Patent Publication Number: US-7914990-B2

Title: Methods and products for in vitro genotyping

Description:
RELATED APPLICATIONS 
     This application is a continuation of, and claims priority to, PCT Patent Application no. PCT/IB2006/000796, filed Jan. 12, 2006, which claims priority to: Spanish patent application P200500089 filed 13 Jan. 2005; Spanish patent application P200502423 filed 5 Oct. 2005; and U.S. Provisional Application No. 60/758,192, filed Jan. 12, 2006, the contents of all of which are incorporated herein by reference in their entirety. 
    
    
     FIELD OF THE INVENTION 
     The invention relates to methods and products for in vitro genotyping by analysis of biological samples. In particular the invention relates to DNA-chips and the use of the chips to detect genetic variations, e.g., polymorphisms or genetic mutations associated with disease, or connected to genotyping of antigens of interest, or associated with resistance to pharmaceutical treatment. The invention further relates to methods for analysing chip data and to computer software based on the methods. 
     BACKGROUND OF THE INVENTION 
     DNA-chips 
     In 2001, the Consortium for the Human Genome Project and the private company Celera presented the first complete example of the human genome with 30,000 genes. From this moment on, the possibility of studying the complete genome or large scale (high-throughput) studies began. So-called “DNA-chips”, also named “micro-arrays”, “DNA-arrays” or “DNA bio-chips” are apparatus that functional genomics can use for large scale studies. Functional genomics studies changes in the expression of genes due to environmental factors and to genetic characteristics of an individual. Gene sequences present small interindividual variations at one unique nucleotide called an SNP (“single nucleotide polymorphism”), which in a small percentage are involved in changes in the expression and/or function of genes that cause certain pathologies. The majority of studies which apply DNA-chips study gene expression, although chips are also used in the detection of SNPs. 
     The first DNA-chip was the “Southern blot” where labelled nucleic acid molecules were used to examine nucleic acid molecules attached to a solid support. The support was typically a nylon membrane. 
     Two breakthroughs marked the definitive beginning of DNA-chip. The use of a solid non-porous support, such as glass, enabled miniaturisation of arrays thereby allowing a large number of individual probe features to be incorporated onto the surface of the support at a density of &gt;1,000 probes per cm 2 . The adaptation of semiconductor photolithographic techniques enabled the production of DNA-chips containing more than 400,000 different oligonucleotides in a region of approximately 20 μm 2 , so-called high density DNA-chips. 
     In general, a DNA-chip comprises a solid support, which contains hundreds of fragments of sequences of different genes represented in the form of DNA, cDNA or fixed oligonucleotides, attached to the solid surface in fixed positions. The supports are generally glass slides for the microscope, nylon membranes or silicon “chips”. It is important that the nucleotide sequences or probes are attached to the support in fixed positions as the robotized localisation of each probe determines the gene whose expression is being measured. DNA-chips can be classified as:
         high density DNA-chips: the oligonucleotides found on the surface of the support, e.g. glass slides, have been synthesized “in situ”, by a method called photolithography.   low density DNA-chips: the oligonucleotides, cDNA or PCR amplification fragments are deposited in the form of nanodrops on the surface of the support, e.g. glass, by means of a robot that prints those DNA sequences on the support. There are very few examples of low density DNA-chips which exist: a DNA-chip to detect 5 mutations in the tyrosinase gene; a DNA-chip to detect mutations in p53 and k-ras; a DNA-chip to detect 12 mutations which cause hypertrophic cardiomypathy; a DNA-chip for genotyping of  Escherichia coli  strains; or DNA-chips to detect pathogens such as  Cryptosporidium parvum  or  rotavirus.          

     For genetic expression studies, probes deposited on the solid surface, e.g. glass, are hybridized to cDNAs synthesized from mRNAs extracted from a given sample. In general the cDNA has been labelled with a fluorophore. The larger the number of cDNA molecules joined to their complementary sequence in the DNA-chip, the greater the intensity of the fluorescent signal detected, typically measured with a laser. This measure is therefore a reflection of the number of mRNA molecules in the analyzed sample and consequently, a reflection of the level of expression of each gene represented in the DNA-chip. 
     Gene expression DNA-chips typically also contain probes for detection of expression of control genes, often referred to as “house-keeping genes”, which allow experimental results to be standardized and multiple experiments to be compared in a quantitive manner. With the DNA-chip, the levels of expression of hundreds or thousands of genes in one cell can be determined in one single experiment. cDNA of a test sample and that of a control sample can be labelled with two different fluorophores so that the same DNA-chip can be used to study differences in gene expression. DNA-chips for detection of genetic polymorphisms, changes or mutations (in general, genetic variations) in the DNA sequence, comprise a solid surface, typically glass, on which a high number of genetic sequences are deposited (the probes), complementary to the genetic variations to be studied. Using standard robotic printers to apply probes to the array a high density of individual probe features can be obtained, for example probe densities of 600 features per cm 2  or more can be typically achieved. The positioning of probes on an array is precisely controlled by the printing device (robot, inkjet printer, photolithographic mask etc) and probes are aligned in a grid. The organisation of probes on the array facilitates the subsequent identification of specific probe-target interactions. Additionally it is common, but not necessary to divide the array features into smaller sectors, also grid-shaped, that are subsequently referred to as sub-arrays. Sub-arrays typically comprise 32 individual probe features although lower (e.g. 16) or higher (e.g. 64 or more) features can comprise each subarray. 
     One strategy used to detect genetic variations involves hybridization to sequences which specifically recognize the normal and the mutant allele in a fragment of DNA derived from a test sample. Typically, the fragment has been amplified, e.g. by using the polymerase chain reaction (PCR), and labelled e.g. with a fluorescent molecule. A laser can be used to detect bound labelled fragments on the chip and thus an individual who is homozygous for the normal allele can be specifically distinguished from heterozygous individuals (in the case of autosomal dominant conditions then these individuals are referred to as carriers) or those who are homozygous for the mutant allele. 
     Another strategy to detect genetic variations comprises carrying out an amplification reaction or extension reaction on the DNA-chip itself. 
     For differential hybridisation based methods there are a number of methods for analysing hybridization data for genotyping:
         Increase in hybridization level: The hybridization level of complementary probes to the normal and mutant alleles are compared.   Decrease in hybridization level: Differences in the sequence between a control sample and a test sample can be identified by a fall in the hybridization level of the totally complementary oligonucleotides with a reference sequence. A complete loss is produced in mutant homozygous individuals while there is only 50% loss in heterozygotes. In DNA-chips for examining all the bases of a sequence of “n” nucleotides (“oligonucleotide”) of length in both strands, a minimum of “2n” oligonucleotides that overlap with the previous oligonucleotide in all the sequence except in the nucleotide are necessary. Typically the size of the oligonucleotides is about 25 nucleotides. The increased number of oligonucleotides used to reconstruct the sequence reduces errors derived from fluctuation of the hybridization level. However, the exact change in sequence cannot be identified with this method; sequencing is later necessary in order to identify the mutation.       

     Where amplification or extension is carried out on the DNA-chip itself, three methods are presented by way of example: 
     In the Minisequencing strategy, a mutation specific primer is fixed on the slide and after an extension reaction with fluorescent dideoxynucleotides, the image of the DNA-chip is captured with a scanner. 
     In the Primer extension strategy, two oligonucleotides are designed for detection of the wild type and mutant sequences respectively. The extension reaction is subsequently carried out with one fluorescently labelled nucleotide and the remaining nucleotides unlabelled. In either case the starting material can be either an RNA sample or a DNA product amplified by PCR. 
     In the Tag arrays strategy, an extension reaction is carried out in solution with specific primers, which carry a determined 5′ sequence or “tag”. The use of DNA-chips with oligonucleotides complementary to these sequences or “tags” allows the capture of the resultant products of the extension. Examples of this include the high density DNA-chip “Flex-flex” (Affymetrix). 
     For genetic diagnosis, simplicity must be taken into account. The need for amplification and purification reactions presents disadvantages for the on-chip extension/amplification methods compared to the differential hybridization based methods. 
     Typically, DNA-chip analysis is carried out using differential hybridization techniques. However, differential hybridization does not produce as high specificity or sensitivity as methods associated with amplification on glass slides. For this reason the development of mathematical algorithms, which increase specificity and sensitivity of the hybridization methodology, are needed (Cutler D J, Zwick M E, Carrasquillo M N, Yohn C T, Tobi K P, Kashuk C, Mathews D J, Shah N, Eichler E E, Warrington J A, Chakravarti A. Geneome Research; 11:1913-1925 (2001). 
     The problems of existing DNA-chips in simultaneously detecting the presence or absence of a high number of genetic variations in a sensitive, specific and reproducible manner has prevented the application of DNA-chips for routine use in clinical diagnosis, of human disease. The inventors have developed a sequential method of processing and interpreting the experimental data generated by genotyping DNA-chips based on an increase in hybridization signal. The method produces high levels of specificity, sensitivity and reproducibility, which allow the DNA-chips developed on the basis of this method to be used for example, for reliable clinical genetic diagnosis. 
     Inflammatory Bowel Disease 
     Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation of the intestine. This pathology presents two clinical forms, Crohns Disease (CD) and Ulcerative Colitis (UC). CD can affect any area of the intestinal tract and is associated with irregular internal injuries of the intestinal wall, while in the case of UC the inflammation is limited to the rectum and colonic mucosa and the injuries are continuous and superficial. The annual rate of UC and CD in Spain is from 4 to 5 and from 1.8 to 2.5 cases per 100,000 people, respectively. In the United States the prevalence of these diseases can reach numbers of 200 to 300 in every 100,000. The disease has a severe effect on quality of life, in particular given its chronic progress, evolution in outbreaks and frequent need for surgery. Patients of both suffer inflammation of the skin, eyes and joints. 
     Treatments for IBD include immunosuppressants, anti-inflammatory agents, such as antibodies targeted against tumour necrosis factor α (TNF-α) and surgery. The molecular biology of the pathogenesis of IBD is still not clear, but causative factors appear to include bacterial infection in the intestinal wall and an imbalance in the regulation of the bowel immune response. 
     CD and UC are classified as autoimmune diseases, both being more prevalent in individuals who have previously had another autoimmune condition. There is a predominance of CD in the female population and of UC in the male, predominantly in the older age bracket with distal proctitis or colitis. 
     Epidemiologic and genetic studies have provided evidence of the presence of genetic susceptibility factors for IBD, increasing expectations that the identification of genes related to IBD could bring a better understanding of the pathogenesis, diagnosis, location, and prognosis and appropriate treatment. Starting from informal studies to evaluate the risk of contracting the disease, such as segregation analysis, evidence has been provided of a genetic origin. Between 10-20% of the relatives of patients affected by CD or UC also suffered from these diseases. However, the tendency to CD and UC is complex and includes various genes as well as environmental factors. IBD is considered to be a complex genetic disease in which inheritance is not considered to be a simple Mendelian trait. Numerous studies of the association between genome and disease susceptibility have recently identified several genes in which one or more genetic variations results in a higher or lower risk of contracting the disease, a better or worse response to drugs or a better or worse prognosis. 
     For this reason, the clinical application of a DNA-chip to characterize the genetic variations associated with IBD will provide benefits for diagnosis and treatment. From a clinical point of view, the early diagnosis, prognosis and location of the disease would influence therapeutic decisions as to treatment of IBD. At least two different groups would benefit from this development:
         relatives of IBD patients who are interested in knowing their likelihood of developing the disease; and   patients who have IBD, in order to be able to choose a personalised therapy, depending on the risk of inflammation or fistulae. The higher the risk of contracting a severe form of IBD, the greater the need for more aggressive therapy.       

     Apart from the contribution to diagnosis and treatment of IBD and the development of new therapeutic strategies, progress in the physiopathology of the inflammatory reaction in IBD will also be of interest in the study of a wide range of autoimmune diseases including several neurodegenerative diseases, rheumatoid arthritis and dermatological conditions such as psoriasis. 
     A DNA-chip, which allows the simultaneous, sensitive, specific and reproducible detection of genetic variations associated with IBD, could be used clinically in diagnosing IBD. 
     Erythrocyte Antigens 
     The blood of each person is so characteristic that it can serve as a means of identification that is nearly as precise as fingerprints; only identical twins have exactly the same blood characteristics. Blood group determination is particularly useful in medical fields such as blood transfusions, haemolytic diseases in fetuses and the new born, medical-legal applications and organ transplantation. 
     The majority of transfusions can be considered safe. However, sometimes they produce slight reactions or possibly a serious and even fatal reaction. Temperature and allergic (hypersensitivity) reactions, occur in 1-2% of transfusions, but more serious incompatibilities do exist which cause the destruction of red cells, (a haemolytic intravascular reaction). 
     Foetal and new born haemolytic disease (HDNF) is a well known immunological condition, in which the potential for survival of the fetus or new born is compromised due to the action of maternal antibodies that pass through the placenta and specifically target antigens of paternal origin present in the red cells of the fetus or new born. It has been determined that EHPN is not only due to antibodies against the D antigen, but that antigens of the RH system, the ABO system and others are also involved. 
     Correct genotyping of blood groups therefore has importance in transfusions (including the detection of rare or infrequent alleles). 
     Blood groups are composed of alloantigens present on the surface of the erythrocyte membrane and red cells, which are transmitted from parents to children according to the laws of Mendelian genetics. 
     The International Society of Blood Transfusions has classified more than 26 different human blood groups. The majority have been defined at a genetic level and include polymorphisms at one unique nucleotide (SNPs), genetic deletions, conversions and other events, which result in genetic variation. The blood group antigens can be classified in two large groups:
         A. Antigens determined by carbohydrates.   B. Antigens determined by proteins.
 
A. Antigens Determined by Carbohydrates
 
Group ABO
       

     This blood group is of clinical importance because it causes the majority of incompatibility reactions in transfusions and organ transplants. The biochemical basis of group ABO depends on the activity of an N-acetylgalactosamine transferase in individuals of blood group A and a galactosyl transferase in blood group B; whilst individuals belonging to group O lack an active transferase enzyme. The genetic basis of the ABO phenotypes is the substitution of amino acids in the ABO gene of glycosyltransferase. This gene is 19,514 bases in size and encodes a membrane bound enzyme that uses GalNAc or UDP-Gal as a substrate. Four amino acid changes in exons 6 and 7 of the ABO gene are responsible for substrate specificity of the transferases A and B respectively, within them the changes Gly235Ser and Leu266Met are vital. The majority of individuals of group O present deletion of one single nucleotide (A261G) which gives rise to a change in the reading frame and results in the production of an inactive transferase protein. Nonetheless, a growing number of O alleles (about 20) exist that result in nonexpression of the transferases A or B. Rare alleles of the subgroup ABO, like A3, Ax, Ael, B3Bx and Bel have been described. These alleles have arisen from genetic recombinations from different alleles of the ABO group. 
     B. Antigens Determined by Proteins. 
     B.1. Antigens Dependent on Expression of Erythrocyte Transferase Molecules. 
     Rh (RH) 
     Incompatibility of RH occurs in a large portion of transfusion reactions and is the main cause of hemolytic disease in newborn and fetuses (HDNF). The RH antigens come from two proteins (RH CcEe and RH D) encoded by the RH locus (1p34-36.2) that contains the genes RHD and RHCE (70 Kb). Possibly the positive D haplotypes present ay configuration of the genes RHD-RHCE of the same orientation, while the negative D haplotypes present a reverse orientation. The negative D phenotype, common in old European populations, is caused by a deletion of the gene RHD. This seems to have been generated by an unequal crossing over between the genes RHCE and RHD. In the African population a pseudogene of RHD is the predominant D negative allele but its frequency diminishes amongst Afro-Americans and Afro-Caribbeans. Recombinations between the genes RHCE and RHD cause rare hybrids that lead to a partial expression of the D antigen. These uncommon antigens on some occasions have been identified as clinically significant. 
     The proteins RH CcEe and RH D co-express themselves with an equivalent glycoprotein (36% identity), the associated glycoprotein RH (RHAG). This erythrocyte specific complex is possibly a hetero tetramer implicated in bidirectional ammonia transport. The mutations in RHAG are the causes of RH null syndrome, associated with defects in transport across the erythrocyte membrane, deficiencies in CD47 and a total absence of ICAM-4. Furthermore, genes related to RHAG, RHBG and RHCG have been found in the regions 1q21.3 and 15q25 respectively. These genes are expressed in different forms in different human tissue. 
     Kidd (JK) 
     The Kidd (JK) antigens occur in the urea transporter hUT-B1 of red cells. The significance of the Kidd antigen has been known for two decades when it was discovered that JK (a − b − ) red cells were resistant to lysis in 2M urea. The molecular basis of the expression of the Kidd antigen is a SNP in nucleotide 838 (G-A) causing a change Asp280Asn (JK*A-JK*B). The Kidd null phenotype, JK (a − b − ) is due to mutations causing fame-shift mutations, premature termination of translation, inappropriate gene splicing and partial deletions in the gene SLC14A1. 
     Diego (DI) 
     The antigens of the blood group Diego (DI) are the most abundant proteins on the surface of red cells (1.1 million copies per cell), and are crucial for carrying CO 2  and acid-base homeostasis. It is thought that Di antigens vary due to multiple SNPs present in the gene SLC4A1. 
     Colton (CO) 
     The CO antigens (COa, COb and CO3) are expressed by the carrier molecule AQP-1. The (COa-COb) antigens are produced by a SNP in AQP-1 that produces a change in codon 45 from alanine to valine. 
     B.2 Antigens Determined by Expression of Red Cell Membrane Enzymes. 
     Kell (KEL) 
     The antigens of the KEL system are very important in transfusions; the k antigen is the second main cause of haemolytic disease in the new born. The glycoprotein KEL is a type II membrane protein. The C-terminal catalytic regions process large endothelins that are potent vasocontrictors. Cysteine 72 of the glycoprotein KEL forms a disulphide bridge with the protein Kx, which might explain why erythrocytes null for KEL (Ko) show activation of levels of the Kx antigen. The antigen of this system with most clinical importance, K (KEL1), is associated with a change Met193Thr that allows Asn-X.ThrN-glycosylation to occur. 
     Dombrock (DO) 
     The variants DOa/DOb are due to an SNP in the gene DOK1, which encodes an enzyme ADP ribosyltransferase, that affects codon 265 (Asn-Asp). The ADP ribosyltransferase of red cells could help eliminate the NAD+ of serum, but it has been noted that it also takes part in the post-transcriptional modification of other proteins. The RGD motif and DOb take part in cellular adhesion. Oddly the allelic variant DO*B is more common in African and Asian populations and could be an evolutionary advantage against the invasion of  Plasmodium falciparum  which expresses RGD proteins during its infection process. 
     B.3. Antigens Determined by Expression of Membrane Receptors of Red Cells. 
     Duffy (FY) 
     The function of the glycoprotein FY as a cytokine receptor of red cells is to accelerate proinflammatory cytokine signalling. The FY glycoprotein is the erythrocyte receptor for the malarial parasite  Plasmodium vivax  and as a consequence FY negative individuals (FY a-b-) are very common in populations where this parasite is found (Western Africa). Three main alleles of FY exist: FY*A, FY*B and FY*A and B which differ due to an SNP which alters codon 42, while phenotype FY (a − b − ) in Africans is caused by a SNP (C-T) in the FY gene promoter that results in an absence of FY glycoprotein in the erythrocytes. 
     MNSs (MNS) 
     The MNS antigens are generated against glycoporin A, while the Ss antigens are against glycoporin B. The genes GYPA and GYPB line up in tandem in the locus 4q28-31 but there is no relationship between glycoporins C and D. Two amino acid changes in the N-terminal region of GPA are responsible for the blood group M-N and a change in amino acid in GPB determines the blood group S-s. A large number of MNS alleles exist due to genetic recombinations, genetic conversions or SNPs. 
     Human blood groups have been defined at a genetic level for the majority of antigens with clinical significance. Nevertheless, genotyping of red cells is still only performed rarely, mainly in prenatal determination of blood groups in cases of haemolytic diseases in newborns and fetuses. 
     The compatibility of blood transfusions between donors and recipients is generally evaluated by serological techniques (antibody-antigen reactions). The use of these techniques can give incorrect results, which could lead to a potential adverse immune reaction in the recipient (patient). No serological tests exist for a high number of the so-called ‘weak’ genes and on various occasions the antibodies used have not been sufficiently specific. The only process capable of preventing problems of this type is that based on complete molecular genotyping of both the donor and the recipient. 
     SNP genotyping will allow both these determinations to be carried out on a large scale and also the genotyping of rare alleles in blood groups that with existing techniques cannot be determined. 
     The appearance of new alleles in certain blood groups (e.g. RH) will continue and will therefore require technology capable of progressing and being constantly monitored. The Human Genome project has identified new SNPs in many proteins in the blood groups concerned, although it still needs to be serologically determined if these SNPs are in antigens related to blood groups. 
     Nowadays genetic molecular analysis is common in transfusions. For example, detection of viral contamination, such as the hepatitis C virus (HCV), the human immunodeficiency virus (HIV) or the hepatitis B virus (HBV), by PCR methodology from small volumes of plasma has been common practice in the European Union (EU) since 1999. Diagnosis based on PCR has practically taken the place of serology in the determination of HLA (human leukocyte antigen); and is routinely used in transfusion centres involved in bone marrow transplants. 
     One of the discoveries of the Human Genome project was the high frequency of polymorphisms in a single nucleotide (SNPs) found in human DNA. Approximately one SNP was found for every kilobase. This discovery has pushed forward the technical development of rapid diagnosis of SNP genotyping, for example by using DNA-chips. This new technology can be applied to developing a rapid method of genotyping of blood groups. 
     Diverse methods of diagnosis for different blood groups have been described. As an illustrative example, U.S. Pat. No. 5,80,4379 relates to a molecular method of diagnosis and a kit to determine the genotypes of the blood group KEL. U.S. Pat. No. 5,723,293 relates to a method and kit to determine the genotypes of the blood group RH. Furthermore a serological diagnostic test to classify blood groups from blood or serum has been described. Likewise new genetic variations of the blood group Duffy have been described as a method of genotyping this blood group. 
     However, no method has been described based on DNA-chip technology capable of being an open platform for genotyping of all the allelic variants of the blood groups with major clinical relevance (including rare variants) that can be used as a method of diagnosis on a huge scale in the population. 
     A DNA-chip which allows the simultaneous, sensitive, specific and reproducible detection of genetic variations associated with determined erythrocyte antigens could be used clinically for genotyping antigens of blood erythrocytes on a large scale in the population and therefore for determining blood groups in humans. 
     Adverse Reactions to Medicine 
     Any medicine is developed with the intention of curing, relieving, preventing or diagnosing an illness or disease but unfortunately these can also produce adverse effects with a risk, which, depending on the specific case, could range from minimal to severe. Although difficult to calculate, the risk of the treatment should not be ignored and the order of magnitude should be known by the doctor and also the patient and accepted, with the understanding that the potential benefit of the medicine compensates any of these risks. 
     An adverse reaction is any harmful or unwanted effect that happens after the administration of the dose usually prescribed to a human being for the prophylaxis, diagnosis or treatment of a disease. Present consensus allows this definition, which was created by the World Health Association in 1972, to be understood in the following manner: “It is any unwanted effect that appears on administering a medicine of adequate dose, for the prophylaxis, diagnosis or treatment of a disease or for the modification of a physiological function.” 
     Developed countries count on systems of drug vigilance to centralize the supervision of security and efficiency of drugs used, which are responsible for collecting and analyzing details of adverse reactions suspected of being produced by the drug used on the market. 
     In Spain the first steps in creating a system of pharmacovigilance were started in the 70s and in 1983, Spain incorporated the International Programme of Pharmacovigilance of Health. In 1992 a computerized database called FEDRA (Spanish Pharmacovigilance of Data of Adverse Reactions) was created. The pharmaceutical industry actively collaborates with this system, and moreover as established by The 1986 General Health Act, and also The 1990 Medicine Act, all public health personnel, including doctors, pharmacists, vets and nurses, are obliged to notify health authorities of any suspicion of adverse reactions to drugs known to them and to collaborate with the Spanish system of pharmacovigilance. Spain also collaborates with the European Medical Evaluation Agency which came into operation in 1995. From the information collected by FEDRA it appears that Spain is within the group of countries with the highest rate of notification, with an average similar to Germany and France although lower than countries such as the USA, Ireland, Norway, New Zealand, The UK or Sweden. 
     Nowadays, in countries like Spain, where the older population is growing and more medicine is being administered, particularly to this age group and also with increasing self-medication, it is only to be expected that the problem of adverse reactions may be important. The Centre for Drug Evaluation and Research of the FDA (U.S. Food and Drug Administration), confirms that more than two million adverse reactions occur annually in the USA, which cause about 100,000 deaths a year, being the fourth cause of death ahead of lung disease, diabetes, AIDS, pneumonia and traffic accidents. The number of patients that die in England and Wales due to errors 
     in prescription of medicines or adverse reactions is growing and the difficulty is that the extent of the problem is not known. In Spain, five out of every hundred casualty cases in public hospitals are due to adverse reactions to drugs and between 10-20% of those hospitalized suffered this medical mishap on receiving medication. Of those affected, 1% die as a consequence. 
     Until May 2000 about 80,000 notifications of adverse reactions to registered drugs had been recorded in the database at the Centre for Pharmaceutical Vigilance in Catalunya. Of these, two thirds were spontaneous and came from primary care. Of those reactions notified most were minor or moderate, whilst 12% were serious and 1% fatal. 50% of reactions were skin, digestive or neurological. The majority of decisions to withdraw drugs are related to hepatic/liver and haematological reactions. What causes concern is that these types of reactions, which represent a small percentage of the total, are those where the majority of drugs are withdrawn. Antibiotics are the main cause of adverse effects, followed by anti-rheumatic drugs and painkillers and drugs to prevent cardiovascular disease. The detection of adverse effects can provoke not only the withdrawal but also the decision to change the use of the drug, or the reformulation or introduction of new directions for specific patients. 
     A DNA-chip, which allows the simultaneous, sensitive, specific and reproducible detection of genetic variations associated with adverse reactions to medicine, could be clinically useful to prevent or reduce the aforementioned reactions in patients receiving medical treatment. 
     SUMMARY OF THE INVENTION 
     The present inventors have developed a sensitive, specific and reproducible method for simultaneously detecting and characterising genetic variations which is useful for the development of products for genotyping. The method is based on a combination of an original trial design for genotyping DNA-chips and the development of a sequential system (algorithm) for processing and interpreting the trial data generated by the chips (based on an increase in hybridization signal), which guarantees high levels of specificity, sensitivity and reproducibility of results and in turn allows the chips to be used, for example, as reliable apparatus in clinical genetic diagnosis. 
     Accordingly the invention provides an in vitro method for genotyping genetic variations in an individual, the method comprising:
     (a) providing a sample containing nucleic acid which comprises the genetic variations to be genotyped (the target DNA);   (b) providing, for each genetic variation to be genotyped, at least 2 oligonucleotide probe pairs, wherein:   (i) one pair consists of probes 1 and 2, and the other pair consists of probes 3 and 4;   (ii) one probe in each pair is capable of hybridising to genetic variation A and the other probe in each pair is capable of hybridising to genetic variation B;   (iii) each probe is provided in replicates; and   (iv) the probe replicates are deposited at positions on a solid support according to a known uniform distribution;   (c) contacting the target DNA with the probes under conditions which allow hybridisation to occur, thereby forming nucleic acid-probe hybridisation complexes, wherein each complex is detectably labelled;   (d) determining the intensity of detectable label at each probe replica position, thereby obtaining a raw intensity value;   (e) optionally amending the raw intensity value to take account of background noise, thereby obtaining a clean intensity value for each replica; and   (e) applying a suitable algorithm to the intensity data from (d) or (e), thereby determining the genotype with respect to each genetic variation, wherein application of the algorithm comprises calculating an average intensity value from the intensity values for each of the replicas of each probe and wherein the algorithm uses three linear functions that characterise each of the three possible genotypes AA, AB or BB for the genetic variation.   

     For genotyping of each of the allelic variant subjected to study, an algorithm has been developed which allows each one of the mutations to be detected with such a sensitivity, specificity and reproducibility that allows the clinical application of the method, on the basis of obtaining the three Fisher Linear Functions, which characterize each of the three possible genotypes. 
                 AA           a   ⁢           ⁢   1   ⁢           ⁢   ratio   ⁢             ⁢             ⁢   1     +     b   ⁢           ⁢   1   ⁢           ⁢   ratio   ⁢             ⁢             ⁢   2     +     c   ⁢           ⁢   1   ⁢           ⁢   Function   ⁢           ⁢   1               AB           a   ⁢           ⁢   2   ⁢           ⁢   ratio   ⁢           ⁢   1     +     b   ⁢           ⁢   2   ⁢           ⁢   ratio   ⁢           ⁢   2     +     c   ⁢           ⁢   2   ⁢           ⁢   Function   ⁢           ⁢   2               BB           a   ⁢           ⁢   3   ⁢           ⁢   ratio   ⁢           ⁢   1     +     b   ⁢           ⁢   3   ⁢           ⁢   ratio   ⁢           ⁢   2     +     c   ⁢           ⁢   3   ⁢           ⁢   Function   ⁢           ⁢   3                 
Wherein
 
     AA represents the genotype of a homozygote subject for the allelic variant 1; 
     AB represents the genotype of a homozygote subject for the allelic variants 1 and 2; 
     BB represents the genotype of a homozygote subject for the allelic variant 2; 
     a1 is the coefficient which accompanies the X in the Fisher Linear Function for the genotype AA; this coefficient is obtained by applying the discriminate analysis to ratios 1 and 2 obtained from analysing 10 patients for the genotype AA, 10 for BB and 10 for AB; 
     b1 is the coefficient which accompanies the Y in the Fisher Linear Function for the genotype AA; this coefficient is obtained by applying the discriminate analysis to ratios 1 and 2 obtained from analysing 10 patients for the genotype AA, 10 for BB and 10 for AB; 
     c1 is the independent term of the first Fisher Linear Function; 
     a2 is the coefficient which accompanies the X in the in the Fisher Linear Function for the genotype AB; this coefficient is obtained by applying the discriminate analysis to ratios 1 and 2 obtained from analysing 10 patients for the genotype AA, 10 for BB and 10 for AB; 
     b2 is the coefficient which accompanies the Y in the Fisher Linear Function for the genotype AB; this coefficient is obtained by applying the discriminate analysis to ratios 1 and 2 obtained from analysing 10 patients for the genotype AA, 10 for BB and 10 for AB; 
     c2 is the independent term of the second Fisher Linear Function; 
     a3 is the coefficient which accompanies the X in the Fisher Linear Function for the genotype BB; this coefficient is obtained by applying the discriminate analysis to ratios 1 and 2 obtained from analysing 10 patients for the genotype AA, 10 for BB and 10 for AB; 
     b3 is the coefficient which accompanies the Y in the Fisher Linear Function for the genotype BB; this coefficient is obtained by applying the discriminate analysis to ratios 1 and 2 obtained from analysing 10 patients for the genotype AA, 10 for BB and 10 for AB; 
     c3 is the independent term of the third linear function; 
     Function 1 is the Fisher Linear Function, which characterizes patients with genotype AA; this function is obtained the same as 2 and 3 when discriminate analysis is applied to the discrimination of 10 patients AA, 10 BB and 10 AB whose ratios 1 and 2 are known; 
     Function 2 is the Fisher Linear Function for genotype AB; 
     Function 3 is the Fisher Linear Function for genotype BB; 
     Ratio 1 is the proportion of the average collected from the intensities of the 10 replicas of the oligo normal 1 which detects the normal allele divided by the average collected from the 10 replicas of the oligo  1  plus the average collected from the 10 replicas from mutant oligo 1 (detects the mutant allele) and can be calculated by the equation: 
     
       
         
           
             
               ratio 
               ⁢ 
               
                   
               
               ⁢ 
               1 
             
             = 
             
               
                 Average 
                 ⁢ 
                 
                     
                 
                 ⁢ 
                 oligo 
                 ⁢ 
                 
                     
                 
                 ⁢ 
                 intensity 
                 ⁢ 
                 
                     
                 
                 ⁢ 
                 normal 
                 ⁢ 
                 
                     
                 
                 ⁢ 
                 1 
               
               
                 
                   
                     
                       
                         Average 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         oligo 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         intensity 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         normal 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         1 
                       
                       + 
                     
                   
                 
                 
                   
                     
                       average 
                       ⁢ 
                       
                           
                       
                       ⁢ 
                       oligo 
                       ⁢ 
                       
                           
                       
                       ⁢ 
                       intensity 
                       ⁢ 
                       
                           
                       
                       ⁢ 
                       mutant 
                       ⁢ 
                       
                           
                       
                       ⁢ 
                       1 
                     
                   
                 
               
             
           
         
       
     
     Ratio 2 is the proportion of the average collected from the intensities of the 10 replicas of the oligo normal 2 which detects the normal allele divided by the average collected from the 10 replicas of the oligo 2 plus the average collected from the 10 replicas from mutant oligo 2 (detecta at mutant allele) and can be calculated by the equation: 
     
       
         
           
             
               ratio 
               ⁢ 
               
                   
               
               ⁢ 
               2 
             
             = 
             
               
                 
                   Average 
                   ⁢ 
                   
                       
                   
                   ⁢ 
                   oligo 
                   ⁢ 
                   
                       
                   
                   ⁢ 
                   intensity 
                   ⁢ 
                   
                       
                   
                   ⁢ 
                   normal 
                   ⁢ 
                   
                       
                   
                   ⁢ 
                   2 
                 
                 
                   
                     
                       
                         
                           Average 
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           oligo 
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           intensity 
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           normal 
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           2 
                         
                         + 
                       
                     
                   
                   
                     
                       
                         average 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         oligo 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         intensity 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         mutant 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         2 
                       
                     
                   
                 
               
               . 
             
           
         
       
     
     The invention additionally provides:
         a DNA chip comprising a plurality of probes deposited on a solid support, the chip being suitable for use in a method of the invention;   a computational method for obtaining a genotype from DNA-chip hybridisation intensity data wherein the method comprises using ratios 1 and 2 in each of three linear functions which characterise each of the three possible genotypes, AA, AB and BB, for a genetic variation wherein:       Function 1 is the linear function that characterises individuals with the genotype AA and consists of a linear combination of ratios 1 and 2;   Function 2 is the linear function that characterises individuals with the genotype AB and consists of a linear combination of ratios 1 and 2;   Function 3 is the linear function that characterises individuals with the genotype BB and consists of a linear combination of ratios 1 and 2; and   the linear functions are formed by coefficients which accompany the variables ratio 1 and 2;   and wherein:   

               ratio   ⁢           ⁢   1     =       average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   1         average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   1     +     
     ⁢           ⁢     average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   2                   and               ratio   ⁢           ⁢   2     =       average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   3         average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   3     +     
     ⁢           ⁢     average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   4               
and wherein:
     probes 1 and 3 detect genetic variation A and probes 2 and 4 detect genetic variation B; and   the average intensity values are obtainable by a method of the invention;
       a method of deriving linear functions for use in a method of the invention, the method comprising, for each of n individuals having genotype AA, n individuals having genotype AB and n individuals having genotype BB with respect to a genetic variation:   
       (a) providing a sample containing nucleic acid which comprises the genetic variation (the target DNA);   (b) providing, for the genetic variation, at least 2 oligonucleotide probe pairs (probes 1+2, and probes 3+4), wherein:   (i) one pair consists of probes 1 and 2 and the other pair consists of probes 3 and 4;   (ii) one probe in each pair is capable of hybridising to genetic variation A and the other probe in each pair is capable of hybridising to genetic variation B;   (iii) each probe is provided in replicates; and   (iv) the probes are deposited at positions on a solid support which comprises additional deposited probes, and the probes are deposited according to a known uniform distribution;   (c) contacting the nucleic acid sample with the probes under conditions which allow hybridisation to occur, thereby forming nucleic acid-probe hybridisation complexes, wherein each complex is detectably labelled;   (d) determining the intensity of detectable label at each probe replica position thereby obtaining a raw intensity value;   (e) optionally amending the raw intensity value to take account of background noise thereby obtaining a clean intensity value for each replica;   (f) applying a suitable algorithm to the intensity data from (d) or (e), wherein application of the algorithm comprises calculating an average intensity value from the intensity values for each of the replicas of each probe and wherein the algorithm uses three linear functions intended to characterise each of the three possible genotypes AA, AB or BB for the genetic variation; and   (g) deriving linear functions which maximise discrimination between the three genotype groups AA, AB and BB in a discriminatory analysis;
       a computational method of deriving linear functions for use in a method of the invention using ratios 1 and 2 obtained for each of n individuals having genotype AA,n individuals having genotype AB and n individuals having genotype BB with respect to a genetic variation, which comprises:   
       (a) applying a suitable algorithm, wherein the algorithm uses three linear functions (Functions 1, 2 and 3) intended to characterise each of the three possible genotypes AA, AB or BB for the genetic variation and wherein:   Function 1 is the linear function that characterises individuals with the genotype AA and consists of a linear combination of ratios 1 and 2;   Function 2 is the linear function that characterises individuals with the genotype AB and consists of a linear combination of ratios 1 and 2;   Function 3 is the linear function that characterises individuals with the genotype BB and consists of a linear combination of ratios 1 and 2; and   the linear functions are formed by coefficients which accompany the variables ratio 1 and 2;   and wherein:   

               ratio   ⁢           ⁢   1     =       average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   1         average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   1     +     
     ⁢           ⁢     average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   2                   and               ratio   ⁢           ⁢   2     =       average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   3         average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   3     +     
     ⁢           ⁢     average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   4               
and wherein:
     probes 1 and 3 detect genetic variation A and probes 2 and 4 detect genetic variation B;   and   (b) deriving linear functions which maximise discrimination between the three genotype groups AA, AB and BB in a discriminatory analysis, thereby obtaining coefficients for each of the three functions;
 
wherein ratios 1 and 2 are obtainable by a method of the invention;
       a computer system comprising a processor and means for controlling the processor to carry out a computational method of the invention;   a computer program comprising computer program code which when run on a computer or computer network causes the computer or computer network to carry out a computational method of the invention;   at least one oligonucleotide selected from:
           the oligonucleotides listed in SEQ ID NOS 255-630;   the oligonucleotides listed in SEQ ID NOS 631-960 and 1429-1652;   the oligonucleotides listed in SEQ ID NOS 961-1316; and   the oligonucleotides of SEQ ID NOs 1-254 and 1317-1428;   
           a pair of PCR primers selected from the pairs of PCR primers in SEQ ID NOs 1-254 and 1317-1428;   a PCR amplification kit comprising at least one pair of primers of the invention;   a pair of oligonucleotide probes for identification of a genetic variation, the pair being selected from the probe pairs in SEQ ID NOS 255-1316 and 1429-1652;   a set of at least 4 oligonucleotide probes, comprising at least 2 pairs of probes according to the invention wherein each pair is for identification of the same genetic variation;   a diagnostic kit comprising a DNA-chip of the invention;   a method of diagnosing IBD or susceptibility to IBD in an individual comprising genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with IBD;   a method of selecting a treatment for an individual having IBD comprising:   
       (a) genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with IBD; and   (b) selecting a suitable treatment based on the genotype determined in (a).
       a method of treating an individual having IBD comprising:   
       (a) genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with IBD; and   (b) selecting a suitable treatment based on the genotype determined in (a); and   (c) administering said treatment to the individual.
       a method of determining blood group in an individual comprising genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with erythrocyte antigens;   a method of determining susceptibility to adverse reactions to pharmaceuticals in an individual comprising genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with adverse reactions to pharmaceuticals;   a method of selecting a pharmaceutical treatment for an individual comprising:   
       (a) genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with adverse reactions to pharmaceuticals; and   (b) selecting a suitable treatment based on the genotype determined in (a);
       a method of treating an individual with a pharmaceutical comprising:   
       (a) genotyping an individual with respect to one or more genetic variations by a method of the invention wherein the genetic variations are associated with adverse reactions to pharmaceuticals;   (b) selecting a suitable treatment based on the genotype determined in (a); and   (c) administering said treatment to the individual;
       a method of identifying genetic variations predictive of a particular IBD phenotype the method comprising:   
       (a) genotyping a plurality of individuals with respect to one or more genetic variations by a method of the invention, wherein the genetic variations are associated with IBD and wherein the IBD phenotype of the individuals is known;   (b) comparing the genotypes of the individuals tested for one or more genetic variations with the known phenotypes of the individuals; and   (c) identifying any genetic variations for which there is a statistically significant association between the genetic variation and the phenotype;
       a method of predicting the likely development of the IBD phenotype of an individual by determining the genotype of the individual with respect to one more genetic variations which have been identified as predictive of development of a particular IBD phenotype by the method of the invention;   a nucleic acid selected from SEQ ID NOS: 1-1652 for use in medicine.   
       

    
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         FIG. 1  shows a representation of ratios 1 and 2 in a study of 15 blood donors, five of genotype 188G189C, five of genotype 188GA189CT and five of genotype 188A1189T (Example 2). 
         FIG. 2  shows a representation of ratios 1 and 2 in a study of 9 patients, 3 of genotype AA, 3 of genotype AT and 3 of genotype TT at genetic variation A2033T in the CSFR1 gene (Example 4). 
         FIGS. 3-10  (Example 6) demonstrate the respective probabilities associated with the development of determined phenotypes (disease prognosis), based on genotypic data obtained with a DNA-chip according to the invention, for each of the eight IBD phenotypes analysed. 
         FIGS. 3-7  show probabilities for development of phenotypes associated with Crohns disease and  FIGS. 8-10  show probabilities associated with the development of phenotypes associated with ulcerative colitis.  FIGS. 11-13  (Example 6) indicate the probabilities associated with the risk of developing resistance to corticosteroid treatment in individuals suffering from IBD. 
     
    
    
     BRIEF DESCRIPTION OF THE SEQUENCES 
     
         
         SEQ ID NOS 1-124 and 1317-1428 are PCR primers suitable for amplifying target DNA regions comprising genetic variations associated with IBD. 
         SEQ ID NOS 125-254 are PCR primers suitable for amplifying target DNA regions comprising genetic variations associated with adverse reactions to pharmaceuticals. 
         SEQ ID NOS 255-630 are probes suitable for detection of genetic variations associated with known erythrocyte antigens, and useful for genotyping for blood groups. 
         SEQ ID NOS 631-960 and 1429-1652 are probes suitable for detection of genetic variations associated with IBD. 
         SEQ ID NOS 961-1316 are probes suitable for detection of genetic variations associated with adverse reactions to pharmaceuticals. 
         SEQ ID NO 1653 is an external control nucleic acid. 
         SEQ ID NOS 1654-1655 are probes suitable for detection of the external control nucleic acid of SEQ ID NO: 1653. 
       
    
     DETAILED DESCRIPTION OF THE INVENTION 
     The present invention relates to a method of genotyping genetic variations in an individual, which is sufficiently sensitive, specific and reproducible as to allow its use in a clinical setting. The inventors have developed DNA-chips with specifically designed probes for use in the method, and a computational method or algorithm for interpreting and processing the data generated by the chips. 
     Thus in one aspect, the invention comprises an in vitro method for genotyping genetic variations in an individual. The in vitro, extracorporeal method is for simultaneous sensitive, specific and reproducible genotyping of multiple human genetic variations present in one or more genes of a subject. The method of the invention allows identification of nucleotide changes, such as, insertions, duplications and deletions and the determination of the genotype of a subject for a given genetic variation. 
     The terms “genetic variation” or “genetic variant”, as they are used in the present description include mutations, polymorphisms and allelic variants. A variation or genetic variant is found amongst individuals within the population and amongst populations within the species. 
     The term “polymorphism” refers to a variation in the sequence of nucleotides of nucleic acid where every possible sequence is present in a proportion of equal to or greater than 1% of a population; in a particular case, when the said variation occurs in just one nucleotide (A, C, T or G) it is called a single nucleotide polymorphism (SNP). 
     The term “genetic mutation” refers to a variation in the sequence of nucleotides in a nucleic acid where every possible sequence is present in less than 1% of a population 
     The terms “allelic variant” or “allele” are used without distinction in the present description and refer to a polymorphism that appears in the same locus in the same population. 
     Thus a genetic variation may comprise a deletion, substitution or insertion of one or more nucleotides. In one aspect the genetic variations to be genotyped according to the present methods comprise SNPs. 
     A given gene may comprise one or more genetic variations. Thus the present methods may be used for genotyping of one or more genetic variations in one or more genes. 
     Typically the individual is a human. 
     Typically, for a given genetic variation there are three possible genotypes:
     AA the individual is homozygous for genetic variation A (e.g homozygous for a wild type allele)   BB the individual is homozygous for genetic variation B (e.g. homozygous for a mutant allele)   AB the individual is heterozygous for genetic variations A and B (e.g. one wild type and one mutant allele)   

     In one aspect the genetic variations, such as SNPs, to be analysed according to the present methods, are associated with a particular phenotype or disease condition. For example, the variations may be associated with particular erythrocyte antigens (and thus often a particular blood group); or with IBD; or with adverse reactions to pharmaceuticals in an individual. 
     Examples of genetic variations associated with IBD which may be assessed by the present methods include those in Table 1 below. 
     
       
         
           
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 Genetic variations associated with IBD 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 The polymorphism G2677T/A/C Ala893Ser/Thr/Pro of the gene 
               
               
                   
                 Multidrug resistance protein 1 (MDR1); 
               
               
                   
                 The polymorphism C3435T of the gene Multidrug resistance 
               
               
                   
                 protein 1 (MDR1); 
               
               
                   
                 The polymorphisms R702W, G908R, 1007insC in the gene Caspase 
               
               
                   
                 recruitment domain-containing protein 15 (CARD15); 
               
               
                   
                 The polymorphism T612C Y113H in the gene Microsomal epoxide 
               
               
                   
                 hydrolase (EPXH1); 
               
               
                   
                 The polymorphism (−2518) G/A of the gene Monocyte chemotactic 
               
               
                   
                 protein 1 (MCP1); 
               
               
                   
                 The polymorphisms (−1082) G/A and G43A (G15R) in the gene 
               
               
                   
                 Interleukin 10 (IL10); 
               
               
                   
                 The polymorphism (−295) T/C in the gene Interleukin 16 
               
               
                   
                 (IL16); 
               
               
                   
                 The polymorphism (−843) C/T in the gene Fas ligand; 
               
               
                   
                 The polymorphisms 94delATTG and −263A/G in the gene Nuclear 
               
               
                   
                 factor kappa-B 1(NFKB1); 
               
               
                   
                 The polymorphism in 3′UTR (G/A) of the gene Nuclear factor 
               
               
                   
                 kappa-B inhibitor alpha (NFKBIA); 
               
               
                   
                 The polymorphism G2964A in the gene Signal transducer and 
               
               
                   
                 activator of transcription 6 (STAT6); 
               
               
                   
                 The polymorphism TCA/TCC of codon 35 in the gene Interleukin 
               
               
                   
                 18 (IL18); 
               
               
                   
                 The polymorphisms E474E, Q476Q, D510D, P588P, −177A/G, 
               
               
                   
                 A165A, R202Q in the gene Mediterranean fever gene (MEFV); 
               
               
                   
                 The polymorphism 113G/A (R30Q) in the gene Discslarge, 
               
               
                   
                   Drosophila , homolog of, 5 (DLG5); 
               
               
                   
                 The polymorphism A2033T in the gene Colony stimulating 
               
               
                   
                 factor receptor 1 (CSFR1); 
               
               
                   
                 The polymorphism 1672C/T (L503F) in the gene Organic cation 
               
               
                   
                 transporter (OCTN1, SLC22A4); 
               
               
                   
                 The polymorphism (−207G/C) in the Organic cation transporter 
               
               
                   
                 (OCTN2, SLC22A5); 
               
               
                   
                 The polymorphisms Asp299Gly and Thr399Ile in the gene Toll- 
               
               
                   
                 like receptor 4 (TLR4); 
               
               
                   
                 The polymorphisms (−511) A/C and 3954 TaqI RFLP in the gene 
               
               
                   
                 Interleukin 1 beta (IL1β); 
               
               
                   
                 The polymorphism Ala16Val in the gene Superoxide dismutase 
               
               
                   
                 2 (SOD2); 
               
               
                   
                 The polymorphism Pro12Ala in the gene Peroxisome 
               
               
                   
                 proliferator-activated receptor gamma (PPARG); 
               
               
                   
                 The polymorphisms K469E, R241G in the gene Intercellular 
               
               
                   
                 adhesion molecule 1 (ICAM1); 
               
               
                   
                 The polymorphisms IGR2060a_1, IGR2198a_1, IGR3096a_1 in the 
               
               
                   
                 locus Inflammatory Bowel Disease 5 (IBD5); 
               
               
                   
                 The polymorphism 1267A/G (Gln351Gln) in the gene Heat shock 
               
               
                   
                 protein 70 (HSP70-2); 
               
               
                   
                 The polymorphism 1237C/T in the gene Toll-like receptor 9 
               
               
                   
                 (TLR9); 
               
               
                   
                 The polymorphism C677T (V222A) in the gene 
               
               
                   
                 Methylinetetrahydrofolate reductase (MTFHR); 
               
               
                   
                 The polymorphisms (−590) C/T, (−34) C/T in the gene 
               
               
                   
                 Interleukin 4 (IL4); 
               
               
                   
                 The polymorphisms Gly54Asp (A/G), Gly57Glu (A/G), Arg52Cys 
               
               
                   
                 (C/T) in the gene Mannose-binding lectin (MBL); 
               
               
                   
                 The polymorphism (−6) A/T in the gene Angiotensinogen 
               
               
                   
                 precursor (AGT); 
               
               
                   
                 The polymorphism 4G/5G in the gene Plasminogen activator 
               
               
                   
                 inhibitor (PAI); 
               
               
                   
                 The polymorphisms (−857C/T), (−308G/A), (−238 G/A) in the 
               
               
                   
                 gene Tumor necrosis factor alpha (TNF-α); 
               
               
                   
                 The polymorphisms G238C, G460A, A719G in the gene TPMT; 
               
               
                   
                 The polymorphisms Trp14Gly, Thr24Ala, Met129Val, Lys173Glu, 
               
               
                   
                 Gly175Ser of the gene Major histocompatibility complex class 
               
               
                   
                 I chain-realted-gene A (MICA) that discriminates the 
               
               
                   
                 alleles MICA*007 and MICA*008; 
               
               
                   
                 The polymorphism of the promoter region (−377 to −222) 
               
               
                   
                 characteristic of allele 7 of the gene Solute carrier family 
               
               
                   
                 11, member 1 (SLC11A1 = NRAMP1); 
               
               
                   
                 The polymorphism (−159) T/C of the gene CD14; 
               
               
                   
                 The polymorphism G4985T (Val158Phe) of the gene 
               
               
                   
                 CD16A = FCGR3A; 
               
               
                   
                 The polymorphism −25385C/T of the gene Nuclear receptor 
               
               
                   
                 subfamily 1, group I, member 2 (NR1I2); 
               
               
                   
                 The polymorphism (T/A) (Cys10Stop) of the gene Caspase 
               
               
                   
                 recruitment domain-containing protein 8 
               
               
                   
                 (TUCAN/CARD8/CARDINAL); 
               
               
                   
                 The polymorphism 738T/C (Cys224Arg) of the gene Inhibitor of 
               
               
                   
                 kappa light chain gene enhancer in B cells-like (IKBL); 
               
               
                   
                 The polymorphisms G593A and T620C of the gene Tumor necrosis 
               
               
                   
                 factor receptor subfamily, member 1B (TNFRSF1B = TNFR2); 
               
               
                   
                 The polymorphism Asp643Asn of the gene Mitogen-Activated 
               
               
                   
                 kinase kinase kinase 1 (MEKK1); 
               
               
                   
                 The polymorphisms 159G/A/C and 282C/T of the gene Major 
               
               
                   
                 Histocompatibility complex, class II, DQ Alpha-1 (HLA-DQ) 
               
               
                   
                 for the identification of the alleles DQB1*0401 and 
               
               
                   
                 DQB1*0402; 
               
               
                   
                 The polymorphisms 109T/C, 119T/C/G/A, 122A/C/G/T, 129A/G, 
               
               
                   
                 161G/A/T, 175A/T/C/G, 184A/C/delA, 286C/A/T, 305C/G for the 
               
               
                   
                 identification of alleles DR2, DR9, DRB1*0103, DR4, DR7, 
               
               
                   
                 DRB3*0301 and DR3 of the gene Major histocompatibility 
               
               
                   
                 complex, class II, DR Beta-1 (HLA-DRB1); 
               
               
                   
                 The polymorphisms 2018T/C and 2073C/T of the gene 
               
               
                   
                 Interleukin 1 receptor antagonist (IL1RN); 
               
               
                   
                 The polymorphism 3954 C/T (TAQI) of the gene Interleukin 1 
               
               
                   
                 receptor, type II (IL1RB); 
               
               
                   
                 The polymorphism (−670) G/A of the gene Fas Antigen; 
               
               
                   
                 The polymorphism 93 C/T of the gene Caspase 9 (CASP9); 
               
               
                   
                 The polymorphism G/C (R80T) of the gene Toll-like receptor 1 
               
               
                   
                 (TLR1); 
               
               
                   
                 The polymorphism A/G (R753G) of the gene Toll-like receptor 
               
               
                   
                 2 (TLR2); 
               
               
                   
                 The polymorphism T/C (S249P) of the gene Toll-like receptor 
               
               
                   
                 6 (TLR6); 
               
               
                   
                 The polymorphism 5A/6A of the gene Matrix metalloproteinase 
               
               
                   
                 3 (MMP3); 
               
               
                   
                 The polymorphism indel +32656 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism DLG5_e26 in the gene Discslarge, 
               
               
                   
                   Drosophila , homolog of, 5 (DLG5); 
               
               
                   
                 The polymorphism with rs20752817 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2975632 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs3020207 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2075818 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2235099 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2075821 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2075822 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2907748 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs5743368 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism with rs2289311 of the gene NOD-1 protein 
               
               
                   
                 (NOD1 = CARD4); 
               
               
                   
                 The polymorphism A1298C in the gene 
               
               
                   
                 Methylinetetrahydrofolate reductase (MTFHR); 
               
               
                   
                 The polymorphism Ile114Thr in the gene N-Acetyl tranferase 
               
               
                   
                 2 (NAT2); 
               
               
                   
                 The polymorphism (A/G) Lys268Arg in the gene N-Acetyl 
               
               
                   
                 tranferase 2 (NAT2); 
               
               
                   
                 The polymorphism with rs9340799 of the gene Estrogen 
               
               
                   
                 receptor 1 (ESR1); 
               
               
                   
                 The polymorphism with rs2234693 of the gene Estrogen 
               
               
                   
                 receptor 1 (ESR1); 
               
               
                   
                 The polymorphism C/T V726A in the gene Mediterranean fever 
               
               
                   
                 gene (MEFV); 
               
               
                   
                 The polymorphism with rs10735810 in the Vitamin D receptor 
               
               
                   
                 (VDR); 
               
               
                   
                 The polymorphism (C/G) E127Q in EGF-like module-contining, 
               
               
                   
                 mucin-like hormone receptor 3 (EMR3); 
               
               
                   
                 The polymorphism (G/T) Q496K in EGF-like module-contining, 
               
               
                   
                 mucin-like hormone receptor 1 (EMR3); 
               
               
                   
                 The polymorphism R653Q in the Methylenetetrahydrofate 
               
               
                   
                 dehydrogenase 1 (MTHFD1); 
               
               
                   
                 The polymorphism 1420 (C/T) in the Serine 
               
               
                   
                 hydroxymethyltransferase (SHMT1); 
               
               
                   
                 The polymorphism Gly286Glu in the gene N-Acetyl tranferase 
               
               
                   
                 2 (NAT2); 
               
               
                   
                 The polymorphism Arg197Gln in the gene N-Acetyl tranferase 
               
               
                   
                 2 (NAT2); 
               
               
                   
                 The polymorphism 191 (G/A) in the gene N-Acetyl tranferase 
               
               
                   
                 2 (NAT2); 
               
               
                   
                 The polymorphism Arg392Stop of the gene Toll-like receptor 
               
               
                   
                 5 (TLR5); 
               
               
                   
                 The polymorphism A49G of the gene cytotoxic T lymphocyte- 
               
               
                   
                 associated 4 (CTLA4); 
               
               
                   
                 The polymorphism D132H of the gene MutL,  E. coli,  homolog 
               
               
                   
                 of, 1 (MLH1); 
               
               
                   
                 The polymorphism 66A/G of the gene Methionine synthase 
               
               
                   
                 reductase (MTRR); 
               
               
                   
                 The polymorphism 94C/A of the gene Inosine Triphosphatase 
               
               
                   
                 (ITPA); 
               
               
                   
                 The polymorphism E148Q in the gene Mediterranean fever gene 
               
               
                   
                 (MEFV); 
               
               
                   
                 The polymorphism R620W in the protein tyrosine phosphatase, 
               
               
                   
                 nonreceptor-type, 22 (PTPN22); 
               
               
                   
                 The polymorphism 3357 A/G in the Low density lipoprotein 
               
               
                   
                 receptor-related protein 5 (LRP-5); 
               
               
                   
                 The polymorphism C318T of the gene cytotoxic T lymphocyte- 
               
               
                   
                 associated 4 (CTLA4); 
               
               
                   
                 The polymorphism rs333 32bpdel of the gene chemokine, CC 
               
               
                   
                 motif, receptor 5 (CCR5); 
               
               
                   
                 The polymorphism −174G/C of the gene interleukin-6(IL6); 
               
               
                   
                 The polymorphism with rs6190 of the gene glucocorticoid 
               
               
                   
                 receptor (GR ER22/23EK); 
               
               
                   
                 The polymorphism Arg72Pro of the gene p53; 
               
               
                   
                 The polymorphism P1371Q in the gene Discslarge,  Drosophila , 
               
               
                   
                 homolog of, 5 (DLG5); 
               
               
                   
                 The polymorphism with rs6189 of the gene glucocorticoid 
               
               
                   
                 receptor (GR ER22/23EK); 
               
               
                   
                 The polymorphism C135242T in the Low density lipoprotein 
               
               
                   
                 receptor-related protein 5 (LRP-5); 
               
               
                   
                 The polymorphism G121513A in the gene Low density 
               
               
                   
                 lipoprotein receptor-related protein 5 (LRP-5); 
               
               
                   
                 The polymorphism C141759T in the gene Low density 
               
               
                   
                 lipoprotein receptor-related protein 5 (LRP-5); 
               
               
                   
                 The polymorphism G138351A in the gene Low density 
               
               
                   
                 lipoprotein receptor-related protein 5 (LRP-5); 
               
               
                   
                 The polymorphism (−298) C/T in the gene Purinergic receptor 
               
               
                   
                 P2X, ligand-gated ion chanel, 7 (P2RX7); 
               
               
                   
                 The polymorphism (−838) G/T in the gene Purinergic receptor 
               
               
                   
                 P2X, ligand-gated ion chanel, 7 (P2RX7); 
               
               
                   
                 The polymorphism E1317Q in the gene Adenomatous polyposis 
               
               
                   
                 of the colon (APC); 
               
               
                   
                 And the polymorphism T64C in the gene CD97 (CD97); 
               
               
                   
               
            
           
         
       
     
     Examples of genetic variations associated with particular erythrocyte antigens which may be assessed by the present methods include those in Table 2 below. 
     
       
         
           
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 Genetic variations associated with erythrocyte antigens 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 The polymorphism GG87_88insG (Genotype O4) (BC008) in exon 2 
               
               
                 of the gene ABO, 
               
               
                 The polymorphism G188A + C189T (Genotype O1v) (BC012) in exon 
               
               
                 4 of the gene ABO, 
               
               
                 The polymorphisms 261delG (Genotype O1/O1v) (BC001), C322T 
               
               
                 (Genotype O5) (BC009) in exon 6 of the gene ABO, 
               
               
                 The polymorphisms C467T (P156L) (Genotype A2) (BC014), G542A 
               
               
                 (Genotype O8) (BC013), T646A (Genotype Ax/O1v) (BC015), 
               
               
                 G703A (Genotype G235S) (B) (BC002), C796A (Genotype L266M) 
               
               
                 (B) (BC003), G802A (Genotype O2) (BC004), G803C (Genotype 
               
               
                 G268A) (B, cisAB-1) (BC005), 798-804insG (Genotype O3, Ael) 
               
               
                 (BC007), C893T (Genotype O6) (BC010), C927A (Genotype O7) 
               
               
                 (BC011), 1059-1061delC (D FS354 + 21aa) (Genotype A2) (BC006) 
               
               
                 in exon 7 of the gene ABO, 
               
               
                 The polymorphisms C8G (S3C) (Genotype weak D type 3) 
               
               
                 (BC040), G48A (W16X) (Genotype RHD W16X) (BC046), C121T 
               
               
                 (Q41X) (Genotype RHD Q41X) (BC047) in exon 1 of the gene 
               
               
                 RHD, 
               
               
                 The polymorphisms A178C, G203A, T307C (exon scanning) 
               
               
                 (BC016, BC017, BC018), T161C (L54P) (Genotype DMH) (BC033), 
               
               
                 G270A (W90X) (Genotype RHD W90X) (BC047), T329C (L110P) 
               
               
                 (Genotype DVII) (BC028) in exon 2 of the gene RHD, 
               
               
                 The polymorphisms C340T (Genotype weak D type 17) (BC043), 
               
               
                 C410T (Genotype DIIIiv) (BC059), C446A (A149D) (Genotype 
               
               
                 weak D type 5) (BC041), A455C (Genotype DIIIa, DIIIiv, DIVa) 
               
               
                 (BC060), IVS3 + 1G &gt; A (Genotype negative allele) (BC049) in 
               
               
                 exon 3 of the gene RHD, 
               
               
                 The polymorphisms 488del4 negative genotype allele (BC050), 
               
               
                 A497C (H166P) (Genotype DFW) (BC030), T509C (M170T) 
               
               
                 (Genotype DOL) (BC027), A514T (Genotype DFRI) (BC065), 
               
               
                 T544A, G577A, A594T (Genotype DVI-I weak D type 4) (exon 
               
               
                 scanning), (BC019, BC020, BC021) in exon 4 of the gene RHD, 
               
               
                 The polymorphisms G635T (G212V) (Genotype RHD G212V) 
               
               
                 (BC051), T667G (Genotype DIIIa, weak D type 4, Dva, DAR, 
               
               
                 DOL, DCS) (BC061), G676C (Genotype DCS, G686A (Genotype DHR) 
               
               
                 (BC031), G697C (E233Q), (Genotype G712A (M238V) (DVI I, weak 
               
               
                 D type 4, DV, DCS) (BC022, BC023), A712G (genotype negative 
               
               
                 allele) (BC023) in exon 5 of the gene RHD, 
               
               
                 The polymorphisms T807G (Genotype pseudogene) (BC044), T809G 
               
               
                 (Genotype weak D type 1) (BC038), G845A (G282D) (Genotype 
               
               
                 weak D type 15, DIM) (BC037), C848T (T283I) (Genotype DHMI) 
               
               
                 (BC029), G854A (C285Y) (Genotype DIM) (BC032), G885T (M295I) 
               
               
                 (Genotype negative allele M295I) (BC053), 906insGGCT 
               
               
                 (Genotype negative allele) (BC054), G916A, A932G (consensus 
               
               
                 exon scanning) (BC062, BC063), IVS6 + 1del4 (Genotype allele 
               
               
                 negative) (BC055) in exon 6 the gene RHD, polymorphisms 
               
               
                 G941T (G314V) (Genotype negative allele) (BC056), C990G 
               
               
                 (Y330X) (Genotype negative allele) (BC057), G1016A (G339E) 
               
               
                 (Genotype weak D type 7) (BC042), T1025C (I342T) (exon 
               
               
                 scanning) (BC024), G1048C (Genotype DIVa, DIVb) (BC094), 
               
               
                 G1057A (G353R) (Genotype DNU) (BC034), C1061A (A354N) 
               
               
                 (Genotype DII) (BC036), G1063A (G355S) (Genotype DNB) 
               
               
                 (BC026), T1073C (Genotype DWI) (BC035) in exon 7 the gene 
               
               
                 RHD, 
               
               
                 The polymorphism IV8 + 1G &gt; A (Genotype negative allele) (BC058) 
               
               
                 in exon 8 of the gene RHD, 
               
               
                 The polymorphisms G1154C (G385A) (Genotype weak D type 2) 
               
               
                 (BC039), A1193T (Genotype DIVb) (BC064), G1227A (K409K) 
               
               
                 (Genotype K409K) (BC045) in exon 9 of the gene RHD, 
               
               
                 The polymorphisms G106A (A36T) (Genotype Cx) (BC068), A122G 
               
               
                 (Q41R) (Genotype Cw) (BC067) in exon 1 of the gene RHCE, 
               
               
                 The polymorphism T307C (S103P) (Genotype RHc) (BC066) in 
               
               
                 exon 2 of the gene RHCE, 
               
               
                 The polymorphism C410T (A137V) (BC059) in exon 3 of the gene 
               
               
                 RHCE, 
               
               
                 The polymorphisms C676G (P226A) (Genotype Ee) (BC025, 
               
               
                 BC069), C733G (L245V) (Genotype VS) (BC070) in exon 5 of the 
               
               
                 gene RHCE, 
               
               
                 The polymorphism G1006T (G336C) (Genotype VS−/VS+) (BC071) 
               
               
                 in exon 7 of the gene RHCE, 
               
               
                 The polymorphisms A697T (Genotype Kk) (BC073), C698T (T193M) 
               
               
                 (Genotype Kk) (BC072) in exon 6 of the gene KEL, 
               
               
                 The polymorphisms T961C (R281W) (Genotype KpaKpb) (BC074), 
               
               
                 G962A (R281Q) (Genotype KpbKpc) (BC075) in exon 8 of the 
               
               
                 gene KEL, 
               
               
                 The polymorphism G1208A (S363N) (Genotype Kmod-1) (BC077) in 
               
               
                 exon 10 of the gene KEL, 
               
               
                 The polymorphism C1910T (L597P) (Genotype JsaJsb) (BC076) in 
               
               
                 exon 17 of the gene KEL, 
               
               
                 The polymorphism I5AG &gt; AA (Genotype Jknull) (BC079) in exon 6 
               
               
                 of the gene SLC14A1 (blood group KIDD), 
               
               
                 The polymorphisms G838A (D280N) (Genotype JkaJkb) (BC078), 
               
               
                 T871C (S291P) (Genotype Jknull) (BC080) in exon 9 of the 
               
               
                 gene SLC14A1 (blood group KIDD), 
               
               
                 The polymorphisms T-33C (Genotype FYGATA) (BC082), G125A 
               
               
                 (D42G) (Genotype FYaFYb) (BC081), C265T (R89C) (Genotype 
               
               
                 FYx) (BC083) in the gene DARC (blood group DUFFY), 
               
               
                 The polymorphisms C59T, G71A, T72G (S20L, G42E, G42E) 
               
               
                 (Genotype MN) (BC084, BC085) in exon 2 of the gene GYPA, 
               
               
                 The polymorphism T143C (M48T) (Genotype Ss) (BC086) in exon 
               
               
                 4 of the gene GYPB, 
               
               
                 The polymorphisms C790A (Genotype GpMUR MiIII) (BC089), 
               
               
                 C850G (Genotype GpMUR MiIII) (BC090) in exon 3 of the gene 
               
               
                 GYPE, 
               
               
                 The polymorphisms C230T (Genotype U) (BC087), I5 + 5GT 
               
               
                 (Genotype U) (BC088) in exon 5 of the gene GYPB, 
               
               
                 The polymorphism T2561C (P854L) (Genotype DiaDib) (BC091) in 
               
               
                 exon 19 of the gene SLC4A1 (blood group DIEGO), 
               
               
                 The polymorphism A793G (Genotype DoaDob) (BC092) in exon 2 
               
               
                 of the gene DOMBROCK, 
               
               
                 The polymorphism C134T (A45V) (Genotype CoaCob) (BC093) in 
               
               
                 exon 1 of the gene COLTON. 
               
               
                   
               
            
           
         
       
     
     Examples of genetic variations associated with adverse reactions to pharmaceuticals which may be assessed by the present methods include those in Table 3 below. 
     
       
         
           
               
             
               
                 TABLE 3 
               
               
                   
               
               
                 Genetic variations associated with adverse reactions to 
               
               
                 pharmaceuticals 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 The polymorphism Arg389Gly in the adrenergic beta 1 receptor 
               
               
                 (ADRB1) 
               
               
                 The polymorphisms Arg16Gly and Gln27Glu in the adrenergic 
               
               
                 beta 2 receptor (ADRB2), 
               
               
                 The polymorphism Ser9Gly of the dopamine receptor D3 (DRD3), 
               
               
                 The polymorphisms His452Tyr and T102C of the serotonin 
               
               
                 receptor 2A (HTR2A), 
               
               
                 The polymorphism Val108Met of Catechol-O-methyltransferase 
               
               
                 (COMT), 
               
               
                 The polymorphism Ile105Val of Glutathione S transferase 
               
               
                 class 1 (GSTP1), 
               
               
                 The polymorphism Gly460Trp of Adducin 1 (ADD1), 
               
               
                 The polymorphism Arg399Gln of the DNA repair protein XRCC1, 
               
               
                 The polymorphism Ile462Val of the cytochrome P450 1A1 
               
               
                 (CYP1A1), 
               
               
                 The polymorphism A1166C of the angiotensin II, type 1 
               
               
                 receptor (AGTR1), 
               
               
                 The polymorphism C-58T of the receptor B2 of bradykinin 
               
               
                 (BDKRB2), 
               
               
                 The polymorphism Met235Thr of angiotensinogen (AGT), 
               
               
                 The polymorphisms C430T, A1075C, 818delA, T1076C and C1080G 
               
               
                 of the cytochrome P450 2C9 (CYP2C9), 
               
               
                 The polymorphisms H324P, V136V, V11M, C882G, C1038T, G4180C, 
               
               
                 A1847G, C-1584G, C100T, 138insT, C1023T, G1659A, 1707T/del, 
               
               
                 G1758A/T, 1863ins9bp, 1973insG, 2539delAACT, 2549A/del, 
               
               
                 2613delAGA, C2850T, G3183A, C3198G, T3277C, G4042A and 
               
               
                 4125insGTGCCCACT of the cytochrome P450 2D6 (CYP2D6), 
               
               
                 The polymorphisms A805T, G416A, A1196G and C792G of the 
               
               
                 cytochrome P450 2C8 (CYP2C8), 
               
               
                 The polymorphisms T341C, C481T, A803G, C282T, G590A, G857A 
               
               
                 and G191A of N-acetyltransferase 2 (NAT2), 
               
               
                 The polymorphisms G636A, G681A, C680T, A1G, IVS5 + 2T &gt; A, 
               
               
                 T358C, G431A and C1297T of the cytochrome P450 2C19 
               
               
                 (CYP2C19), 
               
               
                 The polymorphism C2664T of the glutamate receptor 
               
               
                 ionotropic, N-methyl D-asparate (NMDA) 2B (GRIN2B), 
               
               
                 The polymorphism C3435T of glycoprotein P (ABCB1), 
               
               
                 The polymorphisms A719G and G238C of thiopurine S- 
               
               
                 methyltransferase (TPMT), 
               
               
                 The polymorphism C677T of 5,10- 
               
               
                 methylenetetrahydrofolatereductase (MTHFR) 
               
               
                 The polymorphisms Asp70Gly and Ala539Thr of 
               
               
                 butyrylcholinesterase (BCHE), 
               
               
                 The polymorphism A-392G of the cytochrome P450 3A4 (CYP3A4), 
               
               
                 The polymorphisms A-163C, A-3860G, G3534A and C558A of the 
               
               
                 cytochrome P450 1A2 (CYP1A2), 
               
               
                 The polymorphisms G14690A, C3699T, G19386A, T29753C and 
               
               
                 G6986A of the cytochrome P450 3A5 (CYP3A5), 
               
               
                 The polymorphism 44 bp deletion of the promotor of the 
               
               
                 serotonin transporter (SLC6A4), 
               
               
                 The polymorphism delAGA (allele*B) of Glutathione S- 
               
               
                 transferase M3 (GSTM3), 
               
               
                 The polymorphism null allele of Glutathione S-transferase M1 
               
               
                 (GSTM1), 
               
               
                 The polymorphism null allele of Glutathione S-transferase n1 
               
               
                 (GSTT1), 
               
               
                 The polymorphisms Cys112Arg and Arg158Cys of apolipoprotein 
               
               
                 E (APOE), 
               
               
                 The polymorphism G-308A of Tumor necrosis factor (TNF), and 
               
               
                 The polymorphism G-1082A of Interleukin 10 (IL10) 
               
               
                   
               
            
           
         
       
     
     The sequences of all the genes mentioned in Tables 1-3 are known and recognized on the following websites: GeneBank (NCBI), GeneCard (Weizmann Institute of Sciences) and Snpper.chip.org (Innate Immunity PGA). 
     By permitting clinical genotyping of one or more of the above genetic variations, the present method has use in for example, diagnosing susceptibility to or the presence of IBD or adverse reactions to pharmaceuticals. The methods also allow reliable determination of erythrocyte antigens and are useful in blood grouping or typing. 
     At least one genetic variation is analysed in the present methods. The present methods allow simultaneous genotyping of multiple variations in an individual and typically multiple variations are analysed, in general, at least 10, 12, 14, 16, 18 or 20 genetic variations. For example, 30, 40, 50, 60, 70, 80 or 100 variations or up to 200, 300, 400, 500, or 600 variations may be tested, such as 250, 350 or 450 variations. 
     Thus the present methods may be used for genotyping an individual with respect to all of the variations in any one of Tables 1 to 3, or a selection of the variations in any one of the Tables, as described herein. Thus the variations to be detected may comprise or be selected from any one of Tables 1 to 3. 
     According to the present methods, a sample is provided, containing nucleic acid which comprises at least one of the genetic variations to be tested (the target DNA). The nucleic acid comprises one or more target regions comprising the genetic variation(s) which are to be characterised. 
     The nucleic acid may be obtained from any appropriate biological sample which contains nucleic acid. The sample may be taken from a fluid or tissue, secretion, cell or cell line derived from the human body. 
     For example, samples may be taken from blood, including serum, lymphocytes, lymphoblastoid cells, fibroblasts, platelets, mononuclear cells or other blood cells, from saliva, liver, kidney, pancreas or heart, urine or from any other tissue, fluid, cell or cell line derived from the human body. For example, a suitable sample may be a sample of cells from the buccal cavity. Preferably nucleic acid is obtained from a blood sample. 
     In general, nucleic acid is extracted from the biological sample using conventional techniques. The nucleic acid to be extracted from the biological sample may be DNA, or RNA, typically total RNA. Typically RNA is extracted if the genetic variation to be studied is situated in the coding sequence of a gene. Where RNA is extracted from the biological sample, the methods further comprise a step of obtaining cDNA from the RNA. This may be carried out using conventional methods, such as reverse transcription using suitable primers. Subsequent procedures are then carried out on the extracted DNA or the cDNA obtained from extracted RNA. The term DNA, as used herein, may include both DNA and cDNA. 
     In general the genetic variations to be tested are known and characterised, e.g. in terms of sequence. Therefore nucleic acid regions comprising the genetic variations may be obtained using methods known in the art. 
     In one aspect, DNA regions which contain the genetic variations to be identified (target DNA regions) are subjected to an amplification reaction in order to obtain amplification products which contain the genetic variations to be identified. Any suitable technique or method may be used for amplification. In general, the technique allows the (simultaneous) amplification of all the DNA sequences containing the genetic variations to be identified. In other words, where multiple genetic variations are to be analysed, it is preferable to simultaneously amplify all of the corresponding target DNA regions (comprising the variations). Carrying out the amplification in a single step (or as few steps as possible) simplifies the method. 
     For example, multiplex PCR may be carried out, using appropriate pairs of oligonucleotide PCR primers which are capable of amplifying the target regions containing the genetic variations to be identified. Any suitable pair of primers which allow specific amplification of a target DNA region may be used. In one aspect, the primers allow amplification in the least possible number of PCR reactions. Thus, by using appropriate pairs of oligonucleotide primers and appropriate conditions, all of the target DNA regions necessary for genotyping the genetic variations can be amplified for genotyping (e.g. DNA-chip) analysis with the minimum number of reactions. Suitable PCR primers for amplification of target DNA regions comprising genetic variations associated with erythrocyte antigens, IBD, or adverse reaction to pharmaceuticals, are described herein. In particular, PCR primers for amplification of target DNA regions comprising the genetic variations associated with IBD in Table 1 are listed in SEQ ID NOS 1-124 and 1317-1428. PCR primers for amplification of target DNA regions comprising the genetic variations associated with adverse reaction to drugs in Table 3 are listed in SEQ ID NOS 125-254. The present method may comprise the use of one or more of these primers or one or more of the listed primer pairs. 
     In one instance, the amplification products can be labelled during the amplification reaction with a detectable label. The aim is to be able to later detect hybridisation between the fragments of target DNA containing the genetic variations being analysed and probes fixed on a solid support. The greater the extent of hybridisation of labelled target DNA to a probe, the greater the intensity of detectable label at that probe position. 
     The amplification products may be labelled by conventional methods. For example, a labelled nucleotide may be incorporated during the amplification reaction or labelled primers may be used for amplification. 
     Labelling may be direct using for example, fluorescent or radioactive markers or any other marker known by persons skilled in the art. Examples of fluorophores which can be used, include for example, Cy3 or Cy5. Alternatively enzymes may be used for sample labelling, for example alkaline phosphatase or peroxidase. Examples of radioactive isotopes which can be used include for example  33 P,  125 I, or any other marker known by persons skilled in the art. In one instance, labelling of amplification products is carried out using a nucleotide which has been labelled directly or indirectly with one or more fluorophores. In another example, labelling of amplification products is carried out using primers labelled directly or indirectly with one or more fluorophores. 
     Labelling may also be indirect, using, for example, chemical or enzymatic methods. For example, an amplification product may incorporate one member of a specific binding pair, for example avidin or streptavidin, conjugated with a fluorescent marker and the probe to which it will hybridise may be joined to the other member of the specific binding pair, for example biotin (indicator), allowing the probe/target binding signal to be measured by fluorimetry. In another example, an amplification product may incorporate one member of a specific binding pair, for example, an anti-dioxigenin antibody combined with an enzyme (marker) and the probe to which it will hybridise may be joined to the other member of the specific binding pair, for example dioxigenin (indicator). On hybridization of amplification product to probe the enzyme substrate is converted into a luminous or fluorescent product and the signal can be read by, for example, chemi-luminescence or fluorometry. 
     The nucleic acid comprising the genetic variation(s) to be tested, e.g. the (optionally labelled) amplification products, may further undergo a fragmentation reaction, thereby obtaining some fragmentation products which comprise or contain the genetic variations to be identified or analysed. Typically fragmentation increases the efficiency of the hybridisation reaction. Fragmentation may be carried out by any suitable method known in the art, for example, by contacting the nucleic acid, e.g. the amplification products with a suitable enzyme such as a DNase. 
     If the nucleic acid has not been previously labelled, e.g. during the amplification reaction, (and, typically, where no posthybridisation amplification or ligation is carried out on the solid support) then labelling with a detectable label may be carried out prehybridisation by labelling the fragmentation products. Suitable labelling techniques are known in the art and may be direct or indirect as described herein. Direct labelling may comprise the use of, for example, fluorophores, enzymes or radioactive isotopes. Indirect labelling may comprise the use of, for example, specific binding pairs that incorporate e.g. fluorophores, enzymes, etc. For example, if amplification products have not been labelled during the amplification reaction the fragmentation products may undergo a direct or indirect labelling with one or various markers, for example one or various fluorophores, although other known markers can be used by those skilled in the art. 
     According to the present methods the nucleic acid, e.g. the amplification or fragmentation products, comprising the genetic variation(s) to be detected (target DNA), is contacted with oligonucleotide probes which are capable of detecting the corresponding genetic variations by hybridisation under suitable conditions. 
     Typically the hybridisation conditions allow specific hybridisation between probes and corresponding target nucleic acids to form specific probe/target hybridisation complexes while minimising hybridisation between probes carrying one or more mismatches to the DNA. Such conditions may be determined empirically, for example by varying the time and/or temperature of hybridisation and/or the number and stringency of the array washing steps that are performed following hybridisation and are designed to eliminate all probe-DNA interactions that are inspecific. 
     In the method, the probes are provided deposited on a solid support or surface. The probes are deposited at positions on the solid support according to a predetermined pattern, forming a “DNA-chip”. It has been found that the chips should comply with a number of requirements in order to be used in the present methods, for example in terms of the design of the probes, the number of probes provided for each genetic variation to be detected and the distribution of probes on the support. These are described in detail herein. The inventors have developed suitable genotyping chips for use in the present methods and accordingly in one aspect the invention provides a DNA-chip or (micro)array comprising a plurality of probes deposited or immobilised on a solid support as described herein. 
     In general the solid support or phase comprises oligonucleotide probes suitable for detection of each genetic variation to be tested. The number and type of genetic variations to be tested using a chip may be selected as described herein. 
     Typically there will be at least one probe which is capable of hybridising specifically to genetic variation A (e.g. a wildtype or normal allele) (probe 1) and one probe which is capable of hybridising specifically to genetic variation B (e.g. a mutant allele) (probe 2) under the selected hybridisation conditions. These probes form a probe pair. Probe 1 is for detection of genetic variation A and probe 2 for detection of genetic variation B. Typically the probes can be used to discriminate between A and B (e.g. the wildtype and mutant alleles). 
     The probes may examine either the sense or the antisense strand. Typically, probes 1 and 2 examine the same nucleic acid strand (e.g. the sense strand or antisense strand) although in some cases the probes may examine different strands. In one aspect probes 1 and 2 have the same sequence except for the site of the genetic variation. 
     In one instance, the probes in a probe pair have the same length. In some aspects, where two or more pairs of probes are provided for analysis of a genetic variation, the probes may all have the same length. 
     Preferably more than one probe pair is provided for detection of each genetic variation. Thus, at least 2, 3, 4, 5, 6, 7, 8, 9, 10 or more probe pairs may be provided per genetic variation. In one aspect, (at least) 2 probe pairs are provided. The aim is to reduce the rate of false positives and negatives in the present methods. 
     For example, for a given genetic variation there may be:
     Probe 1 which is capable of hybridising to genetic variation A (e.g. a normal allele)   Probe 2 which is capable of hybridising to genetic variation B (e.g. a mutant allele)   Probe 3 which is capable of hybridising to genetic variation A (e.g. a normal allele)   Probe 4 which is capable of hybridising to genetic variation B (e.g. a mutant allele).   

     The probes may examine the same or different strands. Thus in one embodiment, probes 3 and 4 are the complementary probes of probes 1 and 2 respectively and are designed to examine the complementary strand. In one aspect it is preferred that the probes provided for detection of each genetic variation examine both strands. 
     More than 2 pairs of probes may be provided for analysis of a genetic variation as above. For example, where a genetic variation exists as any one of 4 bases in the same strand (e.g. there are three mutant possibilities), at least one pair of probes may be provided to detect each possibility. Preferably, at least 2 pairs of probes are provided for each possibility. 
     Thus, for example, for the SNP G2677T/A/C, at least one pair of probes may be provided for detection of G2677T, one pair for detection of G2677/A, and one pair for detection of G2677C. Preferably at least two pairs of probes are provided for each of these substitutions. 
     A number of methods are known in the art for designing oligonucleotide probes suitable for use in DNA-chips. 
     A “standard tiling” method may be used. In this method, 4 oligonucleotides are designed that are totally complementary to the reference sequence except in the central position where, typically the 4 possible nucleotides A, C, G and T are examined. An illustrative example of this strategy is the DNA-chip for genotyping of HIV-1 (Affymetrix). 
     In “alternative tiling” 5 oligonucleotides are designed, so that the fifth examines a possible deletion in the sequence. An example of this strategy is the DNA-chip to detect mutations in p53 (Affymetrix). 
     In “block tiling” 4 oligonucleotides are designed that are totally complementary to the normal sequence and another 4 totally complementary to the mutant sequence. The nucleotide which changes is placed in the central position, but a mismatch of one of the 4 bases (A, C, T or G) is placed 2 nucleotides before or after the nucleotide position that it is wished to interrogate. An example of this strategy is the DNA-chip for the detection of mutations in cytochrome p450 (Roche and Affymetrix). 
     A further example is “alternative block tiling” where the “mismatch” is used to increase the specificity of the hybrid not only in one position but also in the positions −4, −1, 0, +1 and +4 to identify the change produced in the central position or 0. An example is the DNA-chip to detect 1,500 SNPs (Affymetrix). 
     Any one or more of these strategies may be used to design probes for the present invention. Preferably standard tiling is used, in particular with 2 pairs of probes e.g. 2 pairs of complementary probes as above. Thus it is preferable that the oligonucleotide sequence is complementary to the target DNA or sequence in the regions flanking the variable nucleotide(s). However, in some cases, one or more mismatches may be introduced, as described above. 
     The oligonucleotide probes for use in the present invention typically present the base to be examined (the site of the genetic variation) at the centre of the oligonucleotide. This is particularly the case where differential hybridisation methods are used, as in general this allows the best discrimination between matched and mismatched probes. In these methods, typically there is formation of specific detectable hybridisation complexes without post-hybridisation on-chip amplification. For example, for precise (single base) mutations, the base which differs between the normal and the mutant allele is typically placed in the central position of the probe. In the case of insertions, deletions and duplications, the first nucleotide which differs between the normal and the mutant sequence is placed in the central position. It is believed that placing the mutation at the centre of the probe maximises specificity. 
     Where post-hybridisation on-chip amplification (e.g. ligation or primer extension methods) is employed, oligonucleotide probes typically present the variable base(s) at the 3′ end of the probe. Where OLA methodology is used, oligonucleotides (labelled directly or indirectly) are also designed which hybridise to probe-target complexes to allow ligation. 
     In general the probes for use in the present invention comprise or in some embodiments consist (essentially) of 17 to 27 nucleotides, for example, 19, 21, 23, or 25 nucleotides or 18, 20, 22, 24 or 26 nucleotides. 
     Preferably the individual probes provided for detection of a genetic variation are capable of hybridising specifically to the normal and mutant alleles respectively under the selected hybridisation conditions. For example, the melting temperature of the probe/target complexes may occur at 75-85 degrees C. and hybridisation may be for one hour, although higher and lower temperatures and longer or shorter hybridisations may also suffice. 
     The probes provided for detection of each genetic variation (as described above) are typically capable of discriminating between genetic variation A and B (e.g. the normal and mutant alleles) under the given hybridisation conditions as above. Preferably the discrimination capacity of the probes is substantially 100%. If the discrimination capacity is not 100%, the probes are preferably redesigned. Preferably the melting temperature of the probe/target complexes occurs at 75-85 degrees C. Methods for testing discrimination capacity are described herein. 
     In one example, the probes provided for detection of a genetic variation examine both strands and have lengths ranging from 19-27 nucleotides. Preferably the probes have 100% discrimination capacity and the melting temperature of probe/target complexes is 75-85 degrees C. 
     Typically in order to obtain probes for use in the present methods, a number of probes are designed and tested experimentally for, e.g. hybridisation specificity and ability to discriminate between genetic variants (e.g. a normal and a mutant allele). Candidate oligonucleotide probe sequences may be designed as described above. These may vary for example in length, strand specificity, position of the genetic variation and degree of complementarity to the sequence flanking the genetic variation in the target DNA. Once probe pairs have been designed, these can be tested for hybridisation specificity and discrimination capacity. The capacity of specific probes to discriminate between the genetic variations A and B (e.g. normal and mutant alleles) depends on hybridisation conditions, the sequence flanking the mutation and the secondary structure of the sequence in the region of the mutation. By using stable hybridisation conditions, appropriate parameters such as strand specificities and lengths can be established in order to maximise discrimination. Preferably, the genetic variation is maintained at the central position in the tested probes. 
     Methods for testing discrimination capacity of probes are described herein. Typically a number of candidate probe pairs are provided and used in a training method as described below. In general two pairs of probes (probes 1 and 2, and probes 3 and 4) are tested in the method. For example, two pairs of probes examining both strands (complementary to each other) may be tested. If it is not possible to obtain 100% discrimination between the three genotyping groups using the probes, the probes are typically redesigned. Hybridisation conditions in the training method are generally maintained stably. Typically the melting temperature of probe/target complexes is 75-85 degrees C. 
     For example, starting from probes of 25 nucleotides which detect a genetic variation (e.g. the normal allele) and another genetic variation (e.g. a mutant allele) in both strands (sense and antisense), in general an average of 8 probes may be experimentally tested to identify two definite pairs. 
     Probes are chosen to have maximum hybridisation specificity and discrimination capacity between genetic variants (e.g. a normal and a mutant allele) under suitable hybridisation conditions. For example, the probes for detection of a given genetic variation, e.g. two probe pairs, typically have substantially 100% discrimination capacity. Typically the melting temperature of probe/target complexes is at 75-85° C. 
     Using the methods herein the inventors have developed oligonucleotide probes suitable for detection of the IBD-associated genetic variations in Table 1. These probes are presented as SEQ ID NOS 631-960 and 1429-1652. The probes are listed in probe sets (133 sets in total), each set being for detection of a given genetic variation. At least two pairs of probes are listed in each set. 
     The inventors have also developed oligonucleotide probes suitable for detection of the erythrocyte antigen-associated genetic variations in Table 2. These probes are presented as SEQ ID NOS 255-630. The probes are listed in probe sets (94 sets in total), each set being for detection of a given genetic variation. At least two pairs of probes are listed in each set. 
     The inventors have also developed oligonucleotide probes suitable for detection of the genetic variations associated with adverse reactions to drugs in Table 3. These probes are presented as SEQ ID NOS 961-1316. The probes are listed in probe sets (89 sets in total), each set being for detection of a given genetic variation. At least two pairs of probes are listed in each set. 
     In one aspect the invention relates to any one or more of the oligonucleotide probes, pairs of probes or sets of probes set out in SEQ ID NOS 255-630, 631-960, 961-1316 or 1429-1652, and to their use in the genotyping, diagnostic or therapeutic methods of the invention. The invention further relates to any one or more of the oligonucleotide probes, pairs of probes or sets of probes set out in SEQ ID NOS 255-630, 631-960, 961-1316 or 1429-1652 for use in medicine, for example in a diagnostic or therapeutic method described herein. A chip of the invention may comprise one or more of the listed probe pairs or sets. 
     In general probes are provided on the support in replicate. Typically, at least 4, 6, 8, 10, 12, 14, 16, 18 or 20 replicates are provided of each probe, in particular, 6, 8 or 10 replicates. Thus for example, the support (or DNA-chip) may comprise or include 10 replicates for each of (at least) 4 probes used to detect each genetic variation (i.e. 40 probes). Alternatively the support (or DNA-chip) may comprise or include 8 replicates for each of (at least) 4 probes used to detect each genetic variation (i.e. 32 probes). Still further the support (or DNA-chip) may comprise or include 6 replicates for each of (at least) 4 probes used to detect each genetic variation (i.e. 24 probes). Using probe replicates helps to minimise distortions in data interpretation from the chip and improves reliability of the methods. 
     In general the support also comprises one or more control oligonucleotide probes. These are also provided in replicate as above. Thus the support (or DNA-chip) may additionally comprise one or more oligonucleotides deposited on the support which are useful as positive and/or negative controls of the hybridisation reactions. If post-hybridisation amplification or ligation reactions are carried out on the chip, there may also be one or more positive or negative controls of these reactions. 
     Typically the chip or array will include positive control probes, e.g., probes known to be complementary and hybridisable to sequences in the target polynucleotide molecules, probes known to hybridise to an external control DNA, and negative control probes, e.g., probes known to not be complementary and hybridizable to sequences in the target polynucleotide molecules. The chip may have one or more controls specific for each target, for example, 2, 3, or more controls. There may also be at least one control for the array. 
     Positive controls may for example be synthesized along the perimeter of the array or in diagonal stripes across the array. The reverse complement for each probe may be synthesized next to the position of the probe to serve as a negative control. In yet another example, sequences from other species of organism may be used as negative controls in order to help determine background (non-specific) hybridisation. 
     As above, the support (or DNA-chip) may include some (one or more) oligonucleotides deposited on the support which are useful as positive and negative controls of the hybridization reactions. In general, each one of the sub-arrays, for example 16, which typically constitute a DNA-chip, is flanked by some external hybridization controls, which serve as reference points allowing allow the points within the grid to be located more easily. 
     In one instance, the nucleotide sequence of an external control DNA is the following (5′→3′): 
                    CEH:                     GTCGTCAAGATGCTACCGTTCAGGAGTCGTCAAG   SEQ ID NO:1653                 ATGCTACCGTTCAGGA            
and the sequences of the oligonucleotides for its detection are the following:
 
     
       
         
           
               
            
               
                 ON1: 
               
            
           
           
               
               
            
               
                 CTTGACGACTCCTGAACGG 
                 SEQ ID NO:1654 
               
               
                   
               
            
           
           
               
            
               
                 ON2: 
               
            
           
           
               
               
            
               
                 CTTGACGACACCTGAACGG 
                 SEQ ID NO:1655 
               
            
           
         
       
     
     Positive control probes are generally designed to hybridise equally to all target DNA samples and provide a reference signal intensity against which hybridisation of the target DNA (sample) to the test probes can be compared. Negative controls comprise either “blanks” where only solvent (DMSO) has been applied to the support or control oligonucleotides that have been selected to show no, or only minimal, hybridisation to the target, e.g. human, DNA (the test DNA). The intensity of any signal detected at either blank or negative control oligonucleotide features is an indication of non-specific interactions between the sample DNA and the array and is thus a measure of the background signal against which the signal from real probe-sample interactions must be discriminated. 
     Desirably, the number of sequences in the array will be such that where the number of nucleic acids suitable for detection of genetic variations is n, the number of positive and negative control nucleic acids is n′, where n′ is typically from 0.01 to 0.4n. 
     In general, the support or chip is suitable for genotyping, in particular, genotyping according to the present methods. The chip typically comprises probes suitable for detection of at least one but preferably multiple, genetic variation(s), typically at least 10, 12, 14, 16, 18 or 20 genetic variations. For example, 30, 40, 50, 60, 70, 80 or 100 variations or up to 200, 300, 400, 500, or 600 variations may be tested, such as 250, 350 or 450 variations. 
     The genetic variations may be those in any one of Tables 1 to 3. Thus an array may comprise probes suitable for genotyping an individual with respect to all of the variations in any one of Tables 1 to 3, or a selection of the variations in any one of the Tables, as described above. 
     The present DNA-chips can be used, in combination with the present methods, to detect practically any human genetic variation of interest, for example, human genetic variations associated with diseases or antigens of interest. Suitable probes will be used for those genetic variations to be detected. As genetic variations associated with the diseases or antigens of interest are identified, suitable probes for their detection can be incorporated in the chips. Probes and DNA-chips for this purpose can be designed in accordance with the teaching of the present invention. 
     The inventors have designed, produced and validated the clinical use of the invention in detection of genetic variations associated with IBD, with known human erythrocyte antigens and with adverse reactions to medicine by developing (designing and producing) corresponding DNA-chips. 
     Therefore, in one particular embodiment, the invention relates to a chip for genotyping of genetic variations associated with IBD (an “IBD-chip”). Typically the DNA-chip allows simultaneous, sensitive, specific and reproducible detection of genetic variations associated with IBD. Non-limiting examples of such variations are given in Table 1. Nevertheless, the number of genetic variations contained in the Table can be increased as other genetic variations are subsequently identified and are associated with IBD. Thus the genetic variations detectable by the chip may comprise, or consist (essentially) of those listed in Table 1 or a selection of these. The chip will comprise probes suitable for detection of these genetic variations as described herein. In one aspect the chip comprises probes selected from those in SEQ ID NOS 631-960 and 1429-1652. The probes are listed in probe sets (133 sets in total), each set being for detection of a given genetic variation. At least two pairs of probes are provided in each set. A chip may comprise at least one probe pair or at least one probe set, or a selection of the probe sets, for example, at least 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130 or all 133 sets, according to the genetic variations being tested. A chip may comprise other probes for detection of variations in Table 1 or other variations associated with IBD instead of or in addition to those specifically listed. 
     In another embodiment the chip is for genotyping of genetic variations associated with erythrocyte antigens (the “blood chip”). Typically the DNA-chip allows the simultaneous, sensitive, specific and reproducible detection of genetic variations associated with determined erythrocyte antigens. Non-limiting examples of such variations are given in Table 2. Nonetheless the number of genetic variations contained in the table can be increased as other genetic variations are subsequently identified and are associated with erythrocyte antigens. Thus the genetic variations detectable by the chip may comprise, or consist (essentially) of those listed in Table 2 or a selection of these. The chip will comprise probes suitable for detection of these genetic variations as described herein. In one aspect the chip comprises probes selected from those in SEQ ID NOS 255-630. The probes are listed in probe sets (94 sets in total), each set being for detection of a given genetic variation. At least two pairs of probes are provided in each set. A chip may comprise at least one probe pair or at least one probe set, or a selection of the probe sets, for example, at least 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or all 94 sets, according to the genetic variations being tested. A chip may comprise other probes for detection of variations in Table 2 or other variations associated with erythrocyte antigens instead of or in addition to those specifically listed. 
     In another embodiment the chip is for genotyping of genetic variations associated with adverse reactions to pharmaceuticals (the “drug chip”). Typically the chip allows the simultaneous, sensitive, specific and reproducible detection of genetic variations associated with adverse reactions to medicine. Non-limiting examples are given in Table 3. Nevertheless, the number of genetic variations contained in the table can be increased as other genetic variations are subsequently identified and are associated with these adverse reactions. Thus the genetic variations detectable by the chip may comprise, or consist (essentially) of those listed in Table 3 or a selection of these. The chip will comprise probes suitable for detection of these genetic variations as described herein. In one aspect the chip comprises probes selected from those in SEQ ID NOS 961-1316. The probes are listed in probe sets (89 sets in total), each set being for detection of a given genetic variation. At least two pairs of probes are provided in each set. A chip may comprise at least one probe pair or at least one probe set, or a selection of the probe sets, for example, at least 5, 10, 20, 30, 40, 50, 60, 70, 80, or all 89 sets, according to the genetic variations being tested. A chip may comprise other probes for detection of variations in Table 3 or other variations associated with adverse reactions to drugs instead of or in addition to those specifically listed. 
     An IBD chip, blood chip or drug chip may additionally comprise oligonucleotide probes for detection of genetic variations not associated with IBD, erythrocyte antigens or adverse reactions to drugs respectively. For example, the chips may comprise probes for detection of genetic variations such as SNPs associated with another (related) condition or other (related) antigen(s). Typically, in an IBD chip, blood chip or drug chip, the number of nucleic acids suitable for detection of genetic variations associated with IBD, erythrocyte antigens or adverse reactions to drugs respectively (e.g. those in Tables 1, 2, or 3) represent at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or more of the nucleic acids in the array. 
     In general the support or chip has from 300 to 40000 nucleic acids (probes), for example, from 400 to 30000 or 400 to 20000. The chip may have from 1000 to 20000 probes, such as 1000 to 15000 or 1000 to 10000, or 1000 to 5000. A suitable chip may have from 2000 to 20000, 2000 to 10000 or 2000 to 5000 probes. For example, a chip may have 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 12000, 14000, 16000, 18000 or 20000 probes. Smaller chips 400 to 1000 probes, such as 400, 500, 600, 700, 800, 900 or 950 probes are also envisaged. 
     In general the array or chip of the invention comprises a support or surface with an ordered array of binding (e.g. hybridisation) sites or probes. Thus the arrangement of probes on the support is predetermined. Each probe (i.e each probe replicate) is located at a known predetermined position on the solid support such that the identity (i.e. the sequence) of each probe can be determined from its position in the array. Typically the probes are uniformly distributed in a predetermined pattern. 
     Preferably, the probes deposited on the support, although they maintain a predetermined arrangement, are not grouped by genetic variation but have a random distribution. Typically they are also not grouped within the same genetic variation. If desired, this random distribution can be always the same. Therefore, typically the probes are deposited on the solid support (in an array) following a predetermined pattern so that they are uniformly distributed, for example, between the two areas that may constitute a DNA-chip, but not grouped according to the genetic variation to be characterised. Distributing probe replicates across the array in this way helps to reduce or eliminate any distortion of signal and data interpretation, e.g. arising from a non-uniform distribution of background noise across the array. 
     As explained above, probes may be arranged on the support in subarrays. 
     The support, on which the plurality of probes is deposited, can be any solid support to which oligonucleotides can be attached. Practically any support, to which an oligonucleotide can be joined or immobilized, and which may be used in the production of DNA-chips, can be used in the invention. For example, the said support can be of a non-porous material, for example, glass, silicone, plastic, or a porous material such as a membrane or filter (for example, nylon, nitrocelullose) or a gel. In one embodiment, the said support is a glass support, such as a glass slide. 
     Microarrays are in general prepared by selecting probes which comprise a given polynucleotide sequence, and then immobilizing such probes to a solid support or surface. Probes may be designed, tested and selected as described herein. In general the probes may comprise DNA sequences. In some embodiments the probes may comprise RNA sequences, or copolymer sequences of DNA and RNA. The polynucleotide sequences of the probes may also comprise DNA and/or RNA analogues, or combinations thereof. For example, the polynucleotide sequences of the probes may be full or partial fragments of genomic DNA. The polynucleotide sequences of the probes may also be synthesized nucleotide sequences, such as synthetic oligonucleotide sequences. The probe sequences can be synthesized either enzymatically in vivo, enzymatically in vitro (e.g., by PCR), or non-enzymatically in vitro. 
     Microarrays or chips can be made in a number of ways. However produced, microarrays typically share certain characteristics. The arrays are reproducible, allowing multiple copies of a given array to be produced and easily compared with each other. Preferably, microarrays are made from materials that are stable under binding (e.g., nucleic acid hybridization) conditions. The microarrays are preferably small, e.g., between 0.25 to 25 or 0.5 to 20 cm 2 , such 0.5 to 20 cm 2  or 0.5 to 15 cm 2 , for example, 1 to 15 cm 2  or 1 to 10 cm 2 , such as 2, 4, 6 or 9 cm 2 . 
     Probes may be attached to the present support using conventional techniques for immobilization of oligonucleotides on the surface of the supports. The techniques used depend, amongst other factors, on the nature of the support used [porous (membranes, micro-particles, etc.) or non-porous (glass, plastic, silicone, etc.)] In general, the probes can be immobilized on the support either by using non-covalent immobilization techniques or by using immobilization techniques based on the covalent binding of the probes to the support by chemical processes. 
     Preparation of non-porous supports (e.g., glass, silicone, plastic) requires, in general, either pre-treatment with reactive groups (e.g., amino, aldehyde) or covering the surface of the support with a member of a specific binding pair (e.g. avidin, streptavidin). Likewise, in general, it is advisable to pre-activate the probes to be immobilized by means of corresponding groups such as thiol, amino or biotin, in order to achieve a specific immobilization of the probes on the support. 
     The immobilization of the probes on the support can be carried out by conventional methods, for example, by means of techniques based on the synthesis in situ of probes on the support (e.g., photolithography, direct chemical synthesis, etc.) or by techniques based on, for example, robotic arms which deposit the corresponding pre-synthesized probe (e.g. printing without contact, printing by contact). 
     In one embodiment, the support is a glass slide and in this case, the probes, in the number of established replicates (for example, 6, 8 or 10) are printed on pre-treated glass slides, for example coated with aminosilanes, using equipment for automated production of DNA-chips by deposition of the oligonucleotides on the glass slides (“micro-arrayer”). Deposition is carried out under appropriate conditions, for example, by means of crosslinking with ultraviolet radiation and heating (80° C.), maintaining the humidity and controlling the temperature during the process of deposition, typically at a relative humidity of between 40-50% and typically at a temperature of 20° C. 
     The replicate probes are distributed uniformly amongst the areas or sectors (sub-arrays), which typically constitute a DNA-chip. The number of replicas and their uniform distribution across the DNA-chip minimizes the variability arising from the printing process that can affect experimental results. Likewise, positive and negative hybridisation controls (as described herein) may be printed. 
     To control the quality of the manufacturing process of the DNA-chip, in terms of hybridization signal, background noise, specificity, sensitivity and reproducibility of each replica as well as differences caused by variations in the morphology of the spotted probe features after printing, a commercial DNA can be used. For example, as a quality control of the printing of the DNA-chips, hybridization may be carried out with a commercial DNA (e.g. k562 DNA High Molecular Weight, Promega) 
     In the first place, the morphology and size of the printed spots are analyzed. In the hybridization with control DNA the parameters described below for determining reliability of genotype determination, are adhered to; specifically the relationship between the signal intensity and background noise, average specificity and sensitivity and reproducibility between replicated copies of the same probe. This method allows the correct genotype of the control DNA to be determined. 
     As above, in accordance with the present method, a nucleic acid sample, e.g. amplification or fragmentation products, comprising the genetic variation(s) to be detected (target DNA) is contacted with a probe array as described herein, under conditions which allow hybridisation to occur between target DNA and the corresponding probes. Specific hybridisation complexes are thus formed between target nucleic acid and corresponding probes. 
     The hybridization of e.g. fragmentation products, with probes capable of detecting corresponding genetic variations deposited on a support may be carried out using conventional methods and devices. In one instance, hybridization is carried out using an automated hybridisation station. For hybridization to occur, the e.g. fragmentation products, are placed in contact with the probes under conditions which allow hybridization to take place. Using stable hybridization conditions allows the length and sequence of the probes to be optimised in order to maximize the discrimination between genetic variations A and B, e.g. between wild type and mutant sequences, as described herein. 
     In one instance, the method relies on differential hybridisation, in particular an increase in hybridisation signal. The method involves formation of specific hybridisation complexes between target DNA and corresponding probes. Thus target DNA bearing the wild type sequence will hybridise to the probes designed to detect the wild type sequence, whereas target DNA bearing a mutant sequence will hybridise to the probes designed to detect that mutant sequence. The hybridisation complexes are detectably labelled by means described herein (e.g. the target DNA is directly labelled, or both target and probe are labelled in such a way that the label is only detectable on hybridisation). By detecting the intensity of detectable label (if any) at the predetermined probe positions it is possible to determine the nature of the target DNA in the sample. In this instance the probes (also referred to as allele specific oligonucleotides, ASOs) preferably have the variable nucleotide(s) at the central position, as described herein. 
     In another instance, hybridisation of target DNA to probes on the solid support (chip) may be followed by on-chip amplification, for example, using primer extension or ligation, e.g. oligonucleotide ligation assay (OLA) technologies (Eggerding F A, Iovannisci D M, Brinson E., Grossman P., Winn-Deen E. S. 1995 Human Mutation, 5:153-65). In this case, the probes on the support typically comprise the variable nucleotide(s) at the 3′ end of the probe. 
     Labelling can be carried out during post hybridisation amplification. The labelling can be by direct labelling using, for example, fluorophores, enzymes, radioactive isotopes, etc. or by indirect labelling using, for example, specific binding pairs which incorporate fluorophores, enzymes etc., by using conventional methods, such as those previously mentioned in relation to labelling amplification or fragmentation products. 
     Post-hybridization amplification may be carried out, for example, using the “primer extension” methodology. Typically, after hybridization, an extension reaction of the hybrid oligonucleotides is carried out on the support (e.g. a glass slide). Extension may be carried out with directly or indirectly labelled nucleotides and will only happen if the extreme 3′ of the oligonucleotide hybridizes perfectly with the amplification product. 
     Primer extension is a known method for genotype discrimination (Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen AC. 2000  Genome Research  10:1031-42.) and can be performed in a number of different ways. In a commonly used approach a set of allele specific oligonucleotide probes are designed to hybridise to the target sequences. The probes differ from one another in their extreme 3′ nucleotide, which for each probe is designed to complement one of the possible polymorphic nucleotides at a given position. 
     When the 3′ nucleotide of the probe complements the sequence under test then the ensuing base pairing allows a DNA polymerase to extend the oligonucleotide primer by incorporation of additional nucleotides that can be directly or indirectly labelled thereby allowing the subsequent identification of those probes that have been extended and those that have not. Probes that are successfully extended carry the complementary nucleotide to the SNP at their 3′ end thus allowing the genotype of the test sample to be determined. Similar approaches, for example the Amplification Refractory Mutation System (ARMS) have also been developed. 
     Alternatively, a post hybridization ligation reaction may be carried out, for example using OLA methodology. After hybridization, a ligation reaction of the hybridised oligonucleotides is carried out on the support (e.g. glass slide) with labelled oligonucleotides. A ligation will only take place if the extreme 3′ end of the probe deposited on the support hybridizes perfectly with the target DNA (e.g. amplification product). 
     The oligonucleotide ligation assay (OLA) is another method for interrogating SNPs (Eggerding F A, Iovannisci D M, Brinson E., Grossman P., Winn-Deen E. S. 1995 Human Mutation, 5:153-65). OLA uses a pair of oligonucleotide probes that hybridize to adjacent segments of target DNA including the variable base. The probe designed to hybridise to the 5′ side of the polymorphic nucleotide is an allele-specific oligonucleotide (ASO) to one of the target alleles. The last base at the 3′ end of this ASO is positioned at the site of the target DNA&#39;s polymorphism; the ASO typically also has a biotin molecule at its 5′ end that functions as a “hook” that can subsequently be used to recover the oligonucleotide by virtue of the highly specific interaction that biotin undergoes with streptavidin. 
     The oligomer on the 3′ or right-hand side of the pair is the common oligomer (the sequence is the same for the two or more different alleles it is wished to test.) The common oligomer is positioned at an invariable site next to the target DNA&#39;s polymorphism and is fluorescently labelled at its 3′ end. 
     If the ASO is perfectly complementary to the target sequence the ASO hybridizes completely when annealed and will lie flat against that target allowing DNA ligase to covalently join the ASO to the common oligomer. After the ligation reaction the biotin hook is used to remove the ASO and the e.g. fluorescently labeled common oligomer will also be removed, producing detectable fluorescence. 
     When the ASO is not a perfect match to the target sequence hybridization is incomplete and the 3′ base of the oligomer will not be base-paired to the target DNA thus preventing ligation. Under these circumstances when the biotin hook is used to remove the ASO, the common oligonucleotide will not be removed and therefore there is no detectable label, e.g. fluorescence, in the molecule removed. 
     To distinguish between two known alleles that differ by a single base, three oligonucleotides are necessary: Two are allele-specific oligonucleotides (ASOs) that differ from each other only in the single 3′ terminal base; the first is complementary to one allele and the second is complementary to the second allele. The third oligonucleotide is complementary to the invariable sequence adjacent to the variant base. 
     Once hybridisation (and optionally post-hybridisation amplification) has taken place, the intensity of detectable label at each probe position (including control probes) can be determined. The intensity of the signal (the raw intensity value) is a measure of hybridisation at each probe. 
     The intensity of detectable label at each probe position (each probe replica) may be determined using any suitable means. The means chosen will depend upon the nature of the label. In general an appropriate device, for example, a scanner, collects the image of the hybridized and developed DNA-chip. An image is captured and quantified. 
     In one instance, e.g. where fluorescent labelling is used, after hybridization, (optionally after post-hybridization amplification or ligation) the hybridized and developed DNA-chip is placed in a scanner in order to quantify the intensity of labelling at the points where hybridization has taken place. Although practically any scanner can be used, in one embodiment a fluorescence confocal scanner is used. In this case, the DNA-chip is placed in the said apparatus and the signal emitted by the fluorpohore due to excitation by a laser is scanned in order to quantify the signal intensity at the points where hybridization has taken place. Non-limiting examples of scanners which can be used according to the present invention, include scanners marketed by the following companies: Axon, Agilent, Perkin Elmer, etc. 
     Typically, in determining the intensity of detectable label at each probe position (i.e for each probe replica), account is taken of background noise, which is eliminated. Background noise arises because of non-specific binding to the probe array and may be determined by means of controls included in the array. Once the intensity of the background signal has been determined, this can be subtracted from the raw intensity value for each probe replica in order to obtain a clean intensity value. Typically the local background, based on the signal intensity detected in the vicinity of each individual feature is subtracted from the raw signal intensity value. This background is determined from the signal intensity in a predetermined area surrounding each feature (e.g. an area of X, Y or Z μm2 centred on the position of the probe). The background signal is typically determined from the local signal of “blank” controls (solvent only). In many instances the device, e.g. scanner, which is used to determine signal intensities will provide means for determining background signal. 
     Thus, for example, where the label is a fluorescent label, absolute fluorescence values (raw intensity values) may be gathered for each probe replica and the background noise associated with each probe replica can also be assessed in order to produce “clean” values for signal intensity at each probe position. 
     Once the target DNA has been hybridised to the chip and the intensity of detectable label has been determined at the probe replica positions on the chip (the raw intensity values), it is necessary to provide a method (model) which can relate the intensity data from the chip to the genotype of the individual. 
     The inventors have found that this can be done by applying a suitable algorithm to the intensity data. The algorithm and computer software developed by the inventors allows analysis of the genetic variations with sufficient sensitivity and reproducibility as to allow use in a clinical setting. The algorithm uses three linear functions which characterise each of the three genotypes AA, AB and BB for a given genetic variation. The method generally involves collating the intensity values for all of the replicas of each probe, to calculate an average intensity value for each probe. Optionally, the raw intensity values for each replica may be amended to take account of background noise (to obtain a clean intensity value) before the intensity values for each of the replicas are collated. 
     In general, for a given genetic variation, analysis and interpretation of a chip comprises the following steps:
     (a) providing the intensity of detectable label at each replica for each of at least four probes (probes 1, 2, 3 and 4) provided for detection of the genetic variation (the raw intensity value), wherein:
       probe 1 detects (is capable of specifically hybridising to) genetic variation A (e.g. a normal allele), and probe 2 detects (is capable of specifically hybridising to) genetic variation B (e.g. a mutant allele);   probe 3 detects (is capable of specifically hybridising to) genetic variation A (e.g. a normal allele)and probe 4 detects (is capable of specifically hybridising to) genetic variation B (e.g. a mutant allele); and   probes 1 and 2 form a first probe pair and probes 3 and 4 form a second probe pair;   
       (b) optionally amending the raw intensity value for each replica to take account of background noise, thus obtaining a clean intensity value;   (c) collating the (optionally clean) intensity values for each of the replicas of each probe and determining an average intensity value for each probe;   (d) calculating ratios 1 and 2 wherein:   

     
       
         
           
             
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         (e) inputting ratios 1 and 2 into each of three linear functions which characterise each of the three possible genotypes, AA, AB and BB, wherein: 
         Function 1 is the linear function that characterises individuals with the genotype AA and consists of a linear combination of ratios 1 and 2; 
         Function 2 is the linear function that characterises individuals with the genotype AB and consists of a linear combination of ratios 1 and 2; 
         Function 3 is the linear function that characterises individuals with the genotype BB and consists of a linear combination of ratios 1 and 2; 
         the linear functions are formed by coefficients which accompany the variables ratio 1 and 2; 
         (f) determining which of the three linear functions has the highest value; and 
         (g) thereby determining the genotype of the individual for the genetic variation. 
       
    
     Thus the linear function corresponding to the genotype of that individual will have the highest absolute value. 
     The inventors have found that the use of replicas and averages calculated from replicas is important for reliable working of the invention. Use of the functions speeds up analysis and allows better discrimination. 
     Preferably the discrimination capacity between the three genotypes is (approximately) 100%. If the discrimination is less than 100% the probes are preferably redesigned. 
     The raw intensity value for each probe replica may be determined according to the methods described above. Thus probe sequences and replicas can be selected as described herein. In one example, 4 probes are used per genetic variation and 6, 8 or 10 replicas are used per probe. 
     Typically, amending the raw intensity value to obtain the clean intensity value for each probe replica comprises subtracting background noise from the raw value. Background noise is typically determined using appropriate controls as described herein. 
     Typically calculating the average intensity value comprises eliminating extreme values or outliers. Thus, when the (optionally clean) intensity values from each of the probe replicas are collated, outlying values can be identified and excluded from further consideration. In one embodiment outliers make up between 10% and 50%, for example, 15, 20, 25, 30, 35, 40 or 45% of the values obtained. In one embodiment, 40% of values are eliminated. In one embodiment, 4 probes are used with 6, 8 or 10 replicas per probe and extreme values or outliers make up between 10% and 50% of the values obtained. 
     A number of suitable linear functions are known in the art. These functions may be used in a linear discriminant analysis for the purposes of the present invention. 
     In one aspect the invention thus relates to a computational method or model (algorithm) for determining genotype with respect to a given genetic variation using ratios 1 and 2 in the three linear functions as defined above (steps e and f). The method can thus in one embodiment produce an output of genotype (AA, AB or BB) from an input of ratios 1 and 2. The method may also include calculating one or both of ratios 1 and 2 (step d). In some embodiments the method additionally comprises calculating an average intensity value for each probe (step c) and/or calculating a clean intensity value for each probe replica (step b). Thus the input to the model may comprise one or more of the average intensity values, clean replica intensity values or raw replica intensity values. The method may additionally comprise determining the raw intensity value for each probe replica (step a). The method may comprise one or more of the above steps. 
     In order to carry out the above methods, the coefficients for the linear functions must first be determined in a training process using data from control individuals whose genotype for the genetic variation is already known. Methods for training are known in the art. Typically in such methods, input data (in this case, typically ratios 1 and 2) is used for which the output (in the present case, genotype) is already known. Coefficients are substituted in the three linear equations at random and the output is calculated. Based on that output, one or more coefficients are altered and the input data is entered again to produce another output. The process is continued until coefficients are obtained which optimise the desired output. These optimised coefficients are then used in the linear functions when the method is applied to test data (where the output is as yet unknown). 
     In order to train the present model, ratios 1 and 2 are obtained for n control individuals having genotype AA (for example, homozygous wild type), n control individuals having genotype AB (heterozygous) and n control individuals having genotype BB (for example, homozygous mutant). The ratios may be obtained using the methods described above. The ratios are inputted as above and the coefficients altered in a discriminatory analysis until three linear functions are obtained which maximise discrimination between the AA, AB and BB groups. These coefficients are then used in the three functions when the model is used on unknown test samples (where the genotype is not predetermined) 
     Thus in one aspect the invention provides a method of deriving linear functions for use in the present genotyping methods. The method typically comprises carrying out the steps of the genotyping methods as described, for n control individuals having genotype AA (for example, homozygous wild type), n control individuals having genotype AB (heterozygous) and n control individuals having genotype BB (for example, homozygous mutant) with respect to a genetic variation. The intensity values obtained for each of the probe replicas are gathered as described and an algorithm is applied. 
     As described for the genotyping methods, application of the algorithm comprises calculating an average intensity value for each probe and the algorithm uses three linear functions intended to characterise each of the three possible genotypes, AA, AB and BB for the given genetic variation. Coefficients are inserted in the functions in a repetitive way until functions are derived which maximise discrimination between the genotypes in a discriminatory analysis. This provides the coefficients for use in the linear functions when the method or algorithm is in operational use (i.e. to determine the genotype of test individuals). 
     The algorithm or method which uses the three linear functions for analysing the intensity data may be as described above. 
     In some cases, the training method allows feedback optimisation. Thus, as intensity values and ratios are obtained for test individuals and these are genotyped, the intensity data, e.g. the ratios, and genotype are inputted and coefficients recalculated for the linear functions. 
     In one aspect the invention relates to a computational method for training. The method can be used to derive linear functions for use in the present genotyping methods by using ratios 1 and 2 obtained for each of n individuals having genotype AA, n individuals having genotype AB and n individuals having genotype BB with respect to a genetic variation. The ratios can be obtained by the methods described above. The method typically comprises applying the algorithm which uses the three linear functions (Functions 1, 2 and 3) intended to characterise each of the three possible genotypes AA, AB or BB for the genetic variation such that:
     Function 1 is the linear function that characterises individuals with the genotype AA and consists of a linear combination of ratios 1 and 2;   Function 2 is the linear function that characterises individuals with the genotype AB and consists of a linear combination of ratios 1 and 2;   Function 3 is the linear function that characterises individuals with the genotype BB and consists of a linear combination of ratios 1 and 2; and   the linear functions are formed by coefficients which accompany the variables ratio 1 and 2;   and deriving linear functions which maximise discrimination between the three genotype groups AA, AB and BB in a discriminatory analysis, so as to obtain the coefficients which can be used in the linear functions when the algorithm is used in a test method (i.e. is in operational use for determining genotype).   

     The algorithm or method which uses the three linear functions for analysing the intensity data may be as described above. 
     The computational training method may additionally involve calculating ratios 1 and 2 from average intensity value provided for each of the probes, and/or collating intensity values from probe replicas to determine an average intensity value for each probe and/or amending a raw intensity value for a probe replica to take account of background noise thereby obtaining clean intensity values for the replica. 
     In some aspects the computational method also allows a feedback optimisation step as described. 
     Typically in training n is ≧3, for example, 3, 4, 5, 6, 7, 8, 9 or 10. In one aspect, n is ≧5. In some cases n may be from 10 to 50 or more, for example, 15 to 40, or 25 to 35, such as 20 or 30. 
     Probes and probe replicas for the training method are selected as described herein. In one embodiment 4 probes are used for each genetic variation, with 6, 8 or 10 replicas of each probe. Once selected, the probes used in training are also used when the model is in operational use (to determine unknown genotype). If the probes are altered, typically the model must be retrained to optimise discrimination with the new probes. 
     Preferably the coefficients are such that the discrimination between the three genotype groups (both in training and in operational use) is substantially 100%. If the discrimination is not 100%, the probes are preferably redesigned. 
     As above, the model may also undergo feedback optimisation when it is in operational use. In that case, the model is first used to determine the genotype of an individual (AA, AB or BB). The ratios 1 and 2 for that individual are then inputted into the model and the coefficients in the linear functions altered as necessary in order to optimise discrimination between the three genotype groups. In this way, the additional data gathered as the model is in use can be used to optimise the discrimination capacity of the linear functions. 
     There are a number of parameters which can be determined and optimised in order to optimise performance and reliability of the analytical model or method.
     (i) In one aspect ratios 1 and 2 determined for an individual fall within the range of ratios 1 and 2 used to train the model (i.e. to optimise the three linear functions). If desired this can thus provide a double test for the genotype of an individual.   (ii) In one aspect the average fluorescence intensity of 4n replicas (where “n” is the number of replicas for each probe, e.g. 6, 8 or 10), for example, 40 replicas, with regard to the background noise is greater than 5.   (iii) In one aspect the variation between intensity values (raw or clean) for replicas of the same probe is a minimum. For example, the coefficient of variation between the intensity values for the replicas of a given probe is preferably less than 0.25   (iv) In one aspect the ratio of the sum of the raw intensity values for all probe replicas on a chip to the intensity of the background noise is greater than 15 when a fluorescence scanner is used.   (v) In one aspect the raw signal intensity value obtained for the negative controls is ≦3 times greater than the intensity value of the background noise. For example, negative controls may include the DMSO “blank” and the non-hybridising oligonucleotides referred to above. The background noise is the signal derived from the regions of the array where no probe has been spotted and may be determined as above.   

     Preferably any one or more of (i) to (v) applies when intensity is fluorescence intensity of a fluorescent label, in particular where the intensity is determined by means of a confocal fluorescent scanner. 
     Ensuring that the model meets one or more of the above helps to provide reliability and reproducibility. Any one or more of (i) to (v) may be true for the model. Preferably the model meets (i) above. In one example, (i), (ii) and (iii) are true. In another example, (iii), (iv), (v) are true. Preferably, all of the above are true for the model. This applies both to training and to operational use. 
     As above, the experimentally derived ratios obtained for a test sample may be compared to the ratios previously obtained for the (n) control samples obtained from individuals of known genotype, where n is as above, usually &gt;5, or &gt;10, or &gt;20. The reference ratios derived from analysis of the control samples permits a genotype to be assigned to the test sample. This can therefore be a double test. 
     In one instance the analytical method or algorithm of the invention comprises a sequence of the following steps: using 4 probes (2 pairs of probes) in replicate (6, 8 or 10 replicas), calculating the average intensity of each probe from the collated intensities of the replicas; calculating ratios 1 and 2 as above for the 2 pairs of probes (to detect the genetic variations A and B); substituting ratios 1 and 2 obtained in three linear equations which have been derived in a discriminatory analysis using ratios 1 and 2 calculated for “n” control patients with genotype AA, “n” control patients with genotype AB and “n” control patients with genotype BB (with respect to the genetic variation) (in one experiment “n” is 5); and determining the genotype of a patient for the genetic variation (for each genetic variation included in the DNA-chip) based on which linear function has the greatest absolute value. The test ratios may also be compared to the ratios of the “n” control patients to determine each genotype.
         In one aspect a genotyping method of the invention comprises:
           extracting DNA from a biological sample provided by a subject;   amplifying the regions of the said nucleic acid which contain the genetic variations to be identified and as an option, labelling these products during the reaction of amplification in order to obtain several products of amplification, optionally labelled, which contain the genetic variations to be identified;   fragmenting the products of amplification to obtain several products of fragmentation which contain the genetic variations and if the said products have not been previously labelled during the amplification stage, labelling the products of fragmentation which contain the genetic variations to be identified;   hybridising the fragmentation products which contain the genetic variations to be identified with probes capable of identifying the genetic variations under conditions which allow hybridization to take place, wherein said probes are deposited on a support and for every genetic variation to be characterized, 4 probes are used following a determined pattern so that they are uniformly distributed but not grouped by genetic variation to be characterized, wherein of the 4 probes, 2 detect one genetic variation and the other two detect another and wherein the number of replicas of each one of the probes is 10, 8 or 6;   introducing the solid support into a scanner and quantifying the intensity of the points where hybridisation has occurred and;   genotyping each one of the genetic variants from the average of the collated intensities of the 10, 8 or 6 replicates of each one of the 4 probes, wherein extreme values are eliminated, by an algorithm developed for such a purpose that permits the detection of each one of the mutations with a sensitivity, specificity and reproducibility that permits this method to be used for clinical applications, based on the fact that it leads to obtaining three linear functions which characterize each one of the possible genotypes.   
               

     The analysis and interpretation above has been described with respect to one genetic variation. However, it is to be understood that the present chip generally includes probes for detection of multiple genetic variations which can be analysed at the same time. Thus the present methods include analysis of multiple genetic variations, as described herein, in parallel. 
     In a further aspect the invention relates to a computer system comprising a processor and means for controlling the processor to carry out a computational method of the invention. 
     The invention additionally relates to a computer program comprising computer program code which when run on a computer or computer network causes the computer or computer network to carry out a computational method of the invention. The computer program may be stored on a computer readable medium. 
     In addition to the probes and chips described herein, the inventors have also designed and validated oligonucleotide primers which are capable of amplifying, e.g. by means of multiplex PCR, the target DNA regions which contain human genetic variations associated with IBD, or adverse reactions to drugs. These primers are therefore useful in preparing nucleic acid for use in the present genotyping, diagnostic and therapeutic methods. 
     Example 3 lists pairs of primers which amplify target DNA regions that contain human genetic variations associated with IBD (SEQ ID NOS 1-124 and 1317-1428) and the corresponding genetic variation. In particular, these primers are useful for amplification of target DNA regions containing the genetic variations in Table 1. 
     Example 5 lists pairs of primers which amplify target DNA regions that contain human genetic variations associated with adverse reactions to drugs (SEQ ID NOS 125-254) and the corresponding genetic variations. In particular, these primers are useful for amplification of target DNA regions containing the genetic variations in Table 3. 
     The listed oligonucleotide primers have the advantage of allowing specific amplification of the said target DNA regions in a very low number of PCR reactions. For example, in the case of detection of genetic variations associated with IBD, the listed primers allow, in a minimum number of multiplex PCR reactions, amplification of all the fragments necessary for genotyping of the genetic variations in Table 1, and which may be analyzed on an IBD-chip as in Example 3. In the case of the detection of genetic variations associated with adverse reactions to drugs the listed primers allow, in only 4 multiplex PCR reactions, amplification of 65 fragments necessary for genotyping of the 89 genetic variations in Table 3 which may be analyzed on a drug-chip as in Example 5. 
     In a further aspect, the present invention relates to each of the PCR primers listed in Examples 3 and 5 (SEQ ID NOS 1-254 and 1317-1428), and in particular to each of the listed pairs of PCR primers and their use in PCR amplification, e.g. in a multiplex PCR reaction, of a target DNA region containing the corresponding genetic variation. The invention in one aspect provides any one of these primers or pairs of primers for use in medicine, in particular for use in the present genotyping, diagnostic or therapeutic methods. 
     The invention further relates to a PCR amplification kit comprising at least one pair of listed PCR primers. The kit may additionally include, for example, a (thermostable) polymerase, dNTPs, a suitable buffer, additional primers, and/or instructions for use, e.g. to amplify a target DNA region containing the corresponding genetic variation. The kit may be used for amplification of target DNA regions from nucleic acid samples, for use in the present methods. 
     In another aspect the present invention relates to a genotyping or diagnostic (preferably in vitro) kit comprising a DNA-chip or array according to the invention. The kit may additionally comprise instructions for use of the chip in a genotyping method of the invention, for example instructions for use in the present analytical method or algorithm. Further components of a kit may include:
         computer software, a computer program or a computer system according to the invention;   one or more PCR primers or pairs of PCR primers according to the invention; and/or   a PCR amplification kit according to the invention.       

     The probes for the chip or PCR primers may be selected as above depending on the genetic variations to be detected or the diagnostic purpose of the kit. 
     The kit may contain one or more positive and/or negative controls of the hybridisation reaction. 
     The kit may be used to detect and analyse genetic variations associated with diseases or antigens of interest. Suitable probes may be designed accordingly. 
     In one aspect the kit is for detection or genotyping of genetic variations associated with known erythrocyte antigens, such as those described herein. The kit may therefore be useful in determining blood group type of an individual. 
     In another aspect the kit is for detection or genotyping of genetic variations associated with IBD, such as those described herein. The kit may therefore be useful in diagnosing IBD or susceptibility to IBD as described herein. 
     In a further aspect the genotyping kit is for detection or genotyping of genetic variations associated with adverse reactions to pharmaceuticals, such as those described herein. The kit may therefore be useful in diagnosing or predicting susceptibility to adverse reactions as described herein. 
     The invention further relates to the use of the kit in a genotyping, diagnostic or therapeutic method of the invention. 
     As described herein, the present methods are useful for diagnosing IBD in a patient or susceptibility to IBD in a patient. The present methods may be used to genotype an individual with respect to one or more genetic variations associated with IBD (e.g. those in Table 1). The results may be used to diagnose IBD or for prognosis and may be useful in determining the appropriate treatment for IBD (e.g. by predicting response to therapy). 
     IBD presents a number of phenotypes. For example, phenotypes observed in sufferers from Crohns disease include the development of fistulae, perianal disease and clinically relevant extraintestinal manifestations, in addition some sufferers require surgical intervention (intestinal resection). Examples of disease phenotypes observed in sufferers from ulcerative colitis include pancolitis and clinically relevant extraintestinal manifestations, in addition surgical intervention may be required (colectomy). 
     Genetic data obtained from a Spanish trial of IBDchip (579 patients) has demonstrated a clear ability to predict the probability (high, moderate, low or minimal) of developing the abovementioned disease phenotypes in individuals suffering from Crohns disease and ulcerative colitis respectively based on their specific genetic profiles (FIGS.  3 - 10 —Example 6). 
     Because of the aggressive nature of IBD, successful treatment often depends on individualising treatment regimens to fit each person&#39;s needs. Treatment typically includes controlling the active inflammation of the disease and maintaining remission through medication. The IBDchip is a genotyping tool that allows clinicians to evaluate the likely course of disease progression based on the individual genetic profiles of their patients as well as providing an indication of the most appropriate therapeutic interventions. A genotype predictive of a rapidly progressing and/or aggressive development of the disease will indicate the need for earlier and more closely monitored treatment regimes as well as indicating the probable need for surgical intervention. Conversely a genotype predictive of less severe disease progression may prevent the use of unnecessary treatment and/or surgery. 
     A wide range of drugs are been used to treat IBD sufferers including: aminosalysilates (e.g. sulfasalazine, olsalazine); antimetabolites (e.g. mercaptopurine, methotrexate); antirheumatics (e.g. azathioprine, 6-mercaptopurine) antibiotics (ciprofloxacin), biologics (e.g. infliximab); as well as a wide range of corticosteroid drugs. However, as discussed above the response of individual patient to these treatments can vary enormously and there is a clear clinical need for better methods of selecting the best therapeutic approach for IBD sufferers. Use of genetic data obtained from the use of IBDchip allowed the identification of individuals with varying probabilities (high, moderate, low and minimal) of developing resistance to corticosteroid treatment (FIGS.  11 - 13 —Example 6). The genotyping methodology described herein can be used to determine similar patterns relating to the genetic influence on drug response in similar clinical trials. 
     The present arrays and methods thus provide a means for clinicians to predict the likely course of disease progression in individual patients and also aid in the selection of the most suitable treatment regime including the likelihood of the need for surgical intervention. They are therefore useful prognostic tools. Genotype information obtained according to the present invention may aid in clinical decision making or diagnosis in cases where symptoms (disease phenotype) are ambiguous. Genetic information provided by IBDchip or other methods could also help in determining the likelihood of disease development in asymptomatic individuals (e.g. immediate family members of IBD sufferers) allowing for example guidance on lifestyle and diet to be provided and indicating the need for continued monitoring of individuals who have a genetic constitution that indicates possible susceptibility to disease development. 
     In one aspect the invention therefore relates to a method of diagnosing IBD or susceptibility to IBD in an individual, or determining the likely course of disease progression in an individual as above. Preferably the method is in vitro. The invention further relates to a method of selecting a treatment, e.g. determining the need for surgical intervention for an individual having IBD, in some cases where the individual has been diagnosed or tested according to the methods of the invention. Still further the invention in some aspects relates to methods of treating an individual suffering from IBD, wherein, after the treatment is selected, the treatment is administered to the individual. 
     Particular genetic variations associated with IBD may be predictive of particular phenotypes or development of particular phenotypes and hence disease progession. In other words, it may be that there is a statistically significant association between e.g. the mutant allele B, of a given genetic variation and the occurrence/development of a particular phenotype. 
     Since the present genotyping methods allow reliable genotyping of multiple genetic variations in a clinical setting, these can be used to genotype individuals of known IBD phenotype, and to thus identify genetic variations predictive of particular IBD phenotypes. 
     In one aspect the invention therefore relates to a method of identifying genetic variations predictive of a particular IBD phenotype, such as the phenotypes listed above. The method involves genotyping a plurality of individuals with respect to one or more genetic variations using a method of the invention, in which the genetic variations are associated with IBD. Typically 300-1000 individuals are genotyped, for example 400, 500 or 600 individuals may be genotyped. The IBD phenotype of each individual is already known. IBD phenotype may be determined by any appropriate method, e.g. the Vienna Classification (Gasche C, Scholmerich J, Brynskov J, et al. A simple classification of Crohn&#39;s disease: report of the Working Party for the World Congresses of Gastroenterology, Vienna 1998. Inflamm Bowel Dis 2000; 6: 8-15) or the Montreal Classification (Silverberg M S, Satsangi J, Ahmad T, Arnott I D, Bernstein C N, Brant S R, Caprilli R, Colombel J F, Gasche C, Geboes K, Jewell D P, Karban A, Loftus Jr E V, Pena A S, Riddell R H, Sachar D B, Schreiber S, Steinhart A H, Targan S R, Vermeire S, Warren B F. Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: Report of a Working Party of the 2005 Montreal World Congress of Gastroenterology.  Can J Gastroenterol . 2005 September;19 Suppl A:5-36) 
     Once the genotypes are obtained, this data is compared with the phenotype data and statistically significant associations between particular genotypes and particular phenotypes are identified. Methods for determining statistical significance are known in the art. 
     The genetic variations identified as predictive of particular phenotypes/disease course can then be used to diagnose these phenotypes/disease courses in test individuals, by genotyping the individuals with respect to the predictive genetic variation(s). Thus it is possible to determine the likely course of disease progression in the individual. Genotyping can be done by any appropriate method, depending on the number of variations to be tested. For example, a genotyping method of the invention may be used. Alternatively, sequence based or other chip-based methods may be appropriate. 
     Thus in one aspect the invention further relates to a method of diagnosing IBD phenotype or predicting the likely course of disease progression in an individual by determining the genotype of the individual with respect to one or more genetic variations which have been identified as predictive (of the particular IBD phenotype or disease course) by the methods described herein. 
     Once the prediction has been made, it will then be possible to select the most suitable therapeutic approach, e.g. to determine the need for surgical intervention. 
     The invention is also useful in determining the blood group of an individual by determining genotype with respect to one or more particular erythrocyte associated antigens (e.g. those in Table 2) Therefore in a further aspect the invention relates to a method (in one aspect in vitro) of determining blood group or type in an individual. Such methods may be useful in for example, blood transfusions, organ transplantation, medical-legal applications ot treatment of haemolytic disease of the fetus and new born. 
     The invention is further useful in determining the likelihood of an adverse reaction to pharmaceuticals in an individual. Therefore in a further aspect the invention relates to a method (in one aspect in vitro) of diagnosing or predicting susceptibility to adverse reaction to pharmaceuticals in an individual. The method comprises determining the genotype of an individual with respect to one or more genetic variations associated with adverse reaction to pharmaceuticals (e.g. those in Table 3) by the present genotyping methods. The genotyping results may be used to select a treatment for the individual which can then be administered. Thus in some aspects the invention further relates to methods of selecting a pharmaceutical treatment for an individual, and methods of treating an individual with the selected pharmaceutical. 
     The diagnostic, predictive and therapeutic methods comprise carrying out a genotyping method of the invention as described herein. Any of the methods may involve carrying out a training method of the invention as described herein in order to derive linear functions for use in determining genotype. Further the methods may comprise the use of a chip, computer system, computer program, oligonucleotide probes or pair or set of probes, oligonucleotide primer or pair of primers, PCR amplification kit or diagnostic kit of the invention as described herein. 
     EXAMPLES 
     Although in general, the techniques mentioned herein are well known in the art, reference may be made in particular to Sambrook et al, 1989, Molecular Cloning: a laboratory manual. 
     Example 1 
     Detection of Human Genetic Variations Associated with Human Erythrocyte Antigens, Using a DNA-Chip for the Identification of Human Blood Groups 
     1.1 Design of the DNA-Chip for Genotyping Blood Groups 
     A DNA-chip was designed and produced to detect human genetic variations associated with several erythrocyte antigens, which permits the simultaneous, sensitive, specific and reproducible detection of the genetic variations. Illustrative examples of the variations which can be determined using the DNA-chip are listed in Table 2. 
     In this case, the DNA-chip designed and produced consists of a support (a glass slide), which comprises a plurality of probes on its surface, which permit the detection of the genetic variations. These probes are capable of hybridizing with (amplified) target gene sequences that encode the erythrocyte antigens to be studied. The DNA sequences of the probes used are listed below. In general, the name of the gene, the mutation (nucleotide change, “ins”: insertion “del”: deletion), the genotype and the exon are indicated. 
                        ABO G261delG GENOTYPE: ABO O1/O1v [probes to detect the           polymorphism G261delG (Genotype ABO O1/O1v) in exon 6 of       the ABO gene]       EXON 6                                 BC001OV01   CAGCCAAGGGGTCACCACGAGGACA   25   SEQ ID NO:255           BC001OV02   CCAGCCAAGGGGTACCACGAGGACA   25   SEQ ID NO:256       BC001OV03   CCAGCCAAGGGGTCACCACGAGGACAT   27   SEQ ID NO:257       BC001OV04   GCCAGCCAAGGGGTACCACGAGGACAT   27   SEQ ID NO:258                             ABO G703A GENOTYPE: ABO B           EXON 7                                 BC002OV01   ACCCTGCACCCCGGCTTCTACGGAA   25   SEQ ID NO:259           BC002OV02   ACCCTGCACCCCAGCTTCTACGGAA   25   SEQ ID NO:260       BC002OV03   CACCCTGCACCCCGGCTTCTACGGAAG   27   SEQ ID NO:261       BC002OV04   CACCCTGCACCCCAGCTTCTACGGAAG   27   SEQ ID NO:262                             ABO C796A GENOTYPE: ABO B           EXON7                                 BC003OV01   AGAACCCCCCCAGGTAGTAGAAATC   25   SEQ ID NO:263           BC003OV02   AGAACCCCCCCATGTAGTAGAAATC   25   SEQ ID NO:264       BC003OV03   AAGAACCCCCCCAGGTAGTAGAAATCG   27   SEQ ID NO:265       BC003OV04   AAGAACCCCCCCATGTAGTAGAAATCG   27   SEQ ID NO:266                             ABO G802A GENOTYPE: ABO O2           EXON7                                 BC004OV01   CCCCGAAGAACCCCCCCAGGTAGTA   25   SEQ ID NO:267           BC004OV02   CCCCGAAGAACCTCCCCAGGTAGTA   25   SEQ ID NO:268       BC004OV03   CCCGAAGAACCCCCCCAGGTAGT   23   SEQ ID NO:269       BC004OV04   CCCGAAGAACCTCCCCAGGTAGT   23   SEQ ID NO:270                             ABO G803C GENOTYPE: ABO B2, cisAB-1           EXON7                                 BC005OV01   CCCCCGAAGAACCCCCCCAGGTAGT   25   SEQ ID NO:271           BC005OV02   CCCCCGAAGAACGCCCCCAGGTAGT   25   SEQ ID NO:272       BC005OV03   ACCCCCGAAGAACCCCCCCAGGTAGTA   27   SEQ ID NO:273       BC005OV04   ACCCCCGAAGAACGCCCCCAGGTAGTA   27   SEQ ID NO:274                             ABO CCC1059-1061 GENOTYPE: ABO A2           EXON7                                 BC006OV01   CGGTCCGGAACCCGTGAGCGGCTGC   25   SEQ ID NO:275           BC006OV02   CGGTCCGGAACCGTGAGCGGCTGCC   25   SEQ ID NO:276       BC006OV03   GCGGTCCGGAACCCGTGAGCGGCTGCC   27   SEQ ID NO:277       BC006OV04   GCGGTCCGGAACCGTGAGCGGCTGCCA   27   SEQ ID NO:273                             ABO GGGGGGG G798_804insG GENOTYPE: ABO O3, Ael           EXON7                                 BC007OV01   CCCCGAAGAACCCCCCCAG   19   SEQ ID NO:279           BC007OV02   CCCGAAGAACCCCCCCCAG   19   SEQ ID NO:280       BC007OV03   CCCCCGAAGAACCCCCCCAGG   21   SEQ ID NO:231       BC007OV04   CCCCGAAGAACCCCCCCCAGG   21   SEQ ID NO:232                             ABO GG87_88insG GENOTYPE: ABO O4           EXON2                                 BC008OV01   TGCTTGTCTTGGTCTTGTTTGGGTA   25   SEQ ID NO:283           BC008OV02   TGCTTGTCTTGGGTCTTGTTTGGGT   25   SEQ ID NO:284       BC008OV03   GCTTGTCTTGGTCTTGTTTGGGT   23   SEQ ID NO:285       BC008OV04   GCTTGTCTTGGGTCTTGTTTGGG   23   SEQ ID NO:286                             ABO C322T GENOTYPE: ABO O5           EXON6                                 BC009OV01   GGAGCCTGAACTGCTCGTTGAGGAT   25   SEQ ID NO:287           BC009OV02   GGAGCCTGAACTACTCGTTGAGGAT   25   SEQ ID NO:288       BC009OV03   TGGAGCCTGAACTGCTCGTTGAGGATG   27   SEQ ID NO:289       BC009OV04   TGGAGCCTGAACTACTCGTTGAGGATG   27   SEQ ID NO:290                             ABO C893T GENOTYPE: ABO O6           EXON7                                 BC010OV01   TCGTGCCACACGGCCTCGATGCCGT   25   SEQ ID NO:291           BC010OV02   TCGTGCCACACGACCTCGATGCCGT   25   SEQ ID NO:292       BC010OV03   CGTGCCACACGGCCTCGATGCCG   23   SEQ ID NO:293       BC010OV04   CGTGCCACACGACCTCGATGCCG   23   SEQ ID NO:294                             ABO C927A GENOTYPE: ABO O7           EXON7                                 BC011OV01   CCTGAACAAGTACCTGCTGCGCCAC   25   SEQ ID NO:295           BC011OV02   CCTGAACAAGTAACTGCTGCGCCAC   25   SEQ ID NO:296       BC011OV03   ACCTGAACAAGTACCTGCTGCGCCACA   27   SEQ ID NO:297       BC011OV04   ACCTGAACAAGTAACTGCTGCGCCACA   27   SEQ ID NO:298                             ABO G188A/C189T GENOTYPE: ABO O1v           EXON4                                 BC012OV01   ACCATCTGCAGCGCGTCTCGTTGCC   25   SEQ ID NO:299           BC012OV02   ACCATCTGCAGCATGTCTCGTTGCC   25   SEQ ID NO:300       BC012OV03   CCATCTGCAGCGCGTCTCGTTGC   23   SEQ ID NO:301       BC012OV04   CCATCTGCAGCATGTCTCGTTGC   23   SEQ ID NO:302                             ABO G542A GENOTYPE: ABO O8           EXON7                                 BC013OV01   GACACGTCCTGCCAGCGCTTGTAGG   25   SEQ ID NO:303           BC013OV02   GACACGTCCTGCTAGCGCTTGTAGG   25   SEQ ID NO:304       BC013OV03   ACACGTCCTGCCAGCGCTTGTAG   23   SEQ ID NO:305       BC013OV04   ACACGTCCTGCTAGCGCTTGTAG   23   SEQ ID NO:306                             ABO C467T GENOTYPE: ABO A2           EXON7                                 BC014OV01   GGCACCGCGGCCGGCTGGTCGGTGA   25   SEQ ID NO:307           BC014OV02   GGCACCGCGGCCAGCTGGTCGGTGA   25   SEQ ID NO:308       BC014OV03   GGGCACCGCGGCCGGCTGGTCGGTGAA   27   SEQ ID NO:309       BC014OV04   GGGCACCGCGGCCAGCTGGTCGGTGAA   27   SEQ ID NO:310                             ABO T646A GENOTYPE: ABO Ax/O1v           EXON7                                 BC015OV01   GTGGACATGGAGTTCCGCGACCACG   25   SEQ ID NO:311           BC015OV02   GTGGACATGGAGATCCGCGACCACG   25   SEQ ID NO:312       BC015OV03   CGTGGACATGGAGTTCCGCGACCACGT   27   SEQ ID NO:313       BC015OV04   CGTGGACATGGAGATCCGCGACCACGT   27   SEQ ID NO:314                             RHD A178C GENOTYPE: RHD DIIIb           EXON2                                 BC016OV01   GTGATGGCGGCCATTGGCTTGGGCT   25   SEQ ID NO:315           BC016OV02   GTGATGGCGGCCCTTGGCTTGGGCT   25   SEQ ID NO:316       BC016OV03   TGATGGCGGCCATTGGCTTGGGC   23   SEQ ID NO:317       BC016OV04   TGATGGCGGCCCTTGGCTTGGGC   23   SEQ ID NO:318                             RHD G203A GENOTYPE: RHD DIIIb           EXON2                                 BC017OV01   TCCTCACCTCGAGTTTCCGGAGACA   25   SEQ ID NO:319           BC017OV02   TCCTCACCTCGAATTTCCGGAGACA   25   SEQ ID NO:320       BC017OV03   TTCCTCACCTCGAGTTTCCGGAGACAC   27   SEQ ID NO:321       BC017OV04   TTCCTCACCTCGAATTTCCGGAGACAC   27   SEQ ID NO:322                             RHD T307C GENOTYPE: RHD DIIIb           EXON 2                                 BC018OV01   AGCCAGTTCCCTTCTGGGAAGGTGG   25   SEQ ID NO:323           BC018OV02   AGCCAGTTCCCTCCTGGGAAGGTGG   25   SEQ ID NO:324       BC018OV03   GAGCCAGTTCCCTTCTGGGAAGGTGGT   27   SEQ ID NO:325       BC018OV04   GAGCCAGTTCCCTCCTGGGAAGGTGGT   27   SEQ ID NO:326                             RHD T544A GENOTYPE: RHD EXON SCANNING           EXON4                                 BC019OV01   TATTTTGGGCTGTCTGTGGCCTGGT   25   SEQ ID NO:327           BC019OV02   TATTTTGGGCTGACTGTGGCCTGGT   25   SEQ ID NO:328       BC019OV03   TTTTGGGCTGTCTGTGGCCTG   21   SEQ ID NO:329       BC019OV04   TTTTGGGCTGACTGTGGCCTG   21   SEQ ID NO:330                             RHD G577A GENOTYPE: RHD EXON SCANNING           EXON4                                 BC020OV01   AGCCTCTACCCGAGGGAACGGAG   23   SEQ ID NO:331           BC020OV02   AGCCTCTACCCAAGGGAACGGAG   23   SEQ ID NO:332       BC020OV03   GCCTCTACCCGAGGGAACGGA   21   SEQ ID NO:333       BC020OV04   GCCTCTACCCAAGGGAACGGA   21   SEQ ID NO:334                             RHD A594T GENOTYPE: RHD EXON SCANNING           EXON4                                 BC021OV01   ACGGAGGATAAAGATCAGACAGC   23   SEQ ID NO:335           BC021OV02   ACGGAGGATAATGATCAGACAGC   23   SEQ ID NO:336       BC021OV03   CGGAGGATAAAGATCAGACAG   21   SEQ ID NO:337       BC021OV04   CGGAGGATAATGATCAGACAG   21   SEQ ID NO:338                             RHD G697C GENOTYPE: RHD Dva (kou, to, yh, sm)           EXON5                                 BC022OV01   AGAAGTCCAATCGAAAGGAAGAATG   25   SEQ ID NO:339           BC022OV02   AGAAGTCCAATCCAAAGGAAGAATG   25   SEQ ID NO:340       BC022OV03   GAAGTCCAATCGAAAGGAAGAAT   23   SEQ ID NO:341       BC022OV04   GAAGTCCAATCCAAAGGAAGAAT   23   SEQ ID NO:342                             RHD G712A GENOTYPE: RHD Dva (to, yh)           EXON5                                 BC023OV01   GGAAGAATGCCGTGTTCAACACC   23   SEQ ID NO:343           BC023OV02   GGAAGAATGCCATGTTCAACACC   23   SEQ ID NO:344       BC023OV03   GAAGAATGCCGTGTTCAACAC   21   SEQ ID NO:345       BC023OV04   GAAGAATGCCATGTTCAACAC   21   SEQ ID NO:346                             RHD T1025C GENOTYPE: RHD DAR (weakDtype4.2)           EXON7                                 BC024OV01   TGGAGAGATCATCTACATTGTGC   23   SEQ ID NO:347           BC024OV02   TGGAGAGATCACCTACATTGTGC   23   SEQ ID NO:348       BC024OV03   GGAGAGATCATCTACATTGTG   21   SEQ ID NO:349       BC024OV04   GGAGAGATCACCTACATTGTG   21   SEQ ID NO:350                             RHD G676C GENOTYPE: RHD DCS, Dva (kou, yh)           EXON5                                 BC025OV01   AGTTTCAACTCTGCTCTGCTGAGAA   25   SEQ ID NO:351           BC025OV02   AGTTTCAACTCTCCTCTGCTGAGAA   25   SEQ ID NO:352       BC025OV03   AATTTTCAACTCTGCTCTGCTGAGAAG   27   SEQ ID NO:353       BC025OV04   AAGTTTCAACTCTCCTCTGCTGAGAAG   27   SEQ ID NO:354                             RHD G1063A GENOTYPE: RHD DNB           EXON7                                 BC026OV01   ACCGTCGGAGCCGGCAATGGCATGT   25   SEQ ID NO:355           BC026OV02   ACCGTCGGAGCCAGCAATGGCATGT   25   SEQ ID NO:356       BC026OV03   TACCGTCGGAGCCGGCAATGGCATGTG   27   SEQ ID NO:357       BC026OV04   TACCGTCGGAGCCAGCAATGGCATGTG   27   SEQ ID NO:358                             RHD T509C GENOTYPE: RHD DFRI, DOL           EXON4                                 BC027OV01   ACATGAACATGATGCACATCTACGT   25   SEQ ID NO:359           BC027OV02   ACATGAACATGACGCACATCTACGT   25   SEQ ID NO:360       BC027OV03   CACATGAACATGATGCACATCTACGTG   27   SEQ ID NO:361       BC027OV04   CACATGAACATGACGCACATCTACGTG   27   SEQ ID NO:362                             RHD T329C GENOTYPE: RHD DVII           EXON2                                 BC028OV01   TGGTCATCACACTGTTCAGGTATTG   25   SEQ ID NO:363           BC028OV02   TGGTCATCACACCGTTCAGGTATTG   25   SEQ ID NO:364       BC028OV03   GGTCATCACACTGTTCAGGTATT   23   SEQ ID NO:365       BC028OV04   GGTCATCACACCGTTCAGGTATT   23   SEQ ID NO:366                             RHD C848T GENOTYPE: RHD DHMi           EXON6                                 BC029OV01   GCTGTGGGTACCTCGTGTCAC   21   SEQ ID NO:367           BC029OV02   GCTGTGGGTATCTCGTGTCAC   21   SEQ ID NO:368       BC029OV03   GGCTGTGGGTACCTCGTGTCACC   23   SEQ ID NO:369       BC029OV04   GGCTGTGGGTATCTCGTGTCACC   23   SEQ ID NO:370                             RHD A497C GENOTYPE: RHD DFW           EXON4                                 BC030OV01   AGACAGACTACCACATGAACATGAT   25   SEQ ID NO:371           BC030OV02   AGACAGACTACCCCATGAACATGAT   25   SEQ ID NO:372       BC030OV03   GACAGACTACCACATGAACATGA   23   SEQ ID NO:373       BC030OV04   GACAGACTACCCCATGAACATGA   23   SEQ ID NO:374                             RHD G686A GENOTYPE: RHD DHR           EXON5                                 BC031OV01   CTGCTCTGCTGAGAAGTCCAATCGA   25   SEQ ID NO:375           BC031OV02   CTGCTCTGCTGAAAAGTCCAATCGA   25   SEQ ID NO:376       BC031OV03   TGCTCTGCTGAGAAGTCCAATCG   23   SEQ ID NO:377       BC031OV04   TGCTCTGCTGAAAAGTCCAATCG   23   SEQ ID NO:378                             RHD G854A GENOTYPE: RHD DIM           EXON6                                 BC032OV01   TGGGTACCTCGTGTCACCTGATCCC   25   SEQ ID NO:379           BC032OV02   TGGGTACCTCGTATCACCTGATCCC   25   SEQ ID NO:380       BC032OV03   GGGTACCTCGTGTCACCTGATCC   23   SEQ ID NO:331       BC032OV04   GGGTACCTCGTATCACCTGATCC   23   SEQ ID NO:382                             RHD T161C GENOTYPE: RHD DMH           EXON2                                 BC033OV01   TTGGCCAAGATCTGACCGTGATGGC   25   SEQ ID NO:383           BC033OV02   TTGGCCAAGATCCGACCGTGATGGC   25   SEQ ID NO:384       BC033OV03   GTTGGCCAAGATCTGACCGTGATGGCG   27   SEQ ID NO:385       BC033OV04   GTTGGCCAAGATCCGACCGTGATGGCG   27   SEQ ID NO:386                             RHD G1057A GENOTYPE: RHD DNU           EXON7                                 BC034OV01   CTTGATACCGTCGGAGCCGGCAATG   25   SEQ ID NO:387           BC034OV02   CTTGATACCGTCAGAGCCGGCAATG   25   SEQ ID NO:388       BC034OV03   GCTTGATACCGTCGGAGCCGGCAATGG   27   SEQ ID NO:389       BC034OV04   GCTTGATACCGTCAGAGCCGGCAATGG   27   SEQ ID NO:390                             RHD T1073C GENOTYPE: RHD DWI           EXON7                                 BC035OV01   CCGGCAATGGCATGTGGGTCACTGG   25   SEQ ID NO:391           BC035OV02   CCGGCAATGGCACGTGGGTCACTGG   25   SEQ ID NO:392       BC035OV03   CGGCAATGGCATGTGGGTCACTG   23   SEQ ID NO:393       BC035OV04   CGGCAATGGCACGTGGGTCACTG   23   SEQ ID NO:394                             RHD C1061A GENOTYPE: RHD DII, DIV IV           EXON7                                 BC036OV01   ATACCGTCGGAGCCGGCAATGGCAT   25   SEQ ID NO:395           BC036OV02   ATACCGTCGGAGACGGCAATGGCAT   25   SEQ ID NO:396       BC036OV03   GCCGGCAATGGCATGTGGGTCACTGGG   27   SEQ ID NO:397       BC036OV04   GCCGGCAATGGCACGTGGGTCACTGGG   27   SEQ ID NO:398                             RHD G845A GENOTYPE: RHD weak D type 15           EXON6                                 BC037OV01   GCGTGGCTGTGGGTACCTCGTGTCA   25   SEQ ID NO:399           BC037OV02   GCGTGGCTGTGGATACCTCGTGTCA   25   SEQ ID NO:400       BC037OV03   GATACCGTCGGAGCCGGCAATGGCATG   27   SEQ ID NO:401       BC037OV04   GATACCGTCGGAGACGGCAATGGCATG   27   SEQ ID NO:402                             RHD T809G GENOTYPE: RHD weak D type 1, psi           EXON6                                 BC038OV01   TGCAGACTTATGTGCACAGTGCGGT   25   SEQ ID NO:403           BC038OV02   TGCAGACTTATGGGCACAGTGCGGT   25   SEQ ID NO:404       BC038OV03   GCAGACTTATGTGCACAGTGCGG   23   SEQ ID NO:405       BC038OV04   GCAGACTTATGGGCACAGTGCGG   23   SEQ ID NO:406                             RHD G1154C GENOTYPE: RHD weak D type 2           EX0N9                                 BC039OV01   GCATTTAAACAGGTTTGCTCCTAAA   25   SEQ ID NO:407           BC039OV02   GCATTTAAACAGCTTTGCTCCTAAA   25   SEQ ID NO:408       BC039OV03   TGCATTTAAACAGGTTTGCTCCTAAAT   27   SEQ ID NO:409       BC039OV04   TGCATTTAAACAGCTTTGCTCCTAAAT   27   SEQ ID NO:410                             RHD C8G GENOTYPE: RHD weak D type 3           EXON1                                 BC040OV01   ACAGGATGAGCTCTAAGTACCCGCG   25   SEQ ID NO:411           BC040OV02   ACAGGATGAGCTGTAAGTACCCGCG   25   SEQ ID NO:412       BC040OV03   CACAGGATGAGCTCTAAGTACCCGCGG   27   SEQ ID NO:413       BC040OV04   CACAGGATGAGCTGTAAGTACCCGCGG   27   SEQ ID NO:414                             RHD C446A GENOTYPE: RHD weak D type 5           EXON3                                 BC041OV01   TGGAGGTGACAGCTTTAGGCAACCT   25   SEQ ID NO:415           BC041OV02   TGGAGGTGACAGATTTAGGCAACCT   25   SEQ ID NO:416       BC041OV03   GGAGGTGACAGCTTTAGGCAACC   23   SEQ ID NO:417       BC041OV04   GGAGGTGACAGATTTAGGCAACC   23   SEQ ID NO:418                             RHD G1016A GENOTYPE: RHD weak D type 7           EXON7                                 BC042OV01   TGGGTCTGCTTGGAGAGATCATCTA   25   SEQ ID NO:419           BC042OV02   TGGGTCTGCTTGAAGAGATCATCTA   25   SEQ ID NO:420       BC042OV03   GGGTCTGCTTGGAGAGATCATCT   23   SEQ ID NO:421       BC042OV04   GGGTCTGCTTGAAGAGATCATCT   23   SEQ ID NO:422                             RHD C340T GENOTYPE: RHD weak D type 17           EXON3                                 BC043OV01   TCCCCCAGTATTCGGCTGGCCACCA   25   SEQ ID NO:423           BC043OV02   TCCCCCAGTATTTGGCTGGCCACCA   25   SEQ ID NO:424       BC043OV03   CTCCCCCAGTATTCGGCTGGCCACCAT   27   SEQ ID NO:425       BC043OV04   CTCCCCCAGTATTTGGCTGGCCACCAT   27   SEQ ID NO:426                             RHD T807G GENOTYPE: RHD PSI           EXON6                                 BC044OV01   TTTGCAGACTTATGTGCACAGTGCG   25   SEQ ID NO:427           BC044OV02   TTTGCAGACTTAGGTGCACAGTGCG   25   SEQ ID NO:428       BC044OV03   TTGCAGACTTATGTGCACAGTGC   23   SEQ ID NO:429       BC044OV04   TTGCAGACTTAGGTGCACAGTGC   23   SEQ ID NO:430                             RHD G1227A GENOTYPE: RHD K409K Dnull           EXON9                                 BC045OV01   AGTTTTCTGGAAGGTAAGATTTTTC   25   SEQ ID NO:431           BC045OV02   AGTTTTCTGGAAAGTAAGATTTTTC   25   SEQ ID NO:432       BC045OV03   AAGTTTTCTGGAAGGTAAGATTTTTCA   27   SEQ ID NO:433       BC045OV04   AAGTTTTCTGGAAAGTAAGATTTTTCA   27   SEQ ID NO:434                             RHD G48A GENOTYPE: RHD W16X Dnull           EXON1                                 BC046OV01   CCTGCCCCTCTGGGCCCTAACACTG   25   SEQ ID NO:435           BC046OV02   CCTGCCCCTCTGAGCCCTAACACTG   25   SEQ ID NO:436       BC046OV03   CTGCCCCTCTGGGCCCTAACACT   23   SEQ ID NO:437       BC046OV04   CTGCCCCTCTGAGCCCTAACACT   23   SEQ ID NO:438                             RHD C121T GENOTYPE: RHD Q41X Dnull           EXON1                                 BC047OV01   TCCTTAGAGGATCAAAAGGGGCTCG   25   SEQ ID NO:439           BC047OV02   TCCTTAGAGGATTAAAAGGGGCTCG   25   SEQ ID NO:440       BC047OV03   CCTTAGAGGATCAAAAGGGGCTC   23   SEQ ID NO:441       BC047OV04   CCTTAGAGGATTAAAAGGGGCTC   23   SEQ ID NO:442                             RHD G270A GENOTYPE: RHD W90X Dnull           EXON2                                 BC048OV01   TGGTGTGCAGTGGGCAATCCTGCTG   25   SEQ ID NO:443           BC048OV02   TGGTGTGCAGTGAGCAATCCTGCTG   25   SEQ ID NO:444       BC048OV03   GGTGTGCAGTGGGCAATCCTGCT   23   SEQ ID NO:445       BC048OV04   GGTGTGCAGTGAGCAATCCTGCT   23   SEQ ID NO:446                             RHD IVS3 + 1G &gt; A GENOTYPE: RHD IVS3 + 1G &gt; A Dneg           EXON3                                 BC049OV01   AATATCTTCAACGTGAGTCATGGTG   25   SEQ ID NO:447           BC049OV02   AATATCTTCAACATGAGTCATGGTG   25   SEQ ID NO:448       BC049OV03   ATATCTTCAACGTGAGTCATGGT   23   SEQ ID NO:449       BC049OV04   ATATCTTCAACATGAGTCATGGT   23   SEQ ID NO:450                             RHD 488del4 GENOTYPE: RHD 488del4 Dnull           EXON4                                 BC050OV01   TTTATTGCAGACAGACTACCACATG   25   SEQ ID NO:451           BC050OV02   TTTATTGCAGACTACCACATGAACA   25   SEQ ID NO:452       BC050OV03   TTATTGCAGACAGACTACCACAT   23   SEQ ID NO:453       BC050OV04   TTATTGCAGACTACCACATGAAC   23   SEQ ID NO:454                             RHD G635T GENOTYPE: RHD G212V Dnull           EXON5                                 BC051OV01   CTGGCCCCCAGGCGCCCTCTTCT   23   SEQ ID NO:455           BC051OV02   CTGGCCCCCAGTCGCCCTCTTCT   23   SEQ ID NO:456       BC051OV03   TGGCCCCCAGGCGCCCTCTTC   21   SEQ ID NO:457       BC051OV04   TGGGCCCCAGTCGCCCTCTTC   21   SEQ ID NO:458                             RHD del711 GENOTYPE: RHD del711 Dnull           EXON5                                 BC052OV01   AAGGAAGAATGCCGTGTTCAACACC   25   SEQ ID NO:459           BC052OV02   AAGGAAGAATGCGTGTTCAACACCT   25   SEQ ID NO:460       BC052OV03   AGGAAGAATGCCGTGTTCAACAC   23   SEQ ID NO:461       BC052OV04   AGGAAGAATGCGTGTTCAACACC   23   SEQ ID NO:462                             RHD G885T GENOTYPE: RHD M295I Dnull, weak D type11           EXON5                                 BC053OV01   GCTTGCCATGGTGCTGGGT   19   SEQ ID NO:463           BC053OV02   GCTTGCCATTGTGCTGGGT   19   SEQ ID NO:464       BC053OV03   GGCTTGCCATGGTGCTGGGTC   21   SEQ ID NO:465       BC053OV04   GGCTTGCCATTGTGCTGGGTC   21   SEQ ID NO:466                             RHD 906insTGGCT GENOTYPE: RHD 906insTGGCT Dnull           EXON6                                 BC054OV01   CTTGTGGCTGGGCTGATCTCCGTCG   25   SEQ ID NO:467           BC054OV02   CTTGTGGCTGGGGGCTCTGATCTCC   25   SEQ ID NO:468       BC054OV03   TTGTGGCTGGGCTGATCTCCGTC   23   SEQ ID NO:469       BC054OV04   TTGTGGCTGGGGGCTCTGATCTC   23   SEQ ID NO:470                             RHD IVS6 + 1del4 GENOTYPE: RHD IVS6 + 1del4 Dnull           EXON6                                 BC055OV01   AGTACCTGCCGGTAAGAAACTAGAC   25   SEQ ID NO:471           BC055OV02   AGTACCTGCCGGAAACTAGACAACT   25   SEQ ID NO:472       BC055OV03   GTACCTGCCGGTAAGAAACTAGA   23   SEQ ID NO:473       BC055OV04   GTACCTGCCGGAAACTAGACAAC   23   SEQ ID NO:474                             RHD G941T GENOTYPE: RHD G314V Dnull           EXON7                                 BC056OV01   CTTGTCCACAGGGGTGTTGTAACCG   25   SEQ ID NO:475           BC056OV02   CTTGTCCACAGGTGTGTTGTAACCG   25   SEQ ID NO:476       BC056OV03   TTGTCCACAGGGGTGTTGTAACC   23   SEQ ID NO:477       BC056OV04   TTGTCCACAGGTGTGTTGTAACC   23   SEQ ID NO:478                             RHD C990G GENOTYPE: RHD Y330X Dnull           EXON7                                 BC057OV01   CATCATGGGCTACAACTTCAGCTTG   25   SEQ ID NO:479           BC057OV02   CATCATGGGCTAGAACTTCAGCTTG   25   SEQ ID NO:480       BC057OV03   ATCATGGGCTACAACTTCAGCTT   23   SEQ ID NO:481       BC057OV04   ATCATGGGCTAGAACTTCAGCTT   23   SEQ ID NO:482                             RHD IVS8 + 1G &gt; A GENOTYPE: RHD IVS8 + 1G &gt; A Dnull           EXON8                                 BC058OV01   GTCTCCTGACAGGTCAGTGTGAGGC   25   SEQ ID NO:483           BC058OV02   GTCTCCTGACAGATCAGTGTGAGGC   25   SEQ ID NO:484       BC058OV03   TCTCCTGACAGGTCAGTGTGAGG   23   SEQ ID NO:485       BC058OV04   TCTCCTGACAGATCAGTGTGAGG   23   SEQ ID NO:486                             RHD C410T GENOTYPE: RHD DIII IV           EXON3                                 BC059OV01   GGTCAACTTGGCGCAGTTGGTGG   23   SEQ ID NO:487           BC059OV02   GGTCAACTTGGTGCAGTTGGTGG   23   SEQ ID NO:488       BC059OV03   GTCAACTTGGCGCAGTTGGTG   21   SEQ ID NO:489       BC059OV04   GTCAACTTGGTGCAGTTGGTG   21   SEQ ID NO:490                             RHD A455C GENOTYPE: RHD DIIIa, DIIIc, DIII IV, DIVa           EXON3                                 BC060OV01   CAGCTTTAGGCAACCTGAGGATGGT   25   SEQ ID NO:491           BC060OV02   CAGCTTTAGGCACCCTGAGGATGGT   25   SEQ ID NO:492       BC060OV03   ACAGCTTTAGGCAACCTGAGGATGGTC   27   SEQ ID NO:493       BC060OV04   ACAGCTTTAGGCACCCTGAGGATGGTC   27   SEQ ID NO:494                             RHD T667G GENOTYPE: RHD DIIIa, DVa (kou, yh), DCS, DAR (weak D           type 4.2), weak D type4, weak D type 4.1, weak D type 29,       DIII V, DOL       EXON5                                 BC061OV01   CTGGCCAAGTTTCAACTCTGC   21   SEQ ID NO:495           BC061OV02   CTGGCCAAGTGTCAACTCTGC   21   SEQ ID NO:496       BC061OV03   TGGCCAAGTTTCAACTCTG   19   SEQ ID NO:497       BC061OV04   TGGCCAAGTGTCAACTCTG   19   SEQ ID NO:498                             RHD G916A RHD [consensus strand] exon scanning           EXON6                                 BC062OV01   GGCTGATCTCCGTCGGGGGAGCC   23   SEQ ID NO:499           BC062OV02   GGCTGATCTCCATCGGGGGAGCC   23   SEQ ID NO:500       BC062OV03   GCTGATCTCCGTCGGGGGAGC   21   SEQ ID NO:501       BC062OV04   GCTGATCTCCATCGGGGGAGC   21   SEQ ID NO:502                             RHD A932G RHD [consensus strand] exon scanning           EXON6                                 BC063OV01   GGGGAGCCAAGTACCTGCCGGTAAG   25   SEQ ID NO:503           BC063OV02   GGGGAGCCAAGTGCCTGCCGGTAAG   25   SEQ ID NO:504       BC063OV03   GGGAGCCAAGTACCTGCCGGTAA   23   SEQ ID NO:505       BC063OV04   GGGAGCCAAGTGCCTGCCGGTAA   23   SEQ ID NO:506                             RHD A1193T GENOTYPE: RHD DIVb           EXON9                                 BC064OV01   GCACCTCATGAGGCTAAATAT   21   SEQ ID NO:507           BC064OV02   GCACCTCATGTGGCTAAATAT   21   SEQ ID NO:508       BC064OV03   AGCACCTCATGAGGCTAAATATT   23   SEQ ID NO:509       BC064OV04   AGCACCTCATGTGGCTAAATATT   23   SEQ ID NO:510                             RHD A514T GENOTYPE: RHD DFRI           EXON4                                 BC065OV01   AACATGATGCACATCTACGTGTTCG   25   SEQ ID NO:511           BC065OV02   AACCTGAGGCACTTCTACGTGTTCG   25   SEQ ID NO:512       BC065OV03   ACATGATGCACATCTACGTGTTC   23   SEQ ID NO:513       BC065OV04   ACCTGAGGCACTTCTACGTGTTC   23   SEQ ID NO:514                             RHCE T307C GENOTYPE: RHCE RHc           EXON2                                 BC066OV01   AGCCAGTTCCCTTCTGGGAAGGTGG   25   SEQ ID NO:515           BC066OV02   AGCCAGTTCCCTCCTGGGAAGGTGG   25   SEQ ID NO:516       BC066OV03   GAGCCAGTTCCCTTCTGGGAAGGTGGT   27   SEQ ID NO:517       BC066OV04   GAGCCAGTTCCCTCCTGGGAAGGTGGT   27   SEQ ID NO:518                             RHCE A122G GENOTYPE: RHCE Cw           EXON1                                 BC067OV01   CTTAGAGGATCAAAAGGGGCTCG   23   SEQ ID NO:519           BC067OV02   CTTAGAGGATCGAAAGGGGCTCG   23   SEQ ID NO:520       BC067OV03   TTAGAGGATCAAAAGGGGCTC   21   SEQ ID NO:521       BC067OV04   TTAGAGGATCGAAAGGGGCTC   21   SEQ ID NO:522                             RHCE G106A GENOTYPE: RHCE Cx           EXON1                                 BC068OV01   ACCCACTATGACGCTTCCTTAGAGG   25   SEQ ID NO:523           BC068OV02   ACCCACTATGACACTTCCTTAGAGG   25   SEQ ID NO:524       BC068OV03   TACCCACTATGACGCTTCCTTAGAGGA   27   SEQ ID NO:525       BC068OV04   TACCCACTATGACACTTCCTTAGAGGA   27   SEQ ID NO:526                             RHCE C676G GENOTYPE: RHCE E/e           EXON5                                 BC069OV01   AGTGTCAACTCTCCTCTGCTGAGAA   25   SEQ ID NO:527           BC069OV02   AGTGTCAACTCTGCTCTGCTGAGAA   25   SEQ ID NO:528       BC069OV03   AAGTGTCAACTCTCCTCTGCTGAGAAG   27   SEQ ID NO:529       BC069OV04   AAGTGTCAACTCTGCTCTGCTGAGAAG   27   SEQ ID NO:530                             RHCE C733G GENOTYPE: RHCE VS           EXON5                                 BC070OV01   ACCTACTATGCTCTAGCAGTCAGTG   25   SEQ ID NO:531           BC070OV02   ACCTACTATGCTGTAGCAGTCAGTG   25   SEQ ID NO:532       BC070OV03   CACCTACTATGCTCTAGCAGTCAGTGT   27   SEQ ID NO:533       BC070OV04   CACCTACTATGCTGTAGCAGTCAGTGT   27   SEQ ID NO:534                             RHCE G1006T GENOTYPE: RHCE VS/V-           EXON7                                 BC071OV01   TTCAGCTTGCTGGGTCTTGCTTGGA   25   SEQ ID NO:535           BC071OV02   TTCAGCTTGCTGTGTCTTGCTTGGA   25   SEQ ID NO:536       BC071OV03   CTTCAGCTTGCTGGGTCTTGCTTGGAG   27   SEQ ID NO:537       BC071OV04   CTTCAGCTTGCTGTGTCTTGCTTGGAG   27   SEQ ID NO:538                             KEL T698C GENOTYPE: KEL K/k           EXON6                                 BC072OV01   AGAAGTCTCAGCATTCGGTTAAAGT   25   SEQ ID NO:539           BC072OV02   AGAAGTCTCAGCGTTCGGTTAAAGT   25   SEQ ID NO:540       BC072OV03   CAGAAGTCTCAGCATTCGGTTAAAGTT   27   SEQ ID NO:541       BC072OV04   CAGAAGTCTCAGCGTTCGGTTAAAGTT   27   SEQ ID NO:542                             KEL A697T GENOTYPE: KEL K           EXON6                                 BC073OV01   AACTTTAACCGAACGCTGAGACTTC   25   SEQ ID NO:543           BC073OV02   AACTTTAACCGATCGCTGAGACTTC   25   SEQ ID NO:544       BC073OV03   AAACTTTAACCGAACGCTGAGACTTCT   27   SEQ ID NO:545       BC073OV04   AAACTTTAACCGATCGCTGAGACTTCT   27   SEQ ID NO:546                             KEL T961C GENOTYPE: KEL Kpa/Kpb           EXON8                                 BC074OV01   ACTGGAACAGCCATGAAGTGATGGA   25   SEQ ID NO:547           BC074OV02   ACTGGAACAGCCGTGAAGTGATGGA   25   SEQ ID NO:548       BC074OV03   AACTGGAACAGCCATGAAGTGATGGAG   27   SEQ ID NO:549       BC074OV04   AACTGGAACAGCCGTGAAGTGATGGAG   27   SEQ ID NO:550                             KEL G962A GENOTYPE: KEL Kpc           EXON8                                 BC075OV01   AACTGGAACAGCCGTGAAGTGATGG   25   SEQ ID NO:551           BC075OV02   AACTGGAACAGCTGTGAAGTGATGG   25   SEQ ID NO:552       BC075OV03   AAACTGGAACAGCCGTGAAGTGATGGA   27   SEQ ID NO:553       BC075OV04   AAACTGGAACAGCTGTGAAGTGATGGA   27   SEQ ID NO:554                             KEL C1910T GENOTYPE: KEL Jsa/Jsb           EXON17                                 BC076OV01   TGGGGGCTGCCCCGCCTGTGACA   23   SEQ ID NO:555           BC076OV02   TGGGGGCTGCCTCGCCTGTGACA   23   SEQ ID NO:556       BC076OV03   GGGGGCTGCCCCGCCTGTGAC   21   SEQ ID NO:557       BC076OV04   GGGGGCTGCCTCGCCTGTGAC   21   SEQ ID NO:558                             KEL G1208A GENOTYPE: KEL Kmod-1           EXON10                                 BC077OV01   AAGATCATGTGGCTCTGCAGAAAGT   25   SEQ ID NO:559           BC077OV02   AAGATCATGTGGTTCTGCAGAAAGT   25   SEQ ID NO:560       BC077OV03   TAAGATCATGTGGCTCTGCAGAAAGTC   27   SEQ ID NO:561       BC077OV04   TAAGATCATGTGGTTCTGCAGAAAGTC   27   SEQ ID NO:562                             KIDD G838A GENOTYPE: KIDD Jka/Jkb           EXON9                                 BC078OV01   GCCCCATTTGAGGACATCTACTTTG   25   SEQ ID NO:563           BC078OV02   GCCCCATTTGAGAACATCTACTTTG   25   SEQ ID NO:564       BC078OV03   CCCCATTTGAGGACATCTACTTT   23   SEQ ID NO:565       BC078OV04   CCCCATTTGAGAACATCTACTTT   23   SEQ ID NO:566                             KIDD Intron5G &gt; A GENOTYPE: KIDD Jknull           EXON6                                 BC079OV01   TCTTGCCCCACAGGTCATTAATAGC   25   SEQ ID NO:567           BC079OV02   TCTTGCCCCACAAGTCATTAATAGC   25   SEQ ID NO:568       BC079OV03   GCTATTAATGACCTGTGGGGCAAGA   25   SEQ ID NO:569       BC079OV04   GCTATTAATGACTTGTGGGGCAAGA   25   SEQ ID NO:570                             KIDD T871C GENOTYPE: KIDD Jknull           EXON9                                 BC080OV01   GGTTTCAACAGCTCTCTGGCCTGCA   25   SEQ ID NO:571           BC080OV02   GGTTTCAACAGCCCTCTGGCCTGCA   25   SEQ ID NO:572       BC080OV03   GGGTTTCAACAGCTCTCTGGCCTGCAT   27   SEQ ID NO:573       BC080OV04   GGGTTTCAACAGCCCTCTGGCCTGCAT   27   SEQ ID NO:574                             DUFFY G125A GENOTYPE: DUFFY FYa/FYb                                     BC081OV01   ATGGAGACTATGGTGCCAACCTGGA   25   SEQ ID NO:575           BC081OV02   ATGGAGACTATGATGCCAACCTGGA   25   SEQ ID NO:576       BC081OV03   GATGGAGACTATGGTGCCAACCTGGAA   27   SEQ ID NO:577       BC081OV04   GATGGAGACTATGATGCCAACCTGGAA   27   SEQ ID NO:578                             DUFFY T-33C GENOTYPE: DUFFY FYGATA-1           PROMOTER                                 BC082OV01   CCTTGGCTCTTATCTTGGAAGCACA   25   SEQ ID NO:579           BC082OV02   CCTTGGCTCTTACCTTGGAAGCACA   25   SEQ ID NO:580       BC082OV03   CTTGGCTCTTATCTTGGAAGCAC   23   SEQ ID NO:581       BC082OV04   CTTGGCTCTTACCTTGGAAGCAC   23   SEQ ID NO:582                             DUFFY C265T GENOTYPE: DUFFY FYx                                     BC083OV01   CCTCTCTTCCGCTGGCAGC   19   SEQ ID NO:583           BC083OV02   CCTCTCTTCCGCTGGCAGC   19   SEQ ID NO:584       BC083OV03   ACCTCTCTTCCGCTGGCAGCT   21   SEQ ID NO:585       BC083OV04   ACCTCTCTTCCGCTGGCAGCT   21   SEQ ID NO:586                             MNS C59T GENOTYPE: MNS MN           EXON2GYPA                                 BC084OV01   GCATATCAGCATCAAGTACCACTGG   25   SEQ ID NO:587           BC084OV02   GCATATCAGCATTAAGTACCACTGA   25   SEQ ID NO:588       BC084OV03   CATATCAGCATCAAGTACCACTG   23   SEQ ID NO:589       BC084OV04   CATATCAGCATTAAGTACCACTG   23   SEQ ID NO:590                             MNS G71A T72G GENOTYPE: MNS MN           EXON2GYPA                                 BC085OV01   CAAGTACCACTGGTGTGGCAATGCA   25   SEQ ID NO:591           BC085OV02   TAAGTACCACTGAGGTGGCAATGCA   25   SEQ ID NO:592       BC085OV03   TCAAGTACCACTGGTGTGGCAATGCAC   27   SEQ ID NO:593       BC085OV04   TTAAGTACCACTGAGGTGGCAATGCAC   27   SEQ ID NO:594                             MNS T143C GENOTYPE: MNS S/s           EXON4GYPB                                 BC086OV01   TTATAGGAGAAATGGGACAACTTGT   25   SEQ ID NO:595           BC086OV02   TTATAGGAGAAACGGGACAACTTGT   25   SEQ ID NO:596       BC086OV03   TTTATAGGAGAAATGGGACAACTTGTC   27   SEQ ID NO:597       BC086OV04   TTTATAGGAGAAACGGGACAACTTGTC   27   SEQ ID NO:598                             MNS C230T GENOTYPE: MNS U           EXON5GYPB                                 BC087OV01   GTATTATTGGAACGATCCTCTTAAT   25   SEQ ID NO:599           BC087OV02   GTATTATTGGAATGATCCTCTTAAT   25   SEQ ID NO:600       BC087OV03   GGTATTATTGGAACGATCCTCTTAATT   27   SEQ ID NO:601       BC087OV04   GGTATTATTGGAATGATCCTGTTAATT   27   SEQ ID NO:602                             MNS INTRON5 + 5GT GENOTYPE: MNS U           EXON5GYPB                                 BC088OV01   TGATAAAGGTGAGAATTCAGTTTTT   25   SEQ ID NO:603           BC088OV02   TGATAAAGGTGATAATTCAGTTTTT   25   SEQ ID NO:604       BC088OV03   AAAAACTGAATTCTCACCTTTATCA   25   SEQ ID NO:605       BC088OV04   AAAAACTGAATTATCACCTTTATCA   25   SEQ ID NO:606                             MNS C790A GENOTYPE: MNS GP.Mur (Mi.III)           EXON3                                 BC089OV01   TATATGCAGATACGCACAAACGGGA   25   SEQ ID NO:607           BC089OV02   TATATGCAGATAAGCACAAACGGGA   25   SEQ ID NO:608       BC089OV03   TTATATGCAGATACGCACAAACGGGAC   27   SEQ ID NO:609       BC089OV04   TTATATGCAGATAAGCACAAACGGGAC   27   SEQ ID NO:610                             MNS C850G GENOTYPE: MNS MNS GP.Mur (Mi.III)           EXON3                                 BC090OV01   GGGGAAACAGTTGTAACAGAAATTT   25   SEQ ID NO:611           BC090OV02   GGGCAAACAGTTCTAACAGAAATTT   25   SEQ ID NO:612       BC090OV03   AGGGGAAACAGTTGTAACAGAAATTTC   27   SEQ ID NO:613       BC090OV04   AGGGCAAACAGTTCTAACAGAAATTTC   27   SEQ ID NO:614                             DIEGO T2561C GENOTYPE: DIEGO DIa/DIb           EXON19                                 BC091OV01   GCCAGGGAGGCCAGCGTGGACTTCA   25   SEQ ID NO:615           BC091OV02   GCCAGGGAGGCCGGCGTGGACTTCA   25   SEQ ID NO:616       BC091OV03   CCAGGGAGGCCAGCGTGGACTTC   23   SEQ ID NO:617       BC091OV04   CCAGGGAGGCCGGCGTGGACTTC   23   SEQ ID NO:618                             DOMBROCK A793G GENOTYPE: DOMBROCK DOa/DOb           EXON2                                 BC092OV01   ACTGCAACCAGTTTCCTCTTGGGTG   25   SEQ ID NO:619           BC092OV02   ACTGCAACCAGTCTCCTCTTGGGTG   25   SEQ ID NO:620       BC092OV03   AACTGCAACCAGTTTCCTCTTGGGTGG   27   SEQ ID NO:621       BC092OV04   AACTGCAACCAGTCTCCTCTTGGGTGG   27   SEQ ID NO:622                             COLTON C134T GENOTYPE: COLTON COa/COb           EXON1                                 BC093OV01   TTGTCCTGGACCGCCGTCTGGTTGT   25   SEQ ID NO:623           BC093OV02   TTGTCCTGGACCACCGTCTGGTTGT   25   SEQ ID NO:624       BC093OV03   TGTCCTGGACCGCCGTCTGGTTG   23   SEQ ID NO:625       BC093OV04   TGTCCTGGACCACCGTCTGGTTG   23   SEQ ID NO:626                             RHD G1048C GENOTYPE: RHD DIVa/DIVb           EXON7                                 BC094OV01   GCTGGTGCTTGATACCGTCGG   21   SEQ ID NO:627           BC094OV02   GCTGGTGCTTCATACCGTCGG   21   SEQ ID NO:628       BC094OV03   TGCTGGTGCTTGATACCGTCGGA   23   SEQ ID NO:629       BC094OV04   TGCTGGTGCTTCATACCGTCGGA   23   SEQ ID NO:630            
1.2 Production of the DNA-chip for Genotyping Blood Groups Printing and Processing of the Glass Slides
 
     The probes capable of detecting the genetic variations previously identified are printed onto aminosilane coated supports (glass slides) using DMSO as a solvent. The printing is carried out using a spotter or printer of oligonucleotides (probes) while controlling the temperature and relative humidity. 
     The joining of the probes to the support (glass slides) is carried out by means of crosslinking with ultraviolet radiation and heating as described in the documentation provided by the manufacturer (for example, Corning Lifesciences; available on the World Wide Web at corning.com). The relative humidity during the deposition process is maintained between 40-50% and the temperature around 20° C. 
     1.3 Validation of the Clinical Usefulness of the DNA-chip to Identify Human Blood Groups: Simultaneous, Sensitive, Specific and Reproducible Detection of Human Genetic Variations Associated with Erythrocyte Antigens 
     1.3.1 Preparation of the Sample to be Hybridized 
     The DNA of the individual is extracted from a blood sample by a standard protocol of filtration. (For example, commercial kits from Macherey Nagel, Qiagene etc). 
     All the exons and introns of interest are amplified by multiplex PCR using appropriate pairs of oligonucleotide primers. Oligonucleotide primers useful for carrying out PCR multiplex for the detection of genetic variations associated with human erythrocyte antigens can be designed by those skilled in the art using the corresponding gene sequences as described in GenBank with, for example, the software: Primer 3 (available on the World Wide Web at frodo.wi.mitedu/cgi-bin/primer3/primer3) or Web Primer (available on the World Wide Web at seq.yeastgenome.org/cgi-bin/web-primer). Practically any pair of oligonucleotide primers can be used that permit the specific amplification of genetic fragments where a genetic variation to be detected may exist. Where possible, those pairs of oligonucleotide primers which permit the said amplifications to be performed in the least possible number of PCR reactions are used. 
     In this case, primers were selected which permitted, in only 3 PCR reactions, amplification of the 36 fragments necessary for genotyping the (94) genetic variations previously mentioned using the DNA-chip for detection of genetic variations associated with erythrocyte antigens. 
     The PCR multiplex reactions are carried out simultaneously under the same conditions of time and temperature which permit specific amplification of the gene fragments in which the genetic variations to be detected can exist. Once the PCR multiplex has finished, agarose gel analysis is used to check that the amplification reaction has taken place. 
     Next, the sample to be hybridized (products of amplification) is subjected to fragmentation with a DNase and the resulting fragmentation products subjected to indirect labelling. A terminal transferase adds a nucleotide, covalently joined to one member of a pair of molecules that show specific binding to one another e.g. biotin, to the end of these small DNA fragments. 
     Before applying the sample to the DNA-chip, the sample is denatured by heating to 95° C. for 5 minutes and then, the “ChipMap Kit Hybridization Buffer” (Ventana Medical System) is added. 
     1.3.2 Hybridization 
     Hybridization is carried out automatically in a hybridisation station such as the Ventana Discovery (Ventana Medical Systems) that has been specifically developed for such a use. Alternatively hybridisation can be performed manually. 
     The prehybridization and blocking of the slides is carried out with BSA. Next, the hybridization solution {ChipMap Kit Hybridization Buffer, Ventana Medical System) is applied to the surface of the DNA-chip which is maintained at 45° C. for 1 hour following the protocol of Ventana 9.0 Europe (Ventana Medical System). Finally the slides are subjected to different cleaning solutions (ChipMap hybridisation Kit Buffers, Ventana Medical System). Once the process of hybridization has finished, the final cleaning and drying of the slides begins. 
     When hybridization has taken place, the DNA chip is developed by incubation with a fluorescently labelled molecule that is able to specifically bind to the molecule incorporated into the amplification product by terminal transferase (e.g. in the case of biotin incorporation a fluorophore coupled to streptavidin such as streptavidin-Cy3 can be used) to label the probe positions where hybridization has occured. 
     1.3.3. Scanning the Slides 
     The slides are placed in a fluorescent confocal scanner, for example Axon 4100 a , and the signal emitted by the fluorophore is scanned when stimulated by the laser. 
     1.3.4 Quantification of the Image 
     The scanner&#39;s own software allows quantification of the image obtained from the signal at the points where hybridization has taken place. 
     1.3.5 Interpretation of the Results: Determination of the Genotype of the Individual, Regarding the Human Genetic Variations Associated with Human Erythrocyte Antigens and the Identification of the Blood Group of the Individual. 
     From the signal obtained with the probes which detect the different genetic variations, the genotype of the individual is established. In the first instance the scanner software executes a function to subtract the local background noise from the absolute signal intensity value obtained for each probe. Next, the replicates for each of the 4 probes that are used to characterize each genetic variation are grouped. The average intensity value for each of 4 probes is calculated using the average collated from the replicates in order to identify abnormal values (outliers) that can be excluded from further consideration. Once the average intensity value for each of the probes is known then two ratios are calculated (ratio 1 and ratio 2): 
               Ratio   ⁢           ⁢   1     =       Average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   1         Average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   1     +     
     ⁢           ⁢     Average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   2                       Ratio   ⁢           ⁢   2     =       Average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   3         Average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   3     +     
     ⁢           ⁢     Average   ⁢           ⁢   intensity   ⁢           ⁢   value   ⁢           ⁢   for   ⁢           ⁢   probe   ⁢           ⁢   4               
wherein probe 1 detects (is capable of specifically hybridising to) genetic variation A (e.g. a normal allele), probe 2 detects (is capable of specifically hybridising to) genetic variation B (e.g. a mutant allele), probe 3 detects (is capable of specifically hybridising to) genetic variation A (e.g. a normal allele) and probe 4 detects (is capable of specifically hybridising to) genetic variation B (e.g. a mutant allele).
 
     These ratios are substituted in three linear functions which characterize each one of the three possible genotypes: 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                   
                 AA 
                 Function 1 
               
               
                   
                 AB 
                 Function 2 
               
               
                   
                 BB 
                 Function 3 
               
               
                   
               
            
           
         
       
     
     The function which presents the highest absolute value determines the genotype of the patient. 
     In this case, the linear functions are obtained by analyzing 5 subjects for each of the three possible genotypes of the genetic variation (AA, AB, BB). With the results, ratios 1 and 2 are calculated for the 15 subjects. These ratios are classification variables for the three groups to create the linear functions, with which the discriminatory capacity of the two pairs of designed probes are evaluated. If the discriminatory capacity is not 100%, the probes are redesigned. New subjects characterized for each of the three genotypes make up new ratios 1 and 2 to perfect the linear functions and in short, to improve the discriminatory capacity of the algorithm based on these three functions. 
     When using a confocal fluorescent scanner, to obtain reliable results it is preferable that ratios 1 and 2 are within the range of the ratios used to build the groups, the average fluorescence intensity of the 4n (for example 40) replicates with regard to background noise is greater than 5 and the coefficient of variation of all of the DNA-chip replicates is below 0.25. 
     Again when a fluorescent confocal scanner is used in the experiment, for a complete hybridization to be considered reliable preferably the ratio of probe fluorescence intensity to background noise of all the DNA-chip probes is above 15. Likewise, the average of all the ratios is preferably above 0.6 and the negative control is preferably less than or equal to 3 times the background noise 
     To sum up, in this case 4 probes (repeated 10 times) are presented on the slide for detection of each mutation. Two of the probes detect one genetic variation (A) and the other two the other genetic variation (B). The examined base is located in the central position of the probes. 
     A subject homozygous for the genetic variation A will not show genetic variation B. Consequently, in the image obtained from the glass support the probes which detect genetic variation B will show a hybridization signal significantly less than that shown by variation A and vice versa. In this case the ratios 1 and 2 will show 1 and the subjects will be assigned as homozygous AA by the software analysis. 
     On the other hand, a heterozygous subject for the determined genetic variation shows both the genetic variations. Therefore, the probes which detect them show an equivalent hybridization signal. The ratios 1 and 2 will show 0.5 and the subject will be assigned as heterozygous AB by the software analysis. 
     Example 2 
     Identification of the Blood Group of 15 Individual Blood Donors, Using the DNA-chip for the Genotyping of Blood Groups 
     2.1 DNA Extraction 
     DNA was extracted from 15 blood donors who responded to serological groups A and 0 by conventional methods. Genetic analysis by sequencing of the region of interest confirmed that 5 of the donors had genotype 188G189C (serological determination A), another 5 donors had genotype 188GA189CT (serological determination 0) and the remaining 5 188A189T (serological determination 0) 
     2.2 Probe Design 
     4 probes were designed for the detection of the polymorphism ABO G188A/C189T genotype ABO O1v as previously described (Example 1): 
                            BC012OV01               ACCATCTGCAGCGCGTCTCGTTGCC   25   SEQ ID NO:299               BC012OV02               ACCATCTGCAGCATGTCTCGTTGCC   25   SEQ ID NO:300               BC012OV03               CCATCTGCAGCGCGTCTCGTTGC   23   SEQ ID NO:301               BC012OV04               CCATCTGCAGCATGTCTCGTTGC   23   SEQ ID NO:302            
2.3 Production of the DNA Chip for the Detection of Human Genetic Variations Associated with Determined Human Erythrocyte Antigens
 
     The designed probes were printed onto glass slides with a micro-arrayer as described in Example 1.2. 
     2.4 PCR and Labelling the Sample 
     The region of the ABO gene for the analysis of the genetic variation of interest (ABO G188A/C189T genotype ABO O1v) was amplified by means of PCR multiplex using specific primers. The product of the amplification was fragmented and labelled as described in Example 1.3.1. 
     2.5 Hybridization of the Samples 
     Hybridization was carried out in an automated hybridisation station, as described in Example 1.3.2. 
     2.6 Analysis of the Results 
     The slides were placed in the scanner. The signal emitted by the bound flurophore on excitation by the laser was measured (Example 1.3.3) and the image obtained from the signal at the points where hybridization had taken place was quantified (Example 1.3.4). 
     The analysis of the results was carried out using the algorithm previously described in Example 1.3.5. The algorithm allowed characterization of this genetic variation for the 15 subjects with a coincidence of 100% compared to serological methods and sequencing. 
       FIG. 1  shows the representation of ratios 1 and 2 and allows characterization of the 15 patients. 
     Table 5 shows the linear functions for the three genotype groups, when the number of replicates of the 4 probes used was 10. “X” is ratio 1; “Y” is ratio 2; “0” corresponds to the genotype 188A189T; “1” corresponds to the genotype 188GA189CT; and “2” corresponds to the genotype 188G189C. 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Coefficients of the functions used for genotyping 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CLASS 
                 0 
                 1 
                 2 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 X 
                 7.338994 
                 101.6024 
                 176.7265 
               
               
                   
                 Y 
                 1227.301 
                 603.8602 
                 81.12664 
               
               
                   
                 (Constant) 
                 −499.132 
                 −163.927 
                 −27.3071 
               
               
                   
               
            
           
         
       
     
     A donor with genotype 188G189C had ratios 1 and 2 of 0.77 and 0.82 respectively. On substituting these ratios for linear functions, it is observed that function 2 shows a greater absolute value. From this we can see how the algorithm of the invention classifies perfectly classifies donors when 10 replicates are used for each one of the 4 probes. 
     Table 6 shows the linear functions obtained when 8 replicates of each of the 4 probes are used. 
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Coefficients of the functions used for genotyping 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CLASS 
                 0 
                 1 
                 2 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 X 
                 178.1139 
                 272.6293 
                 417.9721 
               
               
                   
                 Y 
                 −42.2919 
                 59.0597 
                 132.0375 
               
               
                   
                 (Constant) 
                 −16.0985 
                 −82.5103 
                 −225.228 
               
               
                   
               
            
           
         
       
     
     The same donor with genotype 188G189C had the same ratios 1 and 2 of 0.77 and 0.82, respectively. On substituting these ratios for linear functions, it is observed that function 2 shows a greater absolute value. From this, we can see that the algorithm of the invention perfectly classifies patients when 8 replicates are used for each one of the 4 probes. 
     Table 7 shows the linear functions obtained when 6 replicates of each of the 4 probes are used. 
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Coefficients of the functions used for genotyping 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CLASS 
                 0 
                 1 
                 2 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 X 
                 181.8305 
                 307.0291 
                 477.2833 
               
               
                   
                 Y 
                 −51.0987 
                 15.33189 
                 57.86783 
               
               
                   
                 (Constant) 
                 −15.1285 
                 −79.8083 
                 −218.298 
               
               
                   
               
            
           
         
       
     
     The same donor with genotype 188G189C had the same ratios 1 and 2 of 0.77 and 0.82, respectively. On substituting these ratios for linear functions, it is observed that function 2 shows a greater absolute value. From this, we can see that the algorithm of the invention perfectly classifies patients when 6 replicates are used for each one of the 4 probes. 
     Example 3 
     Detection of Human Genetic Variations Associated with Inflammatory Bowel Disease (IBD), Using a DNA-chip for the Diagnosis, Prognosis and Prediction of Response to Treatment of IBD 
     3.1 Design of the DNA-chip for Genotyping of Genetic Variations Associated with IBD 
     A DNA-chip which permits the simultaneous, sensitive, specific and reproducible detection of human genetic variations associated with IBD was designed and manufactured. The genetic variations are related to a greater or lesser risk of suffering from IBD, a better or worse response to treatment and also a better or worse prognosis of the disease. Table 1 lists illustrative examples of human genetic variations associated with BED which can be determined using this DNA-chip. 
     The DNA-chip designed and produced consists of a support (glass slide) which comprises a plurality of probes on its surface that permit the detection of the genetic variations. These probes are capable of hybridizing with the (amplified) target sequences of the genes related to IBD. The DNA sequences of the probes used are listed below. In general, the name of the gene and the mutation is indicated (change of nucleotide, “ins”: insertion “del” deletion or change of amino acid): 
                    1. - Multidrug resistance protein (MDR-1)        G2677T/A/C Ala893Ser/Thr/Pro) The probes detect       the polymorphisms G2677T (Ala893Ser), G2677A       (Ala893Thr) and G2677C (Ala893Pro) of the gene       Multidrug resistance protein MDR-1)                     TCACCTTCCCAGCACCTTCTAGTTC   SEQ ID NO:631       GAACTAGAAGGTGCTGGGAAGGTGA   SEQ ID NO:632       TCACCTTCCCAGGACCTTCTAGTTC   SEQ ID NO:633       GAACTAGAAGGTCCTGGGAAGGTGA   SEQ ID NO:634       TCACCTTCCCAGAACCTTCTAGTTC   SEQ ID NO:635       GAACTAGAAGGTTCTGGGAAGGTGA   SEQ ID NO:636       TCACCTTCCCAGTACCTTCTAGTTC   SEQ ID NO:637       GAACTAGAAGGTACTGGGAAGGTGA   SEQ ID NO:638                         2. - Multidrug resistance protein (MDR-1) C3435T                     TGCTGCCCTCACAATCTCTTCCTGT   SEQ ID NO:639       ACAGGAAGAGATTGTGAGGGCAGCA   SEQ ID NO:640       TGCTGCCCTCACGATCTCTTCCTGT   SEQ ID NO:641       ACAGGAAGAGATCGTGAGGGCAGCA   SEQ ID NO:642                         3. - CARD15 R702W                     AAGGCCCTGCTCCGGCGCCAGGCCT   SEQ ID NO:643       AGGCCTGGCGCCGGAGCAGGGCCTT   SEQ ID NO:644       AAGGCCCTGCTCTGGCGCCAGGCCT   SEQ ID NO:645       AGGCCTGGCGCCAGAGCAGGGCCTT   SEQ ID NO:646                         4. - CARD15 G908R                     TTCAGATTCTGGGGCAACAGAGTGG   SEQ ID NO:647       CCACTCTGTTGCCCCAGAATCTGAA   SEQ ID NO:648       TTCAGATTCTGGCGCAACAGAGTGG   SEQ ID NO:649       CCACTCTGTTGCGCCAGAATCTGAA   SEQ ID NO:650                         5. - CARD15 1007insC                     TCCTGCAGGCCCCTTGAAAGGAATG   SEQ ID NO:651       CATTCCTTTCAAGGGGCCTGCAGGA   SEQ ID NO:652       TCCTGCAGGCCCTTGAAAGGAATGA   SEQ ID NO:653       TCATTCCTTTCAAGGGCCTGCAGGA   SEQ ID NO:654                         6. - Microsomal epoxide hydrolase (EPXH1) T612C       (Y113H)                     ATTCTCAACAGATACCCTCACTTCA   SEQ ID NO:655       TGAAGTGAGGGTATCTGTTGAGAAT   SEQ ID NO:656       ATTCTCAACAGACACCCTCACTTCA   SEQ ID NO:657       TGAAGTGAGGGTGTCTGTTGAGAAT   SEQ ID NO:658                         7. - Monocyte chemotactic protein 1 (MCP1)       (−2518) G/A                     AGGCAGACAGCTGTCACTTTCCAGA   SEQ ID NO:659       TCTGGAAAGTGACAGCTGTCTGCCT   SEQ ID NO:660       AGGCAGACAGCTATCACTTTCCAGA   SEQ ID NO:661       TCTGGAAAGTGATAGCTGTCTGCCT   SEQ ID NO:662                         8. - Interleukin 10 (IL10) (−1082) G/A                     GCTTCTTTGGGAAGGGGAAGTAGGG   SEQ ID NO:663       CCCTACTTCCCCTTCCCAAAGAAGC   SEQ ID NO:664       GCTTCTTTGGGAGGGGGAAGTAGGG   SEQ ID NO:665       CCCTACTTCCCCCTCCCAAAGAAGC   SEQ ID NO:666                         9. - Interleukin 10 (IL10) G15R G43A                     GTCCTCCTGACTGGGGTGAGGGCCA   SEQ ID NO:667       GTCCTCCTGACTAGGGTGAGGGCCA   SEQ ID NO:668       TGGCCCTCACCCCAGTCAGGAGGAC   SEQ ID NO:669       TGGCCCTCACCCTAGTCAGGAGGAC   SEQ ID NO:670                         10. - Interleukin 16 (IL16) (−295) T/C                     TTGTTCCTATCATAAAGAGTCAGGG   SEQ ID NO:671       CCCTGACTCTTTATGATAGGAACAA   SEQ ID NO:672       TTGTTCCTATCACAAAGAGTCAGGG   SEQ ID NO:673       CCCTGACTCTTTGTGATAGGAACAA   SEQ ID NO:674                         11. - Fas ligand (−843) C/T                     ATGAAAACATTGTGAAATACAAAGC   SEQ ID NO:675       GCTTTGTATTTCACAATGTTTTCAT   SEQ ID NO:676       ATGAAAACATTGCGAAATACAAAGC   SEQ ID NO:677       GCTTTGTATTTCGCAATGTTTTCAT   SEQ ID NO:678                         12. - Nuclear factor kappa-B (NFκB1) 94delATTG                     CCCCGACCATTGGGCCCGGCAGGCG   SEQ ID NO:679       CGCCTGCCGGGCCCAATGGTCGGGG   SEQ ID NO:680       CCCCGACCATTGATTGGGCCCGGCA   SEQ ID NO:681       TGCCGGGCCCAATCAATGGTCGGGG   SEQ ID NO:682                         13. - Nuclear factor kappa-B inhibitor alpha       (NFκKBIA) SNP in the 3′UTR (G/A)                     TGCACACTGCCTGGCCCAAAACGTC   SEQ ID NO:683       TGCACACTGCCTAGCCCAAAACGTC   SEQ ID NO:684       GACGTTTTGGGCCAGGCAGTGTGCA   SEQ ID NO:685       GACGTTTTGGGCTAGGCAGTGTGCA   SEQ ID NO:686                         14. - Signal transducer and activator of transcrip-       tion 6 (STAT6) G2964A                     GCTCTGAGACACGCCCCAACATGCC   SEQ ID NO:687       GGCATGTTGGGGCGTGTCTCAGAGC   SEQ ID NO:688       GCTCTGAGACACACCCCAACATGCC   SEQ ID NO:689       GGCATGTTGGGGTGTGTCTCAGAGC   SEQ ID NO:690                         15. - Interleukin 18 (IL18) TCA/TCC in the codon 35                     GCCAAAGTAATCGGATTCCAGGTTT   SEQ ID NO:691       AAACCTGGAATCCGATTACTTTGGC   SEQ ID NO:692       GCCAAAGTAATCTGATTCCAGGTTT   SEQ ID NO:693       AAACCTGGAATCAGATTACTTTGGC   SEQ ID NO:694                         16. - Mediterranean fever gene (MEFV) E474E                     CTACTTCCTGGAGCAGCAAGAGCAT   SEQ ID NO:695       ATGCTCTTGCTGCTCCAGGAAGTAG   SEQ ID NO:696       CTACTTCCTGGAACAGCAAGAGCAT   SEQ ID NO:697       ATGCTCTTGCTGTTCCAGGAAGTAG   SEQ ID NO:698                         17. - Mediterranean fever gene (MEFV) Q476Q                     CCTGGAGCAGCAGGAGCATTTCTTT   SEQ ID NO:699       AAAGAAATGCTCCTGCTGCTCCAGG   SEQ ID NO:700       CCTGGAGCAGCAAGAGCATTTCTTT   SEQ ID NO:701       AAAGAAATGCTCTTGCTGCTCCAGG   SEQ ID NO:702                         18. - Mediterranean fever gene (MEFV) D510D                     CGCCCTGCTCGACGCGCTGATTGGG   SEQ ID NO:703       CCCAATCAGCGCGTCGAGCAGGGCG   SEQ ID NO:704       CGCCCTGCTCGATGCGCTGATTGGG   SEQ ID NO:705       CCCAATCAGCGCATCGAGCAGGGCG   SEQ ID NO:706                         19. - Mediterranean fever gene (MEFV) P588P                     GCCAATCAGCTCCGGAACTACGGAG   SEQ ID NO:707       CTCCGTAGTTCCGGAGCTGATTGGC   SEQ ID NO:708       GCCAATCAGCTCTGGAACTACGGAG   SEQ ID NO:709       CTCCGTAGTTCCAGAGCTGATTGGC   SEQ ID NO:710                         20. - Discs, large homolog 5 (DLG5) 113G/A (R30Q)                     TCATTCACTTGCCGGTCAGTGAGGA   SEQ ID NO:711       TCCTCACTGACCGGCAAGTGAATGA   SEQ ID NO:712       TCATTCACTTGCTGGTCAGTGAGGA   SEQ ID NO:713       TCCTCACTGACCAGCAAGTGAATGA   SEQ ID NO:714                         21. - Colony stimulating factor receptor 1 (CSFR1)       A2033T                     AAACCCTTATTCACCTAATCACAGC   SEQ ID NO:715       GCTGTGATTAGGTGAATAAGGGTTT   SEQ ID NO:716       AAACCCTTATTCTCCTAATCACAGC   SEQ ID NO:717       GCTGTGATTAGGAGAATAAGGGTTT   SEQ ID NO:718                         22. - Organic cation transporter (OCTN1, SLC22A4)       1672C/T (L503F)                     CTGATTGGAATCCTCACCCTTTTTT   SEQ ID NO:719       AAAAAAGGGTGAGGATTCCAATCAG   SEQ ID NO:720       CTGATTGGAATCTTCACCCTTTTTT   SEQ ID NO:721       AAAAAAGGGTGAAGATTCCAATCAG   SEQ ID NO:722                         23. - Organic cation transporter (OCTN2, SLC22A5)       (−207) G/C                     CCAGGGAAGGTTGCGGGCCTGGGCC   SEQ ID NO:723       GGCCCAGGCCCGCAACCTTCCCTGG   SEQ ID NO:724       CCAGGGAAGGTTCCGGGCCTGGGCC   SEQ ID NO:725       GGCCCAGGCCCGGAACCTTCCCTGG   SEQ ID NO:726                         24. - Toll-like receptor 4 (TLR4) (A/G) Asp299Gly                     ACTACCTCGATGATATTATTGACTT   SEQ ID NO:727       AAGTCAATAATATCATCGAGGTAGT   SEQ ID NO:728       ACTACCTCGATGGTATTATTGACTT   SEQ ID NO:729       AAGTCAATAATACCATCGAGGTAGT   SEQ ID NO:730                         25. - Toll-like receptor 4 (TLR4) (C/T) Thr399Ile                     ATTTTGGGACAACCAGCCTAAAGTA   SEQ ID NO:731       TACTTTAGGCTGGTTGTCCCAAAAT   SEQ ID NO:732       ATTTTGGGACAATCAGCCTAAAGTA   SEQ ID NO:733       TACTTTAGGCTGATTGTCCCAAAAT   SEQ ID NO:734                         26. - Interleukin 1 beta (IL1β) (−511) A/C                     GAAGAGAATCCCAGAGCAGCCTGTT   SEQ ID NO:735       AACAGGCTGCTCTGGGATTCTCTTC   SEQ ID NO:736       GAAGAGAATCCCCGAGCAGCCTGTT   SEQ ID NO:737       AACAGGCTGCTCGGGGATTCTCTTC   SEQ ID NO:738                         27. - Superoxide dismutase 2 (SOD2) (C/T) Ala16Val                     AGCTGGCTCCGGCTTTGGGGTATCT   SEQ ID NO:739       AGATACCCCAAAGCCGGAGCCAGCT   SEQ ID NO:740       AGCTGGCTCCGGTTTTGGGGTATCT   SEQ ID NO:741       AGATACCCCAAAACCGGAGCCAGCT   SEQ ID NO:742                         28. - Peroxisome proliferator-activated receptor       gamma (PPARG) (C/G) Pro12Ala                     TCTCCTATTGACCCAGAAAGCGATT   SEQ ID NO:743       AATCGCTTTCTGGGTCAATAGGAGA   SEQ ID NO:744       TCTCCTATTGACGCAGAAAGCGATT   SEQ ID NO:745       AATCGCTTTCTGCGTCAATAGGAGA   SEQ ID NO:746                         29. - Intercellular adhesion molecule 1 (ICAM1)       (A/G) K469E                     GAGGTCACCCGCAAGGTGACCGTGA   SEQ ID NO:747       TCACGGTCACCTTGCGGGTGACCTC   SEQ ID NO:748       GAGGTCACCCGCGAGGTGACCGTGA   SEQ ID NO:749       TCACGGTCACCTCGCGGGTGACCTC   SEQ ID NO:750                         30. - Intercellular adhesion molecule 1 ICAM1 R241G                     TGTTCCCTGGACAGGCTGTTCCCAG   SEQ ID NO:751       CTGGGAACAGCCTGTCCAGGGAACA   SEQ ID NO:752       TGTTCCCTGGACGGGCTGTTCCCAG   SEQ ID NO:753       CTGGGAACAGCCCGTCCAGGGAACA   SEQ ID NO:754                         31. - IBD5 locus IGR2060a_1                     CCTTGCAACCCTGGCAAAGGTAATG   SEQ ID NO:755       CATTACCTTTGCCAGGGTTGCAAGG   SEQ ID NO:756       CCTTGCAACCCTCGCAAAGGTAATG   SEQ ID NO:757       CATTACCTTTGCGAGGGTTGCAAGG   SEQ ID NO:758                         32. - IBD5 locus IGR2198a_1                     CAGTAGACGAACGATGCAAAATACC   SEQ ID NO:759       GGTATTTTGCATCGTTCGTCTACTG   SEQ ID NO:760       CAGTAGACGAACCATGCAAAATACC   SEQ ID NO:761       GGTATTTTGCATGGTTCGTCTACTG   SEQ ID NO:762                         33. - IBD5 locus IGR3096a_1                     CATCCTGGAGAATAGCTGAGAACCT   SEQ ID NO:763       AGGTTCTCAGCTATTCTCCAGGATG   SEQ ID NO:764       CATCCTGGAGAACAGCTGAGAACCT   SEQ ID NO:765       AGGTTCTCAGCTGTTCTCCAGGATG   SEQ ID NO:766                         34. - Heat shock protein 70 (HSP70-2) 1267A/G       Gln351Gln                     GAAGCTGCTGCAAGACTTCTTCAAC   SEQ ID NO:767       GTTGAAGAAGTCTTGCAGCAGCTTC   SEQ ID NO:768       GAAGCTGCTGCAGGACTTCTTCAAC   SEQ ID NO:769       GTTGAAGAAGTCCTGCAGCAGCTTC   SEQ ID NO:770                         35. - Toll-like receptor (TLR9) 1237C/T                     TCCCTCTGCCTGAAAACTCCCCCAA   SEQ ID NO:771       TTGGGGGAGTTTTCAGGCAGAGGGA   SEQ ID NO:772       TCCCTCTGCCTGGAAACTCCCCCAA   SEQ ID NO:773       TTGGGGGAGTTTCCAGGCAGAGGGA   SEQ ID NO:774                         36. - Methylenetetrahydrofolate reductase (MTFHR)       C677T Val222Ala                     TGTCTGCGGGAGCCGATTTCATCAT   SEQ ID NO:775       ATGATGAAATCGGCTCCCGCAGACA   SEQ ID NO:776       TGTCTGCGGGAGTCGATTTCATCAT   SEQ ID NO:777       ATGATGAAATCGACTCCCGCAGACA   SEQ ID NO:778                         37. - Interleukin 4 (IL4) (−590) C/T                     GGAGAACATTGTCCCCCAGTGCTGG   SEQ ID NO:779       CCAGCACTGGGGGACAATGTTCTCC   SEQ ID NO:780       GGAGAACATTGTTCCCCAGTGCTGG   SEQ ID NO:781       CCAGCACTGGGGAACAATGTTCTCC   SEQ ID NO:782                         38. - Interleukin 4 (IL4) (−34) C/T                     ATAAACTAATTGCCTCACATTGTCA   SEQ ID NO:783       TGACAATGTGAGGCAATTAGTTTAT   SEQ ID NO:784       ATAAACTAATTGTCTCACATTGTCA   SEQ ID NO:785       TGACAATGTGAGACAATTAGTTTAT   SEQ ID NO:786                         39. - Mannose-binding lectin (MBL) (A/G) Gly54Asp                     ATGGGCGTGATGACACCAAGGGAGA   SEQ ID NO:787       TCTCCCTTGGTGTCATCACGCCCAT   SEQ ID NO:788       ATGGGCGTGATGGCACCAAGGGAGA   SEQ ID NO:789       TCTCCCTTGGTGCCATCACGCCCAT   SEQ ID NO:790                         40. - Mannose-binding lectin (MBL) (A/G) Gly57Glu                     ATGGCACCAAGGAAGAAAAGGGGGA   SEQ ID NO:791       TCCCCCTTTTCTTCCTTGGTGCCAT   SEQ ID NO:792       ATGGCACCAAGGGAGAAAAGGGGGA   SEQ ID NO:793       TCCCCCTTTTCTCCCTTGGTGCCAT   SEQ ID NO:794                         41. - Mannose-binding lectin (MBL) (C/T) Arg52Cys                     GGCAAAGATGGGCGTGATGGCACCA   SEQ ID NO:795       TGGTGCCATCACGCCCATCTTTGCC   SEQ ID NO:796       GGCAAAGATGGGTGTGATGGCACCA   SEQ ID NO:797       TGGTGCCATCACACCCATCTTTGCC   SEQ ID NO:798                         42. - Angiotensinogen precursor (AGT) (−6) A/T                     CGTGACCCGGCCAGGGGAAGAAGCT   SEQ ID NO:799       CGTGACCCGGCCGGGGGAAGAAGCT   SEQ ID NO:800       AGCTTCTTCCCCTGGCCGGGTCACG   SEQ ID NO:801       AGCTTCTTCCCCCGGCCGGGTCACG   SEQ ID NO:802                         43. - Plasminogen activator inhibitor (PAI1) 4G/5G                     GGACACGTGGGGGAGTCAGCCGTGT   SEQ ID NO:803       ACACGGCTGACTCCCCCACGTGTCC   SEQ ID NO:804       GGACACGTGGGGAGTCAGCCGTGTA   SEQ ID NO:805       TACACGGCTGACTCCCCACGTGTCC   SEQ ID NO:806                         44. - Tumor necrosis factor alpha (TNF α)       (−857) C/T                     CCCCCCCCTTAACGAAGACAGGGCC   SEQ ID NO:807       GGCCCTGTCTTCGTTAAGGGGGGGG   SEQ ID NO:808       CCCCCCCCTTAATGAAGACAGGGCC   SEQ ID NO:809       GGCCCTGTCTTCATTAAGGGGGGGG   SEQ ID NO:810                         45. - Tumor necrosis factor alpha (TNF α)       (−308) G/A                     TTGAGGGGCATGGGGACGGGGTTCA   SEQ ID NO:811       TGAACCCCGTCCCCATGCCCCTCAA   SEQ ID NO:812       TTGAGGGGCATGAGGACGGGGTTCA   SEQ ID NO:813       TGAACCCCGTCCTCATGCCCCTCAA   SEQ ID NO:814                         46. - Tumor necrosis factor alpha (TNF α)       (−238) G/A                     CCCCTCGGAATCGGAGCAGGGAGGA   SEQ ID NO:815       TCCTCCCTGCTCCGATTCCGAGGGG   SEQ ID NO:816       CCCCTCGGAATCAGAGCAGGGAGGA   SEQ ID NO:817       TCCTCCCTGCTCTGATTCCGAGGGG   SEQ ID NO:818                         47. - TPMT G238C                     GTCCCCGGTCTGCAAACCTGCATAA   SEQ ID NO:819       TTATGCAGGTTTGCAGACCGGGGAC   SEQ ID NO:820       GTCCCCGGTCTGGAAACCTGCATAA   SEQ ID NO:821       TTATGCAGGTTTCCAGACCGGGGAC   SEQ ID NO:822                         48. - TPMT G460A                     TGGGATAGAGGAGCATTAGTTGCCA   SEQ ID NO:823       TGGGATAGAGGAACATTAGTTGCCA   SEQ ID NO:824       TGGCAACTAATGCTCCTCTATCCCA   SEQ ID NO:825       TGGCAACTAATGTTCCTCTATCCCA   SEQ ID NO:826                         49. - TPMT A719G                     TCTGTAAGTAGATATAACTTTTCAA   SEQ ID NO:827       TTGAAAAGTTATATCTACTTACAGA   SEQ ID NO:828       TCTGTAAGTAGACATAACTTTTCAA   SEQ ID NO:829       TTGAAAAGTTATGTCTACTTACAGA   SEQ ID NO:830                         50. - MICA Trp14Gly                     ACGGTGCTGTCCTGGGATGGATCTG   SEQ ID NO:831       ACGGTGCTGTCCGGGGATGGATCTG   SEQ ID NO:832       CAGATCCATCCCAGGACAGCACCGT   SEQ ID NO:833       CAGATCCATCCCCGGACAGCACCGT   SEQ ID NO:834                         51. - MICA Thr24Ala                     TCAGGGTTTCTCGCTGAGGTACATC   SEQ ID NO:835       TCAGGGTTTCTCACTGAGGTACATC   SEQ ID NO:836       GATGTACCTCAGCGAGAAACCCTGA   SEQ ID NO:837       GATGTACCTCAGTGAGAAACCCTGA   SEQ ID NO:838                         52. - MICA Met129Val                     GAGGAATGGACAATGCCCCAGTCCT   SEQ ID NO:839       GAGGAATGGACAGTGCCCCAGTCCT   SEQ ID NO:840       AGGACTGGGGCATTGTCCATTCCTC   SEQ ID NO:841       AGGACTGGGGCACTGTCCATTCCTC   SEQ ID NO:842                         53. - MICA Lys173Glu                     CGGCGATATCTAAAATCCGGCGTAG   SEQ ID NO:843       CGGCGATATCTAGAATCCGGCGTAG   SEQ ID NO:844       CTACGCCGGATTTTAGATATCGCCG   SEQ ID NO:845       CTACGCCGGATTCTAGATATCGCCG   SEQ ID NO:846                         54. - MICA Gly175Ser                     TATCTAAAATCCGGCGTAGTCCTGA   SEQ ID NO:847       TATCTAAAATCCAGCGTAGTCCTGA   SEQ ID NO:848       TCAGGACTACGCCGGATTTTAGATA   SEQ ID NO:849       TCAGGACTACGCTGGATTTTAGATA   SEQ ID NO:850                         55. - SLC11A1 = NRAMP1 in the promoter region       (−377 to −222): allele7                     CGTGTGTGTGTATGTGTGTGTGTGT   SEQ ID NO:851       CGTGTGTGTGTACGTGTGTGTGTGT   SEQ ID NO:852       ACACACACACACATACACACACACG   SEQ ID NO:853       ACACACACACACGTACACACACACG   SEQ ID NO:854                         56. - CD14 (−159) T/C                     TTCCTGTTACGGTCCCCCTCCCTGA   SEQ ID NO:858       TTCCTGTTACGGCCCCCCTCCCTGA   SEQ ID NO:856       TCAGGGAGGGGGACCGTAACAGGAA   SEQ ID NO:857       TCAGGGAGGGGGGCCGTAACAGGAA   SEQ ID NO:858                         57. - CD16A = FCGR3A G4985T Val158Phe                     TGCAGGGGGCTTGTTGGGAGTAAAA   SEQ ID NO:859       TGCAGGGGGCTTTTTGGGAGTAAAA   SEQ ID NO:860       TTTTACTCCCAACAAGCCCCCTGCA   SEQ ID NO:861       TTTTACTCCCAAAAAGCCCCCTGCA   SEQ ID NO:862                         58. - NR1I2 (−25385) C/T                     CAATCCCAGGTTCTCTTTTCTACCT   SEQ ID NO:863       CAATCCCAGGTTTTCTTTTCTACCT   SEQ ID NO:864       AGGTAGAAAAGAGAACCTGGGATTG   SEQ ID NO:865       AGGTAGAAAAGAAAACCTGGGATTG   SEQ ID NO:866                         59. - TUCAN/CARD8/CARDINAL (T/A) Cys10Stop                     GAGCCATTATTGTTCCGTGCTGTTC   SEQ ID NO:867       GAGCCATTATTGATCCGTGCTGTTC   SEQ ID NO:868       GAACAGCACGGAACAATAATGGCTC   SEQ ID NO:869       GAACAGCACGGATCAATAATGGCTC   SEQ ID NO:870                         60. - IKBL +738T/C Cys224Arg                     GCAGAGGGATCCTGTCGACCCCCAC   SEQ ID NO:871       GCAGAGGGATCCCGTCGACCCCCAC   SEQ ID NO:872       GTGGGGGTCGACAGGATCCCTCTGC   SEQ ID NO:873       GTGGGGGTCGACGGGATCCCTCTGC   SEQ ID NO:874                         61. - TNFRSF1B = TNFR2 G593A                     GCAGAGGCAGCGGGTTGTGGAAAGC   SEQ ID NO:875       GCAGAGGCAGCGAGTTGTGGAAAGC   SEQ ID NO:876       GCTTTCCACAACCCGCTGCCTCTGC   SEQ ID NO:877       GCTTTCCACAACTCGCTGCCTCTGC   SEQ ID NO:878                         62. - TNFRSF1B = TNFR2 T620C                     CTGCTGCCATGGCGTGTCCCTCTCG   SEQ ID NO:879       CTGCTGCCATGGTGTGTCCCTCTCG   SEQ ID NO:880       CGAGAGGGACACGCCATGGCAGCAG   SEQ ID NO:881       CGAGAGGGACACACCATGGCAGCAG   SEQ ID NO:882                         63. - MEKK1 Asp643Asn                     AGTGGGAATTATCAATGGACTGCAA   SEQ ID NO:883       AGTGGGAATTATTAATGGACTGCAA   SEQ ID NO:884       TTGCAGTCCATTGATAATTCCCACT   SEQ ID NO:885       TTGCAGTCCATTAATAATTCCCACT   SEQ ID NO:886                         64. - HLA-DQ4 159G/A/C                     CACCAACGGGACGGAGCGCGTGCGG   SEQ ID NO:887       CACCAACGGGACAGAGCGCGTGCGG   SEQ ID NO:888       CACCAACGGGACCGAGCGCGTGCGG   SEQ ID NO:889       CCGCACGCGCTCCGTCCCGTTGGTG   SEQ ID NO:890       CCGCACGCGCTCTGTCCCGTTGGTG   SEQ ID NO:891       CCGCACGCGCTCGGTCCCGTTGGTG   SEQ ID NO:892                         65. - HLA-DQ4 282C/T                     CGAGTACTGGAACAGCCAGAAGGAA   SEQ ID NO:893       CGAGTACTGGAATAGCCAGAAGGAA   SEQ ID NO:894       TTCCTTCTGGCTGTTCCAGTACTCG   SEQ ID NO:895       TTCCTTCTGGCTATTCCAGTACTCG   SEQ ID NO:896                         66. - HLA-DRB 109T/C                     CGACCACGTTTCTTGTGGCAGCTTA   SEQ ID NO:897       TAAGCTGCCACAAGAAACGTGGTCG   SEQ ID NO:898       CGACCACGTTTCCTGTGGCAGCTTA   SEQ ID NO:899       TAAGCTGCCACAGGAAACGTGGTCG   SEQ ID NO:900                         67. - HLA-DRB 119T/C/G/A                     TCTTCTGGCAGCTTAAGTTTGAATG   SEQ ID NO:901       CATTCAAACTTAAGCTGCCACAAGA   SEQ ID NO:902       TCTTGTGGCAGCCTAAGTTTGAATG   SEQ ID NO:903       CATTCAAACTTAGGCTGCCACAAGA   SEQ ID NO:904       TCTTGTGGCAGCGTAAGTTTGAATG   SEQ ID NO:905       CATTCAAACTTACGCTGCCACAAGA   SEQ ID NO:906       TCTTGTGGCAGCATAAGTTTGAATG   SEQ ID NO:907       CATTCAAACTTATGCTGCCACAAGA   SEQ ID NO:908                         68. - HLA-DRB 122A/C/G/T                     TGTGGCAGCTTAAGTTTGAATGTCA   SEQ ID NO:909       TGACATTCAAACTTAAGCTGCCACA   SEQ ID NO:910       TGTGGCAGCTTACGTTTGAATGTCA   SEQ ID NO:911       TGACATTCAAACGTAAGCTGCCACA   SEQ ID NO:912       TGTGGCAGCTTAGGTTTGAATGTCA   SEQ ID NO:913       TGACATTCAAACCTAAGCTGCCACA   SEQ ID NO:914       TGTGGCAGCTTATGTTTGAATGTCA   SEQ ID NO:915       TGACATTCAAACATAAGCTGCCACA   SEQ ID NO:916                         69. - HLA-DRB 129A/G                     GCTTAAGTTTGAATGTCATTTCTTC   SEQ ID NO:917       GAAGAAATGACATTCAAACTTAAGC   SEQ ID NO:918       GCTTAAGTTTGAGTGTCATTTCTTC   SEQ ID NO:919       GAAGAAATGACACTCAAACTTAAGC   SEQ ID NO:920                         70. - HLA-DRB 161G/A/T                     CGGAGCGGGTGCGGTTGCTGGAAAG   SEQ ID NO:921       CTTTCCAGCAACCGCACCCGCTCCG   SEQ ID NO:922       CGGAGCGGGTGCAGTTGCTGGAAAG   SEQ ID NO:923       CTTTCCAGCAACTGCACCCGCTCCG   SEQ ID NO:924       CGGAGCGGGTGCTGTTGCTGGAAAG   SEQ ID NO:925       CTTTCCAGCAACAGCACCCGCTCCG   SEQ ID NO:926                         71. - HLA-DRB 175 T/C/G                     TTGCTGGAAAGATGCATCTATAACC   SEQ ID NO:927       GGTTATAGATGCATCTTTCCAGCAA   SEQ ID NO:928       TTGCTGGAAAGACGCATCTATAACC   SEQ ID NO:929       GGTTATAGATGCGTCTTTCCAGCAA   SEQ ID NO:930       TTGCTGGAAAGAGGCATCTATAACC   SEQ ID NO:931       GGTTATAGATGCCTCTTTCCAGCAA   SEQ ID NO:932                         72. - HLA-DRB 184A/C/delA                     AGATGCATCTATAACCAAGAGGAGT   SEQ ID NO:933       ACTCCTCTTGGTTATAGATGCATCT   SEQ ID NO:934       AGATGCATCTATCACCAAGAGGAGT   SEQ ID NO:935       ACTCCTCTTGGTGATAGATGCATCT   SEQ ID NO:936       AGATGCATCTATACCAAGAGGAGTC   SEQ ID NO:937       GACTCCTCTTGGTATAGATGCATCT   SEQ ID NO:938                         73. - HLA-DRB 286C/A/T                     AGCCAGAAGGACCTCCTGGAGCAGA   SEQ ID NO:939       TCTGCTCCAGGAGGTCCTTCTGGCT   SEQ ID NO:940       AGCCAGAAGGACATCCTGGAGCAGA   SEQ ID NO:941       TCTGCTCCAGGATGTCCTTCTGGCT   SEQ ID NO:942       AGCCAGAAGGACTTCCTGGAGCAGA   SEQ ID NO:943       TCTGCTCCAGGAAGTCCTTCTGGCT   SEQ ID NO:944                         74. - HLA-DRB 305C/G                     AGCAGAGGCGGGCCGCGGTGGACAC   SEQ ID NO:945       GTGTCCACCGCGGCCCGCCTCTGCT   SEQ ID NO:946       AGCAGAGGCGGGGCGCGGTGGACAC   SEQ ID NO:947       GTGTCCACCGCGCCCCGCCTCTGCT   SEQ ID NO:948                         75. - IL1RN 2018 T/C EXON2                     CCAACTAGTTGCTGGATACTTGCAA   SEQ ID NO:949       CCAACTAGTTGCCGGATACTTGCAA   SEQ ID NO:950       TTGCAAGTATCCAGCAACTAGTTGG   SEQ ID NO:951       TTGCAAGTATCCGGCAACTAGTTGG   SEQ ID NO:952                         76. - IL1RN 2073 C/T INTRON 2                     TTGCCAGGAAAGCCAATGTATGTGG   SEQ ID NO:953       TTGCCAGGAAAGTCAATGTATGTGG   SEQ ID NO:954       CCACATACATTGGCTTTCCTGGCAA   SEQ ID NO:955       CCACATACATTGACTTTCCTGGCAA   SEQ ID NO:956                         77. - IL1B 3954 C/T TAQI                     ACCTATCTTCTTCGACACATGGGAT   SEQ ID NO:957       ACCTATCTTCTTTGACACATGGGAT   SEQ ID NO:958       ATCCCATGTGTCGAAGAAGATAGGT   SEQ ID NO:959       ATCCCATGTGTCAAAGAAGATAGGT   SEQ ID NO:960                         78. - Fas −670 G/A                     TCACAGACGTTCCTGGAATGGAC   SEQ ID NO:1429       TCACAGACGTTTCTGGAATGGAC   SEQ ID NO:1430       GTCCATTCCAGGAACGTCTGTGA   SEQ ID NO:1431       GTCCATTCCAGAAACGTCTGTGA   SEQ ID NO:1432                         79. - Caspase 9 C93T                     GTCCTGCTGAGCCGCGAGCTGTT   SEQ ID NO:1433       GTCCTGCTGAGTCGCGAGCTGTT   SEQ ID NO:1434       AACAGCTCGCGGCTCAGCAGGAC   SEQ ID NO:1435       AACAGCTCGCGACTCAGCAGGAC   SEQ ID NO:1436                         80. - TLR1 R80T (G/C)                     TTCTCATAATAGAATCCAGTATC   SEQ ID NO:1437       TTCTCATAATACAATCCAGTATC   SEQ ID NO:1438       GATACTGGATTCTATTATGAGAA   SEQ ID NO:1439       GATACTGGATTGTATTATGAGAA   SEQ ID NO:1440                         81. - TLR2 R753G (A/G)                     CTGCAAGCTGCGGAAGATAATGA   SEQ ID NO:1441       CTGCAAGCTGCAGAAGATAATGA   SEQ ID NO:1442       TCATTATCTTCCGCAGCTTGCAG   SEQ ID NO:1443       TCATTATCTTCTGCAGCTTGCAG   SEQ ID NO:1444                         82. - TLR6 S249P (T/C)                     TCACCAGAGGTCCAACCTTACTG   SEQ ID NO:1445       TCACCAGAGGTTCAACCTTACTG   SEQ ID NO:1446       CAGTAAGGTTGGACCTCTGGTGA   SEQ ID NO:1447       CAGTAAGGTTGAACCTCTGGTGA   SEQ ID NO:1448                         83. - MMP3 5A/6A                     GATGGGGGGAAAAACCATGTCTT   SEQ ID NO:1449       GATGGGGGGAAAAAACCATGTCT   SEQ ID NO:1450       AAGACATGGTTTTTCCCCCCATC   SEQ ID NO:1451       AGACATGGTTTTTTCCCCCCATC   SEQ ID NO:1452                         84. - NOD1 (CARD4) indel +32656                     GCCCGCCCCCCCCCACACACAGC   SEQ ID NO:1453       GCCCGCCCCCCACACACACAGCA   SEQ ID NO:1454       GCTGTGTGTGGGGGGGGGCGGGC   SEQ ID NO:1455       TGCTGTGTGTGTGGGGGGCGGGC   SEQ ID NO:1456                         85. - DLG5 DLG5_e26                     TGGGGTGGGGCAGGGGTCGCCGA   SEQ ID NO:1457       TGGGGTGGGGCGGGGTCGCCGAG   SEQ ID NO:1458       TCGGCGACCCCTGCCCCACCCCA   SEQ ID NO:1459       CTCGGCGACCCCGCCCCACCCCA   SEQ ID NO:1460                         86. - NOD1 rs2075817 C/T                     GGAGGCGGGATCTGCGTGCGGGC   SEQ ID NO:1461       GGAGGCGGGATTTGCGTGCGGGC   SEQ ID NO:1462       GCCCGCACGCAGATCCCGCCTCC   SEQ ID NO:1463       GCCCGCACGCAAATCCCGCCTCC   SEQ ID NO:1464                         87. - NOD 1 rs2975632 C/T                     GAAGGAAGCTGCGCAACACCCCT   SEQ ID NO:1465       GAAGGAAGCTGTGCAACACCCCT   SEQ ID NO:1466       AGGGGTGTTGCGCAGCTTCCTTC   SEQ ID NO:1467       AGGGGTGTTGCACAGCTTCCTTC   SEQ ID NO:1468                         88. - NOD1 rs3020207 A/G                     GAGGTGGGGTGAGCTCTTTCTGT   SEQ ID NO:1469       GAGGTGGGGTGGGCTCTTTCTGT   SEQ ID NO:1470       ACAGAAAGAGCTCACCCCACCTC   SEQ ID NO:1471       ACAGAAAGAGCCCACCCCACCTC   SEQ ID NO:1472                         89. - NOD1 rs2075818 C/G                     TACTTCTCGGCGGAAGATGCGGA   SEQ ID NO:1473       TACTTCTCGGCCGAAGATGCGGA   SEQ ID NO:1474       TCCGCATCTTCCGCCGAGAAGTA   SEQ ID NO:1475       TCCGCATCTTCGGCCGAGAAGTA   SEQ ID NO:1476                         90. - NOD1 rs2235099 C/T                     ATCTACATGGACACCATCATGGA   SEQ ID NO:1477       ATCTACATGGATACCATCATGGA   SEQ ID NO:1478       TCCATGATGGTGTCCATGTAGAT   SEQ ID NO:1479       TCCATGATGGTATCCATGTAGAT   SEQ ID NO:1480                         91. - NOD1 rs2075821 A/G                     AGTGGTCCGGCACGGGAAGACCT   SEQ ID NO:1481       AGTGGTCCGGCGCGGGAAGACCT   SEQ ID NO:1482       AGGTCTTCCCGTGCCGGACCACT   SEQ ID NO:1483       AGGTCTTCCCGCGCCGGACCACT   SEQ ID NO:1484                         92. - NOD1 rs2075822 C/T                     CGGGAATGGCACCATGGACCAGG   SEQ ID NO:1485       CGGGAATGGCATCATGGACCAGG   SEQ ID NO:1486       CCTGGTCCATGGTGCCATTCCCG   SEQ ID NO:1487       CCTGGTCCATGATGCCATTCCCG   SEQ ID NO:1488                         93. - NOD1 rs2907748 C/T                     ATTTCTTAGCCCAGCTACCTGTA   SEQ ID NO:1489       ATTTCTTAGCCTAGCTACCTGTA   SEQ ID NO:1490       TACAGGTAGCTGGGCTAAGAAAT   SEQ ID NO:1491       TACAGGTAGCTAGGCTAAGAAAT   SEQ ID NO:1492                         94. - NOD1 rs5743368 A/G                     AGAACTTGTTTAGAACTTGTCAT   SEQ ID NO:1493       AGAACTTGTTTGGAACTTGTCAT   SEQ ID NO:1494       ATGACAAGTTCTAAACAAGTTCT   SEQ ID NO:1495       ATGACAAGTTCCAAACAAGTTCT   SEQ ID NO:1496                         95. - DLG5 haplotype A rs2289311 C/T                     CAGCAGGGTCTCGATGGCCCTGC   SEQ ID NO:1497       CAGCAGGGTCTTGATGGCCCTGC   SEQ ID NO:1498       GCAGGGCCATCGAGACCCTGCTG   SEQ ID NO:1499       GCAGGGCCATCAAGACCCTGCTG   SEQ ID NO:1500                         96. - MTHFR A1298C                     GACCAGTGAAGAAAGTGTCTTTG   SEQ ID NO:1501       GACCAGTGAAGCAAGTGTCTTTG   SEQ ID NO:1502       CAAAGACACTTTCTTCACTGGTC   SEQ ID NO:1503       CAAAGACACTTGCTTCACTGGTC   SEQ ID NO:1504                         97. - NAT2 Ile114Thr                     GCAGGTGACCACTGACGGCAGGA   SEQ ID NO:1505       GCAGGTGACCATTGACGGCAGGA   SEQ ID NO:1506       TCCTGCCGTCAGTGGTCACCTGC   SEQ ID NO:1507       TCCTGCCGTCAATGGTCACCTGC   SEQ ID NO:1508                         98. - NAT2 Lys268Arg A/G                     AGAAGTGCTGAAAAATATATTTA   SEQ ID NO:1509       AGAAGTGCTGAGAAATATATTTA   SEQ ID NO:1510       TAAATATATTTTTCAGCACTTCT   SEQ ID NO:1511       TAAATATATTTCTCAGCACTTCT   SEQ ID NO:1512                         99. - ESR1 rs9340799 A/G                     GAGTGTGGTCTAGAGTTGGGATG   SEQ ID NO:1513       GAGTGTGGTCTGGAGTTGGGATG   SEQ ID NO:1514       CATCCCAACTCTAGACCACACTC   SEQ ID NO:1515       CATCCCAACTCCAGACCACACTC   SEQ ID NO:1516                         100. - ESR1 rs2234693 C/T                     AATGTCCCAGCCGTTTTATGCTT   SEQ ID NO:1517       AATGTCCCAGCTGTTTTATGCTT   SEQ ID NO:1518       AAGCATAAAACGGCTGGGACATT   SEQ ID NO:1519       AAGCATAAAACAGCTGGGACATT   SEQ ID NO:1520                         101. - MEFV V726A C/T                     GGACTACAGAGCTGGAAGCATCT   SEQ ID NO:1521       GGACTACAGAGTTGGAAGCATCT   SEQ ID NO:1522       AGATGCTTCCAGCTCTGTAGTCC   SEQ ID NO:1523       AGATGCTTCCAACTCTGTAGTCC   SEQ ID NO:1524                         102. - Vit D receptor (VDR) rs10735810 A/G                     CCATTGCCTCCATCCCTGTAAGA   SEQ ID NO:1525       CCATTGCCTCCGTCCCTGTAAGA   SEQ ID NO:1526       TCTTACAGGGATGGAGGCAATGG   SEQ ID NO:1527       TCTTACAGGGACGGAGGCAATGG   SEQ ID NO:1528                         103. - EMR3 E127Q C/G                     TTTCCTGCCCTCGGTTGTCTTTG   SEQ ID NO:1529       TTTCCTGCCCTGGGTTGTCTTTG   SEQ ID NO:1530       CAAAGACAACCGAGGGCAGGAAA   SEQ ID NO:1531       CAAAGACAACCCAGGGCAGGAAA   SEQ ID NO:1532                         104. - EMR1 Q496K G/T                     CTGGTGGTCTTGGAAGAAGCGCT   SEQ ID NO:1533       CTGGTGGTCTTTGAAGAAGCGCT   SEQ ID NO:1534       AGCGCTTCTTCCAAGACCACCAG   SEQ ID NO:1535       AGCGCTTCTTCAAAGACCACCAG   SEQ ID NO:1536                         105. - MTHFD1 R653Q A/G                     CATTGCAGACCAGATCGCACTCA   SEQ ID NO:1537       CATTGCAGACCGGATCGCACTCA   SEQ ID NO:1538       TGAGTGCGATCTGGTCTGCAATG   SEQ ID NO:1539       TGAGTGCGATCCGGTCTGCAATG   SEQ ID NO:1540                         106. - SHMT1 1420C/T                     CAGAGGGAAGAAAGAGGCGAAGC   SEQ ID NO:1541       CAGAGGGAAGAGAGAGGCGAAGC   SEQ ID NO:1542       GCTTCGCCTCTTTCTTCCCTCTG   SEQ ID NO:1543       GCTTCGCCTCTCTCTTCCCTCTG   SEQ ID NO:1544                         107. - NAT2 857G/A Gly286Glu                     ACCTGGTGATGAATCCCTTACTA   SEQ ID NO:1545       ACCTGGTGATGGATCCCTTACTA   SEQ ID NO:1545       TAGTAAGGGATTCATCACCAGGT   SEQ ID NO:1547       TAGTAAGGGATCCATCACCAGGT   SEQ ID NO:1548                         108. - NAT2 Arg197Gln R197Q A/G                     GCTTGAACCTCAAACAATTGAAG   SEQ ID NO:1549       GCTTGAACCTCGAACAATTGAAG   SEQ ID NO:1550       CTTCAATTGTTTGAGGTTCAAGC   SEQ ID NO:1551       CTTCAATTGTTCGAGGTTCAAGC   SEQ ID NO:1552                         109. - NAT2 rs1801279 191 G/A                     AAGAAGAAACCAGGGTGGGTGGT   SEQ ID NO:1553       AAGAAGAAACCGGGGTGGGTGGT   SEQ ID NO:1554       ACCACCCACCCTGGTTTCTTCTT   SEQ ID NO:1555       ACCACCCACCCCGGTTTCTTCTT   SEQ ID NO:1556                         110. - TLR5 Arg392Stop C/T                     CCTTGGATCTCCGAGACAATGCT   SEQ ID NO:1557       CCTTGGATCTCTGAGACAATGCT   SEQ ID NO:1558       AGCATTGTCTCGGAGATCCAAGG   SEQ ID NO:1559       AGCATTGTCTCAGAGATCCAAGG   SEQ ID NO:1560                         111. - CTLA4 A49G                     TGAACCTGGCTACCAGGACCTGG   SEQ ID NO:1561       TGAACCTGGCTGCCAGGACCTGG   SEQ ID NO:1562       CCAGGTCCTGGTAGCCAGGTTCA   SEQ ID NO:1563       CCAGGTCCTGGCAGCCAGGTTCA   SEQ ID NO:1564                         112. - MLH1 D132H C/G                     CAAGTTACTCACATGGAAAACTG   SEQ ID NO:1565       CAAGTTACTCAGATGGAAAACTG   SEQ ID NO:1566       CAGTTTTCCATGTGAGTAACTTG   SEQ ID NO:1567       CAGTTTTCCATCTGAGTAACTTG   SEQ ID NO:1568                         113. - MTRR 66A/G                     GCAGAAGAAATATGTGAGCAAGC   SEQ ID NO:1569       GCAGAAGAAATGTGTGAGCAAGC   SEQ ID NO:1570       GCTTGCTCACATATTTCTTCTGC   SEQ ID NO:1571       GCTTGCTCACACATTTCTTCTGC   SEQ ID NO:1572                         114. - ITPA 94C/A                     GAGATAAGTTTACATGCACTTTG   SEQ ID NO:1573       GAGATAAGTTTCCATGCACTTTG   SEQ ID NO:1574       CAAAGTGCATGTAAACTTATCTC   SEQ ID NO:1575       CAAAGTGCATGGAAACTTATCTC   SEQ ID NO:1576                         115. - MEFV E148Q C/G                     GCAGCCAGCCCCAGGCCGGGAGG   SEQ ID NO:1577       GCAGCCAGCCCGAGGCCGGGAGG   SEQ ID NO:1578       CCTCCCGGCCTGGGGCTGGCTGC   SEQ ID NO:1579       CCTCCCGGCCTCGGGCTGGCTGC   SEQ ID NO:1580                         116. - PTPN22 R620W C/T                     TTCAGGTGTCCATACAGGAAGTG   SEQ ID NO:1581       TTCAGGTGTCCGTACAGGAAGTG   SEQ ID NO:1582       CACTTCCTGTATGGACACCTGAA   SEQ ID NO:1583       CACTTCCTGTACGGACACCTGAA   SEQ ID NO:1584                         117. - LDL-receptor LRP-5 3357A/G                     GCCCTGGTGGTAGACAACACACT   SEQ ID NO:1585       GCCCTGGTGGTGGACAACACACT   SEQ ID NO:1586       AGTGTGTTGTCTACCACCAGGGC   SEQ ID NO:1587       AGTGTGTTGTCCACCACCAGGGC   SEQ ID NO:1588                         118. - CTLA4-C318T                     ATCCAGATCCTCAAAGTGAACAT   SEQ ID NO:1589       ATCCAGATCCTTAAAGTGAACAT   SEQ ID NO:1590       ATGTTCACTTTGAGGATCTGGAT   SEQ ID NO:1591       ATGTTCACTTTAAGGATCTGGAT   SEQ ID NO:1592                         119. - CCR5 rs333 32bpdel                     TTTTCCATACATTAAAGATAGTC   SEQ ID NO:1593       TTTTCCATACATGGTCCTGCCGC   SEQ ID NO:1594       GACTATCTTTAATGTATGGAAAA   SEQ ID NO:1595       GCGGCAGGACCATGTATGGAAAA   SEQ ID NO:1596                         120. - IL6 −174 G/C                     TTGTGTCTTGCCATGCTAAAGGA   SEQ ID NO:1597       TTGTGTCTTGCGATGCTAAAGGA   SEQ ID NO:1598       TCCTTTAGCATGGCAAGACACAA   SEQ ID NO:1599       TCCTTTAGCATCGCAAGACACAA   SEQ ID NO:1600                         121. - GR ER22/23EK rs6190                     TGCTCAGGAGAAGGGAGATGTGA   SEQ ID NO:1601       TGCTCAGGAGAGGGGAGATGTGA   SEQ ID NO:1602       TCACATCTCCCTTCTCCTGAGCA   SEQ ID NO:1603       TCACATCTCCCCTCTCCTGAGCA   SEQ ID NO:1604                         122. - P53 Arg72Pro C/G                     GGCTGCTCCCCCCGTGGCCCCTG   SEQ ID NO:1605       GGCTGCTCCCCGCGTGGCCCCTG   SEQ ID NO:1606       CAGGGGCCACGGGGGGAGCAGCC   SEQ ID NO:1607       CAGGGGCCACGGGGGGAGCAGCC   SEQ ID NO:1608                         123. - DLG5 P1371Q A/C                     TAGCACCCCCCAAGCCAAGCAGA   SEQ ID NO:1609       TAGCACCCCCCCAGCCAAGCAGA   SEQ ID NO:1610       TCTGCTTGGCTTGGGGGGTGCTA   SEQ ID NO:1611       TCTGCTTGGCTGGGGGGGTGCTA   SEQ ID NO:1612                         124. - GR ER22/23EK rs6189                     CTTGCTCAGGAAAGGGGAGATGT   SEQ ID NO:1613       CTTGCTCAGGAGAGGGGAGATGT   SEQ ID NO:1614       ACATCTCCCCTTTCCTGAGCAAG   SEQ ID NO:1615       ACATCTCCCCTCTCCTGAGCAAG   SEQ ID NO:1616                         125. - GR ER22/23EK rs6190                     TGCTCAGGAGAAGGGAGATGTGA   SEQ ID NO:1617       TGCTCAGGAGAGGGGAGATGTGA   SEQ ID NO:1618       TCACATCTCCCTTCTCCTGAGCA   SEQ ID NO:1619       TCACATCTCCCCTCTCCTGAGCA   SEQ ID NO:1620                         126. - LDL-receptor LRP-5 C135242T                     AGCGTGAACCCAAAAATGTGCGG   SEQ ID NO:1621       AGCGTGAACCCGAAAATGTGCGG   SEQ ID NO:1622       CCGCACATTTTTGGGTTCACGCT   SEQ ID NO:1623       CCGCACATTTTCGGGTTCACGCT   SEQ ID NO:1624                         127. - LDL-receptor LRP-5 G121513A                     CTGGGGATGCTACAGAGACCAGA   SEQ ID NO:1625       CTGGGGATGCTGCAGAGACCAGA   SEQ ID NO:1626       TCTGGTCTCTGTAGCATCCCCAG   SEQ ID NO:1627       TCTGGTCTCTGCAGCATCCCCAG   SEQ ID NO:1628                         128. - LDL-receptor LRP-5 C141759T                     ACTGGGACCAACAGAATCGAAGT   SEQ ID NO:1629       ACTGGGACCAATAGAATCGAAGT   SEQ ID NO:1630       ACTTCGATTCTGTTGGTCCCAGT   SEQ ID NO:1631       ACTTCGATTCTATTGGTCCCAGT   SEQ ID NO:1632                         129. - LDL-receptor LRP-5 G138351A                     ACCAAGAAGGCCTCAGGCACGAT   SEQ ID NO:1633       ACCAAGAAGGCTTCAGGCACGAT   SEQ ID NO:1634       ATCGTGCCTGAGGCCTTCTTGGT   SEQ ID NO:1635       ATCGTGCCTGAAGCCTTCTTGGT   SEQ ID NO:1636                         130. - P2X7 −298 C/T                     ATGGGCATTTTCAGAATTCTCCC   SEQ ID NO:1637       ATGGGCATTTTTAGAATTCTCCC   SEQ ID NO:1638       GGGAGAATTCTGAAAATGCCCAT   SEQ ID NO:1639       GGGAGAATTCTAAAAATGCCCAT   SEQ ID NO:1640                         131. - P2X7 −838 G/T                     ACAGCAATTTAGTATAGGATTCC   SEQ ID NO:1641       ACAGCAATTTATTATAGGATTCC   SEQ ID NO:1642       GGAATCCTATACTAAATTGCTGT   SEQ ID NO:1643       GGAATCCTATAATAAATTGCTGT   SEQ ID NO:1644                         132. - APC E1317Q C/G                     CTAGGTCAGCTCAAGATCCTGTG   SEQ ID NO:1645       CTAGGTCAGCTGAAGATCCTGTG   SEQ ID NO:1646       CACAGGATCTTGAGCTGACCTAG   SEQ ID NO:1647       CACAGGATCTTCAGCTGACCTAG   SEQ ID NO:1648                         133. - CD97-T64C A/G                     GTCCCGTCTCCACAGGCTAGGCA   SEQ ID NO:1649       GTCCCGTCTCCGCAGGCTAGGCA   SEQ ID NO:1650       TGCCTAGCCTGTGGAGACGGGAC   SEQ ID NO:1651       TGCCTAGCCTGCGGAGACGGGAC   SEQ ID NO:1652            
3.2 Production of the DNA-chip for Genotyping of Genetic Variations Associated with IBD
 
     Probes are attached to the glass slide by means of crosslinking with ultraviolet radiation and heat as previously described (Example 1.2) maintaining the relative humidity during the deposition process between 40-50% and the temperature around 20° C. 
     3.3 Validation of the Clinical Utility of the DNA-chip for the Diagnosis of IBD: Simultaneous, Sensitive, Specific and Reproducible Detection of Human Genetic Variations Associated with IBD Using a DNA-chip 
     3.3.1 Preparation of the Sample to be Hybridized 
     The DNA of the individual is extracted from a blood sample by a filtration protocol. 
     All the exons and introns of interest are amplified by PCR mutliplex using pairs of oligonucleotide primers. Any suitable pair of oligonucleotides can be used which allow specific amplification of genetic fragments where a genetic variation to be detected might exist. Advantageously, those pairs which permit the said amplification in the least possible number of PCR reactions are used. 
     The oligonucleotide primers used to PCR amplify fragments of the genes to be detected are listed below (with corresponding genetic variations associated with IBD). The oligonucleotide primers represent an additional aspect to the present invention. 
     
       
         
           
               
            
               
                 1. - Multidrug resistance protein (MDR-1) 
               
               
                 G2677T/A/C Ala893Ser/Thr/Pro (oligonucleotides to 
               
               
                 amplify the fragment of the gene “Multidrug 
               
               
                 resistance protein MDR-1” in which may exist the 
               
               
                 polymorphism G2677T/C Ala893Ser/Thr) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1: 
                 GCATAGTAAGCAGTAGGGAGTAACA 
               
               
                 SEQ ID NO 2: 
                 TGCAATAGCAGGAGTTGTTGA 
               
               
                   
               
            
           
           
               
            
               
                 2. - Multidrug resistance protein (MDR-1) C3435T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 3: 
                 TGCTCCCAGGCTGTTTATTT 
               
               
                 SEQ ID NO 4: 
                 TGTTTTCAGCTGCTTGATGG 
               
               
                   
               
            
           
           
               
            
               
                 3. - CARD15 R702W 
               
            
           
           
               
               
            
               
                 SEQ ID NO 5: 
                 AGATCACAGCAGCCTTCCTG 
               
               
                 SEQ ID NO 6: 
                 GGATGGAGTGGAAGTGCTTG 
               
               
                   
               
            
           
           
               
            
               
                 4. - CARD15 G908R 
               
            
           
           
               
               
            
               
                 SEQ ID NO 7: 
                 ACTGCAGAGGGAGGAGGACT 
               
               
                 SEQ ID NO 8: 
                 CCACCTCAAGCTCTGGTGAT 
               
               
                   
               
            
           
           
               
            
               
                 5. - CARD15 1007insC 
               
            
           
           
               
               
            
               
                 SEQ ID NO 9: 
                 ACTGGCTAACTCCTGCAGTC 
               
               
                 SEQ ID NO 10: 
                 GAAAAACTGAGGTTCGGAGA 
               
               
                   
               
            
           
           
               
            
               
                 6. - Microsomal epoxide hydrolase (EPXH1) T612C 
               
               
                 Y113H 
               
            
           
           
               
               
            
               
                 SEQ ID NO 11: 
                 CTCTCAACTTGGGGTCCTGA 
               
               
                 SEQ ID NO 12: 
                 GGCGTTTTGCAAACATACCT 
               
               
                   
               
            
           
           
               
            
               
                 7. - Monocyte chemotactic protein 1 (MCP1) 
               
               
                 (−2518) G/A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 13: 
                 CCAGCCAAATGCATTCTCTT 
               
               
                 SEQ ID NO 14: 
                 CACAGGGAAGGTGAAGGGTA 
               
               
                   
               
            
           
           
               
            
               
                 8. - Interleukin 10 (IL10) (−1082) G/A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 15: 
                 CAACTGGCTCCCCTTACCTT 
               
               
                 SEQ ID NO 16: 
                 ATGGAGGCTGGATAGGAGGT 
               
               
                   
               
            
           
           
               
            
               
                 9. - Interleukin 10 (IL10) G15R G43A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 17: 
                 AGAGGCCTCCCTGAGCTTAC 
               
               
                 SEQ ID NO 18: 
                 TCTCGGAGATCTCGAAGCAT 
               
               
                   
               
            
           
           
               
            
               
                 10. - Interleukin 16 (IL16) (−295) T/C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 19: 
                 AACTGAAGCAATGCCAGTCC 
               
               
                 SEQ ID NO 20: 
                 CAGAGCCAGCACCTCCTAGA 
               
               
                   
               
            
           
           
               
            
               
                 11.- Fas ligand (−843) C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 21: 
                 CTTGAGCCCAGGAGTTTGAG 
               
               
                 SEQ ID NO 22: 
                 ATCAGAGGCTGCAAACCAGT 
               
               
                   
               
            
           
           
               
            
               
                 12.- Nuclear factor kappa-B (NFKB1) 94dtheATTG 
               
            
           
           
               
               
            
               
                 SEQ ID NO 23: 
                 TGGACCGCATGACTCTATCA 
               
               
                 SEQ ID NO 24: 
                 GGCTCTGGCTTCCTAGCAG 
               
               
                   
               
            
           
           
               
            
               
                 13.- Nuclear factor kappa-B inhibitor alpha 
               
               
                 (NFKBIA) SNP in the 3′UTR (G/A) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 25: 
                 CCAGCCATCATTTCCACTCT 
               
               
                 SEQ ID NO 26: 
                 CCTGCACCCTGTAATCCTGT 
               
               
                   
               
            
           
           
               
            
               
                 14. - Signal transducer and activator of 
               
               
                 transcription 6 (STAT6) G2964A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 27: 
                 AGCCAATCCACTCCTTCCTT 
               
               
                 SEQ ID NO 28: 
                 CATGCCCTAACCTGTGCTCT 
               
               
                   
               
            
           
           
               
            
               
                 15. - Interleukin 18 (IL18) TCA/TCC in the codon 35 
               
            
           
           
               
               
            
               
                 SEQ ID NO 29: 
                 ATAGAGGCCGATTTCCTTGG 
               
               
                 SEQ ID NO 30: 
                 TTCTGGAACAGAAGATTGTCATT 
               
               
                   
               
            
           
           
               
            
               
                 16. - Mediterranean fever gene (MEFV) E474E 
               
            
           
           
               
               
            
               
                 SEQ ID NO 31: 
                 GCTCCCCAGAAACAAACTGA 
               
               
                 SEQ ID NO 32: 
                 CACCTGCAGAAGTTCCCATT 
               
               
                   
               
            
           
           
               
            
               
                 17. - Mediterranean fever gene (MEFV) Q476Q 
               
            
           
           
               
               
            
               
                 SEQ ID NO 33: 
                 GCTCCCCAGAAACAAACTGA 
               
               
                 SEQ ID NO 34: 
                 CACCTGCAGAAGTTCCCATT 
               
               
                   
               
            
           
           
               
            
               
                 18. - Mediterranean fever gene (MEFV) D510D 
               
            
           
           
               
               
            
               
                 SEQ ID NO 35: 
                 AGGAAGCTGGAGCAGGTGTA 
               
               
                 SEQ ID NO 36: 
                 CCATTCTGACTGGCACTCCT 
               
               
                   
               
            
           
           
               
            
               
                 19. - Mediterranean fever gene (MEFV) P588P 
               
            
           
           
               
               
            
               
                 SEQ ID NO 37: 
                 TCTTCTGGAACGTGGTAGGG 
               
               
                 SEQ ID NO 38: 
                 CTAAGCAGGGGGTTCCTTGT 
               
               
                   
               
            
           
           
               
            
               
                 20. - Discs large homolog 5 (DLG5) 113G/A (R30Q) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 39: 
                 CGGCGCAATTACTACCTCTT 
               
               
                 SEQ ID NO 40: 
                 CGTGAATGCCAGATGAACAC 
               
               
                   
               
            
           
           
               
            
               
                 21. - Colony stimulating factor receptor 1 (CSFR1) 
               
               
                 A2033T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 41: 
                 CTCCTTGCTTGCTTTCCTTG 
               
               
                 SEQ ID NO 42: 
                 AGTAGGGATGGGATGGATGG 
               
               
                   
               
            
           
           
               
            
               
                 22. - Organic cation transporter (OCTN1, SLC22A4) 
               
               
                 1672C/T (L503F) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 43: 
                 CAAGAGTGCCCAGAGAGTCC 
               
               
                 SEQ ID NO 44: 
                 TTCTCCCTAAGGCATTTTGGT 
               
               
                   
               
            
           
           
               
            
               
                 23. - Organic cation transporter (OCTN2, SLC22A5) 
               
               
                 (−207G/C) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 45: 
                 CTTACATAGGGCGCACGAC 
               
               
                 SEQ ID NO 46: 
                 AGTCCCGCTGCCTTCCTA 
               
               
                   
               
            
           
           
               
            
               
                 24. - Toll-like receptor 4 (TLR4)  Asp299Gly (A/G) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 47: 
                 CTCTAGAGGGCCTGTGCAAT 
               
               
                 SEQ ID NO 48: 
                 TCAATGTGGGAAACTGTCCA 
               
               
                   
               
            
           
           
               
            
               
                 25. - Toll-like receptor 4 (TLR4) Thr399Ile (C/T) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 49: 
                 CAACAAAGGTGGGAATGCTT 
               
               
                 SEQ ID NO 50: 
                 TTTCAAATTGGAATGCTGGA 
               
               
                   
               
            
           
           
               
            
               
                 26. - Interleukin 1 beta -(IL1β) (−511) A/C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 51: 
                 AGGCAGAGAGGGAAGGAGAG 
               
               
                 SEQ ID NO 52: 
                 AAACAGCGAGGGAGAAACTG 
               
               
                   
               
            
           
           
               
            
               
                 27. - Superoxide dismutase 2 (SOD2) Ala16Val C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 53: 
                 GGCTGTGCTTTCTCGTCTTC 
               
               
                 SEQ ID NO 54: 
                 GGTGACGTTCAGGTTGTTCA 
               
               
                   
               
            
           
           
               
            
               
                 28. - Peroxisome proliferator-activated receptor 
               
               
                 gamma (PPARG) Pro12Ala C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 55: 
                 AGCAAACCCCTATTCCATGC 
               
               
                 SEQ ID NO 56: 
                 TACATAAATGCCCCCACGTC 
               
               
                   
               
            
           
           
               
            
               
                 29. - Intercellular adhesion molecule 1 (ICAM1) 
               
               
                 K469E (A/G) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 57: 
                 CTTGAGGGCACCTACCTCTG 
               
               
                 SEQ ID ND 58: 
                 CATTATGACTGCGGCTGCTA 
               
               
                   
               
            
           
           
               
            
               
                 30. - Intercellular adhesion molecule 1 ICAM1 R241G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 59: 
                 GAATGAAATGCCCCAGAGAA 
               
               
                 SEQ ID NO 60: 
                 ACTGTGGGGTTCAACCTCTG 
               
               
                   
               
            
           
           
               
            
               
                 31. - IBD5 locus IGR2060a_1 
               
            
           
           
               
               
            
               
                 SEQ ID NO 61: 
                 CATACAGCACCTTCGGGTCT 
               
               
                 SEQ ID NO 62: 
                 GGGCAGACTTTGGAACTCAG 
               
               
                   
               
            
           
           
               
            
               
                 32. - IBD5 locus IGR2198a_1 
               
            
           
           
               
               
            
               
                 SEQ ID NO 63: 
                 CATAATCAGGGGTTGCATGA 
               
               
                 SEQ ID NO 64: 
                 CCAGAGACACTGGGACATCA 
               
               
                   
               
            
           
           
               
            
               
                 33. - IBD5 locus IGR3096a_1 
               
            
           
           
               
               
            
               
                 SEQ ID NO 65: 
                 CCAAGGCCATGGTGTATAGC 
               
               
                 SEQ ID NO 66: 
                 GTGCCACCTCCCATCTCTAA 
               
               
                   
               
            
           
           
               
            
               
                 34. - Heat shock protein 70 (HSP70-2) 1267A/G 
               
               
                 Gln351Gln 
               
            
           
           
               
               
            
               
                 SEQ ID NO 67: 
                 CTGTTTGAGGGCATCGACTT 
               
               
                 SEQ ID NO 68: 
                 GGGGTTGATGCTCTTGTTCA 
               
               
                   
               
            
           
           
               
            
               
                 35. - Toll-like receptor (TLR9)  1237C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 69: 
                 AGTCAAAGCCACAGTCCACA 
               
               
                 SEQ ID NO 70: 
                 CCCTGTTGAGAGGGTGACAT 
               
               
                   
               
            
           
           
               
            
               
                 36. - Methylenetetrahydrofolate reductase (MTFHR) 
               
               
                 C677T Val222Ala 
               
            
           
           
               
               
            
               
                 SEQ ID NO 71: 
                 GCCTCTCCTGACTGTCATCC 
               
               
                 SEQ ID NO 72: 
                 TCACAAAGCGGAAGAATGTG 
               
               
                   
               
            
           
           
               
            
               
                 37. - Interleukin 4 (IL4)  (−590) C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 73: 
                 ACCCAAACTAGGCCTCACCT 
               
               
                 SEQ ID NO 74: 
                 ACAGGTGGCATCTTGGAAAC 
               
               
                   
               
            
           
           
               
            
               
                 38. - Interleukin 4 (IL4)  (−34) C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 75: 
                 TCATTTTCCCTCGGTTTCAG 
               
               
                 SEQ ID NO 76: 
                 AGAACAGAGGGGGAAGCAGT 
               
               
                   
               
            
           
           
               
            
               
                 39. - Mannose-binding lectin (MBL) (A/G) Gly54Asp 
               
            
           
           
               
               
            
               
                 SEQ ID NO 77: 
                 TGGCAGCGTCTTACTCAGAA 
               
               
                 SEQ ID NO 78: 
                 AGAACAGCCCAACACGTACC 
               
               
                   
               
            
           
           
               
            
               
                 40. - Mannose-binding lectin (MBL) (A/G) Gly57Glu 
               
            
           
           
               
               
            
               
                 SEQ ID NO 79: 
                 GTTCCCCTTGCACGTTCC 
               
               
                 SEQ ID NO 80: 
                 TTGTTGGAAGAAAAGAATTGTCC 
               
               
                   
               
            
           
           
               
            
               
                 41. - Mannose-binding lectin (MBL) (C/T) Arg52Cys 
               
            
           
           
               
               
            
               
                 SEQ ID NO 81: 
                 CAACCTCAGCCAGACAAGGT 
               
               
                 SEQ ID NO 82: 
                 CAGCCACGTGATTGTCTAGG 
               
               
                   
               
            
           
           
               
            
               
                 42. - Angiotensinogen precursor (AGT) (−6) A/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 83: 
                 GCTTCTGGCATCTGTCCTTC 
               
               
                 SEQ ID NO 84: 
                 CCGGCTTACCTTCTGCTGTA 
               
               
                   
               
            
           
           
               
            
               
                 43. - Plasminogen activator inhibitor (PAI1) 4G/5G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 85: 
                 ACCTGGTCCCCAAAAGAAAT 
               
               
                 SEQ ID NO 86: 
                 AAAGTTGGGGACACACAAGC 
               
               
                   
               
            
           
           
               
            
               
                 44. - Tumor necrosis factor alpha (TNF α) 
               
               
                 (−857) C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 87: 
                 ACCACAGCAATGGGTAGGAG 
               
               
                 SEQ ID NO 88: 
                 TGGTTTCAGTCTTGGCTTCC 
               
               
                   
               
            
           
           
               
            
               
                 45. - Tumor necrosis factor alpha (TNF α) (−308) 
               
               
                 G/A y (−238) G/A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 89: 
                 ACCTGGTCCCCAAAAGAAAT 
               
               
                 SEQ ID NO 90: 
                 AAAGTTGGGGACACACAAGC 
               
               
                   
               
            
           
           
               
            
               
                 46. - TPMT G238C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 91: 
                 AAAACTTTTGTGGGGATATGGA 
               
               
                 SEQ ID NO 92: 
                 CCCTCTATTTAGTCATTTGAAAACA 
               
               
                   
               
            
           
           
               
            
               
                 47. - TPMT G460A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 93: 
                 CCAGGTCCACACATTCCTCT 
               
               
                 SEQ ID NO 94: 
                 TTACCATTTGCGATCACCTG 
               
               
                   
               
            
           
           
               
            
               
                 48. - TPMT A719G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 95: 
                 CATCCATTACATTTTCAGGCTTT 
               
               
                 SEQ ID NO 96: 
                 GGTTGATGCTTTTGAAGAACG 
               
               
                   
               
            
           
           
               
            
               
                 49. - MICA Trp14Gly and Thr24Ala 
               
            
           
           
               
               
            
               
                 SEQ ID NO 97: 
                 GAGCCCCACAGTCTTCGTTA 
               
               
                 SEQ ID NO 98: 
                 TTTCCGTTCCCTGTCAAGTC 
               
               
                   
               
            
           
           
               
            
               
                 50. - MICA Met129Val, Lys173Glu and Gly175Ser 
               
            
           
           
               
               
            
               
                 SEQ ID NO 99: 
                 GCTCTTCCTCTCCCAAAACC 
               
               
                 SEQ ID NO 100: 
                 CACCATGGGGGGCACTGTTC 
               
               
                   
               
            
           
           
               
            
               
                 51. - SLC11A1 = NRAMP1 in the promoter region 
               
               
                 (−377 to −222): allele 7 
               
            
           
           
               
               
            
               
                 SEQ ID NO 101: 
                 AACGAGGGGTCTTGGAACTC 
               
               
                 SEQ ID NO 102: 
                 GTGTTCTGTGCCTCCCAAGT 
               
               
                   
               
            
           
           
               
            
               
                 52. - CD14  (−159)T/C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 103: 
                 CACCCACCAGAGAAGGCTTA 
               
               
                 SEQ ID NO 104: 
                 ATCACCTCCCCACCTCTCTT 
               
               
                   
               
            
           
           
               
            
               
                 53. - CD16A = FCGR3A  G4985T Val158Phe 
               
            
           
           
               
               
            
               
                 SEQ ID NO 105: 
                 CCAAAAGCCACACTCAAAGAC 
               
               
                 SEQ ID NO 106: 
                 CTTGAGTGATGGTGATGTTCA 
               
               
                   
               
            
           
           
               
            
               
                 54. - NR1I2  (−25385)C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 107: 
                 TCACCAGGGCTGGATTAAAG 
               
               
                 SEQ ID NO 108: 
                 GCCTCTGGCAACAGTAAAGC 
               
               
                   
               
            
           
           
               
            
               
                 55. - TUCAN/CARD8/CARDINAL  (T/A) Cys10Stop 
               
            
           
           
               
               
            
               
                 SEQ ID NO 109: 
                 CTGCCGAGACGGGTATACAG 
               
               
                 SEQ ID NO 110: 
                 GCAAATGTCTCCTGGGAATG 
               
               
                   
               
            
           
           
               
            
               
                 56. - IKBL  +738T/C  Cys224Arg 
               
            
           
           
               
               
            
               
                 SEQ ID NO 111: 
                 TGAGTCCTTCTCAGCCTGGT 
               
               
                 SEQ ID NO 112: 
                 CTCTCACGCAGCTCTTCCTC 
               
               
                   
               
            
           
           
               
            
               
                 57. - TNFRSF1B = TNFR2  G593A y T620C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 113: 
                 TTCTGGGCCAAGTTCCTCTA 
               
               
                 SEQ ID NO 114: 
                 GGGGCAGGTCACAGAGAGT 
               
               
                   
               
            
           
           
               
            
               
                 58. - MEKK1  Asp643Asn 
               
            
           
           
               
               
            
               
                 SEQ ID NO 115: 
                 CTGGAAAGTTTGCCAACCA 
               
               
                 SEQ ID NO 116: 
                 ACCCAAAGTCTGGGCTCTTT 
               
               
                   
               
            
           
           
               
            
               
                 59. - HLA-DQ4  159G/A/C and 282C/T (DQB1*0401 and 
               
               
                 DQB1*0402) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 117: 
                 GTTTAAGGGCATGTGCTAC 
               
               
                 SEQ ID NO 118: 
                 AGCTCCAACTGGTAGTTGTG 
               
               
                   
               
            
           
           
               
            
               
                 60. - HLA-DRB  109T/C, 119T/C/G/A, 122A/C/G/T, 
               
               
                 129A/G, 161G/A/T, 175A/T/C/G, 184A/C/dtheA,  
               
               
                 286C/A/T, 305C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 119: 
                 GCGCTTCGACAGCGACGTGGG 
               
               
                 SEQ ID NO 120: 
                 CTCGCCGCTGCACTGTGAAG 
               
               
                   
               
            
           
           
               
            
               
                 61. - IL1RN 2018 T/C EXON 2 AND 2073 C/T INTRON 2 
               
            
           
           
               
               
            
               
                 SEQ ID NO 121: 
                 ACAAGTTCTGGGGGACACAG 
               
               
                 SEQ ID NO 122: 
                 ATTGCACCTAGGGTTTGTGC 
               
               
                   
               
            
           
           
               
            
               
                 62. - IL1B 3954 C/T TAQI 
               
            
           
           
               
               
            
               
                 SEQ ID NO 123: 
                 TGTTCTTAGCCACCCCACTC 
               
               
                 SEQ ID NO 124: 
                 GTGATCGTACAGGTGCATCG 
               
               
                   
               
            
           
           
               
            
               
                 63. - Fas −670 G/A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1317: 
                 AGTTGGGGAGGTCTTGAAGG 
               
               
                 SEQ ID NO 1318: 
                 CCTATGGCGCAACATCTGTA 
               
               
                   
               
            
           
           
               
            
               
                 64. - Caspase 9 C93T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1319: 
                 GGAAGAGCTGCAGGTGGAC 
               
               
                 SEQ ID NO 1320: 
                 GAATCGCTTTAGCGAACACC 
               
               
                   
               
            
           
           
               
            
               
                 65. - TLR1  R80T (G/C) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1321: 
                 TCTGAGCTTTGGACTTCTGACA 
               
               
                 SEQ ID NO 1322: 
                 AGGGTGGCAAGAAATCTTCA 
               
               
                   
               
            
           
           
               
            
               
                 66. - TLR2 R753G (A/G) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1323: 
                 TCCCATTTCCGTCTTTTTGA 
               
               
                 SEQ ID NO 1324: 
                 CAAAATCCTTCCCGCTGAG 
               
               
                   
               
            
           
           
               
            
               
                 67. - TLR6 S249P (T/C) 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1325: 
                 ACTTTAGGGTGCTTACAACTGACT 
               
               
                 SEQ ID NO 1326: 
                 GACTCTGACCAGGCATTTCC 
               
               
                   
               
            
           
           
               
            
               
                 68. - MMP3 5A/6A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1327: 
                 GCCTCAACCTCTCAAAGTGC 
               
               
                 SEQ ID NO 1328: 
                 AATTCACATCACTGCCACCA 
               
               
                   
               
            
           
           
               
            
               
                 69. - NOD1 (CARD4) indel +32656 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1329: 
                 CACTATCTCTCCCCGACAGC 
               
               
                 SEQ ID NO 1330: 
                 TGGCTGTGAAGAACAGCAAA 
               
               
                   
               
            
           
           
               
            
               
                 70. - DLG5 DLG5_e26 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1331: 
                 GAGAATGCCCAGAAGATCCA 
               
               
                 SEQ ID NO 1332: 
                 AAGCAGAATCCCTCCTCCAG 
               
               
                   
               
            
           
           
               
            
               
                 71. - NOD1 rs2075817  C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1333: 
                 GGCTGCGAAGTCTGTAAACC 
               
               
                 SEQ ID NO 1334: 
                 CGCTACATGCTTCAAACTCG 
               
               
                   
               
            
           
           
               
            
               
                 72. - NOD 1 rs2975632  C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1335: 
                 GCGGCGATTACAGAAAACAT 
               
               
                 SEQ ID NO 1336: 
                 AATGCCATGCTCCATTCTTT 
               
               
                   
               
            
           
           
               
            
               
                 73. - NOD1 rs3020207  A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1337: 
                 GAGAAACCCCACAACCAGTG 
               
               
                 SEQ ID NO 1338: 
                 AGCGGCTACTTTTCCCAAAT 
               
               
                   
               
            
           
           
               
            
               
                 74. - NOD1 rs2075818 C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1339: 
                 CAGAGTCTCACCCCCACATT 
               
               
                 SEQ ID NO 1340: 
                 CTCAGATCAGCAGGGAGAGG 
               
               
                   
               
            
           
           
               
            
               
                 75. - NOD1 rs2235099 C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1341: 
                 TCCCTCCAGTGAGCAGGTAT 
               
               
                 SEQ ID NO 1342: 
                 GCATCACCCAGGATGAAGAT 
               
               
                   
               
            
           
           
               
            
               
                 76. - NOD1 rs2075821 A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1343: 
                 TCAGGTTCTTCCAGGAGTGG 
               
               
                 SEQ ID NO 1344: 
                 CTGTTTGGCTTTGGACAACA 
               
               
                   
               
            
           
           
               
            
               
                 77. - NOD1 rs2075822 C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1345: 
                 CGCCTCACTGTTCTCAGGT 
               
               
                 SEQ ID NO 1346: 
                 AAGCTTTGCACCTTGACCTC 
               
               
                   
               
            
           
           
               
            
               
                 78. - NOD1 rs2907748 C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1347: 
                 TCACTTGCTGAGAACCCAGA 
               
               
                 SEQ ID NO 1348: 
                 GGACCCTGGGACTAGAGGAG 
               
               
                   
               
            
           
           
               
            
               
                 79. - NOD1 rs5743368 A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1349: 
                 ACTTAATTGCCTGGGTGACG 
               
               
                 SEQ ID NO 1350: 
                 GCAATTCACCAAACTGATCG 
               
               
                   
               
            
           
           
               
            
               
                 80. - DLG5 haplotype A rs2289311 C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1351: 
                 CCACCTTTGCTTTTCTCACC 
               
               
                 SEQ ID NO 1352: 
                 CTGCGTTTGTGCTTGTGTTT 
               
               
                   
               
            
           
           
               
            
               
                 81. - MTHFR A1298C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1353: 
                 TTTGGGGAGCTGAAGGACTA 
               
               
                 SEQ ID NO 1354: 
                 CTTTGTGACCATTCCGGTTT 
               
               
                   
               
            
           
           
               
            
               
                 82. - NAT2 Ile114Thr 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1355: 
                 TGGTGTCTCCAGGTCAATCA 
               
               
                 SEQ ID NO 1356: 
                 GGCTGATCCTTCCCAGAAAT 
               
               
                   
               
            
           
           
               
            
               
                 83. - NAT2 Lys268Arg A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1357: 
                 ACTGTTTGGTGGGCTTCATC 
               
               
                 SEQ ID NO 1358: 
                 AGGGATCCATCACCAGGTTT 
               
               
                   
               
            
           
           
               
            
               
                 84. - ESR1 rs9340799 A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1359: 
                 AGGGTTATGTGGCAATGACG 
               
               
                 SEQ ID NO 1360: 
                 ACCAATGCTCATCCCAACTC 
               
               
                   
               
            
           
           
               
            
               
                 85. - ESR1 rs2234693 C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1361: 
                 CATGAACCACCATGCTCAGT 
               
               
                 SEQ ID NO 1362: 
                 ACCACACTCAGGGTCTCTGG 
               
               
                   
               
            
           
           
               
            
               
                 86. - MEFV V726A C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1363: 
                 AGAATGGCTACTGGGTGGTG 
               
               
                 SEQ ID NO 1364: 
                 AGAGCAGCTGGCGAATGTAT 
               
               
                   
               
            
           
           
               
            
               
                 87. - Vit D receptor (VDR) rs10735810 A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1365: 
                 TCAAAGTCTCCAGGGTCAGG 
               
               
                 SEQ ID NO 1366: 
                 AGGGCGAATCATGTATGAGG 
               
               
                   
               
            
           
           
               
            
               
                 88. - EMR3 E127Q  C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1367: 
                 CATCCCCATTTGCTCACTTT 
               
               
                 SEQ ID NO 1368: 
                 GCCTGGTCACTCTCAGTTCC 
               
               
                   
               
            
           
           
               
            
               
                 89. - EMR1 Q496K  G/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1369: 
                 CGAGGAGTTCCCAACAGGTA 
               
               
                 SEQ ID NO 1370: 
                 GGCTTTTGTCTCCTTTGTGG 
               
               
                   
               
            
           
           
               
            
               
                 90. - MTHFD1 R653Q  A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1371: 
                 TCCAGTGTTTGTCCATGCTG 
               
               
                 SEQ ID NO 1372: 
                 TTCCCCTGATGTTAAAAGAAACA 
               
               
                   
               
            
           
           
               
            
               
                 91. - SHMT1 1420C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1373: 
                 GTCAACAGTTCCCCTTTGGA 
               
               
                 SEQ ID NO 1374: 
                 TGGCAGGGGATAAGTACCAG 
               
               
                   
               
            
           
           
               
            
               
                 92. - NAT2 857G/A  Gly286Glu 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1375: 
                 ACTGTTTGGTGGGCTTCATC 
               
               
                 SEQ ID NO 1376: 
                 GGGTGATACATACACAAGGGTTT 
               
               
                   
               
            
           
           
               
            
               
                 93. - NAT2 Arg197Gln  R197Q  A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1377: 
                 CCTGCCAAAGAAGAAACACC 
               
               
                 SEQ ID NO 1378: 
                 GATGAAGCCCACCAAACAGT 
               
               
                   
               
            
           
           
               
            
               
                 94. - NAT2 rs1801279 191 G/A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1379: 
                 GGGGATCATGGACATTGAAG 
               
               
                 SEQ ID NO 1380: 
                 TGTGGTCAGAGCCCAGTACA 
               
               
                   
               
            
           
           
               
            
               
                 95. - TLR5 Arg392Stop C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1381: 
                 CCTTCTGGGGGAACTTTACA 
               
               
                 SEQ ID NO 1382: 
                 CGCTGTAAGGTTGATCTTTGG 
               
               
                   
               
            
           
           
               
            
               
                 96. - CTLA4 A49G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1383: 
                 CTGAACACCGCTCCCATAAA 
               
               
                 SEQ ID NO 1384: 
                 CCTCCTCCATCTTCATGCTC 
               
               
                   
               
            
           
           
               
            
               
                 97. - MLH1 D132N C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1385: 
                 CCGGGATCAGGAAAGAAGAT 
               
               
                 SEQ ID NO 1386: 
                 AGGGGCTTTCAGTTTTCCAT 
               
               
                   
               
            
           
           
               
            
               
                 98. - MTRR 66A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1387: 
                 TGTGTGGGTATTGTTGCATTG 
               
               
                 SEQ ID NO 1388: 
                 CCATGTACCACAGCTTGCTC 
               
               
                   
               
            
           
           
               
            
               
                 99. - ITPA 94C/A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1389: 
                 CTCATTGGTGGGGAAGAAGA 
               
               
                 SEQ ID NO 1390: 
                 CGAACTGCCTCCTGACATTT 
               
               
                   
               
            
           
           
               
            
               
                 100. - MEFV E148Q C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1391: 
                 GCCCAGGAGCCTGAAGAC 
               
               
                 SEQ ID NO 1392: 
                 CCTTCTCTCTGCGTTTGCTC 
               
               
                   
               
            
           
           
               
            
               
                 101. - PTPN22 R620W C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1393: 
                 GGCCTCAATGAACTCCTCAA 
               
               
                 SEQ ID NO 1394: 
                 GGATAGCAACTGCTCCAAGG 
               
               
                   
               
            
           
           
               
            
               
                 102. - LDL-receptor LRP-5 3357A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1395: 
                 ACTTCACCAACATGCAGGAC 
               
               
                 SEQ ID NO 1396: 
                 CAGGTCACAGCTCTCAATGC 
               
               
                   
               
            
           
           
               
            
               
                 103. - CTLA4 -C318T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1397: 
                 TGGTTAAGGATGCCCAGAAG 
               
               
                 SEQ ID NO 1398: 
                 CGAAAAGACAACCTCAAGCAC 
               
               
                   
               
            
           
           
               
            
               
                 104. - CCR5 rs333 32bpdel 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1399: 
                 CTGTCGTCCATGCTGTGTTT 
               
               
                 SEQ ID NO 1400: 
                 GACCAGCCCCAAGATGACTA 
               
               
                   
               
            
           
           
               
            
               
                 105. - IL6 −174 G/C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1401: 
                 GCCTCAATGACGACCTAAGC 
               
               
                 SEQ ID NO 1402: 
                 TCATGGGAAAATCCCACATT 
               
               
                   
               
            
           
           
               
            
               
                 106. - GR ER22/23EK rs6190 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1403: 
                 AAGAAAACCCCAGCAGTGTG 
               
               
                 SEQ ID NO 1404: 
                 GCCTTTTGGAAAATCAACCA 
               
               
                   
               
            
           
           
               
            
               
                 107. - P53 Arg72Pro C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1405: 
                 GAAGACCCAGGTCCAGATGA 
               
               
                 SEQ ID NO 1406: 
                 ACTGACCGTGCAAGTCACAG 
               
               
                   
               
            
           
           
               
            
               
                 108. - DLG5 P1371Q A/C 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1407: 
                 CTGTCATCGACCCACTGATG 
               
               
                 SEQ ID NO 1408: 
                 GACACAGGGAAGGCTCACA 
               
               
                   
               
            
           
           
               
            
               
                 109. - GR ER22/23EK rs6189 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1409: 
                 AAGAAAACCCCAGCAGTGTG 
               
               
                 SEQ ID NO 1410: 
                 GCCTTTTGGAAAATCAACCA 
               
               
                   
               
            
           
           
               
            
               
                 110. - GR ER22/23EK rs6190 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1411: 
                 AAGAAAACCCCAGCAGTGTG 
               
               
                 SEQ ID NO 1412: 
                 GCCTTTTGGAAAATCAACCA 
               
               
                   
               
            
           
           
               
            
               
                 111. - LDL-receptor LRP-5 C135242T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1413: 
                 GTAGATGAAGTCCCCCAGCA 
               
               
                 SEQ ID NO 1414: 
                 GCATTGAACCCGTCTTGTTT 
               
               
                   
               
            
           
           
               
            
               
                 112. - LDL-receptor LRP-5 G121513A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1415: 
                 GCACCGACATTTACTGACACC 
               
               
                 SEQ ID NO 1416: 
                 ATGAGGCTGGAGAAGAAGCA 
               
               
                   
               
            
           
           
               
            
               
                 113. - LDL-receptor LRP-5 C141759T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1417: 
                 GAGCACGTGGTGGAGTTTG 
               
               
                 SEQ ID NO 1418: 
                 TTGTCCAAGTCCCTCCACAC 
               
               
                   
               
            
           
           
               
            
               
                 114. - LDL-receptor LRP-5 G138351A 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1419: 
                 ATGGCCACGTCGTTGTTATT 
               
               
                 SEQ ID NO 1420: 
                 AGCCACCTGTGCTTCTTCAC 
               
               
                   
               
            
           
           
               
            
               
                 115. - P2X7 −298 C/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1421: 
                 GTGTTCAGAGGATGGGCATT 
               
               
                 SEQ ID NO 1422: 
                 GGGGCTGAATAAAGGGTTGT 
               
               
                   
               
            
           
           
               
            
               
                 116. - P2X7 −838 G/T 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1423: 
                 GAGCTACGCACATCACCAAA 
               
               
                 SEQ ID NO 1424: 
                 GGTCCTCTTTGCAATCCAGA 
               
               
                   
               
            
           
           
               
            
               
                 117. - APC E1317Q C/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1425: 
                 CAGACGACACAGGAAGCAGA 
               
               
                 SEQ ID NO 1426: 
                 TGTCTGAGCACCACTTTTGG 
               
               
                   
               
            
           
           
               
            
               
                 118. - CD97 -T64C A/G 
               
            
           
           
               
               
            
               
                 SEQ ID NO 1427: 
                 GGGAAAGAGTGAGTGGGACA 
               
               
                 SEQ ID NO 1428: 
                 CCCCTGGGTCTGTGTTTTTA 
               
            
           
         
       
     
     The multiplex PCRs are carried out simultaneously under the same time and temperature conditions which permit specific amplification of the gene fragments where the genetic variation to be detected might exist. Once the PCR multiplex has finished, agarose gel analysis is used to check that amplification has taken place 
     Next, the sample to be hybridized (product of the amplification) is subjected to fragmentation with a DNase and the resulting fragmentation products are then subjected to indirect labelling. A terminal transferase adds a nucleotide, joined to one member of a pair of molecules that specifically bind to one another (e.g. biotin allowing subsequent binding to streptavidin) to the ends of these small DNA fragments. 
     Before applying the sample to the DNA-chip, the sample is denatured by heating to 95° C. for 5 minutes and, the “ChipMap Kit Hybridization Buffer” (Ventana Medical System) is added. 
     Next, the stages of hybridization are performed, scanning the slide, quantification of the image and interpretation of the results, following the procedure described in the sections 1.3.2, 1.3.3, 1.3.4 and 1.3.5 of Example 1. 
     Example 4 
     Identification of the Genotype of 9 Individuals for the Human Genetic Variations Associated with IBD Using a DNA-chip 
     4.1 DNA Extraction 
     DNA was extracted from 9 individuals (patients) by conventional methods to characterize the genetic variations found in these individuals with regard to the genetic variation A2033T of the gene CSFR1 associated with the development of Crohn&#39;s Disease. Genetic analysis of the region of interest by sequencing determined that 3 of the patients had genotype AA, another 3 genotype AT (heterozygotes) and the other 3 genotype TT. 
     4.2 Design of the Probes 
     4 probes were designed for the detection of the genetic variation A2033T CSFR1S: 
                                AAACCCTTATTCACCTAATCACAGC   SEQ ID NO: 715                   GCTGTGATTAGGTGAATAAGGGTTT   SEQ ID NO: 716                   AAACCCTTATTCTCCTAATCACAGC   SEQ ID NO: 717                   GCTGTGATTAGGAGAATAAGGGTTT   SEQ ID NO: 718            
4.3 Production of the DNA-chip for the Detection of Human Genetic Variations Associated with IBD
 
     The designed oligonucleotides were printed onto the slide with a microarrayer as described in Example 3.2. 
     4.4 PCR and Labelling the Sample 
     The region of the gene CSFR1 which permitted the analysis of the genetic variation of interest was amplified by means of PCR multiplex using specific primers (SEQ ID NO 41 and SEQ ID NO 42). The product of the amplification was fragmented and labelled as indicated in Example 1.3.1. 
     4.5 Hybridization of the Samples 
     Hybridization was carried out in an automatic hybridization station as described in Example 1.3.2. 
     4.6 Analysis of the Results 
     The slides were placed in the scanner. The signal emitted by the bound fluorophore on being stimulated by the laser was scanned (Example 1.3.3) and the image obtained from the signal at the points where hybridization had taken place was quantified (Example 1.3.4). 
     The analysis of the results was carried out using the algorithm described in Example 1.3.5. Using this algorithm allowed the characterization of the genotypes for each of the 9 subjects tested with complete correspondence to the genotypes obtained by nucleotide sequence analysis of the subjects&#39; samples. 
       FIG. 2  shows the representation of ratios 1 and 2 and allows the genotypes of the 9 patients to be characterised. 
     Table 8 shows the linear functions obtained for the three genotype groups where 10 replicates of each of the 4 probes were used; “X” is ratio 1; “Y” is ratio 2; “0” corresponds to the genotype TT; “1” corresponds to the genotype AT; and “2” corresponds to the genotype AA. 
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Coefficients of the functions used for genotyping 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CLASS 
                 0 
                 1 
                 2 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 X 
                 427.052 
                 863.0399 
                 1270.836 
               
               
                   
                 Y 
                 8937.156 
                 16216.35 
                 21969.05 
               
               
                   
                 (Constant) 
                 −1514.27 
                 −5026.28 
                 −9293.69 
               
               
                   
               
            
           
         
       
     
     A donor with genotype AA had ratios 1 and 2 of 0.26 and 0.32 respectively. On substituting these ratios in the linear functions, it is observed that function 2 shows a greater absolute value. From this we can see how the algorithm of the invention perfectly classifies donors when 10 replicates of each of the 4 probes are used. 
     Table 9 shows the linear functions obtained when 8 replicates of each of the 4 probes were used. 
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 Coefficients of the functions used for genotyping 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CLASS 
                 0 
                 1 
                 2 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 X 
                 751.6869 
                 1446.046 
                 2065.363 
               
               
                   
                 Y 
                 10369.47 
                 18620.87 
                 25204.48 
               
               
                   
                 (Constant) 
                 −1813.36 
                 −5892.27 
                 −10868.5 
               
               
                   
               
            
           
         
       
     
     The same donor with genotype AA had the same ratios 1 and 2 of 0.26 and 0.32, respectively. On substituting these ratios in the linear functions, it is observed that function 2 shows a greater absolute value. From this, we can see the algorithm of the invention perfectly classifies patients when 8 replicates of each of the 4 probes are used. 
     Table 10 shows the linear functions obtained when 6 replicates of each of the 4 probes are used. 
     
       
         
           
               
             
               
                 TABLE 10 
               
             
            
               
                   
               
               
                 Coefficients of the functions used for genotyping 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CLASS 
                 0 
                 1 
                 2 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 X 
                 227.5676 
                 531.6475 
                 798.1821 
               
               
                   
                 Y 
                 11864.89 
                 21269.96 
                 28789.95 
               
               
                   
                 (Constant) 
                 −1992.22 
                 −6460.62 
                 −11889.5 
               
               
                   
               
            
           
         
       
     
     The same donor with genotype AA had the same ratios 1 and 2 of 0.26 and 0.32, respectively. On substituting these ratios in the linear functions, it is observed that function 2 shows a greater absolute value. From this, we can see the algorithm of the invention perfectly classifies patients when 6 replicates are used for each of the 4 probes. 
     Example 5 
     Detection of Human Genetic Variations Associated with Adverse Reactions to Drugs, Using a DNA-chip 
     5.1 Design of the DNA-chip for the Detection of Human Genetic Variations Associated with Adverse Reactions to Drugs 
     A DNA-chip was designed and produced to detect adverse pharmaceutical reactions. The chip permits the simultaneous, sensitive, specific and reproducible detection of genetic variations associated with adverse reactions to drugs. Illustrative examples of these human genetic variations are listed in Table 3. 
     In this case, the DNA-chip consists of a support which comprises a plurality of probes on its surface which permit the detection of the genetic variations. These probes are capable of hybridizing with (amplified) target sequences of genes associated with the adverse reactions to be studied. The DNA sequences of each of the probes used are listed below. In general, the name of the gene and the genetic variation (change of amino acid, change of nucleotide, “ins”: insertion, “del”: deletion)] are given. 
                    1. - Beta-1-adrenergic receptor (ADRB1) Arg389 Gly       (probes to detect the polymorphism Arg389 Gly in       the gene of the Beta-1 adrenergic receptor)                     AAGGCCTTCCAGCGACTGCTCTGCT   SEQ ID NO: 961       AAGGCCTTCCAGGGACTGCTCTGCT   SEQ ID NO: 962       AGCAGAGCAGTCGCTGGAAGGCCTT   SEQ ID NO: 963       AGCAGAGCAGTCCCTGGAAGGCCTT   SEQ ID NO: 964                         2. - Beta-2-adrenergic receptor (ADRB2) Arg16Gly                     CTGGCACCCAATGGAAGCCATGCGC   SEQ ID NO: 965       CTGGCACCCAATAGAAGCCATGCGC   SEQ ID NO: 966       GCGCATGGCTTCCATTGGGTGCCAG   SEQ ID NO: 967       GCGCATGGCTTCTATTGGGTGCCAG   SEQ ID NO: 968                         3. - Beta-2-adrenergic receptor (ADRB2) Gln27Glu                     GACGTCACGCAGCAAAGGGACGAGG   SEQ ID NO: 969       GACGTCACGCAGGAAAGGGACGAGG   SEQ ID NO: 970       CCTCGTCCCTTTGCTGCGTGACGTC   SEQ ID NO: 971       CCTCGTCCCTTTCCTGCGTGACGTC   SEQ ID NO: 972                         4. - Dopamine D3 receptor (DRD3) Ser9Gly                     AGTTCAGGTGGCCACTCAGCTGGCT   SEQ ID NO: 973       AGTTCAGGTGGCTACTCAGCTGGCT   SEQ ID NO: 974       AGCCAGCTGAGTGGCCACCTGAACT   SEQ ID NO: 975       AGCCAGCTGAGTAGCCACCTGAACT   SEQ ID NO: 976                         5. - Serotonin 2A receptor (HTR2A) His452Tyr                     CTAGGAAAGCAGCATTCTGAAGAGG   SEQ ID NO: 977       CTAGGAAAGCAGTATTCTGAAGAGG   SEQ ID NO: 978       CCTCTTCAGAATGCTGCTTTCCTAG   SEQ ID NO: 979       CCTCTTCAGAATACTGCTTTCCTAG   SEQ ID NO: 980                         6. - Serotonin 2A receptor (HTR2A) T102C                     GTTAGCTTCTCCGGAGTTAAAGTCA   SEQ ID NO: 981       GTTAGCTTCTCCAGAGTTAAAGTCA   SEQ ID NO: 982       TGACTTTAACTCCGGAGAAGCTAAC   SEQ ID NO: 983       TGACTTTAACTCTGGAGAAGCTAAC   SEQ ID NO: 984                         7. - Catechol-O-methyltransferase (COMT) Val108Met                     GATTTCGCTGGCGTGAAGGACAAGG   SEQ ID NO: 985       GATTTCGCTGGCATGAAGGACAAGG   SEQ ID NO: 986       CCTTGTCCTTCACGCCAGCGAAATC   SEQ ID NO: 987       CCTTGTCCTTCATGCCAGCGAAATC   SEQ ID NO: 988                         8. - Glutathione S transferase class 1 (GSTP1)       Ile105Val                     CGCTGCAAATACATCTCCCTCATCT   SEQ ID NO: 989       CGCTGCAAATACGTCTCCCTCATCT   SEQ ID NO: 990       AGATGAGGGAGATGTATTTGCAGCG   SEQ ID NO: 991       AGATGAGGGAGACGTATTTGCAGCG   SEQ ID NO: 992                         9. - Adducin 1 (ADD1) Gly460Trp                     GCTTCCGAGGAAGGGCAGAATGGAA   SEQ ID NO: 993       GCTTCCGAGGAATGGCAGAATGGAA   SEQ ID NO: 994       TTCCATTCTGCCCTTCCTCGGAAGC   SEQ ID NO: 995       TTCCATTCTGCCATTCCTCGGAAGC   SEQ ID NO: 996                         10. - DNA Repair Enzyme XRCC1 Arg399Gln                     GGCTGCCCTCCCGGAGGTAAGGCCT   SEQ ID NO: 997       GGCTGCCCTCCCAGAGGTAAGGCCT   SEQ ID NO: 998       AGGCCTTACCTCCGGGAGGGCAGCC   SEQ ID NO: 999       AGGCCTTACCTCTGGGAGGGCAGCC   SEQ ID NO: 1000                         11. - Cytochrome P450 1A1 (CYP1A1) Ile462Val                     ATCGGTGAGACCATTGCCCGCTGGG   SEQ ID NO: 1001       ATCGGTGAGACCGTTGCCCGCTGGG   SEQ ID NO: 1002       CCCAGCGGGCAATGGTCTCACCGAT   SEQ ID NO: 1003       CCCAGCGGGCAACGGTCTCACCGAT   SEQ ID NO: 1004                         12. - Angiotensin II receptor, type 1 (AGTR1) A1166C                     TACCAAATGAGCATTAGCTACTTTT   SEQ ID NO: 1005       TACCAAATGAGCCTTAGCTACTTTT   SEQ ID NO: 1006       AAAAGTAGCTAATGCTCATTTGGTA   SEQ ID NO: 1007       AAAAGTAGCTAAGGCTCATTTGGTA   SEQ ID NO: 1008                         13. - Bradykinin receptor B2 (BDKRB2) C-58T                     TGCCATCTAACCATCTTTTCTTCTC   SEQ ID NO: 1009       TGCCATCTAACCGTCTTTTCTTCTC   SEQ ID NO: 1010       GAGAAGAAAAGATGGTTAGATGGCA   SEQ ID NO: 1011       GAGAAGAAAAGACGGTTAGATGGCA   SEQ ID NO: 1012                         14. - Angiotensinogen (AGT) Met235Thr                     GCTGCTCCCTGACGGGAGCCAGTGT   SEQ ID NO: 1013       GCTGCTCCCTGATGGGAGCCAGTGT   SEQ ID NO: 1014       ACACTGGCTCCCGTCAGGGAGCAGC   SEQ ID NO: 1015       ACACTGGCTCCCATCAGGGAGCAGC   SEQ ID NO: 1016                         15. - Cytochrome P450 2C9 (CYP2C9) C430T                     AGCATTGAGGACCGTGTTCAAGAGG   SEQ ID NO: 1017       AGCATTGAGGACTGTGTTCAAGAGG   SEQ ID NO: 1018       CCTCTTGAACACGGTCCTCAATGCT   SEQ ID NO: 1019       CCTCTTGAACACAGTCCTCAATGCT   SEQ ID NO: 1020                         16. - Cytochrome P450 2C9 (CYP2C9) A1075C                     GTCCAGAGATACATTGACCTTCTCC   SEQ ID NO: 1021       GTCCAGAGATACCTTGACCTTCTCC   SEQ ID NO: 1022       GGAGAAGGTCAATGTATCTCTGGAC   SEQ ID NO: 1023       GGAGAAGGTCAAGGTATCTCTGGAC   SEQ ID NO: 1024                         17. - Cytochrome P450 2C9 (CYP2C9) 818delA                     TGAAAATGGAGAAGGTAAAATGTAA   SEQ ID NO: 1025       TGAAAATGGAGAGGTAAAATGTAAA   SEQ ID NO: 1026       TTACATTTTACCTTCTCCATTTTCA   SEQ ID NO: 1027       TTTACATTTTACCTCTCCATTTTCA   SEQ ID NO: 1028                         18. - Cytochrome P450 2C9 (CYP2C9) T1076C                     TCCAGAGATACATTGACCTTCTCCC   SEQ ID NO: 1029       TCCAGAGATACACTGACCTTCTCCC   SEQ ID NO: 1030       GGGAGAAGGTCAATGTATCTCTGGA   SEQ ID NO: 1031       GGGAGAAGGTCAGTGTATCTCTGGA   SEQ ID NO: 1032                         19. - Cytochrome P450 2C9 (CYP2C9) C1080G                     GAGATACATTGACCTTCTCCCCACC   SEQ ID NO: 1033       GAGATACATTGAGCTTCTCCCCACC   SEQ ID NO: 1034       GGTGGGGAGAAGGTCAATGTATCTC   SEQ ID NO: 1035       GGTGGGGAGAAGCTCAATGTATCTC   SEQ ID NO: 1036                         20. - Cytochrome P450 2D6 (CY2D6) H324P                     TGCACATCCGGAGGTAGGATCATGA   SEQ ID NO: 1037       TGCACATCCGGATGTAGGATCATGA   SEQ ID NO: 1038       TCATGATCCTACCTCCGGATGTGCA   SEQ ID NO: 1039       TCATGATCCTACATCCGGATGTGCA   SEQ ID NO: 1040                         21. - Cytochrome P450 2D6 (CYP2D6) V136V                     GCGCTTCTCCGTGTCCACCTTGCGC   SEQ ID NO: 1041       GCGCTTCTCCGTCTCCACCTTGCGC   SEQ ID NO: 1042       GCGCAAGGTGGACACGGAGAAGCGC   SEQ ID NO: 1043       GCGCAAGGTGGAGACGGAGAAGCGC   SEQ ID NO: 1044                         22. - Cytochrome P450 2D6 (CYP2D6) V11M                     GTGCCCCTGGCCGTGATAGTGGCCA   SEQ ID NO: 1045       GTGCCCCTGGCCATGATAGTGGCCA   SEQ ID NO: 1046       TGGCCACTATCACGGCCAGGGGCAC   SEQ ID NO: 1047       TGGCCACTATCATGGCCAGGGGCAC   SEQ ID NO: 1048                         23. - Cytochrome P450 2D6 (CYP2D6) C882G                     GCGGCGCCGCAACTGCAGAGGGAGG   SEQ ID NO: 1049       GCGGCGCCGCAAGTGCAGAGGGAGG   SEQ ID NO: 1050       CCTCCCTCTGCAGTTGCGGCGCCGC   SEQ ID NO: 1051       CCTCCCTCTGCACTTGCGGCGCCGC   SEQ ID NO: 1052                         24. - Cytochrome P450 2D6 (CYP2D6) C1038T                     GATCCTGGGTTTCGGGCCGCGTTCC   SEQ ID NO: 1053       GATCCTGGGTTTTGGGCCGCGTTCC   SEQ ID NO: 1054       GGAACGCGGCCCGAAACCCAGGATC   SEQ ID NO: 1055       GGAACGCGGCCCAAAACCCAGGATC   SEQ ID NO: 1056                         25. - Cytochrome P450 2D6 (CYP2D6) G4180C                     CTTTCCTGGTGAGCCCATCCCCCTA   SEQ ID NO: 1057       CTTTCCTGGTGACCCCATCCCCCTA   SEQ ID NO: 1058       TAGGGGGATGGGCTCACCAGGAAAG   SEQ ID NO: 1059       TAGGGGGATGGGGTCACCAGGAAAG   SEQ ID NO: 1060                         26. - Cytochrome P450 2D6 (CYP2D6) A1847G                     CTCCCACCCCCAGGACGCCCCTTTC   SEQ ID NO: 1061       CTCCCACCCCCAAGACGCCCCTTTC   SEQ ID NO: 1062       GAAAGGGGCGTCCTGGGGGTGGGAG   SEQ ID NO: 1063       GAAAGGGGCGTCTTGGGGGTGGGAG   SEQ ID NO: 1064                         27. - Cytochrome P450 2D6 (CYP2D6) C-1584G                     CTTGGAAGAACCCGGTCTCTACAAA   SEQ ID NO: 1065       CTTGGAAGAACCGGGTCTCTACAAA   SEQ ID NO: 1066       TTTGTAGAGACCGGGTTCTTCCAAG   SEQ ID NO: 1067       TTTGTAGAGACCCGGTTCTTCCAAG   SEQ ID NO: 1068                         28. - Cytochrome P450 2D6 (CYP2D6) C100T                     GCTGCACGCTACCCACCAGGCCCCC   SEQ ID NO: 1069       GCTGCACGCTACTCACCAGGCCCCC   SEQ ID NO: 1070       GGGGGCCTGGTGGGTAGCGTGCAGC   SEQ ID NO: 1071       GGGGGCCTGGTGAGTAGCGTGCAGC   SEQ ID NO: 1072                         29. - Cytochrome P450 2D6 (CYP2D6) 138insT                     GCTGGGCAACCTGCTGCATGTGGAC   SEQ ID NO: 1073       GCTGGGCAACCTTGCTGCATGTGGA   SEQ ID NO: 1074       GTCCACATGCAGCAGGTTGCCCAGC   SEQ ID NO: 1075       TCCACATGCAGCAAGGTTGCCCAGC   SEQ ID NO: 1076                         30. - Cytochrome P450 2D6 (CYP2D6) C1023T                     CTGTGCCCATCACCCAGATCCTGGG   SEQ ID NO: 1077       CTGTGCCCATCATCCAGATCCTGGG   SEQ ID NO: 1078       CCCAGGATCTGGGTGATGGGCACAG   SEQ ID NO: 1079       CCCAGGATCTGGATGATGGGCACAG   SEQ ID NO: 1080                         31. - Cytochrome P450 2D6 (CYP2D6) G1659A                     AGGCGCTTCTCCGTGTCCACCTTGC   SEQ ID NO: 1081       AGGCGCTTCTCCATGTCCACCTTGC   SEQ ID NO: 1082       GCAAGGTGGACACGGAGAAGCGCCT   SEQ ID NO: 1083       GCAAGGTGGACATGGAGAAGCGCCT   SEQ ID NO: 1084                         32. - Cytochrome P450 2D6 (CYP2D6) 1707T/del                     TCGCTGGAGCAGTGGGTGACCGAGG   SEQ ID NO: 1085       TCGCTGGAGCAGGGGTGACCGAGGA   SEQ ID NO: 1086       CCTCGGTCACCCACTGCTCCAGCGA   SEQ ID NO: 1087       TCCTCGGTCACCCCTGCTCCAGCGA   SEQ ID NO: 1088                         33. - Cytochrome P450 2D6 (CYP2D6) G1758A                     GCCAACCACTCCGGTGGGTGATGGG   SEQ ID NO: 1089       GCCAACCACTCCAGTGGGTGATGGG   SEQ ID NO: 1090       CCCATCACCCACCGGAGTGGTTGGC   SEQ ID NO: 1091       CCCATCACCCACTGGAGTGGTTGGC   SEQ ID NO: 1092                         34. - Cytochrome P450 2D6 (CYP2D6) G1758T                     GCCAACCACTCCGGTGGGTGATGGG   SEQ ID NO: 1093       GCCAACCACTCCTGTGGGTGATGGG   SEQ ID NO: 1094       CCCATCACCCACCGGAGTGGTTGGC   SEQ ID NO: 1095       CCCATCACCCACAGGAGTGGTTGGC   SEQ ID NO: 1096                         35. - Cytochrome P450 2D6 (CYP2D6) 1863ins9bp                     CCCTTTCGCCCCAACGGTCTCTTGG   SEQ ID NO: 1197       CCCTTTCGCCCCTTTCGCCCCAACG   SEQ ID NO: 1198       CCAAGAGACCGTTGGGGCGAAAGGG   SEQ ID NO: 1199       CGTTGGGGCGAAAGGGGCGAAAGGG   SEQ ID NO: 1100                         36. - Cytochrome P450 2D6 (CYP2D6) 1973insG                     ACCTAGCTCAGGAGGGACTGAAGGA   SEQ ID NO: 1101       ACCTAGCTCAGGGAGGGACTGAAGG   SEQ ID NO: 1102       TCCTTCAGTCCCTCCTGAGCTAGGT   SEQ ID NO: 1103       CCTTCAGTCCCTCCCTGAGCTAGGT   SEQ ID NO: 1104                         37. - Cytochrome P450 2D6 (CYP2D6) 2539delAACT                     GGATGAGCTGCTAACTGAGCACAGG   SEQ ID NO: 1105       GGATGAGCTGCTGAGCACAGGATGA   SEQ ID NO: 1106       CCTGTGCTCAGTTAGCAGCTCATCC   SEQ ID NO: 1107       TCATCCTGTGCTCAGCAGCTCATCC   SEQ ID NO: 1108                         38. - Cytochrome P450 2D6 (CYP2D6) 2549A/del                     CTAACTGAGCACAGGATGACCTGGG   SEQ ID NO: 1109       CTAACTGAGCACGGATGACCTGGGA   SEQ ID NO: 1110       CCCAGGTCATCCTGTGCTCAGTTAG   SEQ ID NO: 1111       TCCCAGGTCATCCGTGCTCAGTTAG   SEQ ID NO: 1112                         39. - Cytochrome P450 2D6 (CYP2D6) 2613delAGA                     TGGCAGAGATGGAGAAGGTGAGAGT   SEQ ID NO: 1113       TGGCAGAGATGGAGGTGAGAGTGGC   SEQ ID NO: 1114       ACTCTCACCTTCTCCATCTCTGCCA   SEQ ID NO: 1115       GCCACTCTCACCTCCATCTCTGCCA   SEQ ID NO: 1116                         40. - Cytochrome P450 2D6 (CYP2D6) C2850T                     GATGAGAACCTGCGCATAGTGGTGG   SEQ ID NO: 1117       GATGAGAACCTGTGCATAGTGGTGG   SEQ ID NO: 1118       CCACCACTATGCGCAGGTTCTCATC   SEQ ID NO: 1119       CCACCACTATGCACAGGTTCTCATC   SEQ ID NO: 1120                         41. - Cytochrome P450 2D6 (CYP2D6) G3183A                     GAGATCGACGACGTGATAGGGCAGG   SEQ ID NO: 1121       GAGATCGACGACATGATAGGGCAGG   SEQ ID NO: 1122       CCTGCCCTATCACGTCGTCGATCTC   SEQ ID NO: 1123       CCTGCCCTATCATGTCGTCGATCTC   SEQ ID NO: 1124                         42.- Cytochrome P450 2D6 (CYP2D6) C3198G                     ATAGGGCAGGTGCGGCGACCAGAGA   SEQ ID NO: 1125       ATAGGGCAGGTGGGGCGACCAGAGA   SEQ ID NO: 1126       TCTCTGGTCGCCGCACCTGCCCTAT   SEQ ID NO: 1127       TCTCTGGTCGCCCCACCTGCCCTAT   SEQ ID NO: 1128                         43. - Cytochrome P450 2D6 (CYP2D6) T3277C                     GCTTTGGGGACATCGTCCCCCTGGG   SEQ ID NO: 1129       GCTTTGGGGACACCGTCCCCCTGGG   SEQ ID NO: 1130       CCCAGGGGGACGATGTCCCCAAAGC   SEQ ID NO: 1131       CCCAGGGGGACGGTGTCCCCAAAGC   SEQ ID NO: 1132                         44. - Cytochrome P450 2D6 (CYP2D6) G4042A                     TCCCCACAGGCCGCCGTGCATGCCT   SEQ ID NO: 1133       TCCCCACAGGCCACCGTGCATGCCT   SEQ ID NO: 1134       AGGCATGCACGGCGGCCTGTGGGGA   SEQ ID NO: 1135       AGGCATGCACGGTGGCCTGTGGGGA   SEQ ID NO: 1136                         45. - Cytochrome P450 2D6 (CYP2D6) 4125ins       GTGCCCACT                     TCGGTGCCCACTGGACAGCCCCGGC   SEQ ID NO: 1137       TCGGTGCCCACTGTGCCCACTGGAC   SEQ ID NO: 1138       GCCGGGGCTGTCCAGTGGGCACCGA   SEQ ID NO: 1139       GTCCAGTGGGCACAGTGGGCACCGA   SEQ ID NO: 1140                         46. - Cytochrome P450 2C8 (CYP2C8) A805T                     GATTGCTTCCTGATCAAAATGGAGC   SEQ ID NO: 1141       GATTGCTTCCTGTTCAAAATGGAGC   SEQ ID NO: 1142       GCTCCATTTTGATCAGGAAGCAATC   SEQ ID NO: 1143       GCTCCATTTTGAACAGGAAGCAATC   SEQ ID NO: 1144                         47. - Cytochrome P450 2C8 (CYP2C8) G416A                     GGATGGGGAAGAGGAGCATTGAGGA   SEQ ID NO: 1145       GGATGGGGAAGAAGAGCATTGAGGA   SEQ ID NO: 1146       TCCTCAATGCTCCTCTTCCCCATCC   SEQ ID NO: 1147       TCCTCAATGCTCTTCTTCCCCATCC   SEQ ID NO: 1148                         48. - Cytochrome P450 2C8 (CYP2C8) A1196G                     TTAGGAAATTCTTTGTCATCATGTA   SEQ ID NO: 1149       TTAGGAAATTCTCTGTCATCATGTA   SEQ ID NO: 1150       TACATGATGACAAAGAATTTCCTAA   SEQ ID NO: 1151       TACATGATGACAGAGAATTTCCTAA   SEQ ID NO: 1152                         49. - Cytochrome P450 2C8 (CYP2C8) C792G                     TCGGGACTTTATCGATTGCTTCCTG   SEQ ID NO: 1153       TCGGGACTTTATGGATTGCTTCCTG   SEQ ID NO: 1154       CAGGAAGCAATCGATAAAGTCCCGA   SEQ ID NO: 1155       CAGGAAGCAATCCATAAAGTCCCGA   SEQ ID NO: 1156                         50. - N-acetyltransferase 2 (NAT2) T341C                     TGCAGGTGACCATTGACGGCAGGAA   SEQ ID NO: 1157       TGCAGGTGACCACTGACGGCAGGAA   SEQ ID NO: 1158       TTCCTGCCGTCAATGGTCACCTGCA   SEQ ID NO: 1159       TTCCTGCCGTCAGTGGTCACCTGCA   SEQ ID NO: 1160                         51. - N-acetyltransferase 2 (NAT2) C481T                     GGAATCTGGTACCTGGACCAAATCA   SEQ ID NO: 1161       GGAATCTGGTACTTGGACCAAATCA   SEQ ID NO: 1162       TGATTTGGTCCAGGTACCAGATTCC   SEQ ID NO: 1163       TGATTTGGTCCAAGTACCAGATTCC   SEQ ID NO: 1164                         52. - N-acetyltransferase 2 (NAT2) A803G                     AAGAAGTGCTGAAAAATATATTTAA   SEQ ID NO: 1165       AAGAAGTGCTGAGAAATATATTTAA   SEQ ID NO: 1166       TTAAATATATTTTTCAGCACTTCTT   SEQ ID NO: 1167       TTAAATATATTTCTCAGCACTTCTT   SEQ ID NO: 1168                         53. - N-acetyltransferase 2 (NAT2) C282T                     AGGGTATTTTTACATCCCTCCAGTT   SEQ ID NO: 1169       AGGGTATTTTTATATCCCTCCAGTT   SEQ ID NO: 1170       AACTGGAGGGATGTAAAAATACCCT   SEQ ID NO: 1171       AACTGGAGGGATATAAAAATACCCT   SEQ ID NO: 1172                         54. - N-acetyltransferase 2 (NAT2) G590A                     CGCTTGAACCTCGAACAATTGAAGA   SEQ ID NO: 1173       CGCTTGAACCTCAAACAATTGAAGA   SEQ ID NO: 1174       TCTTCAATTGTTCGAGGTTCAAGCG   SEQ ID NO: 1175       TCTTCAATTGTTTGAGGTTCAAGCG   SEQ ID NO: 1176                         55. - N-acetyltransferase 2 (NAT2) G857A                     AACCTGGTGATGGATCCCTTACTAT   SEQ ID NO: 1177       AACCTGGTGATGAATCCCTTACTAT   SEQ ID NO: 1178       ATAGTAAGGGATCCATCACCAGGTT   SEQ ID NO: 1179       ATAGTAAGGGATTCATCACCAGGTT   SEQ ID NO: 1180                         56. - N-acetyltransferase 2 (NAT2) G191A                     TAAGAAGAAACCGGGGTGGGTGGTG   SEQ ID NO: 1181       TAAGAAGAAACCAGGGTGGGTGGTG   SEQ ID NO: 1182       CACCACCCACCCCGGTTTCTTCTTA   SEQ ID NO: 1183       CACCACCCACCCTGGTTTCTTCTTA   SEQ ID NO: 1184                         57. - Cytochrome P450 2C19 (CYP2C19) G636A                     AAGCACCCCCTGGATCCAGGTAAGG   SEQ ID NO: 1185       AAGCACCCCCTGAATCCAGGTAAGG   SEQ ID NO: 1186       CCTTACCTGGATCCAGGGGGTGCTT   SEQ ID NO: 1187       CCTTACCTGGATTCAGGGGGTGCTT   SEQ ID NO: 1188                         58. - Cytochrome P450 2C19 (CYP2C19) G681A                     TGATTATTTCCCGGGAACCCATAAC   SEQ ID NO: 1189       TGATTATTTCCCAGGAACCCATAAC   SEQ ID NO: 1190       GTTATGGGTTCCCGGGAAATAATCA   SEQ ID NO: 1191       GTTATGGGTTCCTGGGAAATAATCA   SEQ ID NO: 1192                         59. - Cytochrome P450 2C19 (CYP2C19) C680T                     TTGATTATTTCCCGGGAACCCATAA   SEQ ID NO: 1193       TTGATTATTTCCTGGGAACCCATAA   SEQ ID NO: 1194       TTATGGGTTCCCGGGAAATAATCAA   SEQ ID NO: 1195       TTATGGGTTCCCAGGAAATAATCAA   SEQ ID NO: 1196                         60. - Cytochrome P450 2C19 (CYP2C19) A1G                     GAGAAGGCTTCAATGGATCCTTTTG   SEQ ID NO: 1197       GAGAAGGCTTCAGTGGATCCTTTTG   SEQ ID NO: 1198       CAAAAGGATCCATTGAAGCCTTCTC   SEQ ID NO: 1199       CAAAAGGATCCACTGAAGCCTTCTC   SEQ ID NO: 1200                         61. - Cytochrome P450 2C19 (CYP2C19) IVS5 + 2T &gt; A                     AAATGGAGAAGGTAAAATGTTAACA   SEQ ID NO: 1201       AAATGGAGAAGGAAAAATGTTAACA   SEQ ID NO: 1202       TGTTAACATTTTACCTTCTCCATTT   SEQ ID NO: 1203       TGTTAACATTTTTCCTTCTCCATTT   SEQ ID NO: 1204                         62. - Cytochrome P450 2C19 (CYP2C19) T358C                     AATGGAAAGAGATGGAAGGAGATCC   SEQ ID NO: 1205       AATGGAAAGAGACGGAAGGAGATCC   SEQ ID NO: 1206       GGATCTCCTTCCATCTCTTTCCATT   SEQ ID NO: 1207       GGATCTCCTTCCGTCTCTTTCCATT   SEQ ID NO: 1208                         63. - Cytochrome P450 2C19 (CYP2C19) G431A                     GCATTGAGGACCGTGTTCAAGAGGA   SEQ ID NO: 1209       GCATTGAGGACCATGTTCAAGAGGA   SEQ ID NO: 1210       TCCTCTTGAACACGGTCCTCAATGC   SEQ ID NO: 1211       TCCTCTTGAACATGGTCCTCAATGC   SEQ ID NO: 1212                         64. - Cytochrome P450 2C19 (CYP2C19) C1297T                     TTTTCAGGAAAACGGATTTGTGTGG   SEQ ID NO: 1213       TTTTCAGGAAAATGGATTTGTGTGG   SEQ ID NO: 1214       CCACACAAATCCGTTTTCCTGAAAA   SEQ ID NO: 1215       CCACACAAATCCATTTTCCTGAAAA   SEQ ID NO: 1216                         65. - Glutamate receptor, ionotropic, N-methyl       D-asparate (NMDA) 2B(GRIN2B) C2664T                     GTTCATGGTTGCGGTGGGGGAGTTC   SEQ ID NO: 1217       GTTCATGGTTGCAGTGGGGGAGTTC   SEQ ID NO: 1218       GAACTCCCCCACCGCAACCATGAAC   SEQ ID NO: 1219       GAACTCCCCCACTGCAACCATGAAC   SEQ ID NO: 1220                         66. - Glycoprotein P (ABCB1) C3435T                     TGCTGCCCTCACAATCTCTTCCTGT   SEQ ID NO: 1221       TGCTGCCCTCACGATCTCTTCCTGT   SEQ ID NO: 1222       ACAGGAAGAGATTGTGAGGGCAGCA   SEQ ID NO: 1223       ACAGGAAGAGATCGTGAGGGCAGCA   SEQ ID NO: 1224                         67. - Thiopurine methyltransferase (TPMT) A719G                     TTGAAAAGTTATATCTACTTACAGA   SEQ ID NO: 1225       TTGAAAAGTTATGTCTACTTACAGA   SEQ ID NO: 1226       TCTGTAAGTAGATATAACTTTTCAA   SEQ ID NO: 1227       TCTGTAAGTAGACATAACTTTTCAA   SEQ ID NO: 1228                         67. - Thiopurine methyltransferase (TPMT) G238C                     GTCCCCGGTCTGGAAACCTGCATAA   SEQ ID NO: 1229       GTCCCCGGTCTGCAAACCTGCATAA   SEQ ID NO: 1230       TTATGCAGGTTTCCAGACCGGGGAC   SEQ ID NO: 1231       TTATGCAGGTTTGCAGACCGGGGAC   SEQ ID NO: 1232                         69. - 5,10-methylenetetrahydrofolate reductase       (MTHFR) C677T                     TGTCTGCGGGAGCCGATTTCATCAT   SEQ ID NO: 1233       TGTCTGCGGGAGTCGATTTCATCAT   SEQ ID NO: 1234       ATGATGAAATCGGCTCCCGCAGACA   SEQ ID NO: 1235       ATGATGAAATCGACTCCCGCAGACA   SEQ ID NO: 1236                         70. - Butyrylcholinesterase (BCHE) Asp70Gly                     GTCAGAACATAGATCAAAGTTTTCC   SEQ ID NO: 1237       GTCAGAACATAGGTCAAAGTTTTCC   SEQ ID NO: 1238       GGAAAACTTTGATCTATGTTCTGAC   SEQ ID NO: 1239       GGAAAACTTTGACCTATGTTCTGAC   SEQ ID NO: 1240                         71. - Butyrylcolinesterase (BCHE) Ala539Thr                     AATATTGATGAAGCAGAATGGGAGT   SEQ ID NO: 1241       AATATTGATGAAACAGAATGGGAGT   SEQ ID NO: 1242       ACTCCCATTCTGCTTCATCAATATT   SEQ ID NO: 1243       ACTCCCATTCTGTTTCATCAATATT   SEQ ID NO: 1244                         72. - Cytochrome P450 3A4 (CYP3A4) A-392G                     GAGACAAGGGCAAGAGAGAGGCGAT   SEQ ID NO: 1245       GAGACAAGGGCAGGAGAGAGGCGAT   SEQ ID NO: 1246       ATCGCCTCTCTCTTGCCCTTGTCTC   SEQ ID NO: 1247       ATCGCCTCTCTCCTGCCCTTGTCTC   SEQ ID NO: 1248                         73. - Cytochrome P450 1A2 (CYP1A2) A-163C                     AGCTCTGTGGGCACAGGACGCATGG   SEQ ID NO: 1249       AGCTCTGTGGGCCCAGGACGCATGG   SEQ ID NO: 1250       CCATGCGTCCTGTGCCCACAGAGCT   SEQ ID NO: 1251       CCATGCGTCCTGGGCCCACAGAGCT   SEQ ID NO: 1252                         74. - Cytochrome P450 1A2 (CYP1A2) A-3860G                     CCTCCGCCTCTCGGATTCAAGCAAT   SEQ ID NO: 1253       CCTCCGCCTCTCAGATTCAAGCAAT   SEQ ID NO: 1254       ATTGCTTGAATCCGAGAGGCGGAGG   SEQ ID NO: 1255       ATTGCTTGAATCTGAGAGGCGGAGG   SEQ ID NO: 1256                         75. - Cytochrome P450 1A2 (CYP1A2) G3534A                     CAACCATGACCCGTGAGTACATACC   SEQ ID NO: 1257       CAACCATGACCCATGAGTACATACC   SEQ ID NO: 1258       GGTATGTACTCACGGGTCATGGTTG   SEQ ID NO: 1259       GGTATGTACTCATGGGTCATGGTTG   SEQ ID NO: 1260                         76. - Cytochrome P450 1A2 (CYP1A2) C558A                     GCCTGGGCACTTCGACCCTTACAAT   SEQ ID NO: 1261       GCCTGGGCACTTAGACCCTTACAAT   SEQ ID NO: 1262       ATTGTAAGGGTCGAAGTGCCCAGGC   SEQ ID NO: 1263       ATTGTAAGGGTCTAAGTGCCCAGGC   SEQ ID NO: 1264                         77. - Cytochrome P450 3A5 (CYP3A5) G14690A                     GGAGAGCACTAAGAAGTTCCTAAAA   SEQ ID NO: 1265       GGAGAGCACTAAAAAGTTCCTAAAA   SEQ ID NO: 1266       TTTTAGGAACTTCTTAGTGCTCTCC   SEQ ID NO: 1267       TTTTAGGAACTTTTTAGTGCTCTCC   SEQ ID NO: 1268                         78. - Cytochrome P450 3A5 (CYP3A5) C3699T                     AGATATGGGACCCGTACACATGGAC   SEQ ID NO: 1269       AGATATGGGACCTGTACACATGGAC   SEQ ID NO: 1270       GTCCATGTGTACGGGTCCCATATCT   SEQ ID NO: 1271       GTCCATGTGTACAGGTCCCATATCT   SEQ ID NO: 1272                         79. - Cytochrome P450 3A5 (CYP3A5) G19386A                     AAGGAGATTGATGCAGTTTTGCCCA   SEQ ID NO: 1273       AAGGAGATTGATACAGTTTTGCCCA   SEQ ID NO: 1274       TGGGCAAAACTGCATCAATCTCCTT   SEQ ID NO: 1275       TGGGCAAAACTGTATCAATCTCCTT   SEQ ID NO: 1276                         80. - Cytochrome P450 3A5 (CYP3A5) T29753C                     TTGGCATGAGGTTTGCTCTCATGAA   SEQ ID NO: 1277       TTGGCATGAGGTCTGCTCTCATCAA   SEQ ID NO: 1278       TTCATGAGAGCAAACCTCATGCCAA   SEQ ID NO: 1279       TTCATGAGAGCAGACCTCATGCCAA   SEQ ID NO: 1280                         81. - Cytochrome P450 3A5 (CYP3A5) G6986A                     TTTTGTCTTTCAGTATCTCTTCCCT   SEQ ID NO: 1281       TTTTGTCTTTCAATATCTCTTCCCT   SEQ ID NO: 1282       AGGGAAGAGATACTGAAAGACAAAA   SEQ ID NO: 1283       AGGGAAGAGATATTGAAAGACAAAA   SEQ ID NO: 1284                         82. - Serotonin transporter (SLC6A4) promoter 44bp       deletion                     ATCCCCCCTGCACCCCCCAGCATCC   SEQ ID NO: 1285       ATCCCCCCTGCACCCCCAGCATCCC   SEQ ID NO: 1286       GGATGCTGGGGGGTGCAGGGGGGAT   SEQ ID NO: 1287       GGGATGCTGGGGGTGCAGGGGGGAT   SEQ ID NO: 1288                         83. - Gluthatione S-transferase M3 (GSTM3) delAGA       (allele*B)                     AGGGAAAAGAAGAGGATACTTCTCT   SEQ ID NO: 1289       AGGGAAAAGAAGATACTTCTCTATC   SEQ ID NO: 1290       AGAGAAGTATCCTCTTCTTTTCCCT   SEQ ID NO: 1291       GATAGAGAAGTATCTTCTTTTCCCT   SEQ ID NO: 1292                         84. - Gluthatione S-transferase M1 (GSTM1) allele       [nulo?]                     CACACATTCTTGGCCTTCTGCAGAT   SEQ ID NO: 1293       CACACATTCTTGACCTTCTGCAGAT   SEQ ID NO: 1294       ATCTGCAGAAGGCCAAGAATGTGTG   SEQ ID NO: 1295       ATCTGCAGAAGGTCAAGAATGTGTG   SEQ ID NO: 1296                         85. - Gluthathione S-transferase n1 (GSTT1) null       allele                     CTGCCTAGTGGGTTCACCTGCCCAC   SEQ ID NO: 1297       CTGCCTAGTGGGGTCACCTGCCCAC   SEQ ID NO: 1298       GTGGGCAGGTGAACCCACTAGGCAG   SEQ ID NO: 1299       GTGGGCAGGTGACCCCACTAGGCAG   SEQ ID NO: 1300                         86. - Apolipoprotein E (APOE) Arg158Cys                     GACCTGCAGAAGCGCCTGGCAGTGT   SEQ ID NO: 1301       ACACTGCCAGGCGCTTCTGCAGGTC   SEQ ID NO: 1302       GACCTGCAGAAGTGCCTGGCAGTGT   SEQ ID NO: 1303       ACACTGCCAGGCACTTCTGCAGGTC   SEQ ID NO: 1304                         87. - Apolipoprotein E (APOE) Cys112Arg                     ATGGAGGACGTGTGCGGCCGCCTGG   SEQ ID NO: 1305       CCAGGCGGCCGCACACGTCCTCCAT   SEQ ID NO: 1306       ATGGAGGACGTGCGCGGCCGCCTGG   SEQ ID NO: 1307       CCAGGCGGCCGCGCACGTCCTCCAT   SEQ ID NO: 1308                         88. - Tumor necrosis factor (TNF) G-308A                     TTGAGGGGCATGGGGACGGGGTTCA   SEQ ID NO: 1309       TTGAGGGGCATGAGGACGGGGTTCA   SEQ ID NO: 1310       TGAACCCCGTCCCCATGCCCCTCAA   SEQ ID NO: 1311       TGAACCCCGTCCTCATGCCCCTCAA   SEQ ID NO: 1312                         89. - Interleukin 10 (IL10) G-1082A                     GCTTCTTTGGGAAGGGGAAGTAGGG   SEQ ID NO: 1313       GCTTCTTTGGGAGGGGGAAGTAGGG   SEQ ID NO: 1314       CCCTACTTCCCCTTCCCAAAGAAGC   SEQ ID NO: 1315       CCCTACTTCCCCCTCCCAAAGAAGC   SEQ ID NO: 1316            
5.2 Production of the DNA-chip for Genotyping Genetic Variations Associated with Adverse Reactions to Drugs
 
5.2.1 Printing of the Glass Slides
 
     The probes capable of detecting the genetic variations of interest are printed or deposited on the support (glass slides) using DMSO as solvent. The printing is carried out with a spotter or printer of oligonucleotides while controlling the temperature and relative humidity. 
       5 . 2 . 2  Processing of the Glass Slides 
     Probes are attached to the support (glass slides) by means of crosslinking with ultraviolet radiation and heating as previously described (Example 1.2) maintaining the relative humidity during the deposition process between 40-50% and the temperature around 20° C. 
     5.3 Validation of the Clinical Utility of the DNA-chip for the Simultaneous, Sensitive, Specific and Reproducible Detection of Human Genetic Variations Associated with Adverse Reactions to Pharmaceutical Drugs 
     5.3.1 Preparation of the Sample to be Hybridized 
     DNA is extracted from a blood sample of an individual by means of a filtration protocol. 
     All the exons and introns of interest are amplified by multiplex PCR using appropriate pairs of oligonucleotide primers. Any suitable pair of oligonucleotides can be used that allows specific amplification of genetic fragments where a genetic variation to be detected might exist. Advantageously, those pairs which permit the said amplification in the least possible number of PCR reactions are used. 
     The oligonucleotide primers used to PCR amplify the fragments of the genes to be detected are listed below with corresponding genetic variations associated with adverse reactions to pharmaceutical drugs. 
     
       
         
           
               
            
               
                 1. - Beta-1-adrenergic receptor (ADRB1) Arg3B9Gly 
               
               
                 (oligonucleotides to amplify the fragment where 
               
               
                 the polymorphism Arg389Gly might exist in the 
               
               
                 Beta-1-adrenergic receptor gene (ADRB1) 
               
               
                 SEQ ID NO 125: GCCTTCAACCCCATCATCTA 
               
               
                 SEQ ID NO 126: CAGGCTCGAGTCGCTGTC 
               
               
                   
               
               
                 2. - Beta-2-adrenergic receptor (ADRB2) Arg16Gly 
               
               
                 and Gln27Glu (oligonucleotides to amplify the 
               
               
                 fragment where the polymorphism Arg389Gly might 
               
               
                 exist in the Beta-2-adrenergic receptor gene 
               
               
                 (ADRB2) 
               
               
                 SEQ ID NO 227: GCTCACCTGCCAGACTGC 
               
               
                 SEQ ID NO 128: GCCAGGACGATGAGAGACAT 
               
               
                   
               
               
                 3. - Dopamine D3 receptor (DRD3) Ser9Gly 
               
               
                 SEQ ID NO 129: CGCAGTAGGAGAGGGCATAG 
               
               
                 SEQ ID NO 130: CAAGCCCCAAAGAGTCTGAT 
               
               
                   
               
               
                 4. - Serotonin 2A receptor (HTR2A) His452Tyr 
               
               
                 SEQ ID NO 131: AGCAAGATGCCAAGACAACA 
               
               
                 SEQ ID NO 132: CAGTGTGCCTTCCACAGTTG 
               
               
                   
               
               
                 5. - Serotonin 2A receptor (HTR2A) T102C 
               
               
                 SEQ ID NO 133: AGGAGAGACACGACGGTGAG 
               
               
                 SEQ ID NO 134: CAAGTTCTGGCTTAGACATGGA 
               
               
                   
               
               
                 6. - Catechol-Q-methyltransferase (COMT) Val108Met 
               
               
                 SEQ ID NO 135: GGGCCTACTGTGGCTACTCA 
               
               
                 SEQ ID NO 136: CCCTTTTTCCAGGTCTGACA 
               
               
                   
               
               
                 7. - Glutathione S transferase class 1 (GSTP1) 
               
               
                 Ile105Val 
               
               
                 SEQ ID NO 137: TGGTGGACATGGTGAATGAC 
               
               
                 SEQ ID NO 138: GTGCAGGTTGTGTCTTGTCC 
               
               
                   
               
               
                 8. - Adducin-1 (ADD1) Gly460Trp 
               
               
                 SEQ ID NO 139: TTGCTAGTGACGGTGATTCG 
               
               
                 SEQ ID NO 140: GAGACTGCAGCAAGGGTTTC 
               
               
                   
               
               
                 9. - DNA repair enzyme XRCC1 Arg399Gln 
               
               
                 SEQ ID NO 141: TGTCTCCCCTGTCTCATTCC 
               
               
                 SEQ ID NO 142: ATTGCCCAGCACAGGATAAG 
               
               
                   
               
               
                 10. - Cytochrome P450 1A1 (CYP1A1) Ile462Val 
               
               
                 SEQ ID NO 143: CTCACCCCTGATGGTGCTAT 
               
               
                 SEQ ID NO 144: TTTGGAAGTGCTCACAGCAG 
               
               
                   
               
               
                 11. - Angiotensin II receptor, type 1 (AGTR1) 
               
               
                 A1166C 
               
               
                 SEQ ID NO 145: GAGAACATTCCTCTGCAGCAC 
               
               
                 SEQ ID NO 146: TGTGGCTTTGCTTTGTCTTG 
               
               
                   
               
               
                 12. - Bradykinin receptor (BDKRB2) C-58T 
               
               
                 SEQ ID NO 147: GAGCAATGTCTGGCTTCTCC 
               
               
                 SEQ ID NO 148: CCAGGGAGAGAACATTTGGA 
               
               
                   
               
               
                 13. - Angiotensinogen (AGT) Met235Thr 
               
               
                 SEQ ID NO 149: AGGCTGTGACAGGATGGAAG 
               
               
                 SEQ ID NO 150: GGTGGTCACCAGGTATGTCC 
               
               
                   
               
               
                 14. - Cytochrome P450 2C9 (CYP2C9) C430T 
               
               
                 SEQ ID NO 151: CCTGGGATCTCCCTCCTAGT 
               
               
                 SEQ ID NO 152: CCACCCTTGGTTTTTCTCAA 
               
               
                   
               
               
                 15. - Cytochrome P450 2C9 (CYP2C9) A1075C, T1076C 
               
               
                 and C1080G 
               
               
                 SEQ ID NO 153: CCACATGCCCTACACAGATG 
               
               
                 SEQ ID NO 154: TCGAAAACATGGAGTTGCAG 
               
               
                   
               
               
                 16. - Cytochrome P450 2C9 (CYP2C9) 818delA 
               
               
                 SEQ ID NO 155: CCGGGAACTCACAACAAATTA 
               
               
                 SEQ ID NO 156: CACAAATTCACAAGCAGTCACA 
               
               
                   
               
               
                 17. - Cytochrome P450 2D6 31G &gt; A, 100C &gt; T and 
               
               
                 138insT 
               
               
                 SEQ ID NO 157: CAGGTATGGGGCTAGAAGCA 
               
               
                 SEQ ID NO 158: ACCTGGTCGAAGCAGTATGG 
               
               
                   
               
               
                 18. - Cytochrome P450 2D6 883G &gt; C, 1023C &gt; T, 
               
               
                 1039C &gt; T 
               
               
                 SEQ ID NO 159: GATCCTGGCTTGACAAGAGG 
               
               
                 SEQ ID NO 160: TCCCACGGAAATCTGTCTCT 
               
               
                   
               
               
                 19. - Cytochrome P450 2D6 1659G &gt; A, 1661G &gt; C, 
               
               
                 1707T &gt; del, 1758G &gt; A and 1758G &gt; T 
               
               
                 SEQ ID NO 161: GTGGGGCTAATGCCTTCAT 
               
               
                 SEQ ID NO 162: CTTCCCAGTTCCCGCTTT 
               
               
                   
               
               
                 20. - Cytochrome P450 2D6 1846G &gt; A and 1863ins9 bp 
               
               
                 SEQ ID NO 163: GTGGGTGATGGGCAGAAG 
               
               
                 SEQ ID NO 164:  GAGGGTCGTCGTACTCGAAG   
               
               
                   
               
               
                 21. - Cytochrome P450 2D6 1973insG 
               
               
                 SEQ ID NO 165: AGCCGTGAGCAACGTGAT 
               
               
                 SEQ ID NO 166: CTGCAGAGACTCCTCGGTCT 
               
               
                   
               
               
                 22. - Cytochrome P450 2D6 2539delAACT, 2549A &gt; del, 
               
               
                 2613delAGA 
               
               
                 SEQ ID NO 167: CAAGGTCCTACGCTTCCAAA 
               
               
                 SEQ ID NO 168: GATGCACTGGTCCAACCTTT 
               
               
                   
               
               
                 23. - Cytochrome P450 2D6 2850C &gt; T and 2935A &gt; C 
               
               
                 SEQ ID NO 169: GGAACCCTGAGAGCAGCTT 
               
               
                   
               
               
                 SEQ ID NO 170: GGTGTCCCAGCAAAGTTCAT 
               
               
                   
               
               
                 24. - Cytochrome P450 2D6 3183G &gt; A, 3198C &gt; G and 
               
               
                 3277T &gt; C 
               
               
                 SEQ ID NO 171: GGAGGCAAGAAGGAGTGTCA 
               
               
                 SEQ ID NO 172: CGATGTCACGGGATGTCATA 
               
               
                   
               
               
                 25. - Cytochrome P450 2D6 4042G &gt; A and 
               
               
                 4125insGTGCCCACT 
               
               
                 SEQ ID NO 173: GGAGTCTTGCAGGGGTATCA 
               
               
                 SEQ ID NO 174: TCACCAGGAAAGCAAAGACA 
               
               
                   
               
               
                 26. - Cytochrome P450 2C8 (CYP2C8) C792G and A805T 
               
               
                 SEQ ID NO 175: GAACACCAAGCATCACTGGA 
               
               
                 SEQ ID NO 176: GATGTTTAGTGCAGGCCCATA 
               
               
                   
               
               
                 27. - Cytochrome P450 2C8 (CYP2C8) G416A 
               
               
                 SEQ ID NO 177: CTCACAACCTTGCGGAATTT 
               
               
                 SEQ ID NO 178: CTTCAAATCTCCCTCCACCA 
               
               
                   
               
               
                 28. - Cytochrome P450 2C8 (CYP2C8) A1196G 
               
               
                 SEQ ID NO 179: ACCTGCTGAGAAAGGCATGA 
               
               
                 SEQ ID NO 180: TTCCAGGGCACAACCATAAT 
               
               
                   
               
               
                 29. - N-acetyltransferase 2 (NAT2) 191G &gt; A and 
               
               
                 282C &gt; T 
               
               
                 SEQ ID NO 181: CCATGGAGTTGGGCTTAGAG 
               
               
                 SEQ ID NO 182: CCATGCCAGTGCTGTATTTG 
               
               
                   
               
               
                 30. - N-acetyltransferase 2 (NAT2) T341C 
               
               
                 SEQ ID NO 183: TGGTGTCTCCAGGTCAATCA 
               
               
                 SEQ ID NO 184: GGCTGATCCTTCCCAGAAAT 
               
               
                   
               
               
                 31. - N-acetyltransferase 2 (NAT2) C481T 
               
               
                 SEQ ID NO 185: TGACGGCAGGAATTACATTG 
               
               
                 SEQ ID NO 186: TGTTTCTTCTTTGGCAGGAGA 
               
               
                   
               
               
                 32. - N-acetyltransferase 2 (NAT2) A803G 
               
               
                 SEQ ID NO 187: ACTGTTTGGTGGGCTTCATC 
               
               
                 SEQ ID NO 188: AGGTTTGGGCACGAGATTT 
               
               
                   
               
               
                 33. - N-acetyltransferase 2 (NAT2) G590A 
               
               
                 SEQ ID NO 189: CCTGCCAAAGAAGAAACACC 
               
               
                 SEQ ID NO 190: GATGAAGCCCACCAAACAGT 
               
               
                   
               
               
                 34. - N-acetyltransferase 2 (NAT2) G857A 
               
               
                 SEQ ID NO 191: ACTGTTTGGTGGGCTTCATC 
               
               
                 SEQ ID NO 192: GGGTGATACATACACAAGGGTTT 
               
               
                   
               
               
                 35. - Cytochrome P450 2C19 (CYP2C19) G636A 
               
               
                 SEQ ID NO 193: ACCCTGTGATCCCACTTTCA 
               
               
                 SEQ ID NO 194: TGTACTTCAGGGCTTGGTCA 
               
               
                   
               
               
                 36. - Cytochrome P450 2C19 (CYP2C19) C680T and 
               
               
                 G681A 
               
               
                 SEQ ID NO 195: CAACCAGAGCTTGGCATATTG 
               
               
                 SEQ ID NO 196: TAAAGTCCCGAGGGTTGTTG 
               
               
                   
               
               
                 37. - Cytochrome P450 2C19 (CYP2C19) A1G 
               
               
                 SEQ ID NO 197: TAGTGGGCCTAGGTGATTGG 
               
               
                 SEQ ID NO 198: TTTCCAATCACTGGGAGAGG 
               
               
                   
               
               
                 38. - Cytochrome P450 2C19 (CYP2C19) IVS5 + 2T &gt; A 
               
               
                 SEQ ID NO 199: CAACCCTCGGGACTTTATTG 
               
               
                 SEQ ID NO 200: CAAGCATTACTCCTTGACCTGTT 
               
               
                   
               
               
                 39. - Cytochrome P450 2C19 (CYP2C19) T358C 
               
               
                 SEQ ID NO 201: CCCAGTGTCAGCTTCCTCTT 
               
               
                 SEQ ID NO 202: GTCCTCAATGCTCCTCTTCC 
               
               
                   
               
               
                 40. - Cytochrome P450 2C19 (CYP2C19) G431A 
               
               
                 SEQ ID NO 203: GAATCGTTTTCAGCAATGGAA 
               
               
                 SEQ ID NO 204: GTATGTTCACCCACCCTTGG 
               
               
                   
               
               
                 41. - Cytochrome P450 2C19 (CYP2C19) C1297T 
               
               
                 SEQ ID NO 205: TCACCGAACAGTTCTTGCAT 
               
               
                 SEQ ID NO 206: GTCAAGGTCCTTTGGGTCAA 
               
               
                   
               
               
                 42. - Glutamate receptor, ionotropic, N-methyl 
               
               
                 D-aspartate (NMDA) 2B (GRIN2B) C2664T 
               
               
                 SEQ ID NO 207: GCAGGATGTTGGAGTGTGTG 
               
               
                 SEQ ID NO 208: GCAATTATTGGTGGGAGAGTG 
               
               
                   
               
               
                 43. - Glycoprotein P (ABCB1) C3435T 
               
               
                 SEQ ID NO 209: TGCTCCCAGGCTGTTTATTT 
               
               
                 SEQ ID NO 210: TGTTTTCAGCTGCTTGATGG 
               
               
                   
               
               
                 44. - Thiopurine methyltransferase (TPMT) A719G 
               
               
                 SEQ ID NO 211: GGTTGATGCTTTTGAAGAACG 
               
               
                 SEQ ID NO 212: CATCCATTACATTTTCAGGCTTT 
               
               
                   
               
               
                 45. - Thiopurine methyltransferase (TPMT) G238C 
               
               
                 SEQ ID NO 213: AAAACTTTTGTGGGGATATGGA 
               
               
                 SEQ ID NO 214: AACCCTCTATTTAGTCATTTGAAAACA 
               
               
                   
               
               
                 46. - 5,10-methylenetetra hydrofolate reductase 
               
               
                 (MTHFR) C677T 
               
               
                 SEQ ID NO 215: TCCCTGTGGTCTCTTCATCC 
               
               
                 SEQ ID NO 216: CAAAGCGGAAGAATGTGTCA 
               
               
                   
               
               
                 47. - Butyrylcholinesterase (BCHE) Asp70Gly 
               
               
                 SEQ ID NO 217: AAAGCCACAGTCTCTGACCAA 
               
               
                 SEQ ID NO 218: GGTGCTGGAATCCATACATTT 
               
               
                   
               
               
                 48. - Butyrylcholinesterase (BCHE) Ala539Thr 
               
               
                 SEQ ID NO 219: GAGAAAATGGCTTTTGTATTCG 
               
               
                 SEQ ID NO 220: TGATTTTTCCAGTCCATCATGT 
               
               
                   
               
               
                 49. - Cytochrome P450 3A4 (CYP3A4) A-392G 
               
               
                 SEQ ID NO 221: CAGGGGAGGAAATGGTTACA 
               
               
                 SEQ ID NO 222: TGGAGCCATTGGCATAAAAT 
               
               
                   
               
               
                 50. - Cytochrome P450 1A2 (CYP1A2) A-163C 
               
               
                 SEQ ID NO 223: AGAGAGCCAGCGTTCATGTT 
               
               
                 SEQ ID NO 224: CTGATGCGTGTTCTGTGCTT 
               
               
                   
               
               
                 51. - Cytochrome P450 1A2 (CYP1A2) A-3860G 
               
               
                 SEQ ID NO 225: GAGTGCAGTGGTGCGATCT 
               
               
                 SEQ ID NO 226: TGAGGCCAGGAGTTCAAGAC 
               
               
                   
               
               
                 52. - Cytochrome P450 1A2 (CYP1A2) G3534A 
               
               
                 SEQ ID NO 227: GGTGGAGGTAGGAGCAACAC 
               
               
                 SEQ ID NO 228: CTGCTGAACCTGCACACATT 
               
               
                   
               
               
                 53. - Cytochrome P450 1A2 (CYP1A2) C558A 
               
               
                 SEQ ID NO 229: CCTCATCCTCCTGCTACCTG 
               
               
                 SEQ ID NO 230: GAGGCAGTCTCCACGAACTC 
               
               
                   
               
               
                 54. - Cytochrome P450 3A5 (CYP3A5) G14690A 
               
               
                 SEQ ID NO 231: GCCTACAGCATGGATGTGA 
               
               
                 SEQ ID NO 232: TGGAATTGTACCTTTTAAGTGGA 
               
               
                   
               
               
                 55. - Cytochrome P450 3A5 (CYP3A5) C3699T 
               
               
                 SEQ ID NO 233: TCACAATCCCTGTGACCTGA 
               
               
                 SEQ ID NO 234: GGGGCATTTTTACTGATGGA 
               
               
                   
               
               
                 56. - Cytochrome P450 3A5 (CYP3A5) G19386A 
               
               
                 SEQ ID NO 235: TGAAACCACCAGCAGTGTTC 
               
               
                 SEQ ID NO 236: AAAATTCTCCTGGGGAGTGG 
               
               
                   
               
               
                 57. - Cytochrome P450 3A5 (CYP3A5) T29753C 
               
               
                 SEQ ID NO 237: ACCCCTAACATGTAACTCTGTGG 
               
               
                 SEQ ID NO 238: TTTGAAGGAGAAGTTCTGAAGGA 
               
               
                   
               
               
                 58. - Cytochrozne P450 3A5 (CYP3A5) G6986A 
               
               
                 SEQ ID NO 239: CACCCAGCTTAACGAATGCT 
               
               
                 SEQ ID NO 240: CCAGGAAGCCAGACTTTGAT 
               
               
                   
               
               
                 59. - Serotonin transporter (SLC6A4) promoter 44 bp 
               
               
                 deletion 
               
               
                 SEQ ID NO 241: ACCCCTAATGTCCCTACTGC 
               
               
                 SEQ ID NO 242: GGAGATCCTGGGAGAGGTG 
               
               
                   
               
               
                 60. - Glutathione S-transferase M3 (GSTM3) delAGA 
               
               
                 (allele*B) 
               
               
                 SEQ ID NO 243: TTCTGGGGAAATTCTCATGG 
               
               
                 SEQ ID NO 244: TCAGGTTTGGGAACTCATCC 
               
               
                   
               
               
                 61. - Glutathione S-transferase M1 (GSTM1) null  
               
               
                 allele 
               
               
                 SEQ ID NO 245: ATGGTTTGCAGGAAACAAGG 
               
               
                 SEQ ID NO 246: AAAGCGGGAGATGAAGTCCT 
               
               
                   
               
               
                 62. - Glutathione S-transferase n1 (GSTT1) null 
               
               
                 allele 
               
               
                 SEQ ID NO 247: GGCAGCATAAGCAGGACTTC 
               
               
                 SEQ ID NO 248: GTTGCTCGAGGACAAGTTCC 
               
               
                   
               
               
                 63. - Apolipoprotein E (APOE) Arg158Cys and  
               
               
                 Cys112Arg 
               
               
                 SEQ ID NO 249: GCACGGCTGTCCAAGGA 
               
               
                 SEQ ID NO 250: GCGGGCCCCGGCCTGGT 
               
               
                   
               
               
                 64. - Tumor necrosis factor (TNF) G-308A 
               
               
                 SEQ ID NO 251: ACCTGGTCCCCAAAAGAAAT 
               
               
                 SEQ ID NO 252: AAAGTTGGGGACACACAAGC 
               
               
                   
               
               
                 65. - Interleukin 10 (IL10) G-1082A 
               
               
                 SEQ ID NO 253: CACACACACACACAAATCCAAG 
               
               
                 SEQ ID NO 254:  GATGGGGTGGAAGAAGTTGA   
               
            
           
         
       
     
     The multiplex PCR is carried out simultaneously under the same conditions of time and temperature that permit specific amplification of the gene fragments in which the genetic variations to be detected are located. Following the multiplex PCR agarose gel analysis of the reactions is performed to determine if the amplification reaction has been successful. 
     Next, the sample to be hybridized (products of amplification) is subjected to fragmentation with a DNase and the resulting fragmentation products subjected to indirect labelling. A terminal transferase adds a nucleotide, joined to one member of a pair of specifically interacting molecules, (e.g. biotin for subsequent binding to a chemically labelled streptavidin molecule) to the end of these small DNA fragments. 
     Before applying the sample to the DNA-chip, it is denatured by heating to 95° C. for 5 minutes and then, ChipMap Kit Hybridization Buffer (Ventana Medical System) is added. 
     Next, the stages of hybridization are performed, scanning the slide, quantification of the image and interpretation of the results, following the procedure described in the sections 1.3.2, 1.3.3, 1.3.4 and 1.3.5 of Example 1. 
     Example 6 
     Application of the IBDchip for Prognosis of Disease Progression and Response to Therapy in Individuals Suffering from Inflammatory Bowel Disease 
     The value of the IBDchip in predicting disease progression and response to corticosteroid treatment was assessed based on the results of a clinical validation using blood samples obtained from 579 individuals with inflammatory bowel disease (IBD), of which 335 suffered from Crohns disease and 244 from ulcerative colitis. All samples were from individuals with at least a five year history of IBD. 
     Prognosis of disease progression is based on the positive likelihood ratio (LR+, measured as sensitivity/[1-specificity]), which defines the probability of developing a given disease phenotype or response to therapy. An LR+ value of ≧10 indicates a high probability of developing a defined phenotype; an LR+ value≧5 but &lt;10 indicates a moderate probability of developing a defined phenotype; a value≧2 but &lt;5 indicates a low probability of developing a defined phenotype; a value ≧1 but &lt;2 indicates a minimal chance of developing a given phenotype. 
       FIGS. 3-10  demonstrate the respective probabilities associated with the development of determined phenotypes (disease prognosis), based on genotypic data obtained with a DNA-chip, for each of the eight phenotypes analysed.  FIGS. 3-7  show probabilities for development of phenotypes associated with Crohns disease and  FIGS. 8-10  show probabilities associated with the development of phenotypes associated with ulcerative colitis.  FIGS. 11-13  indicate the probabilities associated with the risk of developing resistance to corticosteroid treatment in individuals suffering from IBD.