bluuebunny/crossref_metadata_2025_split huggingface dataset:
HLA CLASS I NON‐CODING NUCLEOTIDE SEQUENCES, 1992
Authors: Summers C.W. , Hampson V.J. , Taylor G.M. 
Published: April 2007

SUMMARYWe present a compilation of the nucleotide sequences of the non‐coding regions of the human HLA class I genes which complements previously published information on exon sequences. The listing includes the 5’and 3’untranslated (UT) regions, and introns 1–7. The HLA class I loci and their alleles from which non‐coding sequences were derived are listed in Table 1, together with source references. Where possible, locus and allele designations follow the Nomenclature for factors of the HLA system 1991(Bodmer et al.,1992).In aligning sequences, nucleotides which are conserved between all class I genes are specified only by the consensus sequence, and are indicated by a hyphen (‐). To maintain the alignment between different alleles, an asterisk (*) is inserted where there is a gap in the sequence. An unavailable sequence is indicated by a period (.). Regions of sequence too diverse to be accurately compared are represented by an exclamation mark (!). Sequence motifs previously classified as having an important role in HLA class I regulation or processing, such as enhancer sequences, are identified at the bottom of the sequence comparison.It is not our intention in this paper to present an analysis of the many features revealed by this compilation. However, we hope that the information will provide important reference material for studies of HLA class I mRNA processing (Cianetti et al., 1989), promoter regulation (David‐Watine et al., 1990) and in the design of allele, locus or region specific PCR primers (Summers et al., 1991).We hope to update this compilation in due course, and we would welcome sequence information not included in this publication, as well as comments and corrections that help to maintain the accuracy of the information.
SEROLOGICAL AND BIOCHEMICAL DETECTION OF B‐CELL ANTIGENS IN GOATS
Authors: Ruff G. , Joosten I. , Howald M. , Davis W. C. , Lazary S. 
Published: April 2007

SUMMARYThe production of B‐cell specific alloantisera by lymphocyte transfusion between class I matched, MLR positive goats is described. Furthermore, the usefulness of preceding IEF typing is demonstrated in the selection of immunization pairs. After suitable absorptions and cluster analysis the detected B‐cell specific antigens were designated BeDl‐BeD6. The specificity BeD3 could also be detected by two class II‐specific murine anti‐H2 monoclonal antibodies. IEF class II typing of 34 animals gave concordant results between the two techniques. One additional allelic variant could be detected by IEF typing. The detected products segregated in close linkage to the earlier described caprine class I antigens. One recombinant has been found in 78 offspring. The reactivity of cells in mixed lymphocyte cultures (MLC) was correlated with the compatibility of the test cells for their B‐cell specific antigens. Three of the B‐cell specific sera were characterized by immunoprecipitation. The precipitated antigens corresponded in molecular weight to MHC class II products as described in other species indicating that the here described caprine products are of class II nature.
POLYMORPHISM OF THE 5’ FLANKING REGION OF THE HLA‐DQA1 GENE IN COELIAC DISEASE
Authors: de la Paz Bettinotti M. , Kolek A. , Brünnler G. , Haas P. , Paul C. , Hochberger M. , Bartova A. , Kimura A. , Sasazuki T. , Albert E. D. 
Published: April 2007

SUMMARYCoeliac disease (CD) is associated with particular HLA genotypes. The susceptibility gene (or genes) has been mapped to the class II region, most probably to the DQ loci. Polymorphism of the upstream promoter region of the DQA1 gene (QAP) has been recently reported. At least ten variants or QAP alleles have been found, some of which are present in the as‐acting regulatory sequences. Allelic differences in DQ molecule expression may play a role in susceptibility to CD. We investigated the QAP polymorphism in 102 CD patients and 142 unrelated healthy controls of Czech origin using polymerase chain reaction amplification (PCR) of genomic DNA and oligonucleotide probes. We found a significant frequency increase of the alleles QAP 4.1 (RR = 10.3, p.c. = 10‐6) and QAP 2.1 (RR = 2.4, p.c. = 0.017) in patients over controls. An increased susceptibility is provided by the presence of both alleles, as is shown by the higher proportion of QAP 4.1, 2.1 heterozygotes among patients than expected from the Hardy‐Weinberg equilibrium and by the comparison of the odds ratios for these alleles. There is a strong linkage disequilibrium between the QAP alleles and the DQA1, DQB1, and DRB1 loci. Two haplotypes carrying the QAP alleles whose frequency is increased are predominant in this group of CD patients: DQB1* 0201, DQA1* 0501, QAP 4.1, DRB1* 0301 and DQB1* 0201, DQA1* 0201, QAP 2.1, DRB1* 0701. Thus, the QAP variants are increased as part of these haplotypes and we cannot discriminate if they are responsible for the primary association.
HLA CLASS II TYPING IN A MICROTITRE PLATE FORMATE USING DIGOXIGENIN‐LABELLED AMPLIFIED DNA AND BIOTIN‐LABELLED OLIGONUCLEOTIDE PROBES
Authors: Nevinny‐Stickel C. , Albert E. D. 
Published: April 2007

SUMMARYWe describe a new, non‐radioactive microtitre plate assay for the analysis of genetic variations at the DNA level. The new method combines hybridization of oligonucleotides with PCR amplified DNA in liquid phase with detection in solid phase using an elisa‐reader. Genomic DNA is labelled with digoxigenin during PCR using a nucleotide mix containing DIG‐11‐2′‐deoxy‐uridine‐5′‐triphosphate (DIG‐11‐dUTP) DIG labelled, amplified genomic DNA is hybridized in solution with an oligon de which is labelled with one biotin at its 3′‐end, using biotin‐16,2′,3′‐dideoxy ine‐5′‐triphosphate (BIO‐16‐ddUTP) and DNA deoxynucleotidylexo‐transferase (TdT). The hybridized complex is immobilized in a streptavidin (SA) coated microtitre plate via the biotin and detection of digoxigenin is performed using anti‐digoxigenin horseradish peroxidase, fab fragments (anti‐DIG‐POD), and the colorimetric substrate 2,2′‐Azino‐di‐(3‐ethylbenzthiazolinsulfonat[6]) (ABTS®). The resulting absorbtion of the assay is analysed in a microtitre plate reader. This method results in highly specific and sensitive hybridization signals and with the 15 oligonucleotides chosen, allows the typing of DR1‐DR10.
HLA DR AND DQ RFLP ANALYSIS IN CROHN'S DISEASE
Authors: Wassmuth R. , Eastman S. , Kockum I. , Holmberg E. , Starck M. , Lindhagen T. , Kalden J. R. , Lernmark Å. , Sundkvist G. , Lindgren S. 
Published: April 2007

SUMMARYA study of 109 Swedish patients and 85 healthy Swedish controls with Crohn's disease (CD) by HLA class II RFLP genotyping was carried out. There was no significant association for any single DR or DQ specificity or phenotypic combination of DR and/or DO specificities among our study group of Caucasian extraction.
HLA DOA‐DQB HAPLOTYPES IN A SWEDISH POPULATION
Authors: & A. Langö , Lindblom B. 
Published: April 2007

SUMMARYSamples from 94 Swedish blood donors were analysed for HLA‐DQA1 and ‐DQB1 alleles by the PCR‐SSO technique used in the XIth Histocompatibility Workshop. Seven DQA1 and 12 DQB1 alleles were identified and a total of 17 haplotype combinations were found deduced from the most probable allele combinations. Frequencies calculated from these haplotypes were compared to those calculated from the phenotypes according to Mattiuz et al. (1970). There was no significant difference in the frequencies of the 17 haplotype combinations deduced. Eight haplotype combinations had exactly the same frequencies and four had approximately the same frequencies independent of the calculation method used. The DQA1*0301‐DQB 1*0302, DQA1*0501‐DQB1*0201, DQA1* 0101‐DQB1* 0501, and DQA1*0102‐DQB1*0602 were the most frequent haplotypes with frequencies over 0.130.
DISCRIMINATION OF HUMAN HLA‐DRB1 ALLELES BY PCR‐SSCP (SINGLE‐STRAND CONFORMATION POLYMORPHISM) METHOD
Authors: Bannai M. , Tokunaga K. , Lin L. , Kuwata S. , Mazda T. , Amaki I. , Fujisawa K. , Juji T. 
Published: April 2007

SUMMARYA single‐strand conformation polymorphism (PCR‐SSCP) method has been adopted for discrimination of human HLA‐DRB1 alleles. This method enabled the detection of DN A polymorphisms including point mutations at a variety of positions in the DN A fragments of the HLA‐DRB1 gene. A total of 27 HLA‐DRB1 alleles from 172 healthy donors were analysed using a combination of PCR‐SSCP with group‐specific amplifications. Application of a small amount of amplified and denatured DNA to non‐denaturing electrophoresis followed by silver staining resulted in distinct banding patterns. Samples possessing a single allele in each amplification group showed two‐band patterns which correspond to the sense and antisense strands, while heterozygotes in the same group or a mixture of two single‐type samples showed four‐band patterns. All of the analysed alleles were discriminated in each DRB1 group. The method described here may be somewhat complicated for routine typing of HLA‐DRB1 alleles. However, it is useful in the screening of ‘new’ alleles as well as the donor‐recipient molecular matching of HLA class II genes for various purposes, e.g. selection of bone marrow transplant donors.
RECOMBINATION FRACTIONS IN THE HLA SYSTEM BASED ON THE DATA SET ‘PROVINCES FRANÇAISES’: INDICATIONS OF HAPLOTYPE‐SPECIFIC RECOMBINATION RATES
Authors: Thomsen M. , Neugebauer M. , Arnaud J. , Borot N. , Sevin A. , Baur M. , Cambon‐Thomsen A. 
Published: April 2007

SUMMARYIn the large genetic survey ‘Provinces Françaises’ the recombination fractions in the HLA system have been estimated by a family analysis programme (FAP). A total of 1332 families were analysed and in general the findings were in agreement with recombination fractions reported previously. The maternal recombination rates were on average 1.8 times higher than the corresponding ones for males. The comparison of the recombination fractions with the corresponding physical distances suggests the existence of hot spots of recombination. The analysis did not show deviations from expected values for HLA‐A and B alleles on HLA‐A/B recombinant haplotypes. However, analysis of HLA‐B/DR recombinant haplotypes showed a skewed distribution of B and DR alleles. The significance of the findings is difficult to evaluate as all results are estimated numbers and frequencies but a manual analysis of the recombinant families confirmed the observations. HLA‐B/DR recombinant haplotypes carried often HLA‐DR3 and DR11 whereas DR2 and DR7 were more rarely present on recombinant haplotypes. DR4 had an increased incidence on BF/DR recombinant haplotypes but not on A/B or B/BF recombinant haplotypes. Some of the haplotypes with the strongest linkage disequilibria as A1, B8, DR3 and A3, B7, DR2 seem to be less frequently involved in recombinations than other haplotypes. Variations of recombination rates depending on certain alleles or haplotypes might partially explain the conservation of some haplotypes or part of haplotypes in Caucasoids.
HLA‐DRB AND ‐DBQ TYPING BY PCR AMPLIFICATION USING SEQUENCE‐SPECIFIC PRIMERS (PCR‐SSP): ASSESSMENT AFTER 1 YEAR OF ROUTINE USE BY THREE LABORATORIES
Authors: Mercier B. , Daccak R. Al , Samaan A. , David F. , Carta A. , Cracco P. , Raguenes O. , Dufosse F. , Ferec C. , Charron D. , Loiseau P. 
Published: April 2007

SUMMARYUsing sequence‐specific amplifications, a practical and fast technique for DRB and DQB typing has been developed. The primers are chosen in order to amplify groups of alleles corresponding to the same serological specificity. In a second step, precise allelic determination is obtained by studying the restriction fragment length polymorphism of the PCR products.The experience of three laboratories using this technique in the context of organ or bone marrow transplantation is reported.
TAP GENE ASSOCIATIONS IN UK CAUCASOIDS
Authors: Donn R. P. , Davies E. J. , Thomson W. , Hillarby M. C. , Ollier W. E. R. 
Published: April 2007

SUMMARYThe authors determined the allele frequencies of the TAP1 and TAP2 transporter genes in a healthy UK Caucasoid population by ARMS‐PCR. TAP1A was the most frequent TAP1 allele by far, being present in 76% of subjects. TAP1 alleles could not be assigned in 24% of subjects, since the combinations TAP 1 A/1B and TAP1C/1D cannot be separated. TAP2A was the most frequent TAP2 alleles (75% of subjects) followed by TAP2B (43%), TAP2C (11%), TAP2D (8%) and TAP2E (6%). The authors also identified an individual with a previously undescribed TAP2 allele, TAP2H (isoleucine at amino acid [aa] 379, alanine at aa 565, alanine at aa 665).It was not possible to assign unequivocally TAP2 alleles in 15 individuals (9%) as TAP2A/D and TAP2C/E cannot be distinguished from each other.To address this problem a separate study of families of rheumatoid arthritis (RA) patients selected for this ambiguity were studied. In all five informative families, TAP2A/2D was confirmed as the combination present.In the population studied no evidence was found for linkage disequilibrium between TAP1 and TAP2 or between the TAP genes and HLA‐DP. There was no evidence for extensive linkage disequilibrium between the TAP genes and HLA‐DQ/DR, although TAP2B was associated with DR1 (Δ= 0.056, correctedP< 0.01) and TAP2D with DR4 (Δ= 0.018). In the RA families studied, TAP2D was found on DRB1 *0401 ‐bearing haplotypes.
A NOVEL HUMAN COMPLEMENT COMPONENT C7 PHENOTYPE DETECTED IN SOUTH AFRICA AND PROPOSED DESIGNATION OF THE ALLELE AS C7*10
Authors: Orren A. , Würzner R. , Lachmann P. J. , Hobart M. J. 
Published: April 2007

SUMMARYA novel allotype of the seventh component of human complement was detected by isoelectric focusing. The band pattern showed a complete band‐interval shift towards the cathode compared with the C7 1 allotype and it is proposed that the designation is C7 10. The allele C7* 10 segregated in two South African Cape Coloured families and had a gene frequency of 0.006. It was also found to segregate together with a C6*rare allele.
HLA CLASS II AND SUSCEPTIBILITY AND RESISTANCE TO INSULIN‐DEPENDENT DIABETES MELLITUS IN A POPULATION FROM THE NORTHWEST OF SPAIN
Authors: Baranda F. Setién , Coto E. , Déaz J. Menéndez , Martinez‐Naves E. , Marténez V. Alvarez , López‐Larrea C. 
Published: April 2007

SUMMARYThe role of HLA class II alleles in genetic predisposition to insulin‐dependent diabetes mellitus(IDDM) was examined using Polymerase Chain Reaction/oligonucleotide probe typing (PCR/SSOs) of eight HLA class II loci in 58 IDDM patients and 50 healthy controls from the Northwest of Spain (Asturias). We compared the distribution of HLA class II alleles, haplotypes and genotypes between IDDM patients and controls, and tested three recently proposed HLA‐IDDM susceptibility theories. By using the aetiologic fraction (δ) as an almost absolute measure of the strongest linkage of disequilibrium of a HLA marker to the putative Type I susceptibility locus, it has been found that the strength of association of the HLA markers may be quantified as follows: DQA1 *03‐DQB1 *0302 or DQA1 *0501‐DQB1 *0201 > DR3 or DR4; presence of more than one dimer DQαβ of the six proposed by Rønningen > non‐Asp57 DQβ and Arg52 DQα > Arg52 DQα > non‐Asp57 DQβ/non‐Asp57 DQβ > DRB1*0301; DQA1*0501‐DQB1*0201 > DQA1*03‐DQB1*0302; DQB1*0302. The presence of at least one Asp57 DQβ allele was the best protection HLA marker to IDDM in our population. Therefore, the above data confirm that IDDM susceptibility to HLA locus is linked more to DQ than DR.
MOLECULAR ANALYSIS OF CYP21 GENE MUTATIONS CARRIED ON HLA‐B14 POSITIVE HAPLOTYPES
Authors: Dondi E. , Cuccia M. , Keller E. , Martinetti M. , Larizza D. , Albert E. D. 
Published: April 2007

SUMMARYHLA‐B14 positive haplotypes have increased frequencies in a group of patients with puberty disorders, IgA deficiency and cancer of the ovary. Clinical investigations demonstrated that all these patients have high values of 170H progesteron after the ACTH test which suggests an alterated function of 21 hydroxylase enzyme. In order to investigate whether these B14 positive haplotypes carry the same CYP21 mutation in the various diseases and controls, we have amplified by polymerase chain reaction (PCR) the sections of CYP21B gene which include amino acid positions 172 and 281 where typical mutations are known to occur in 21 hydroxylase deficiency. The presence or absence of the defined mutations was tested by oligonucleotide hybridization using oligonucleotides, labelled with DIG‐ddUTP, designed to hybridize with the mutated or with the normal sequence. It was found that regardless of whether the subject tested was a patient or a healthy control the mutation at position 281 was found in all cases carrying HLA‐B14, DR1 haplotype. Interestingly, this mutation does not seem to be in association with HLA‐B14, DR7 haplotype.These findings suggest that CYP21 gene plays a role in all these differing diseases although it must be stressed that there may be alternative explanations for the observed data.
DPB1 LOCUS PCR‐RFLP TYPING OF THE FOURTH ASIA‐OCEANIA HISTOCOMPATIBILITY WORKSHOP CELL PANEL REVEALS A NOVEL DPB1 ALLELE
Authors: Naughton M. J. , Limm T. M. , Ashdown M. L. , Simons M. J. 
Published: April 2007

SUMMARYDPB1 locus typing of the 155 cell 4AOHW panel was performed using a PCR‐RFLP method. Ambiguity of allele assignment was resolved by amplification using sequence‐specific primers. Of the 150 cells for which typings were achieved, three exhibited unusual restriction enzyme fragment patterns, suggesting the possibility of novel DPB1 alleles. Sequence analysis revealed one allele present in the currently reported 46, one novel allele (4AOHW/107) not present among the 46, and one from a non‐human primate which is being investigated. Twenty‐six (26) of the 34 10IHW cells have been studied previously by cDNA RFLP, and strong haplotypic associations have been demonstrated between DPA1 and DPB1 locus alleles. It is proposed that exploitation of intron polymorphisms marking haplotypes will be an integral part of future DPB 1 typing as a ‘first‐pass’ stratification process to minimize the requirement for sequence‐based methods to definitively assign DPB 1 alleles.
DETECTION EFFICACY OF SOLUBLE HLA‐A, B ANTIGENS USING 1D‐IEF
Authors: Kubens B. S. , Päbler M. , Grosse‐Wilde H. 
Published: April 2007

SUMMARYSoluble HLA class I alloantigens (sHLA class I) can be typed according to their isoelectric points (IEP) after immunoprecipitation by w6/32 monoclonal antibody (mAb) coupled to immunomagnetic beads and focusing. In order to prove the large scale efficacy of this methodology, EDTA‐plasma samples from 344 probands HLA‐A, B typed by serology were analysed by one‐dimensional isoelectric focusing and HLA class I specific Westernblot (1D‐IEF). In addition, detergent solubilized HLA class I membrane molecules from approximately one half of the probands were studied too. Soluble HLA‐A24, B7, B18, B62 antigens were identified in nearly all experiments, whereas A28, B13, and B51 could be detected in about 50%. A third group of HLA antigens (A26, B8, B44) could be visualized rarely. The difficulties of detection might be due to the different affinity of mAb w6/32 to certain sHLA class I gene products or to variable amounts of sHLA class I in the plasma specimens. Some modifications of the antigen capture technique have already led to a slightly better degree of antigen recognition in 25 probands tested.Thus, HLA‐A, B typing using sHLA molecules and 1D‐IEF in the assay format presented does not yet seem to be a definitive alternative for HLA class I serology or biochemistry of membrane‐bound HLA class I molecules but it should be a promising technique if no cells are available or donor‐derived sHLA allotypes are to be monitored after HLA mismatched organ transplantation.
THE POLYMORPHIC HUMAN TLX‐B/CD46/MCP SYSTEM AND ITS IMPLICATIONS IN TRANSPLANTATION AND REPRODUCTION
Authors: Petränyi G. , Padányi A. , Szelényi J. , Sármay G. , Gyódi É. , Fülöp V. , Kassai M. , Illés P. , Réti M. , Szigetvári I. , Boros P. 
Published: April 2007

SUMMARYTLX antigens have been found on most peripheral blood cells, trophoblasts, seminal vesicle cells and sperms. These antigens seem to be associated with the membrane co‐factor protein (MCP) and the CD46 antigen. Alloantibodies to TLX antigens with FctRII‐blocking features were obtained by transfusion of leucocytes or platelets. Preliminary population studies revealed that alloantibodies to TLX/CD46/MCP recognize four overlapping specificities. The terminology TLX‐B was introduced with specificities TLX‐BI, B2, B3, B4 and frequencies obtained in the population were: 38%, 46%, 42% and 26%, respectively. Family studies showed an independent segregation of the TLX and HLA alleles.At the cellular protein on trophoblast, the alloantibody detected a glycoprotein of 66‐67 kDa molecular mass, which may correspond to the a chain of the TLX/CD46/MCP isotypes. A direct association of the alloantibody with FctRII could be excluded thus its FctR blocking feature is probably based on an indirect functional effect.After transfusion and in pregnancy the induction of TLX alloantibody production depended on the mismatching in the TLX/CD46/MCP phenotypes. Probable associations were revealed in the case of recurrent habitual abortion between the lack of FCTR blocking antibody production and the matched TLX specificities of the couples. After transfusion, TLX alloantibody production with FCTR and MLR blocking function was induced only when the recipient was lacking the TLX specificities expressed on the donor cells. Suppression of MLR was found only when TLX specificity in sera corresponded to the TLX specificity of the effector cell. The immunopathological importance of these findings in transplantation and reproductive medicine has yet to be clarified.
DNA MUTATION INDUCED IN THE SEQUENCE UPSTREAM OF THE SECRETED MYU C‐TERMINAL CODING SEQUENCE BY ULTRAVIOLET IRRADIATION IN THE CELL LINE OF BLOOM'S SYNDROME
Authors: Ozawa T. , Kondo N. , Motoyoshi F. , Kasahara K. , Orii T. 
Published: April 2007

SUMMARYSelective IgM deficiency is commonly found in Bloom's syndrome (BS). We reported that membrane‐bound μ (μ m) mRNA was well transcribed but secreted μ (μ s) mRNA was not, although there was no mutation or deletion in the sequence including the (is C‐terminal coding sequence in the patients with BS. Furthermore, we have shown previously, preferential damage to IgM production by ultraviolet (UV) irradiation of the cells of the patient. In the study described here, mutation in the sequence which is upstream of the 5’ end of the μ s C‐terminal coding sequence was induced by UV irradiation in the lymphoblastoid cell line (LCL) of BS patient. These results suggest that abnormal repair of DNA damage is present in this LCL, and that preferential damage to IgM production by UV irradiation in this LCL may be due to the abnormal repair of DNA damage.
IMMUNOGENETIC ANALYSIS OF HLA‐DR10 HOMOZYGOUS INDIVIDUALS
Authors: Young N. T. , Thompson J. , Gibson K. , Dewar K. , Darke C. 
Published: April 2007

SUMMARYMolecular, cellular and serological analysis of Major Histocompatibility Complex alleles was performed on three individuals who appeared to be HLA‐DR10 homozygous by DNA restriction fragment analysis. Each donor was of different ethnic origin: Caucasoid, Asian Indian and African Negroid.The results of our studies show that the Caucasoid and Asian donors are indeed homozygous for the HLA‐DR 10 allele, while the African donor also possesses the DRB1*0103 allele. Homozygosity for the HLA‐A1B37‐Cw6‐DR10‐DQ5 haplotype in the Caucasoid donor was confirmed by familial segregation analysis. The B‐lymphoblastoid cell line produced from this donor should prove useful in studies of HLA immunogenetics.