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Screening of the ARX gene in 682 retarded males.

The newly identified gene, ARX, when mutated has been shown to cause both syndromic and nonsyndromic forms of mental retardation. It seems that the less severe forms are due to polyalanine expansions and missense mutations in the gene. We screened 682 developmentally retarded males for polyalanine expansions in ARX in order to examine the contribution of ARX mutations to the causes of developmental retardation. We also reinvestigated 11 putative MRX and three MR families where no cause of mental retardation had been found, by mutational analysis of ARX. Mutational analysis was also performed in 11 probands with autism from families with two or more affected males. We find that previously described polyalanine expansions of ARX are not a common cause of mental retardation.

Noninvasive diagnosis of the 3243A > G mitochondrial DNA mutation using urinary epithelial cells.

The 3243A > G mutation is one of the most frequently observed mutations of mitochondrial DNA (mtDNA), and is associated with numerous clinical presentations including mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), progressive external ophthalmoplegia (PEO) and diabetes and deafness. The routine diagnosis of the 3243A > G mutation in blood is difficult as mutation levels are known to decrease in this tissue over time, while in some patients it may be absent. We have directly compared the levels of the 3243A > G mutation in skeletal muscle, blood and urinary epithelial cells in 18 patients and observed a striking correlation between the mutation load in postmitotic muscle and urinary epithelium, a mitotic tissue. These data strongly support the use of urinary epithelial cells as the tissue of choice in the noninvasive diagnosis of the 3243A > G mutation.

Hereditary breast and ovarian cancer: what the primary care physician should know.

In recent years, testing for cancer susceptibility genes has entered the clinical setting. The practicing physician needs to be familiar with this evolving area of medicine to be able to counsel and/or refer high-risk patients such as those with a strong personal or family history of cancer. The following is a review of the clinically pertinent information regarding hereditary breast and ovarian cancers resulting from mutations in BRCA genes. A special emphasis is placed on the different options available for BRCA mutation carriers, because many interventions have already proven to be highly efficacious. The increased risk of cancer seen in hereditary nonpolyposis colorectal cancer (HNPCC) is not part of this review but is mentioned briefly.

Maternal activating mutation of the calcium-sensing receptor: implications for calcium metabolism in the neonate.

Two infants were studied born of a mother with autosomal dominant hypocalcemia who is heterozygous for an activating mutation in the calcium-sensing receptor gene. Both infants had serum calcium levels in the low-normal range and parathyroid hormone levels in the high-normal range and were healthy. The mother's hypocalcemia had been treated with calcium carbonate and calcitriol and she has nephrocalcinosis and mild renal insufficiency. By genetic testing, both infants were shown to have normal calcium-sensing receptor gene alleles, i.e., they had not inherited the activating mutation from their mother. This provided reassurance to the family and ensured that treatment to correct apparent hypocalcemia would not be necessary. The fact that the infants had high normal parathyroid hormone levels with normal calcium may be due to the fact that with a normal calcium-sensing receptor their parathyroid glands responded in utero to the maternal hypocalcemia with an increase in parathyroid hormone.

Use of a real-time polymerase chain reaction-based fluorogenic 5' nuclease assay to evaluate insect vectors of Corynebacterium pseudotuberculosis infections in horses.

To develop and use a sensitive molecular assay for detecting the phospholipase D (PLD) exotoxin gene of Corynebacterium pseudotuberculosis in an attempt to identify insect vectors that may be important in transmission of clinical disease in horses.</AbstractText>2,621 flies of various species.</AbstractText>A real-time polymerase chain reaction (PCR)-based fluorogenic 5' nuclease (TaqMan) system (ie, TaqMan PCR assay) was developed for the detection of the PLD gene in insects. Flies were collected monthly (May to November 2002) from 5 farms in northern California where C. pseudotuberculosis infection in horses is endemic. Three of the 5 farms (which housed a total of 358 horses) had diseased horses during the study period. A total of 2,621 flies of various species were tested for the PLD gene of C. pseudotuberculosis.</AbstractText>Evidence of bacterial DNA for the PLD gene was detected in skin biopsy specimens from clinically affected horses and from 3 fly species collected from farms where affected horses were housed. Farms with a high incidence of diseased horses had a high proportion of insects carrying the organism. High percentages of flies with positive results for the PLD gene were observed in October, when most clinically affected horses were observed.</AbstractText>Our results are consistent with the hypothesis that C. pseudotuberculosis may be vectored to horses by flies. Three potential vectors were identified, including Haematobia irritans, Stomoxys calcitrans, and Musca domestica. The organism can be identified in up to 20% of house flies (Musca domestica) in the vicinity of diseased horses.</AbstractText>

Simple method of zygosity identification in transgenic mice by real-time quantitative PCR.

To determine zygosity in transgenic (Tg) mice, a new technology, real-time quantitative PCR, has recently been introduced in transgenic research to overcome several drawbacks (time-consuming, specialized techniques and/or ambiguity in the results) of previously established methods, for example, Southern blot hybridization, dot blot hybridization, fluorescence in situ hybridization (FISH), etc. However, the previous real-time quantitative PCR method still possesses several drawbacks, for example, it needs two sets of primers/probes and the complicated setting up of appropriate conditions, both of which are expensive and remain time-consuming. We therefore developed an improved real-time quantitative PCR system for determination of zygosity, which is easy, rapid and less expensive, because the technique needs only two experimental processes: estimation of DNA concentration and CYBR Green PCR. We found that homozygous, hemizygous and non-Tg animals could easily be distinguished among F1 littermates in crosses of hemizygous EGFP- and DsRed2-Tg mice. Our improved method will be applicable to any Tg mouse strains, when a primer set is matched to the corresponding transgene.

Proteasomal expression, induction of immunoproteasome subunits, and local MHC class I presentation in myofibrillar myopathy and inclusion body myositis.

Inclusion body myositis (IBM) and myofibrillar myopathy (MM) are diseases characterized by the abnormal accumulation of proteins in muscle fibers, including desmin, alphaB-crystallin, gelsolin, actin, kinases, and phospho-tau, along with ubiquitin in muscle fibers, suggesting abnormal protein degradation as a possible cause of the surplus myopathy. Since the ubiquitin-proteasome system plays a crucial role in non-lysosomal protein degradation, the present study has examined by immunohistochemistry the expression of components of the catalytic core of 20S proteasomes and its regulators: 19S and PA28alpha/beta, and the expression of immunoproteasome subunits LMP2, LMP7, and MECL1 in 8 patients with MM and 10 patients with IBM. The patients with MM were from 6 unrelated families, 2 sporadic cases, I with autosomal recessive and 5 with autosomal dominant inheritance. One sporadic patient had a de novo R406W mutation in the desmin gene, and 1 patient with autosomal dominant MM had a single amino acid deletion at position 366 in the desmin gene. Increased immunoreactivity to 20S, 19S, and PA28alpha/beta colocalizing abnormal protein deposits, as revealed in consecutive serial sections, was seen in all cases with MM and IBM. In all cases, the subunits of the immunoproteasome LMP2, LMP7, and MECL1 colocalized with proteasomal immunoreactivity and abnormal protein accumulation. Immunohistochemistry revealed focal MHC class I immunoreactivity in the cytoplasmic membrane of muscle fibers in IBM and in association with protein aggregates in IBM, and to a lesser degree, in MM. The present findings provide a link between abnormal protein accumulation and altered proteasomal expression in IBM and MM.

Health and ecological effects of adiponitrile.

Adiponitrile (ADN) has moderate acute toxicity with an oral LD50 in rats of 100 to 500 mg/kg and a 4-hr LC50 in rats of 1.71 mg/L (vapor plus aerosol). ADN produced slight eye but no skin irritation in rabbits. Repeated exposures by inhalation produced changes in the hematologic profile with effects seen at 100 or 300 mg/m3. The hematologic changes were reversible upon cessation of further inhalation exposures. Dogs fed up to 500 ppm (equivalent to 12-15 mg/kg) showed no effects but 1,000 ppm produced vomiting and nausea which limited further testing at that concentration. ADN was not a genetic toxin, developmental toxin, reproductive toxin nor did it produce an increase in tumors in a 2-yr drinking water study in rats. Human experience reports are limited to one accidental poisoning case and a few skin exposures resulting in transient irritation and inflammation. ADN is rapidly absorbed and excreted by mammals, and is metabolized to some extent although unchanged ADN is readily detected in urine, and does not bioaccumulate.

Identifying candidate causal variants responsible for altered activity of the ABCB1 multidrug resistance gene.

The difficulty of fine localizing the polymorphisms responsible for genotype-phenotype correlations is emerging as an important constraint in the implementation and interpretation of genetic association studies, and calls for the definition of protocols for the follow-up of associated variants. One recent example is the 3435C&gt;T polymorphism in the multidrug transporter gene ABCB1, associated with protein expression and activity, and with several clinical conditions. Available data suggest that 3435C&gt;T may not directly cause altered transport activity, but may be associated with one or more causal variants in the poorly characterized stretch of linkage disequilibrium (LD) surrounding it. Here we describe a strategy for the follow-up of reported associations, including a Bayesian formalization of the associated interval concept previously described by Goldstein. We focus on the region of high LD around 3435C&gt;T to compile an exhaustive list of variants by (1) using a relatively coarse set of marker typings to assess the pattern of LD, and (2) resequencing derived and ancestral chromosomes at 3435C&gt;T through the associated interval. We identified three intronic sites that are strongly associated with the 3435C&gt;T polymorphism. One of them is associated with multidrug resistance in patients with epilepsy (chi2 = 3.78, P = 0.052), and sits within a stretch of significant evolutionary conservation. We argue that these variants represent additional candidates for influencing multidrug resistance due to P-glycoprotein activity, with the IVS 26+80 T&gt;C being the best candidate among the three intronic sites. Finally, we describe a set of six haplotype tagging single-nucleotide polymorphisms that represent common ABCB1 variation surrounding 3435C&gt;T in Europeans.

Advances in preimplantation genetic diagnosis.

Strategies for preimplantation genetic diagnosis (PGD) have become increasingly complex. For single gene disorders it is now usual for several DNA fragments to be simultaneously amplified using multiplex-PCR. This allows redundant diagnostic loci to be analyzed, reducing the chance of misdiagnosis due to allele dropout (ADO). Additionally, hypervariable 'fingerprinting' loci can be amplified, revealing the presence of DNA contaminants. Chromosomal screening has also increased in complexity. Current FISH techniques investigate up to nine chromosomes per cell and are offered to an increasingly wide range of patients, including women of advanced reproductive age and those with a history of repeated spontaneous abortion. Technical limitations, which preclude a full assessment of all chromosomes using FISH, have encouraged the development alternative tests. These include nuclear conversion, comparative genomic hybridization (CGH) and the use of DNA microarray 'chip' technology. This paper discusses technical innovations that have improved the scope and accuracy of PGD, as well as the emergence of new indications for PGD that are sometimes considered controversial (e.g. HLA-typing).

Genetics of gametes and embryos.

Chromosome analysis of oocytes, sperm and embryos has mainly relied on fluorescent in situ hybridisation (FISH) and karyotyping. FISH studies have been performed on sperm from fertile and infertile men as well as men carrying known chromosomal translocations. Molecular DNA analyses has aided in the identification and treatment of men with Y chromosome deletions. In oocytes FISH and karyotyping have identified non-disjunction of univalents and predivision of chromatids. Analysis of the chromosomes from human embryos has shown that a high proportion of embryos are mosaic or chaotic, in addition to embryos beings uniformly and abnormal. FISH and PCR have also been used clinically for preimplantation genetic diagnosis (PGD). For patients at risk of transmitting a specific genetic or chromosomal abnormality, 1-2 blastomeres are biopsied from embryos and specific genes or chromosomes analysed. Normal embryos are then transferred to the uterus.

Langerhans cell histiocytosis in adults: more questions than answers?

Langerhans cell histiocytosis (LCH) may affect patients of any age but in adults the features of this disease are still poorly defined. Most reports are based on single-specialty experience and there are only a few describing relatively large series of patients. Although child and adult patients share several features of the disease, and may either have localised or disseminated disease, the proportion of cases with lung involvement is much higher in adults and is partly explained by cigarette smoking. Persisting uncertainty about the pathogenesis of LCH has certainly limited current treatment alternatives. In particular, no clinical trial has been conducted in adults so far and most information derives from description of one or a few cases, often reported retrospectively. On the basis of the background provided by the data collected in its International Registry, the Histiocyte Society is about to start the first prospective, cooperative adult LCH study, aimed at: (a) establishing a common platform for clinical evaluation; (b) testing in adult patients the efficacy of the best standard chemotherapy regimen for children-a combination of prednisone and vinblastine-developed by the Society's trials; (c) describing the natural history of the disease, the impact of cigarette smoking withdrawal and the efficacy of steroid monotherapy in pulmonary LCH. Research studies, ancillary to this trial, offer unique opportunities of addressing some of the open questions in LCH including: the genetic component of the disease as supported by evidence of familial clustering and chromosomal instability, the issue of 'LCH cells' clonality, the relation between pulmonary disease, cigarette smoking, and immune system polymorphisms that might increase individual susceptibility to LCH. A concerted joint effort between paediatricians and adult specialists could be the key to the development of insights into LCH in all age groups affected by this distressing and often debilitating condition.

How (not) to protect genomic data privacy in a distributed network: using trail re-identification to evaluate and design anonymity protection systems.

The increasing integration of patient-specific genomic data into clinical practice and research raises serious privacy concerns. Various systems have been proposed that protect privacy by removing or encrypting explicitly identifying information, such as name or social security number, into pseudonyms. Though these systems claim to protect identity from being disclosed, they lack formal proofs. In this paper, we study the erosion of privacy when genomic data, either pseudonymous or data believed to be anonymous, are released into a distributed healthcare environment. Several algorithms are introduced, collectively called RE-Identification of Data In Trails (REIDIT), which link genomic data to named individuals in publicly available records by leveraging unique features in patient-location visit patterns. Algorithmic proofs of re-identification are developed and we demonstrate, with experiments on real-world data, that susceptibility to re-identification is neither trivial nor the result of bizarre isolated occurrences. We propose that such techniques can be applied as system tests of privacy protection capabilities.

Using genomics to help predict drug interactions.

This article proposes using genomic information to help tailor the output of a drug interaction program for a patient. This paper focuses on a particular CYP450 enzyme to illustrate adding genomic information to an existing drug interaction database. The data are formatted as an Extensible Markup Language (XML) document. The additional interaction information based on genomics for a patient is added to an XML document using XML tags. The suggestion is to combine specifics about a patient's genome with genomic information in the drug interactions database to increase the accuracy and details of a drug interaction program.

The genetic family history assessment in gastroenterology nursing practice.

Genetic factors influence the risk for disease and the overall health of persons throughout their lifespan. The systematic collection of family history information in a three-generation format is the most important approach for the identification of individuals with a genetic susceptibility to most common diseases, and applying genetic concepts in healthcare. The detailed family history can play a critical role in diagnosis, lay the foundation for accurate risk assessment, and be used to develop subsequent education, individualized monitoring and management of the disease, and prevention measures. The purpose of this article is to familiarize nurses with why, what, how, when, where and for whom a genetic family history assessment should be used in gastroenterology nursing practice. Risk assessment specific to the development and prevention of colorectal cancer will be described.

Identification of integrin beta subunit mutations that alter heterodimer function in situ.

We conducted a genetic screen for mutations in myospheroid, the gene encoding the Drosophila betaPS integrin subunit, and identified point mutants in all of the structural domains of the protein. Surprisingly, we find that mutations in very strongly conserved residues will often allow sufficient integrin function to support the development of adult animals, including mutations in the ADMIDAS site and in a cytoplasmic NPXY motif. Many mutations in the I-like domain reduce integrin expression specifically when betaPS is combined with activating alphaPS2 cytoplasmic mutations, indicating that integrins in the extended conformation are unstable relative to the inactive, bent heterodimers. Interestingly, the screen has identified alleles that show gain-of-function characteristics in cell culture, but have negative effects on animal development or viability. This is illustrated by the allele mys(b58); available structural models suggest that the molecular lesion of mys(b58), V409&gt;D, should promote the "open" conformation of the beta subunit I-like domain. This expectation is supported by the finding that alphaPS2betaPS (V409&gt;D) promotes adhesion and spreading of S2 cells more effectively than does wild-type alphaPS2betaPS, even when betaPS is paired with alphaPS2 containing activating cytoplasmic mutations. Finally, comparisons with the sequence of human beta8 suggest that evolution has targeted the "mys(b58)" residue as a means of affecting integrin activity.

Measuring environmental factors can enhance the search for disease causing genes?

The value of the concurrent measurement of environmental factors in studies aimed at the discovery of disease causing genes has been questioned on the grounds that such an approach fails to increase study power. This report discusses the issue and shows with examples from the recent literature that the examination of a gene disease association within an environmental subgroup can provide enhanced opportunities for detecting gene effects. The concurrent collection of environmental as well as genetic factors in studies of disease aetiology may enhance study informativeness and validity in several ways, including an increase in the power of the study to detect gene disease associations.

Persistence of low levels of simian immunodeficiency virus in macaques that were transiently viremic by conventional testing.

Transient SIV viremia after experimental SIV challenge has been documented. Whether SIV persists in these transiently viremic macaques remains unclear. In the present study, we applied a sensitive PCR and found persistent low levels of SIVmne infection (LLSI) (range: 0.1-5.3 SIV DNA copies/10(6) PBMC) in seven macaques that were transiently positive by conventional assays, which was 10(2)- to 10(6)-fold less than those of SIVmne infected monkeys with typical disease progression. SIV envelope V1 sequences remained homogeneous in these macaques for the 6-year study period, with a mean evolution rate of 0.005% per site per year, which was not different from zero (P = 0.612) and significantly lower than that (0.56-1.18%) in macaques with progressive infection of SIVmne. LLSI macaques have remained free from SIV-associated illness, and are still alive 10 years after virus inoculation. Understanding the mechanisms underlying this outcome may provide valuable insight into therapy and vaccine development.

No association between two MLH3 variants (S845G and P844L)and colorectal cancer risk.

Recently we identified a new variant, S845G, in the MLH3 gene in 7 out of 327 patients suspected of hereditary nonpolyposis colorectal cancer but not fulfilling the Amsterdam criteria and in 1 out of 188 control subjects. As this variant might play a role in causing sporadic colorectal cancer, we analyzed its prevalence in sporadic colorectal cancer patients. We analyzed a small part of exon 1 of the MLH3 gene, including the S845G variant, in germline DNA of 467 white sporadic colorectal cancer patients and 497 white controls. The S845G variant was detected in five patients and eight controls; the results thus indicate that this variant does not confer an increased colorectal cancer risk. Another variant (P844L) was clearly a polymorphism. Three other missense variants were rare and the sample size of the study was too small to conclude whether they are pathogenic. In conclusion, no association was observed between two MLH3 variants (P844L and S845G) and colorectal cancer risk.

[Polymorphism and multiplex amplification of 3 X-chromosome specific short tandem repeat loci].

To devise a multiplex PCR system of three X-chromosome specific short tandem repeat (X-STR) loci and study the genetic polymorphism.</AbstractText>DXS6799, DXS6804 and DXS6854 were amplified simultaneously using a multiplex system and were typed by polyacrylamide gel electrophoresis and silver staining.</AbstractText>A total of 262 male and 255 female individuals from Guangdong Han population were tested; each locus showed 7 alleles. 73 haplotypes were detected in the male individuals. The haplotype diversity reached 0.9674.</AbstractText>The 3 X-STR multiplex system is relatively abundant in polymorphic information for forensic identification and paternity testing.</AbstractText>

[Carrier detection of Duchenne/Becker muscular dystrophy in Chinese families by microsatellite analysis].

To screen and detect the female carriers from the DMD/BMD family members for prenatal or preimplantation genetic diagnosis.</AbstractText>For the detection of DMD/BMD carriers from 27 family members in 4 families, PCR to five microsatellite markers(located in 5' terminus and intron 44, 45, 49, 50) and analysis of the short tandem repeat(STR) sequence polymorphism with the use of genescan were implemented.</AbstractText>Six of the 17 female members were obligate DMD gene carriers according to the haplotype analysis of the results of the genescan, which conformed with the pedigree analysis. Besides, the authors detected five carriers and five normal females in these families with the use of the haplotype analysis only. The most polymorphic locus was STR 49, and the least was STR 50.</AbstractText>The STR haploid linkage analysis using (CA)n repeats within the human dystrophin gene is a rapid,accurate, objective method and is well suited for routine use in clinical laboratories engaged in DMD/BMD linkage analysis for the detection of carrier.</AbstractText>

A novel permutation testing method implicates sixteen nicotinic acetylcholine receptor genes as risk factors for smoking in schizophrenia families.

Smoking is a common correlate of schizophrenia, which leads to medical morbidity. Although twin and adoption studies have consistently implicated genes in the etiology of both smoking and schizophrenia, finding genes has been difficult. Several authors have suggested that clinical or neurobiological features associated with schizophrenia, such as smoking, might improve the ability to detect schizophrenia susceptibility genes by identifying genes related to the etiology of that feature. The objective of this study is to assess evidence for linkage of sixteen nicotinic acetylcholine receptor genes and smoking in schizophrenia families, using data from the NIMH Genetics Initiative for schizophrenia. Sixteen nicotinic acetylcholine receptor genes were selected prior to analysis. We used a multipoint sibling pair linkage analysis program, SIBPAL2, with a smoking trait in schizophrenia families. The significance of the group of candidate genes, in addition to each individual candidate gene, was assessed using permutation testing, which adjusted for multiple comparisons. The group of genes showed significant linkage to the smoking trait after adjusting for multiple comparisons through permutation testing (p = 0.039). In addition, two of the individual candidate genes were significant (CHRNA2, p = 0.044) and (CHRNB2, p = 0.015) and two genes were marginally significant (CHRNA7, p = 0.095; CHRNA1, p = 0.076). The significance of the complex hypothesis, involving sixteen genes, implicates the nicotinic system in smoking for schizophrenic families. Individual gene analysis suggests that CHRNA2 and CHRNB2 may play a particular role in this involvement. Such findings help prioritize genes for future case control studies. In addition, we provide a novel permutation method that is useful in future analyses involving a single hypothesis, with multiple candidate genes.

Identification of autoantigens in psoriatic plaques using expression cloning.

To search for autoantigens in psoriatic plaques, we screened cDNA libraries of plaque epidermis with psoriatic serum samples. This approach has been highly successful in identifying tumor antigens, but has not been widely applied to autoimmune disease. We identified 11 autoantigens including three with prominent reactivity and plausible disease relevance. These are keratin 13 (K13), heterogeneous nuclear ribonucleoprotein-A1 (hnRNP-A1), and a previously uncharacterized protein, FLJ00294. Serum antibody screening for these demonstrated reactivity in 40%, 38%, and 27% of psoriasis patients, respectively. Most positive samples reacted with all three, and we found that this was due to cross-reactivity among them. Enzyme-linked immunospot assay (ELISPOT) analysis of psoriatic peripheral blood T cells confirmed that these autoantigens are also recognized by T cells. This demonstrates that this is a feasible method to identify autoantigens in an autoimmune target tissue, and suggests that these antigens warrant further study in psoriasis. Furthermore, but peripheral blood of normal controls reacted to these autoantigens with essentially the same frequencies as patients, suggesting that psoriatics may have not only an immune system which is capable of reacting to certain autoantigens, but also to a skin immunoregulatory alteration which allows this normal reactivity to develop into abnormal inflammation.

The evolution to stool DNA testing for colorectal cancer.

Despite a variety of screening strategies and recent trends showing death rate stabilization, colorectal cancer still remains the second leading cause of overall cancer death. Current screening tools suffer from performance limitations, low patient acceptability, and marginal reliable access within the health care system. Noninvasive strategies present the lowest risk with the highest potential for patient satisfaction. However, serious implementation barriers exist requiring consistent programmatic screening, strict patient adherence, and poor sensitivity for adenomas. Colonoscopy remains an invasive screening test with the best sensitivity and specificity, but faces large financial costs, manpower requirements, patient access and adherence. Development of advanced molecular techniques identifying altered DNA markers in exfoliated colonocytes signify early or precancerous growth. Stool-based DNA testing provides an entirely noninvasive population-based screening strategy which patients can perform easier than faecal occult blood testing (FOBT). Large-scale prospective randomized control trials currently pending should help characterize accurate test performance, screening intervals, cost-effectiveness, direct comparison to FOBT and analysis of patient adherence. As tumour development pathways and potential target genes are further elucidated, refinements in multi-assay stool-based DNA testing portend enhanced test characteristics to detect and treat this genetically heterogeneous disease.

People who influence women's decisions and preferred sources of information about prenatal testing for birth defects.

More than half of Victorian pregnant women are undergoing prenatal testing for birth defects, although little is known about the factors that are influencing their decisions.</AbstractText>To examine whom women perceived as influencing their decision about prenatal testing for birth defects, with whom they would have liked to talk more, and what sources of information they preferred.</AbstractText>A total of 737 pregnant women aged 37 years and over, who either had or had not undergone prenatal testing (screening and/or diagnosis) completed a questionnaire in 18 hospitals throughout Victoria.</AbstractText>Over 90% reported that they themselves had a strong influence on their decision, and 70% reported their partner as strongly influencing their decision. Approximately 30% of women who had both screening and diagnosis and more than 20% of women who had no prenatal testing, would like to have discussed prenatal testing with women who had previously had testing. Face-to-face counselling with a doctor or counsellor was the preferred source of information, followed by a pamphlet as the second choice.</AbstractText>Given that both tested and untested women felt so strongly that they were responsible for their own decisions about prenatal testing, it is unlikely that universal acceptance and uptake will occur, even in this group of women of advanced maternal age. A support network of women who have already had testing could supplement existing sources of support. However, there continues to be a need for face-to-face sessions with a doctor or counsellor in combination with printed material.</AbstractText>

Preservation of C-peptide secretion in subjects at high risk of developing type 1 diabetes mellitus--a new surrogate measure of non-progression?

Individuals at high risk of developing type 1 diabetes mellitus can be identified using immunologic, genetic, and metabolic parameters. In the Diabetes Prevention Trial-1 (DPT-1), annual intravenous infusions of low doses of regular insulin, together with daily subcutaneous injection of a single low dose of Ultralente insulin at nighttime, failed to prevent or delay the onset of type 1 diabetes in high-risk non-diabetic relatives. In our study, we attempted to achieve beta-cell rest by administering higher doses of neutral protamine Hagedorn (NPH) insulin twice daily to high-risk non-diabetic subjects in an effort to prevent or delay the onset of the disease. The maximum tolerable dose was given with the dose reduced for any hypoglycemia (mean dose 0.33 +/- 0.15; range 0.09-0.66 units/kg/d). We treated 26 subjects who were confirmed to have islet cell antibodies (ICAs) and a low first-phase insulin response (FPIR) to intravenous glucose. Fourteen had normal glucose tolerance and 12 impaired glucose tolerance (IGT). The median duration of follow-up was 5.5 yr. Diabetes occurred in 10 of 12 subjects with IGT and five of 14 subjects with normal glucose tolerance. The cumulative incidence of diabetes was the same as with that seen in a matched, observation group (subjects followed prospectively as part of the University of Florida natural history studies) (age, sex, ICA, insulin autoantibodies, duration of ICA prior to enrollment, FPIR, and glucose intolerance; p = 0.39), as was the rate of progression (p = 0.79). There was a higher rate of progression to diabetes in the group with abnormal glucose tolerance at baseline than in those with normal baseline glucose tolerance (p = 0.003). Interestingly, in non-progressors, as opposed to progressors, there was no fall in C-peptide (peak and area under the curve) production regardless of the type of tolerance testing (mixed meal, oral or intravenous) over time (p &lt; 0.001). In this study, in the dose and regimen of NPH insulin used, insulin did not delay or prevent the development of type 1 diabetes. However, preservation of C-peptide production in the prediabetic period appears to indicate non-progression to clinical disease and may serve as a new surrogate for determining response to preventative efforts.

Screening for the breast cancer gene (BRCA1) using a biochip system and molecular beacon probes immobilized on solid surfaces.

We describe the use of a biochip based on complementary metal oxide semiconductor (CMOS) technology for detection of specific genetic sequences using molecular beacons (MB) immobilized on solid surfaces as probes. The applicability of this miniature detection system for screening for the BRCA1 gene is evaluated using MB probes, designed especially for the BRCA1 gene. MB probes are immobilized on a zeta-probe membrane by biotin-streptavidin immobilization. Two immobilization strategies are investigated to obtain optimal assay sensitivity. The MB is immobilized by manual spotting on zeta-probe membrane surfaces with the use of a custom-made stamping system. The detection of the BRCA1 gene using an MB probe is successfully demonstrated and expands the use of the CMOS biochip for medical applications.

Nonlinear matching measure for the analysis of on-off type DNA microarray images.

We propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by a template-matching method. The proposed measure is obtained by binary thresholding over the entire template region and taking the number of white pixels inside the spotted area. This measure is compared with the normalized covariance method in terms of classifying the ability to successfully locate markers. The proposed measure was evaluated for scanned images of human papillomavirus (HPV) DNA microarrays where locating markers is a critical issue because of the small number of spots. The targeting spots of HPV DNA chips are designed for genotyping twenty-two types of the human papillomavirus. The proposed measure is proven to give a more discriminative response, reducing the missed cases of successful marker location. The locating accuracy of the proposed method is also shown to have the same performance as that of the normalized covariance.

DNA testing for type III von Willebrand disease in Dutch Kooiker dogs.

Von Willebrand disease type III is widespread in Dutch Kooiker dogs. To eradicate von Willebrand disease from the breed, affected dogs and nonsymptomatic carriers must be excluded from breeding. Previous efforts to detect carriers in Kooiker dogs by a von Willebrand factor antigen assay were not satisfactory because of considerable overlap of plasma concentrations in normal dogs and carriers. The aim of this study was to develop and apply a DNA test for the detection of von Willebrand disease carriers in the Kooiker breed. Two mutations in the von Willebrand factor gene in affected Kooiker dogs have been described previously, a splice site mutation at the border of intron 16 and exon 16 and a missense mutation in exon 3. We have developed polymerase chain reaction tests for both mutations in genomic DNA. The missense mutation most likely is a neutral variant and appears to be a polymorphism present in many breeds. The allele-specific oligonucleotide test for the splice site mutation was applied in the selection of animals cleared to breed by the Dutch breeding club. In a few years, the mutation has been eliminated from the breeding stock without apparent increase of inbreeding or preferential sire usage.

Selection-subtraction approach (SSA): a universal genetic screening technique that enables negative selection.

Screening of expression libraries for bioactive clones that modulate the growth of mammalian cells has been limited largely to positive selections incapable of revealing growth suppressive or lethal genetic elements. We have developed a technique, selection-subtraction approach (SSA), that allows growth-modulating clones to be isolated based on alterations in their relative abundance in growing cell populations that have been transduced with an expression library. SSA utilizes tagged retroviral libraries in bacteriophage lambda vectors (retrophages). Nylon prints from retrophage libraries are used to determine the relative abundance of tags in library-transduced cells to identify biological activity of individual clones. Applications of SSA for gene discovery, target discovery, and generation of mutant proteins have been demonstrated, by using p53 and ataxia telangiectasia mutated (ATM) as models to isolate growth inhibitory proteins, peptides and antisense RNAs, and temperature-sensitive mutant proteins.

Europe plans gene testing framework.

Genetic testing is set to enter mainstream healthcare and further population research but needs new regulation according to a European report, writes Nigel Williams.

Preventing and managing antiretroviral drug resistance.

Development of resistance to antiretroviral drugs (ARVs) is a major impediment to optimum treatment of HIV-1 infection. Although resistance testing can help to select subsequent regimens when virologic failure occurs, cross-resistance, which affects all classes of ARVs, may make it more difficult to achieve optimum control of HIV. We have known for some time that our first choice of antiretroviral therapy offers the best chance to control HIV replication and that initial therapy should be selected with an eye on future options. Potency is the first line of defense against the development of resistance. Other factors that affect resistance development include: tolerability, potential for optimum adherence, and genetic and pharmacologic barriers to development of resistance. If resistance emerges, only a single drug may be affected initially, and a rapid change in ARVs may preserve the efficacy of other components. One cautionary note is that we can no longer assume that a patient's HIV is fully susceptible to all ARVs even in the initial regimen. Transmission of drug-resistant HIV means that the genetic composition may be that of an "experienced" virus with reduced susceptibility to ARVs. Resistance testing at the time of transmission is most likely to reveal this resistance, but over time the dominant genetic pattern may revert to wild-type, and be missed by resistance testing. Because "archived" resistant HIV may emerge quickly once treatment is initiated, we need to keep this in mind when selecting initial therapy.

Differences in the expressed HLA class I alleles effect the differential clustering of HIV type 1-specific T cell responses in infected Chinese and caucasians.

China is a region of the world with a rapidly spreading HIV-1 epidemic. Studies providing insights into HIV-1 pathogenesis in infected Chinese are urgently needed to support the design and testing of an effective HIV-1 vaccine for this population. HIV-1-specific T cell responses were characterized in 32 HIV-1-infected individuals of Chinese origin and compared to 34 infected caucasians using 410 overlapping peptides spanning the entire HIV-1 clade B consensus sequence in an IFN-gamma ELISpot assay. All HIV-1 proteins were targeted with similar frequency in both populations and all study subjects recognized at least one overlapping peptide. HIV-1-specific T cell responses clustered in seven different regions of the HIV-1 genome in the Chinese cohort and in nine different regions in the caucasian cohort. The dominant HLA class I alleles expressed in the two populations differed significantly, and differences in epitope clustering pattern were shown to be influenced by differences in class I alleles that restrict immunodominant epitopes. These studies demonstrate that the clustering of HIV-1-specific T cell responses is influenced by the genetic HLA class I background in the study populations. The design and testing of candidate vaccines to fight the rapidly growing HIV-1 epidemic must therefore take the HLA genetics of the population into account as specific regions of the virus can be expected to be differentially targeted in ethnically diverse populations.

Preimplantation genetic diagnosis: choosing the "good enough" child.

Preimplantation genetic diagnosis (PGD) raises serious moral questions concerning the parent-child relationship. Good parents accept their children unconditionally: they do not reject/attack them because they do not have the features they want. There is nothing wrong with treating a child as someone who can help promote some other worthwhile end, providing the child is also respected as an end in him or herself. However, if the child's presence is not valued in itself, regardless of any further benefits it brings, the child is not being treated as an end in the full sense of the term, in this paper, I argue that these principles apply to human embryos, as well as to born human offspring: the human moral subject is a bodily being, whose interests and rights begin with the onset of his or her bodily life. The rights of the living, bodily human individual include a righ not to be attacked/abandoned because of his or her genetic profile. PGD is harmful to the parent-child relationship, and we give mixed messages to parents by expecting them to show unconditional commitment to offspring after birth, while inviting them to take a very different approach at the prenatal stage.

A rare transthyretin mutation (Asp18Glu) associated with cardiomyopathy.

The identification of a rare transthyretin (TTR) gene mutation (Asp18Glu) in a middle-aged male with biopsy proven amyloid disease featuring cardiomyopathy is described. The more commonly occurring light chain amyloidosis (AL) was initially considered, but negative hematologic testing prompted screening for a pathologic TTR mutation. A differential diagnosis of familial transthyretin type amyloidosis (ATTR) was established using a combination of molecular genetic and biochemical techniques. Single-strand conformation polymorphism (SSCP) screening of exons 2, 3 and 4 of the TTR gene indicated the presence of atypical DNA. SSCP testing was performed using a new non-radioactive, silver stained minigel technique. The genetic abnormality was identified by direct DNA sequence analysis as a T to A transversion at the third base position in codon 18. This result was confirmed by restriction fragment length polymorphism (RFLP) testing. The presence of the variant protein, TTR Asp18Glu, in serum from the proband was confirmed by mass spectrometric analysis.

Increased cancer risk of heterozygotes with NBS1 germline mutations in Poland.

It has been suggested based on familial data that Nijmegen breakage syndrome (NBS) heterozygotes have an increased risk of malignant tumors. We found 15 carriers of the 657del5 mutation and 8 carriers of the R215W molecular variant of the NBS1 gene among 1,289 consecutive patients from Central Poland with various cancers and only 10 and 4 such carriers, respectively, in 1,620 controls from this region. Most of the 657del5 mutation carriers were found among patients with melanoma (4/105), non-Hodgkin lymphoma (2/42) and breast cancer (4/224) and of the 234 patients with colorectal carcinoma 3 carried the 657del5 mutation and 3 others the R215W molecular variant. The frequencies of 657del5 mutation carriers among patients with melanoma and non-Hodgkin lymphoma and of R215W carriers in patients with colorectal cancer were significantly higher than in controls (p &lt; 0.01, &lt; 0.05 and &lt; 0.05 respectively). The pooled frequencies of 657del5 and R215W mutations in all cancer patients were also significantly higher than in controls (p &lt; 0.05). Two carriers of the 657del5 mutation had second primary tumors. Malignant tumors among parents and siblings of 657del5 mutation carriers (14/77) were twice more frequent than in population controls. Three carriers of this mutation (2 probands with melanoma) reported melanoma in relatives. These results suggest strongly that NBS1 heterozygosity may be associated with elevated risk of some cancers. Larger studies are needed to evaluate the impact of the high frequency of germline NBS1 mutations on the cancer burden in the Slav populations.

A critical role for the chimpanzee model in the study of hepatitis C.

Chimpanzees remain the only recognized animal model for the study of hepatitis C virus (HCV). Studies performed in chimpanzees played a critical role in the discovery of HCV and are continuing to play an essential role in defining the natural history of this important human pathogen. In the absence of a reproducible cell culture system, the infectivity titer of HCV challenge pools can be determined only in chimpanzees. Recent studies in chimpanzees have provided new insight into the nature of host immune responses-particularly the intrahepatic responses-following primary and secondary experimental HCV infections. The immunogenicity and efficacy of vaccine candidates against HCV can be tested only in chimpanzees. Finally, it would not have been possible to demonstrate the infectivity of infectious clones of HCV without chimpanzees. Chimpanzees became infected when RNA transcripts from molecular clones were inoculated directly into the liver. The infection generated by such transfection did not differ significantly from that observed in animals infected intravenously with wild-type HCV. The RNA inoculated into chimpanzees originated from a single sequence, and the animals therefore had a monoclonal HCV infection. Monoclonal infection simplifies studies of HCV, because virus interaction with the host is not confounded by the quasispecies invariably present in a natural infection. It furthermore permits true homologous challenge in studies of protective immunity and in testing the efficacy of vaccine candidates. Finally, this in vivo transfection system has made it possible to test for the first time the importance of genetic elements for HCV infectivity.

Molecular mapping of deletion breakpoints on chromosome 4 of Drosophila melanogaster.

As part of our effort to induce and identify mutations in all genes on chromosome 4 of Drosophila melanogaster, we have mapped the breakpoints of eight chromosome 4 deficiencies relative to the predicted genes along this chromosome. Although the approximate locations of Df(4)G, Df(4)C3, Df(4)M101-62f, Df(4)M101-63a, Df(4)J2, Df(4)O2, Df(4)C1-10AT, and Df(4)B2-2D are known (some from cytological observations and others predicted from P element locations), the extents of these deletions have not been mapped with respect to the predicted genes identified by the Drosophila Genome Project. Polymerase chain reaction primers were designed to amplify the predicted exons of all chromosome 4 genes, and homozygous embryos for each deficiency were identified and their DNA used to test for the presence or absence of these exons. By testing for the inability to amplify various exons along the length of the chromosome, we were able to determine which predicted genes are missing in each deficiency. The five deficiencies, Df(4)G, Df(4)C3, Df(4)C1-10AT, and Df(4)B2-20 (all terminal deletions), and Df(4)M101-62f (a proximal interstitial deletion), enabled us to partition the gene-containing, right arm of chromosome 4 into five regions. Region A [uncovered by Df(4)M101-62f] contains the proximal-most 21 genes; region B [uncovered by Df(4)B2-2D] contains the next 12 genes; region C [uncovered by Df(4)B2-2D and Df(4)C1-10AT] contains the next 17 genes; region D [uncovered by Df(4)B2-2D, Df(4)C1-10AT, and Df(4)C3] contains the next 21 genes; and region E [uncovered by Df(4)B2-2D, Df(4)C1-10AT, Df(4)C3, and Df(4)G] contains the distal-most ten genes. By using Df(4)M101-62f, Df(4)B2-2D, Df(4)C1-10AT, Df(4)C3, and Df(4)G in complementation tests, we can assign newly induced recessive lethal mutations to one of the five regions on chromosome 4. This will substantially reduce the amount of DHPLC analysis required to match each mutation to a predicted transcript on chromosome 4.

Longitudinal changes in cognition and behavior in asymptomatic carriers of the APOE e4 allele.

To determine whether memory loss is detectable before the symptomatic presentation of mild cognitive impairment (MCI) in those at greater genetic risk for Alzheimer disease (AD) based upon presence or absence of the e4 allele of APOE.</AbstractText>Participants were age 50 years or older who responded to newspaper advertisements. A total of 212 cognitively normal individuals of known APOE genotype were initially enrolled in a match paradigm that included e4 homozygotes, e3/4 heterozygotes, and e4 noncarriers in a 1:1:2 ratio (53 sets). Of the original 212 individually matched participants, 180 completed at least two epochs of testing including 45 APOE e4/4 homozygotes, 42 APOE e3/4 heterozygotes, and 93 APOE e4 noncarriers, mean age 60 (+/-6.2) years. Of these, four developed MCI or AD during the follow-up period and were excluded from analysis. Longitudinal neuropsychological study included two verbal (Auditory Verbal Learning Test [AVLT], Selective Reminding Test [SRT]) and two visual (Complex Figure Test [CFT], Visual Retention Test) memory tests.</AbstractText>Multiple measures on both verbal memory tests showed poorer performance over a mean interval of 33 months in e4 carriers than noncarriers: AVLT total learning, long term delayed recall; SRT free and cued recall. Among those age 50 to 59 years, AVLT long term delayed recall, SRT free and cued recall, and CFT recall declined more in APOE e4 carriers. No differences were found in the domains of language, spatial skills, or executive function.</AbstractText>Memory declined in APOE e4 carriers before the symptomatic presentation of MCI in a cohort whose mean age was 60 years over a median period of 33 months. The decline began prior to age 60.</AbstractText>

NFI-C2 negatively regulates alpha-sarcoglycan promoter activity in C2C12 myoblasts.

alpha-Sarcoglycan striated muscle-specific protein is a member of the sarcoglycan-sarcospan complex. Positive and negative transcriptional regulation of sarcoglycan genes are important in sarcoglycan's intracellular localization and sarcolemmal stability. In the present work we assessed the function of NFI transcription factors in the regulation of alpha-sarcoglycan promoter through the C2C12 cell line differentiation. NFI factors act alternatively as activators and negative modulators of alpha-sarcoglycan promoter activity. In myoblasts NFI-A1.1 and NFI-B2 are activators, whereas NFI-C2 and NFI-X2 are negative regulators. In myotubes, all NFI members are activators, being NFI-C2 the less potent. We identified the alpha-sarcoglycan promoter NFI-C2 response element by testing progressive deletion constructs and point mutations in C2C12 cells over-expressing NFI-C2. Gel-shift and chromatin immunoprecipitation experiments demonstrated that NFI factors are indeed interacting in vitro and in vivo with the binding sequence. These results suggest a NFI role in C2C12 cell differentiation.

HSV-1 amplicon-mediated transfer of 128-kb BMP-2 genomic locus stimulates osteoblast differentiation in vitro.

In previous studies, we developed mouse genetic models and discovered genetic components of quantitative trait loci on mouse chromosomes that contribute to phenotypes such as bone size, bone density, and fracture healing. However, these regions contain dozens of genes in several overlapping bacterial artificial chromosomes (BACs) and are difficult to clone by physical cloning strategies. A feasible and efficient approach of identifying candidate genes is to transfer the genomic loci in BAC clones into mammalian cells for functional studies. In this study, we retrofitted a BAC construct into herpes simplex virus-1 amplicon and packaged it into an infectious BAC (iBAC) to test gene function in a cell-based system, using a 128-kb clone containing the complete bone morphogenetic protein-2 (BMP-2) gene. We transduced MC3T3-E1 cells with the iBAC bearing BMP-2 gene and examined transgene expression and function. Our results have demonstrated that an iBAC can efficiently deliver a BMP-2 genomic locus into preosteoblast cells and express functional BMP-2 protein, inducing a phenotype of cell differentiation, as indicated by an increase in alkaline phosphatase activity. Therefore, this experimental system provides a rapid, efficient cell-based model of high-throughput phenotypic screening to identify the BAC clones from physically mapped regions that are important for osteoblast differentiation. It also illustrates the potential of iBAC technology in functional testing of single nucleotide polymorphisms located in the distal promoter or/and intron regions responsible for low bone density.

Accuracy and completeness in reporting family history of prostate cancer by unaffected men.

To determine the accuracy of prostate cancer reports and completeness of the family history provided by unaffected men with a family history of prostate cancer. A positive family history is associated with increased prostate cancer risk and could influence surveillance recommendations and patient selection for genetic testing in the future. However, the accuracy of prostate cancer reports and completeness of the family history provided by unaffected men is poorly understood.</AbstractText>Eligible respondents were ascertained through participation in a population-based study of prostate cancer. The family history was collected by questionnaire and compared with the verified research pedigree. Information about the family history was also independently collected from spouses. A standard statistical method was used to determine the variables associated with accuracy and failure to report cases.</AbstractText>A total of 154 unaffected men (51%) responded. Most (82%) reports of prostate cancer cases were verified. Overall, 63% reported a family history that precisely matched the verified family history. The respondents' wives contributed little additional information. Age and degree of relationship to an affected person were associated with both accuracy and completeness of the family history. Verification altered the empirical risk category of 29% of the respondents; however, most (93%) remained at increased risk.</AbstractText>Unaffected men with a family history of prostate cancer generally provide a reliable family history. We conclude that surveillance advice can be reasonably based on a man's reported family history. However, the identification of certain high-risk individuals, which may be relevant for selection for genetic testing in the future, requires more extensive ascertainment of the family history.</AbstractText>

Accurate mapping of mutations of pyrazinamide-resistant Mycobacterium tuberculosis strains with a scanning-frame oligonucleotide microarray.

The increasing emergence of drug-resistant Mycobacterium tuberculosis poses significant threat to the treatment of tuberculosis. Conventional susceptibility testing for the front-line tuberculosis drug pyrazinamide (PZA) is difficult, because of the requirement for acid pH for the drug to show activity. Resistance to PZA in M. tuberculosis is caused by mutations in the pncA gene, and detection of pncA mutations can be an indicator of PZA resistance. In this study, we examined the feasibility of a microarray-based approach exploiting short overlapping oligonucleotides (sliding-frame array) to rapidly detect pncA mutations (substitutions, deletions, and insertions) in multiple strains of PZA-resistant M. tuberculosis. The genetic mapping of these mutations is necessary to link the gene sequence to the protein function defined by mutant phenotype. Microarray analysis was performed in a blind manner using 57 isolates of M. tuberculosis for which the sequence of the pncA gene was previously determined. Our results showed that all mutations could be unambiguously detected, suggesting that microarray can be a routine and valuable tool for rapid identification of drug-resistant M. tuberculosis isolates. We expect that mutation mapping with a sliding-frame microarray will accelerate the molecular analysis of drug-resistant M. tuberculosis bacteria and the microorganism populations.

Anterior basement membrane corneal dystrophy and pseudo-unilateral lattice corneal dystrophy in a patient with recurrent corneal erosions.

To report the utility of genetic testing in the diagnosis and management of patients with suspected corneal dystrophies.</AbstractText>Case report.</AbstractText>A 58-year-old man with a history of recurrent corneal erosions was diagnosed with bilateral anterior basement membrane dystrophy and unilateral lattice corneal dystrophy. All 17 exons of the TGFBI gene were screened for mutations previously associated with lattice corneal dystrophy as well as novel coding region changes.</AbstractText>No mutations were found in the 17 exons of the TGFBI gene. A nucleotide change in exon 6 (651C&gt;G) did not result in a change in the encoded amino acid (Leu217Leu).</AbstractText>In cases of suspected TGFBI corneal dystrophies, genetic testing is a useful tool to confirm the clinical diagnosis. In this case of suspected unilateral lattice corneal dystrophy, screening of the TGFBI gene ruled out the diagnosis, raising the possibility that the corneal changes were related to the coexistent anterior basement membrane dystrophy.</AbstractText>

Complex phenotypic assays in high-throughput screening.

High-throughput screening (HTS), systematically testing thousands of small molecules to find candidates for lead optimization, primarily involves exposure of purified proteins to arrayed collections of small molecules. More complex phenotypic assays, such as cell-based or whole-organism assays, traditionally have flanked HTS, preceding it to validate new therapeutic targets, and following it to characterize new lead compounds in cellular contexts. Recently, however, cell- and organism-based phenotypic assays have increasingly been adopted as a primary screening platform for annotating small molecules.

Expression of rabbit IL-4 by recombinant myxoma viruses enhances virulence and overcomes genetic resistance to myxomatosis.

Rabbit IL-4 was expressed in the virulent standard laboratory strain (SLS) and the attenuated Uriarra (Ur) strain of myxoma virus with the aim of creating a Th2 cytokine environment and inhibiting the development of an antiviral cell-mediated response to myxomatosis in infected rabbits. This allowed testing of a model for genetic resistance to myxomatosis in wild rabbits that have undergone 50 years of natural selection for resistance to myxomatosis. Expression of IL-4 significantly enhanced virulence of both virulent and attenuated virus strains in susceptible (laboratory) and resistant (wild) rabbits. SLS-IL-4 completely overcame genetic resistance in wild rabbits. The pathogenesis of SLS-IL-4 was compared in susceptible and resistant rabbits. The results support a model for resistance to myxomatosis of an enhanced innate immune response controlling virus replication and allowing an effective antiviral cell-mediated immune response to develop in resistant rabbits. Expression of IL-4 did not overcome immunity to myxomatosis induced by immunization.

Allele frequencies of two polymorphisms associated with the factor IX gene in Iranian population.

Indirect genetic diagnosis using polymorphic DNA markers can be useful in large-scale screening programs, which is technically simpler, more rapid and amenable. The main objective of this study was to test the informativeness of two common intragenic markers (TaqI and XmnI) in Iranian haemophilia B families to detect the carriers by using a strategy that would be accurate and informative, yet less expensive compared to direct mutation analysis. The efficacy of these sites has been examined in 50 unrelated Iranian haemophilia B families and 50 normal females. The method used was polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP), which is economical and the enzymes XmnI and TaqI are cheap enough to be accessible in most of laboratories in developing countries. Our results show that 25% of X-chromosomes had the restriction site for TaqI enzyme. The XmnI site was 21%. The heterozygosity rates for TaqI and XmnI polymorphisms were 37% and 38%, respectively. Using the two polymorphisms together, the informative rate reached 46%. Taking advantage of TaqI and XmnI polymorphisms, carrier detection was performed for seven females with unknown status in five haemophilia B families (including one large extended family) with positive history. Six of the girls were normal and one was haemophilia B carrier. Therefore, carrier detection might be possible for informative Iranian haemophilia B families in the familial cases. Additionally, similarities in term of heterozygosity rates for these two polymorphic sites were seen between some European and Iranian populations.

Multiplex PCR-single-base extension genotyping of multiple glutathione S-transferase polymorphisms.

Identification of genetic polymorphisms has recently gained increased interest, since they can be used as markers to identify the genes that predispose to disease. This emerging role of genetic polymorphism in clinical association has created the need for high-throughput genotyping methodologies. The present study describes the development of an SBE (single-base extension) methodology for the parallel identification of genetic polymorphisms in glutathione S-transferase genes, a superfamily of phase II drug-metabolizing enzymes. Oligonucleotide PCR primers were designed for simultaneous amplification of GSTM1, GSTP1 and GSTT1 gene loci SBE primers were also designed to be specific for each loci and to stop one nucleotide 5'-upstream of the polymorphic location. A specific tag was associated with each SBE primer to guarantee further discrimination by length. After simultaneous amplification of the target gene loci from genomic DNA extracted from human blood samples, SBE reactions were performed with fluorescently labelled dideoxynucleotide triphosphates. Individual genotypes were identified after separation of each tag-SBE probe by PAGE. The multiplex/SBE methodology was validated with previously genotyped DNA samples extracted from 21 individuals and it was used in a blind assay to genotype additional 64 individuals. The results show that SBE leads to the same results as the current 'gold standard' restriction-fragment-length-polymorphism-based genotyping methodologies, since SBE is a robust and accurate genotyping methodology that enables the parallel identification of multiple polymorphisms in the same reaction.

Fine mapping of a murine growth locus to a 1.4-cM region and resolution of linked QTL.

Previous work identified a QTL affecting murine size (particularly tail length) in a cross between C57BL/6J and DBA/2J mice and refined its location to an 8-cM region between D1Mit30 and D1Mit57. The present study used recombinant progeny testing to fine map this QTL. Individuals from a partially congenic strain carrying chromosomes recombinant between D1Mit30 and D1Mit57 were mated to DBA/2J, generating 942 progeny. Two QTL affecting 10-week tail length were identified in this population: one at 9.7 cM distal to D1Mit30 (the position estimated in previous work), and another of smaller effect near D1Mit30. A second population ( n = 787) was generated by mating siblings from the progeny test population that were heterozygous for the same segment of chromosome, including only recombinants between D1Mit265 and D1Mit57. In the latter population, two QTL were also identified: one at 10.2 cM distal to D1Mit30, and another of smaller effect at the distal end of the mapped region (at D1Mit150). When the two populations were analyzed together, the estimated location of the central QTL was 10.2 cM distal to D1Mit30 and there was marginally significant evidence of the distal QTL. The central QTL explained approximately 7% of the phenotypic variance, and the 95% confidence interval for its position (determined by bootstrapping) was a 1.4-cM region, approximately the region from D1Mit451 to D1Mit219. The central QTL also affected tail length and body mass at 3 and 6 weeks of age, but to a lesser degree than 10-week tail length.

Genetic complexity of an obesity QTL ( Fob3) revealed by detailed genetic mapping.

Obesity is proving to be a serious health concern in the developed world as well as an unwanted component of growth in livestock production. While recent advances in genetics have identified a number of monogenic causes of obesity, these are responsible for only a small proportion of human cases of obesity. By divergent selection for high and low fat content over 60 generations, we have created Fat (F) and Lean (L) lines of mice that represent a model of polygenic obesity similar to the situation in human populations. From previous crosses of these lines, four body fat quantitative trait loci (QTL) were identified. We have created congenic lines (F(chr15L)), by recurrent marker-assisted backcrossing, to introgress the QTL region with the highest LOD score, Fob3 on Chr 15, from the L-Iine into the F-line background. We have further mapped this QTL by progeny testing of recombinants, produced from crosses between the F-line and congenic F(chrl5L) mice, showing that the Fob3 QTL region is a composite of at least two smaller effect QTL-the proximal QTL Fob3a is a late-onset obesity QTL, whereas the distal Fob3b is an early-onset obesity QTL.

Cancer vaccine development: protein transfer of membrane-anchored cytokines and immunostimulatory molecules.

Many tumor cells escape host-immune recognition by the downregulation or lack of immunostimulatory molecules. Expression of immunostimulatory molecules on tumor cells by gene transfer can be used to induce an antitumor immune response. However, we have previously shown that protein transfer of glycosyl-phosphatidylinositol (GPI)-linked costimulatory molecules is a successful alternative to traditional gene transfer in preparing such a tumor vaccine. Vaccination with membranes modified by protein transfer to express GPI-linked B7.1 (CD80), a costimulatory adhesion molecule, induces protective immunity in mice and allogeneic antitumor T-cell proliferation in humans in vitro. Our goal is to develop an optimal tumor vaccine using tumor membranes modified by protein transfer to target and stimulate antigen-presenting cells (APCs) and T cells. We have investigated the efficacy of expressing GPI-anchored cytokine molecules on the surface of tumor cells. Expression of interleukin-12 (IL-12) on tumor-cell membranes in a GPI-anchored form induces a strong antitumor immune response that is comparable to the effects of secretory IL-12. Because many cytokines act synergistically, we are testing the membrane expression and immunostimulatory effects of cytokines individually as well as in combination to determine potential complementary effects of coexpression on the antitumor immune response. Ultimately, the protein-transfer vaccination may be used in humans alone or in multimodal combination therapies to induce tumor regression and to serve as a protective measure to prevent postsurgical secondary metastases.

Constitutive expression of EIL-like transcription factor partially restores ripening in the ethylene-insensitive Nr tomato mutant.

Climacteric fruit ripening is regulated by the phytohormone ethylene. ETHYLENE-INSENSITIVE3 (EIN3) is a transcription factor that functions downstream from the ethylene receptors in the Arabidopsis ethylene signal transduction pathway. Three homologues of the Arabidopsis EIN3 gene have been identified in tomato, Lycopersicon esculentum, EIN3-like or LeEIL, LeEIL1, LeEIL2, and LeEIL3. These transcription factors have been proposed to be functionally redundant positive regulators of multiple ethylene responses. In order to test the role of such factors in the ethylene signal transduction pathway during ripening, EIL1 fused to green fluorescent protein (GFP) has been over-expressed in the ethylene-insensitive non-ripening Nr mutant of tomato. Increased levels of LeEIL1 compensated for the normally reduced levels of LeEIL1 in the Nr mutant, and transgenic Nr plants that exhibited high-level constitutive expression of LeEIL1GFP phenotypically resembled wild-type plants, the fruit ripened and the leaves exhibited epinasty, unlike Nr plants. The EIL1GFP fusion protein was located in the cell nuclei of ripe tomato fruit. The mRNA profile of these plants showed that the expression of certain ethylene-dependent ripening genes was up-regulated, including polygalacturonase and TOMLOX B. However, not all ripening genes and ethylene responses, such as seedling triple response, were restored. These results demonstrate that expressing candidate genes in the Nr ethylene-insensitive background is a valuable general approach for testing the role of putative downstream components in the ethylene-signalling pathway.

Transcriptional profiling of dysplastic lesions in K14-HPV16 transgenic mice using laser microdissection.

In the K14-HPV16 transgenic mouse model of human papillomavirus (HPV)-associated squamous cell cancers, HPV16 E6 and E7 oncogenes and E1 and E2 regulatory genes are driven by the K14 keratinocyte-specific promoter. HPV transcription varies within the different layers of the epithelium. The correlation between HPV transcription patterns and disease pathogenesis is not well understood. Understanding these patterns is critical to designing and testing new HPV-specific therapeutic strategies. We examined HPV gene expression in homogenous populations of cells microdissected from the stratum basale, stratum spinosum, and stratum corneum of lesions from the transgenic mice using PALM microlaser technology. RNA extracted from each cell layer was subjected to two-step gene-specific RT-PCR and real-time quantitative nested PCR. To ensure specific amplification of spliced transcripts, the primers used for real-time nested PCR spanned the splice sites. High levels of E2 were detected in the basal and supra-basal layers of hyperplastic and dysplastic lesions. E7 and E6* levels increased significantly over time in stratum basale and stratum spinosum. E6** was expressed at much lower levels. We showed that the transgenic mice express correctly spliced E2 transcripts and are suitable as a preclinical model to test a therapeutic strategy using transcriptional regulation by the E2 protein.

Progression of multiple sclerosis is associated with exon 1 CTLA-4 gene polymorphism.

Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system which is widely believed to have a T-cell-mediated etiology. The cytotoxic T-lymphocyte antigen-4 (CTLA-4) antigen molecule plays a key role in the downregulation of T-cell responses. To examine the genetic association of the CTLA-4 gene locus with MS, we analyzed an exon 1 (A49G) transition.</AbstractText>One hundred and fifty-two MS patients and 154 controls were examined. The A/G transition was genotyped by a polymerase chain reaction followed by labeling with a SNaPshot kit and detection using a capillary genetic analyzer.</AbstractText>The genotype, allele and phenotype frequencies did not differ significantly between MS patients and controls. Those MS patients with AA and AG genotypes had 4.36 times greater risk of progressing from the relapsing-remitting to the secondary progressive form of the disease than those with the GG genotype.</AbstractText>The results of our study indicate that CTLA-4 (A49G) exon 1 polymorphism is associated with MS progression.</AbstractText>

Single-molecule spectroscopy for nucleic acid analysis: a new approach for disease detection and genomic analysis.

Recently developed single-molecule spectroscopy (SMS) permits the analysis of fluorescent mixtures one molecule at a time. SMS methods provide the means to make rapid measurements on small, complex samples without the need for separations and target amplification enabling a new class of ultrasensitive nucleic acid assays. Here we give a brief overview of the current state of the art of SMS nucleic acid analysis and discuss ongoing work in our laboratory on two-color single-molecule fluorescence detection of specific nucleic acid sequences. In the future, two-color SMS nucleic acid assays will be used for a variety of applications including: gene expression analysis, disease detection and genomics.

Mouse models for Usher syndrome 1B.

Photoreceptor cell degeneration was not detected in any of the shaker1 alleles, except for a small but significant loss of photoreceptor cells found in Myo7a(4626SB/4626SB) mice that were also homozygous mutant for Cdh23v. Perhaps greater and/or faster photoreceptor cell loss that is dependent on mutant Myo7a can be effected by having additional mutant USH1 genes in the genetic background. In any case, it is argued that shaker1 mice are a useful model for testing USH1B gene therapy, due to the presence of mutant phenotypes other than photoreceptor cell death.

Medullary thyroid carcinoma. Genetic screening and prophylactic thyroidectomies.

Medullary thyroid cancer is a rare, neuroendocrine, tumor. It arises from parafollicular or C-cells with the ability to produce and secrete different bioactive substances like calcitonin (TC) and CEA (1-5) TC is ideal tumor marker in early diagnosis, in patents' follow up and in evaluation of their treatment. TC determinations after ca/pentagastrine stimulation test give us even more accurate results and the procedure is used for biochemical family screening. MTC occurs as a sporadic tumor or in hereditary settings MEN 2A, MEN 2B and FMCT. Germ/line point mutations in RET proto/onkogene are responsible for tumor arise and inheritance of settings. Genetic screening provides information of these RET mutations in family members even before pathologic changes occur. These individuals with MEN 2A, 2B and FMCT characteristic RET mutations are almost certain to acquire MTC (95% penetrance) in their lives and are candidates for preventive total thyroidectomy (TT), with or without central neck dissection (CND). Surgery is still the treatment of choice for MTC and only C-cell hyperplasia and early stage of MTC can be cured. Prophylactic thyroid surgery eliminates the possibility of MTC but doesn't influence appearance of other diseases (PHEO, HPTH) of MEN 2 syndromes.

Deafness due to A1555G mitochondrial mutation without use of aminoglycoside.

<AbstractText Label="OBJECTIVES/HYPOTHESIS" NlmCategory="OBJECTIVE">The objective was to clarify the characteristics of deafness associated with the A1555G mutation within mitochondrial 12S ribosomal RNA gene in the absence of aminoglycoside exposure.</AbstractText>Clinical and genetic studies in family members with the A1555G mitochondrial mutation were performed.</AbstractText>The subjects were 123 maternally related members of a large Japanese family with the A1555G mutation. All subjects had no previous history of exposure to aminoglycosides. Hearing disability and handicap, tinnitus, and medical histories were analyzed by interviews in all of the subjects, genetic testing was performed in 41 subjects, and pure-tone audiometry was conducted in 26 subjects with hearing disability and handicap.</AbstractText>The A1555G mutation was detected in a homoplasmic form (meaning that all the mitochondrial DNA carries the mutation) in all 41 subjects who were screened. The risk for developing postlingual hearing loss was likely to be much higher in the present subjects than in the general population. Both the severity and age at onset of the phenotype were similar in affected subjects within the same sibling group. Pure-tone averages were significantly worse in subjects who developed hearing loss before age 10 years than in those who developed hearing loss later.</AbstractText>The present study demonstrated that the prevalence of deafness in individuals with the A1555G mitochondrial mutation was likely to be high even in the absence of aminoglycoside exposure and clearly showed the association of severe to profound hearing loss with the onset of hearing loss before age 10 years.</AbstractText>

Genetic amniocentesis complications: is the incidence overrated?

To estimate the complication rate of 2nd-trimester amniocentesis and to determine the associated risk factors.</AbstractText>A retrospective chart review of genetic amniocenteses performed at a single tertiary care institution, from 1996 to 1998, was done. The variables studied included gestational age, indication for amniocentesis, number and site of needle punctures, and amniotic fluid color. Complications included fetal loss, rupture of membranes, and bleeding.</AbstractText>Out of the 1,347 procedures analyzed, the most common indications were advanced maternal age (72.3%) and abnormal triple screen (20.3%). Transplacental genetic amniocenteses totaled 234 (17.4%). Clear fluid was observed in 98.2% of the patients. Twenty-two complications (1.6%) were observed: fetal loss (0.22%), bleeding (0.59%), and rupture of membranes (0.82%). An abnormal karyotype was detected in 34 (2.5%) fetuses. In separate univariate logistic regression analyses, complications were significantly associated with gestational age [odds ratio OR = 1.19; 95% confidence interval CI = (1.08, 1.32); p = 0.001], number of punctures [OR = 8.2; 95% CI = (1.76, 37.97); p = 0.007], and ultrasound anomalies [OR = 5.82; 95% CI = (1.65, 20.58); p = 0.006]. Gestational age and number of punctures remained significant in multivariate logistic regression analysis.</AbstractText>Genetic amniocentesis performed at a tertiary care institution is rather safe, and the fetal loss rate of 0.22% is significantly lower (p &lt; 0.001) than the previously published incidence of 1/200. The risk of complications is significantly and independently associated with advanced gestational age and number of punctures.</AbstractText>

Coexistence of tuberous sclerosis and Friedreich ataxia.

Tuberous sclerosis (TS) is caused by point mutations in the TSC1 or TSC2 genes on chromosomes 9q33-34 or 16p13, respectively. Clinical manifestations can be quite variable but are primarily limited to cutaneous, neurologic, and cardiovascular abnormalities. Phenotypes range from neurologically devastated to those with silent lesions. A 34-year-old patient with genetically documented TSC1 developed progressive ataxia over a decade, without TS lesions to correlate with this finding. After evaluation of common causes including long-term antiepileptic regimens, DNA testing for hereditary ataxias was performed and revealed the presence of an additional mutation on chromosome 9. The patient was homozygous for the Friedreich ataxia (FA) mutation, with 500 and 700 GAA repeats in the FRDA gene on chromosome 9q13. There is no established relationship between these two disorders and the occurrence of two mutations on the same chromosome is probably coincidental but emphasizes the importance of searching for additional genetic causes when the phenotype does not fit with an established genetic diagnosis.

A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region.

The human Y chromosome is replete with amplicons-very large, nearly identical repeats-which render it susceptible to interstitial deletions that often cause spermatogenic failure. Here we describe a recurrent, 1.8-Mb deletion that removes half of the azoospermia factor c (AZFc) region, including 12 members of eight testis-specific gene families. We show that this "b2/b3" deletion arose at least four times in human history-likely on inverted variants of the AZFc region that we find exist as common polymorphisms. We observed the b2/b3 deletion primarily in one family of closely related Y chromosomes-branch N in the Y-chromosome genealogy-in which all chromosomes carried the deletion. This branch is known to be widely distributed in northern Eurasia, accounts for the majority of Y chromosomes in some populations, and appears to be several thousand years old. The population-genetic success of the b2/b3 deletion is surprising, (i) because it removes half of AZFc and (ii) because the gr/gr deletion, which removes a similar set of testis-specific genes, predisposes to spermatogenic failure. Our present findings suggest either that the b2/b3 deletion has at most a modest effect on fitness or that, within branch N, its effect has been counterbalanced by another genetic, possibly Y-linked, factor.

Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function.

Over 520 different amino acid substitution variants have been previously identified in the systematic screening of 91 human DNA repair genes for sequence variation. Two algorithms were employed to predict the impact of these amino acid substitutions on protein activity. Sorting Intolerant from Tolerant (SIFT) classified 226 of 508 variants (44%) as "Intolerant." Polymorphism Phenotyping (PolyPhen) classed 165 of 489 amino acid substitutions (34%) as "Probably or possibly damaging." Another 9-15% of the variants were classed as "Potentially intolerant or damaging." The results from the two algorithms are highly associated, with concordance in predicted impact observed for approximately 62% of the variants. Twenty-one to thirty-one percent of the variant proteins are predicted to exhibit reduced activity by both algorithms. These variants occur at slightly lower individual allele frequency than do the variants classified as "Tolerant" or "Benign." Both algorithms correctly predicted the impact of 26 functionally characterized amino acid substitutions in the APE1 protein on biochemical activity, with one exception. It is concluded that a substantial fraction of the missense variants observed in the general human population are functionally relevant. These variants are expected to be the molecular genetic and biochemical basis for the associations of reduced DNA repair capacity phenotypes with elevated cancer risk.

The neurofibromatoses: hereditary predisposition to multiple peripheral nerve tumors.

Neurosurgeons must be aware of the neuro-fibromatoses because they frequently present with nervous system tumors. Such patients develop numerous peripheral nerve sheath tumors; fortunately, only a few of these tumors are symptomatic or malignant. The tumor burden in individual patients can be remarkable, however, producing significant morbidity and requiring extensive or repeated care by a skilled neurosurgeon. Because it is impossible to predict which of the deep neurofibromas will undergo malignant transformation, it behooves clinicians and patients to be aware of any change in symptoms or growth of tumors, because early resection of MPNST offers the only chance for cure. Neurosurgical professionals should be familiar with the diagnostic criteria of the neurofibromatoses, because the patient who presents with an initial neurofibroma or schwannoma immediately falls into a category in which those disorders must be ruled out. In this regard, a family history of nerve sheath tumors is revealing and should prompt referral for a clinical genetics evaluation. Cutaneous manifestations of NFI can confirm the diagnosis at initial presentation. Missing the initial presentation of a patient with NF2 can lead to marked morbidity, such as deafness,because surveillance for subsequent tumors was inadequate. Tumorigenesis in all neurofibromatoses involves loss of tumor suppressor genes. These disorders illustrate that the two-hit loss of tumor suppressor gene model, which applies best for NF2, is oversimplified. As with most cancers,a theory of multistep progressive acquisition of genetic changes that promote unregulated grow this emerging in schwannomatosis. In addition, the hyperpigmentation and learning disability of NF 1 highlight that loss of one copy of the gene is sufficient to cause nontumoral manifestations of the disorder. Genetic counseling and testing have an important role in the diagnosis of NFI and NF2 as well as in the management of all the neurofibromatoses.

Novel UBA domain mutations of SQSTM1 in Paget's disease of bone: genotype phenotype correlation, functional analysis, and structural consequences.

Three novel missense mutations of SQSTM1 were identified in familial PDB, all affecting the UBA domain. Functional and structural analysis showed that disease severity was related to the type of mutation but was unrelated to the polyubiquitin-binding properties of the mutant UBA domain peptides.</AbstractText>Mutations affecting the ubiquitin-associated (UBA) domain of Sequestosome 1 (SQSTM1) gene have recently been identified as a common cause of familial Paget's disease of bone (PDB), but the mechanisms responsible are unclear. We identified three novel SQSTM1 mutations in PDB, conducted functional and structural analyses of all PDB-causing mutations, and studied the relationship between genotype and phenotype.</AbstractText>Mutation screening of the SQSTM1 gene was conducted in 70 kindreds with familial PDB. We characterized the effect of the mutations on structure of the UBA domain by protein NMR, studied the effects of the mutant UBA domains on ubiquitin binding, and looked at genotype-phenotype correlations.</AbstractText>Three novel missense mutations affecting the SQSTM1 UBA domain were identified, including a missense mutation at codon 411 (G411S), a missense mutation at codon 404 (M404V), and a missense mutation at codon 425 (G425R). We also identified a deletion leading to a premature stop codon at 394 (L394X). None of the mutations were found in controls. Structural analysis showed that M404V and G425R involved residues on the hydrophobic surface patch implicated in ubiquitin binding, and consistent with this, the G425R and M404V mutants abolished the ability of mutant UBA domains to bind polyubiquitin chains. In contrast, the G411S and P392L mutants bound polyubiquitin chains normally. Genotype-phenotype analysis showed that patients with truncating mutations had more extensive PDB than those with missense mutations (bones involved = 6.05 +/- 2.71 versus 3.45 +/- 2.46; p &lt; 0.0001). This work confirms the importance of UBA domain mutations of SQSTM1 as a cause of PDB but shows that there is no correlation between the ubiquitin-binding properties of the different mutant UBA domains and disease occurrence or extent. This indicates that the mechanism of action most probably involves an interaction between SQSTM1 and a hitherto unidentified protein that modulates bone turnover.</AbstractText>

Clinical biochemical genetics in the twenty-first century.

Genetic disorders are recognized to play an increasing role in pediatrics. Close to 10% of diseases among hospitalized children have been ascribed to Mendelian traits inherited as single gene defects, not a surprising figure considering that approximately 1000 inborn errors of metabolism (IEM) have been identified to date, primarily through the detection of endogenous metabolites abnormally accumulated in biological fluids and tissues. The laboratory discipline that covers the biochemical diagnosis of IEM is known as clinical biochemical genetics, and is defined as one concerned with the evaluation and diagnosis of patients and families with inherited metabolic disease, monitoring of treatment, and distinguishing heterozygous carriers from non-carriers by metabolite and enzymic analysis of physiological fluids and tissues. The biochemical genetics laboratory differs from the clinical chemistry laboratory in the extent of interpretation necessary to make its results meaningful to the clinician. While dramatic advances in molecular genetics have greatly changed the landscape of diagnostic options for many genetic disorders, a biochemical approach remains the dominant force for the diagnosis and monitoring of IEM. Owing to the stereotypical clinical presentation of many of these disorders, a major role of the biochemical genetics laboratory is to analyze ever more complex metabolic profiles to reach a preliminary diagnosis, which then needs to be confirmed by enzymic and/or molecular studies in vitro. Accordingly, the role of biochemical genetics in the pediatric practice of the 21st century is to provide a multicomponent screening process that can be divided into four major components: (i) at-risk screening (prenatal diagnosis); (ii) newborn screening (testing of presymptomatic patients); (iii) high-risk screening (testing of symptomatic patients); and (iv) postmortem screening (metabolic autopsy). The focus of our laboratory is to apply state-of-the-art technology such as tandem mass spectrometry to bring as many as possible IEM within the boundaries of newborn screening programs, and to investigate the role played by individual disorders in maternal complications of pregnancy, pediatric acute/fulminant liver failure, and sudden and unexpected death in early life.

A molecular description of brain trauma pathophysiology using microarray technology: an overview.

It has been estimated that 50% of human transcriptome, the collection of mRNA in a cell, is expressed in the brain, making it one of the most complex organs to understand in terms of genomic responses to injury. The availability of genome sequences for several organisms coupled with the increasing affordability of microarray technologies makes it feasible to monitor the mRNA levels of thousands of genes simultaneously. In this paper, we provide an overview of findings using both cDNA- and oligonucleotide-based microarray analyses after experimental traumatic brain injury (TBI). Specifically, the utility of this methodology as a means of cataloging the biochemical sequelae of brain trauma and elucidating novel genes or pathways for further study is discussed. Furthermore, we offer future directions for the continued evaluation of microarray results and discuss the usefulness of microarray techniques as a testing format for determining the efficacy of mechanism-based therapies.

Implantation of tumoral XC cells induces chronic, endothelin-dependent, thermal hyperalgesia in mice.

1. We describe here the alterations in the nociceptive sensitivity of Swiss CD1 mice receiving an intraplantar (i.pl.) administration of XC Rous sarcoma-virus-transformed rat fibroblasts (XC cells). 2. Histological studies reveal that XC cells remain at the injection site 2-3 weeks after implantation, a time at which an inflammatory reaction is also detected. No tumoral growth was found and 5 weeks after inoculation neither XC cells nor inflammatory reaction were observed. 3. Measures to different types of noxious stimuli were performed. At week 1 after XC cell inoculation, hyperalgesia to thermal, but not mechanical, stimuli as well as to capsaicin injection is present in the implanted paw. At week 5 after XC cell implantation, only thermal hyperalgesia is present, and this enhanced reactivity persisted for even 25 weeks after the disappearance of XC tumoral cells. 4. Pharmacological studies on thermal hyperalgesia were conducted at two different stages, week 1 and week 5 after XC cell inoculation. The systemic administration of morphine (1-10 mg/kg i.p. (intraperitoneal); 30 min before testing) prevents this thermal hyperalgesic reaction both at week 1 and week 5. The endothelin type A (ETA) receptor antagonist BQ-123 (10 nmol; i.pl.; 90 min before testing) abolishes both the early (week 1) and the late (week 5) thermal hyperalgesia. In contrast, the selective endothelin type B (ETB) receptor antagonist, BQ-788 (10 nmol; i.pl.; 90 min before) abolishes thermal hyperalgesia only at week 1, but not at week 5 after XC cell inoculation. 5. It might be concluded that endothelins are probably involved in this type of long-term thermal hyperalgesia produced by the transitory presence of the XC tumoral cell line.

Renal transplantation in amyloidosis: effects of HLA matching and donor type on recurrence of primary disease.

The aim of this study is to evaluate the effect of HLA-matching and donor type on recurrence of amyloidosis after renal transplantation. The study includes 30 patients with systemic amyloidosis who received kidney transplants between 1985 and 2001. Donor source and HLA tissue typing of the donor and recipient were evaluated in each case. Of the 30 patients, 20 developed a recurrence of amyloidosis in their allografts, as confirmed by biopsy. The time from transplantation to diagnosis of amyloidosis in the graft ranged from 18 months to 10 years. Of the 20 patients with recurrence, 18 had received their grafts from living related donors (LRDs), and 2 had received their grafts from cadaveric donors (P &lt; 0.01). There was a strong correlation between amyloidosis recurrence and degree of HLA-DR matching (P &lt; 0.05). Furthermore, in the recipients of LRD grafts, the risk of amyloidosis recurrence was much higher if the donor-recipient pair were HLA-identical than if they were not perfectly matched (P &lt; 0.01). The incidence of amyloidosis recurrence in our patients was significantly higher than the rates reported for other series. Most of the cases in previous reports involved cadaveric grafts. The higher rate of amyloidosis recurrence in our patients may be explained by the high proportion of LRD grafts and by genetic susceptibility.

Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

Genomic imprinting is an epigenetic chromosomal modification in the gametes or zygotes that results in a non-random monoallelic expression of specific autosomal genes depending upon their parent of origin. Approximately 44 human genes have been reported to be imprinted. A majority of them are clustered, including some on chromosome segment 11p15.5. We report here the imprinting status of the SLC22A1LS gene from the human chromosome segment 11p15.5</AbstractText>In order to test for allele specific expression patterns, PCR primer sets from the SLC22A1LS gene were used to look for heterozygosity in DNA samples from 17 spontaneous abortuses using PCR-SSCP and DNA sequence analyses. cDNA samples from different tissues of spontaneous abortuses showing heterozygosity were subjected to PCR-SSCP analysis to determine the allele specific expression pattern. PCR-SSCP analysis revealed heterozygosity in two of the 17 abortuses examined. DNA sequence analysis showed that the heterozygosity is caused by a G&gt;A change at nucleotide position 473 (c.473G&gt;A) in exon 4 of the SLC22A1LS gene. PCR-SSCP analysis suggested that this gene is paternally imprinted in five fetal tissues examined.</AbstractText>This study reports the imprinting status of the SLC22A1LS gene for the first time. The results suggest imprinting of the paternal allele of this gene in five fetal tissues: brain, liver, placenta, kidneys and lungs.</AbstractText>

Meta-analysis of genome-wide studies of psoriasis susceptibility reveals linkage to chromosomes 6p21 and 4q28-q31 in Caucasian and Chinese Hans population.

Ten genome-wide scans have been conducted over the past few years in the search for psoriasis susceptibility genes, but only one potential susceptibility region has been consistently replicated. A meta-analysis using the genome-search meta-analysis method was undertaken combining the results of six of these psoriasis genome-wide studies. The results of this analysis revealed linkage to the major histocompatibility complex on chromosome 6p21 that includes the PSORS1 locus. In addition, linkage was also recorded to a region on chromosome 4q28-q31 previously identified only in a Chinese Hans population. Both these regions were statistically significant even after correction for multiple testing. A possible reason for the erratic replication of findings could be the large effect of the PSORS1 locus (6p21) masking the effect of other loci involved in psoriasis. To overcome this problem, we suggest that future studies condition on the effect of the PSORS1 locus.

Novel targeted agents in the treatment of lung cancer.

Lung cancer is the leading cause of cancer-related mortality in the US. Although an improvement in outcome is possible with the continued advancement of cytotoxic-based treatment, clinical research is currently focused on utilising novel molecular targets with proven efficacy in preclinical models and a low toxicity profile. This is the result of advances in understanding of tumour biology and molecular pathways that have been implicated in cancer pathogenesis and progression. Novel agents targeting cell cycle regulation, angiogenesis and signal transduction pathways have reached clinical testing in lung cancer and are discussed in this review.

HIV pharmacogenomics: closer to personalized therapy?

Pharmacogenomics classically focuses on host nuclear genetic polymorphisms that can be used to predict adverse drug reactions (ADRs). Because ADRs are defined as any noxious, unintended, and undesired drug effects, loss of efficacy due to the development of antiretroviral drug resistance and both acute and cumulative adverse effects of antiretroviral therapy can be considered ADRs. In order to address these types of antiretroviral-associated ADRs, pharmacogenomic testing methods have expanded to include molecular assays that characterize extranuclear genetic material (e.g. HIV and mitochondrial genomes), as well as the host nuclear genetic material. Recent molecular advances permit high resolution resistance testing that detects loss of therapeutic efficacy through the use of phenotypic, genotypic and/or virtual phenotypic resistance testing. These assays use complex technical and interpretative methods to improve the therapeutic efficacy of antiretroviral therapy. The resistance assays demonstrate the utility of pharmacogenomic testing for patients undergoing lifelong and complex antiretroviral therapies. Future applications of antiretroviral-directed pharmacogenomic tests range from quantitative detection of mitochondrial depletion as an early surrogate marker for drug toxicity, to qualitative analysis of host immune haplotypes, and metabolic/transporter genetic polymorphisms for predicting disease progression. In summary, pharmacogenomic testing for HIV-positive patients provides proof of principle that these tests can be used clinically to improve outcomes for patients undergoing complex and sustained drug regimens.

Screening of coeliac disease in north Italian children with type 1 diabetes: limited usefulness of HLA-DQ typing.

To determine the contribution of HLA-DQA1* and HLA-DQB1* genes to the risk of coeliac disease (CD) in a cohort of children with type 1 diabetes mellitus (T1DM) from northern Italy.</AbstractText>Three hundred and fifty-seven children with T1DM, attending the Childhood Diabetes Unit of the University of Verona, have been regularly tested for serum IgA endomysial antibodies (EMA). All patients with positive EMA underwent small bowel biopsy to confirm the diagnosis of CD. HLA typing was performed in subjects with T1DM and CD, and in a control group of 79 EMA-negative patients with T1DM.</AbstractText>Of the 357 patients tested, 25 (7%) had CD. The frequency of HLA-DQA1*0501-DQB1*0201 (T1DM + CD 68% vs T1DM 62%) and of DQA1*0301-DQB1*0302 (T1DM + CD 40% vs T1DM 35%) haplotypes, between T1DM patients with and without CD, was statistically comparable. A trend towards a reduction of the risk of CD (p = 0.055, OR: 0.22, CI 0.05: 1.04) was observed in patients with T1DM (28% vs T1DM + CD 2%) who did not carry either the HLA-DQA1*0501-DQB1*0201 or the DQA1*0301-DQB1*0302 haplotype.</AbstractText>A high prevalence of HLA-DQA1* and -DQB1* susceptibility haplotypes for CD was observed both in EMA-negative diabetics and in those with associated CD. The implementation of screening programmes of CD in a T1DM population, based on the identification of HLA susceptibility haplotypes, seems to be of limited usefulness. Serial serologic screening of diabetic patients remains the advisable strategy.</AbstractText>

Linkage and association with the NOS2A locus on chromosome 17q11 in multiple sclerosis.

A large body of research supports a multifactorial cause in multiple sclerosis (MS), with an underlying genetic susceptibility likely acting in concert with undefined environmental exposures. Here, we used a highly efficient multilocus genotyping assay to study single nucleotide polymorphisms representing variation in 34 genes from inflammatory pathways in a well-characterized MS familial data set. Evidence of transmission distortion was present for several polymorphisms. Results for the NOS2A locus (exon 10 C/T, D346D) on chromosome 17q11 remained significant after correction for multiple testing and were reproduced in a second independent African American MS data set. In addition, linkage to a NOS2A promoter region polymorphism, (CCTTT)(n), was present in a third data set of multicase MS families. Our results provide strong evidence for linkage and association to a new candidate disease gene on chromosome 17q11 in MS and suggest that variation within NOS2A or a nearby locus contributes to disease susceptibility.

Population-based newborn screening for genetic disorders when multiple mutation DNA testing is incorporated: a cystic fibrosis newborn screening model demonstrating increased sensitivity but more carrier detections.

Newborn screening for cystic fibrosis (CF) provides a model to investigate the implications of applying multiple-mutation DNA testing in screening for any disorder in a pediatric population-based setting, where detection of affected infants is desired and identification of unaffected carriers is not. Widely applied 2-tiered CF newborn screening strategies first test for elevated immunoreactive trypsinogen (IRT) with subsequent analysis for a single CFTR mutation (DeltaF508), systematically missing CF-affected infants with any of the &gt;1000 less common or population-specific mutations. Comparison of CF newborn screening algorithms that incorporate single- and multiple-mutation testing may offer insights into strategies that maximize the public health value of screening for CF and other genetic disorders. The objective of this study was to evaluate technical feasibility and practical implications of 2-tiered CF newborn screening that uses testing for multiple mutations (multiple-CFTR-mutation testing).</AbstractText>We implemented statewide CF newborn screening using a 2-tiered algorithm: all specimens were assayed for IRT; those with elevated IRT then had multiple-CFTR-mutation testing. Infants who screened positive by detection of 1 or 2 mutations or extremely elevated IRT (&gt;99.8%; failsafe protocol) were then referred for definitive diagnosis by sweat testing. We compared the number of sweat-test referrals using single- with multiple-CFTR-mutation testing. Initial physician assessments and diagnostic outcomes of these screened-positive infants and any affected infants missed by the screen were analyzed. We evaluated compliance with our screening and follow-up protocols. All Massachusetts delivery units, the Newborn Screening Program, pediatric health care providers who evaluate and refer screened-positive infants, and the 5 Massachusetts CF Centers and their affiliated genetic services participated. A 4-year cohort of 323 506 infants who were born in Massachusetts between February 1, 1999, and February 1, 2003, and screened for CF at approximately 2 days of age was studied.</AbstractText>A total of 110 of 112 CF-affected infants screened (negative predictive value: 99.99%) were detected with IRT/multiple-CFTR-mutation screening; 2 false-negative screens did not show elevated IRT. A total of 107 (97%) of the 110 had 1 or 2 mutations detected by the multiple- CFTR-mutation screen, and 3 had positive screens on the basis of the failsafe protocol. In contrast, had we used single-mutation testing, only 96 (87%) of the 110 would have had 1 or 2 mutations detectable by single-mutation screen, 8 would have had positive screens on the basis of the failsafe protocol, and an additional 6 infants would have had false-negative screens. Among 110 CF-affected screened-positive infants, a likely "genetic diagnosis" was made by the multiple-CFTR-mutation screen in 82 (75%) versus 55 (50%) with DeltaF508 alone. Increased sensitivity from multiple-CFTR-mutation testing yielded 274 (26%) more referrals for sweat testing and carrier identifications than testing with DeltaF508 alone.</AbstractText>Use of multiple-CFTR-mutation testing improved sensitivity and postscreening prediction of CF at the cost of increased referrals and carrier identification.</AbstractText>

A new scoring system for the chances of identifying a BRCA1/2 mutation outperforms existing models including BRCAPRO.

To develop a simple scoring system for the likelihood of identifying a BRCA1 or BRCA2 mutation.</AbstractText>DNA samples from affected subjects from 422 non-Jewish families with a history of breast and/or ovarian cancer were screened for BRCA1 mutations and a subset of 318 was screened for BRCA2 by whole gene screening techniques. Using a combination of results from screening and the family history of mutation negative and positive kindreds, a simple scoring system (Manchester scoring system) was devised to predict pathogenic mutations and particularly to discriminate at the 10% likelihood level. A second separate dataset of 192 samples was subsequently used to test the model's predictive value. This was further validated on a third set of 258 samples and compared against existing models.</AbstractText>The scoring system includes a cut-off at 10 points for each gene. This equates to &gt;10% probability of a pathogenic mutation in BRCA1 and BRCA2 individually. The Manchester scoring system had the best trade-off between sensitivity and specificity at 10% prediction for the presence of mutations as shown by its highest C-statistic and was far superior to BRCAPRO.</AbstractText>The scoring system is useful in identifying mutations particularly in BRCA2. The algorithm may need modifying to include pathological data when calculating whether to screen for BRCA1 mutations. It is considerably less time-consuming for clinicians than using computer models and if implemented routinely in clinical practice will aid in selecting families most suitable for DNA sampling for diagnostic testing.</AbstractText>

Changes in the utilization of prenatal diagnosis.

The impact of prenatal screening for Down syndrome has largely been assessed under the assumption that screening protocols and policies are fully used. To measure the overall effectiveness in actual clinical practice, we analyzed the tests performed by a single cytogenetics laboratory.</AbstractText>We reviewed all amniotic fluid and chorionic villus samples (CVS) processed by the University of Connecticut Health Center's cytogenetics laboratory for the years 1991 to 2002. We evaluated trends in the use of prenatal testing, referral indications, and the numbers of cytogenetic abnormalities identified.</AbstractText>The number of women receiving amniocentesis or CVS declined more than 50% from 1,988 in 1991 to 933 in 2002 (P &lt;.001), despite an increase in the number of women of advanced maternal age in the population served. There was a 68% decline in the number of women who underwent invasive prenatal testing solely on the basis of their age (1,314 in 1991 to 423 in 2002, P &lt;.001). The number of Down syndrome fetuses detected prenatally increased from 20 to 31 (P =.08), representing approximately one half of the affected pregnancies present in the population served. Between 1991 and 2002, the proportion of antenatal cytogenetic tests with a significant chromosomal abnormality increased from 1 in 43 (2.3%) to 1 in 14 (7.0%; P &lt;.001).</AbstractText>Advances in maternal serum screening and second-trimester ultrasonography have resulted in more judicious use of amniocentesis and chorionic villus sampling.</AbstractText>II-2</AbstractText>

Society and ethics - the genetics of disease.

Established guidance for the protection of human subjects in research has provided the framework for research and clinical practice in genetics. Three key principles to emerge are the requirements for consent, privacy and confidentiality. However, recent research on genetic susceptibility to common diseases indicates that it may be more difficult to decide if and when genetic testing will be appropriate. Risks of disease may be low and interventions may not be available. Today, debate is primarily focussed on ethical issues raised by the use and storage of genetic information. One of the earliest experiences of genetic testing for some people is likely to be in the area of pharmacogenetics. Debate about ethical issues has been focused on the implications of patient stratification, particularly with regard to the availability of medicines for small groups and the significance of racial variation in response to medicines. The possible use of personal genetic information by insurance companies and employers has also been an issue that legislators have taken seriously.

Increased rates of spontaneous sister chromatid exchange in lymphocytes of BRCA2+/- carriers of familial breast cancer clusters.

Heterozygous carriers of germ-line mutations of the BRCA2 breast cancer susceptibility gene are predisposed to breast, ovarian, pancreatic and other cancers. The BRCA2 protein is implicated in the maintenance of chromosome stability through its essential function in double-strand DNA repair and recombination. Our previous studies had revealed multiple intrachromosomal rearrangements, duplications, inversions and deletions on 9p23-24 in lymphocytes and fibroblasts of BRCA2+/- members from independently ascertained familial breast cancer clusters. In pursuit of evaluating if there is a subtle genomic instability in BRCA2+/- individuals, we have determined frequencies of spontaneous sister chromatid exchanges (SCEs) in BRCA2 wild-types and BRCA2 mutation carriers of two familial breast cancer clusters. Here, we demonstrate an average increase of 65% of spontaneous SCEs in BRCA2+/- versus BRCA2+/+ family members. In one cluster, the number of metaphases with multiple SCEs was 5-times higher in BRCA2+/- compared to wild-type members, while in the second cluster BRCA2+/- members had 8.9% of metaphases with multiple SCEs compared to a level below detection in BRCA2 wild types. To investigate the correlation between SCE and genomic instability in 9p, we performed fluorescence detection of SCEs and FISH analysis with 9p probes. The frequency of SCE in 9p of BRCA2 mutation carriers was 3-4 fold (P = 0.005) higher compared to BRCA2 wild-types. Collectively, the increased rates of SCE in BRCA2 heterozygous mutation carriers indicate a BRCA2 haploinsufficiency, which might be an important factor for the accumulation of structural chromosomal alterations with the consequence of damage in as yet unidentified genes.

Lack of evidence for association between serotonin transporter gene (5-HTTLPR) and obsessive-compulsive disorder by case control and family association study in humans.

Association studies of the serotonin transporter (SLC6A4) gene in obsessive-compulsive disorder (OCD) have generated discrepant results. Here, we genotyped the 5-HTTLPR polymorphism in 106 French OCD patients and 171 healthy controls (case control study). We also performed a family association study on 116 trios including an OCD patient (73 French and 43 German). No association was detected between the 5-HTTLPR polymorphism and OCD in either the case control study or the family study.

Exclusion of CYP46 and APOM as candidate genes for Alzheimer's disease in a French population.

Alzheimer's disease (AD) is a complex, multifactorial disorder, probably resulting from an interaction between environmental and genetic factors. Increasing evidence points to a link between cholesterol turnover and AD, suggesting that genes implicated in brain cholesterol homeostasis may be potential candidate genes for AD. With this background, we tested the potential association of the CYP46, APOM and APOF genes with the risk of developing AD. CYP46 encodes the enzyme cholesterol 24-hydrolase, which plays a key role in brain cholesterol turnover, and APOF and APOM encode apolipoproteins belonging to the large lipocalin family, which also includes ApoE. In contrast to two previous reports but in accordance with one other, we were unable to detect an association between an intron 2 polymorphism of CYP46 and AD. We also searched for polymorphisms within the APOM and APOF by dHPLC. We were unable to detect any polymorphisms in the coding and exon/intron sequences of the APOF. Finally, we excluded APOM as a genetic determinant of AD in our large French case control population.

Lack of association of interleukin-1beta polymorphism with Alzheimer's disease in the Jewish population.

A growing body of evidence suggests that Alzheimer's disease (AD) is associated with local inflammation processes, including the activation of inflammatory cytokines. We performed a case-control association study between sporadic AD patients and the exon 5 position +3953 polymorphism in the potent pro-inflammatory cytokine, interleukin-1beta (IL-1B). Recent association studies of this locus with AD revealed conflicting results, suggesting that the association - if it exists - is not universal but rather population specific. In our study no association was detected with AD: neither as a risk factor nor as a modifier gene affecting the age at onset and disease progression. These findings show no evidence for an association between the IL-1B +3953 polymorphism and AD in the Jewish population.

No evidence for tau duplications in frontal temporal dementia families showing genetic linkage to the tau locus in which tau mutations have not been found.

Given the remarkable similarities between the genetics of tau diseases and the genetics of alpha-synuclein diseases, and given the fact that we have recently found a triplication of the alpha-synuclein locus in a family in which we had shown linkage to the alpha-synuclein locus, we determined to test whether some of the several families with autosomal dominant frontal temporal dementia which show genetic linkage to the tau locus but in which tau mutations have not been found could be caused by similar structural mutations. We did not find any such mutations.

Rapid, comprehensive screening of the human medium chain acyl-CoA dehydrogenase gene.

Newborn screening by tandem mass spectrometry (MS/MS) identifies patients with medium chain acyl-CoA dehydrogenase (MCAD) deficiency the most frequently observed disorder of fatty acid oxidation. Molecular genetic analysis is becoming a common tool to confirm those identified as affected by prospective screening and for carrier detection in family studies. The A985G (K304E) mutation accounts for approximately 80% of mutant alleles in MCAD deficient patients, presenting symptomatically, while greater variability of mutant alleles is observed among cases identified through prospective screening. Aside from A985G, the mutation spectrum in MCAD deficient patients is heterogeneous such that comprehensive gene analysis is required. Traditionally the MCAD gene is assayed by sequencing the entire coding region. Although effective and definitive, this approach is expensive, turn around time is slow, and is poorly amenable to a clinical service molecular genetics laboratory. Dye-binding/high-resolution thermal denaturation is a rapid and homogeneous method by which to scan a PCR product for evidence of sequence aberration. PCR is performed in capillaries in the presence of the dsDNA-binding dye LCGreen I and subsequently the DNA/dye complexes are analyzed by high-resolution thermal denaturation. DNA sequencing was limited to fragments displaying abnormal melting profiles. Of 18 specimens analyzed, 11 have a genotype consistent with MCAD deficiency and seven have a genotype consistent with carrier status. Clinical and biochemical data corroborate that the genotype results identified the affected patients and differentiates them from carriers. The entire process is homogeneous requiring no post-PCR manipulation and is completed in under 3 h.

Development and implementation of a database system to manage a large-scale mouse ENU-mutagenesis program.

A mouse ENU-mutagenesis program at RIKEN GSC has been initiated to conduct a large-scale, genome-wide, early- and late-onset phenotypic screen of mutant mice. We screened about a hundred mice every week with a comprehensive set of phenotype assays including behavioral tests based on a modified SHIRPA protocol, blood tests (both clinical biochemical testing and hemogram), and measurement of locomotor activity in their home cages. To manage the entire program, we developed a client/server architecture database system and named it MUSDB (Mutagenesis Universal Support DataBase). It manages mouse husbandry, mating protocols, procedures for ENU injection and phenotypic screens, phenotype inheritance tests, preservation of sperm and organs, and other materials generated during the program. We have implemented MUSDB in quite a large-scale system that includes 150 client computers. It has, helped reduce typographical errors and provided simple and efficient operation via its front-end user interface. It significantly contributed to the communication within and between workgroups in the program and in the accumulation of various phenotypic and inheritance data.

Cognitive impairment associated with chemotherapy for cancer: report of a workshop.

Cognitive dysfunction may occur in some patients who receive chemotherapy. We provide a summary of an April 2003 workshop on this topic, that included medical oncologists, radiologists, clinical and experimental psychologists, and patient advocates. Current studies indicate that cognitive deficits are often subtle, although they are observed consistently in a proportion of patients, may be durable, and can be disabling. Deficits have been observed in a range of cognitive functions. Underlying mechanisms are unknown, although preliminary studies suggest there may be genetic predisposition and that cognitive impairment may be accompanied by changes in the brain detectable by neuroimaging. The following priorities were established for future research: (1) large-scale clinical studies that use both a longitudinal design and concurrent evaluation of patients with cancer who do not receive chemotherapy-such studies should address the probability and magnitude of cognitive deficits, factors that predict them, and underlying mechanisms; (2) exploration of discrepancies between subjective reports of cognitive dysfunction and the objective results of cognitive testing; (3) studies of cognitive function in patients receiving treatment for diseases other than breast cancer, and in both men and women, to address the hypothesis that underlying mechanisms relate to changes in serum levels of sex hormones and/or to chemotherapy-induced menopause; (4) development of interventions to alleviate these problems; and (5) development of animal models and the use of imaging techniques to address mechanisms that might cause cognitive impairment associated with chemotherapy.

3-T proton MRS investigation of glutamate and glutamine in adolescents at high genetic risk for schizophrenia.

Glutamate and glutamine were examined in vivo in nonpsychotic adolescents at high genetic risk for schizophrenia by using 3-T proton magnetic resonance spectroscopy ((1)H-MRS).</AbstractText>Spectra from the right medial frontal lobe of 20 adolescents who had a parent with schizophrenia (high-risk group; mean age=16.4 years) were compared with spectra obtained from adolescent offspring of parents with no history of schizophrenia (low-risk group; mean age=16.7 years).</AbstractText>Glutamate/glutamine was significantly higher in the adolescents at high genetic risk for schizophrenia than in the low-risk offspring. Age, premorbid adjustment scale scores, and other (1)H-MRS metabolites did not differ between groups. Global Assessment of Functioning Scale scores and socioeconomic status were lower in the high-risk group.</AbstractText>The finding of glutamate/glutamine abnormalities in a group of subjects at high genetic risk for schizophrenia lends support for both the glutamate dysfunction and neurodevelopmental hypotheses for schizophrenia.</AbstractText>

SEREX identification of the autoantibodies that are prevalent in the cerebrospinal fluid of patients with moyamoya disease.

We performed SEREX (serological analysis of recombinant cDNA expression library) to identify autoantibodies that are prevalent in the cerebrospinal fluid of patients with moyamoya disease. These autoantibodies include PC326 (of unknown function), SRY (sex determining region Y), and peroxisomal D3,D2-enoyl-CoA isomerase.

Identification and evaluation of 55 genetic variations in the BRCA1 and the BRCA2 genes of patients from 50 Japanese breast cancer families.

We sequenced approximately 23 kb genomic regions containing all the coding exons and their franking introns of two breast cancer susceptibility genes, BRCA1 and BRCA2, of 55 individuals from 50 unrelated Japanese breast cancer families. We identified 55 single-nucleotide polymorphisms (SNPs) (21 in BRCA1 and 34 in BRCA2) containing nine pathogenic protein-truncating mutations (four in BRCA1 and five in BRCA2 from ten patients). Among the remaining 46 SNPs, allele frequencies of 40 were examined in both the breast cancer patients and 28 healthy volunteers with no breast cancer family history by PCR-RFLP or by direct DNA sequencing. Twenty-eight SNPs were common and were also found in the healthy volunteers and/or a SNP database. The remaining 18 were rare (allele frequency &lt;0.05) and were not found in the healthy volunteers and/or the database. The pathogenic significance of these coding SNPs (cSNPs) remains to be clarified. The SNP information from this study will be useful in the future genetic testing of both BRCA1 and BRCA2 genes in the Japanese population.

The effect of CYP3A5 and MDR1 (ABCB1) polymorphisms on cyclosporine and tacrolimus dose requirements and trough blood levels in stable renal transplant patients.

Cyclosporine and tacrolimus are immunosuppressive drugs largely used in renal transplantation. They are characterized by a wide inter-individual variability in their pharmacokinetics with a potential impact on their therapeutic efficacy or induced toxicity. CYP3A5 and P-glycoprotein appear as important determinants of the metabolism of these drugs. The objective of this study was to investigate the effect of CYP3A5 and MDR1 (ABCB1) polymorphisms on cyclosporine and tacrolimus dose requirements and trough blood concentrations in stable transplant patients. Stable renal transplant recipients receiving cyclosporine (n = 50) or tacrolimus (n = 50) were genotyped for CYP3A5*3 and *6, and MDR1 C1236T, G2677T/A and C3435T. Dose-adjusted trough blood levels (ng/ml per mg/kg body weight) as well as doses (mg/kg body weight) required to achieve target blood concentrations were compared among patients according to allelic status for CYP3A5 and MDR1. Dose-adjusted trough concentrations were three-fold and 1.6-fold higher in CYP3A5*3/*3 patients than in CYP3A5*1/*3 patients for tacrolimus and cyclosporine, respectively. In the case of tacrolimus, the difference was even more striking when considering CYP3A5*1/*1 patients showing dose-adjusted trough concentrations 5.8-fold lower than CYP3A5*3/*3 patients. For both drugs, no association was found between trough blood concentrations or dose requirement and MDR1 genotype. Multiple regression analyses showed that CYP3A5*1/*3 polymorphism explained up to 45% of the variability in dose requirement in relation to tacrolimus use. Given the importance of rapidly achieving target blood concentrations after transplantation, further prospective studies should consider the immediate post-graft period and assess the influence of this specific polymorphism. Beside non-genetic factors (e.g. steroids dosing, drugs interactions), CYP3A5 pharmacogenetic testing performed just before transplantation could contribute to a better individualization of immunosuppressive therapy.

Serotonin transporter promoter gene polymorphism and long-term outcome of antidepressant treatment.

This study investigates the relationship between the serotonin transporter linked polymorphic region (5-HTTLPR) and the long-term outcome of antidepressant treatment.</AbstractText>One hundred and twenty-eight patients with major depressive disorder were evaluated for long-term outcome (up to 3 years) of antidepressant treatment. The severity and improvement of depression were assessed with the Clinical Global Impression scale. The genotypes of 5-HTTLPR in the patients were determined using polymerase chain reaction.</AbstractText>During the long-term treatment of antidepressants (1-3 years of treatment), clinical improvement of depressive symptoms was more significant for carriers of the long (l) allele [l/l and l/short (s) genotypes] than for those possessing the s/s genotype (P=0.025 at 1 year, P=0.005 at 2 years, P=0.005 at 3 years). A response to treatment was also significantly more frequent in carriers of the l allele than in those with the s/s genotype (P=0.015).</AbstractText>These findings show that patients with major depressive disorder possessing the 5-HTTLPR l allele may exhibit a better long-term outcome when treated with antidepressants.</AbstractText>

High occurrence of simultaneous mutations in target enzymes and MtrRCDE efflux system in quinolone-resistant Neisseria gonorrhoeae.

Emergence of multidrug-resistant Neisseria gonorrhoeae resulting from new genetic mutations is a serious threat to controlling gonorrhea.</AbstractText>To determine 1) antimicrobial susceptibilities and the corresponding genetic mutations and 2) the role of MtrRCDE efflux system in gonococcal resistance to fluoroquinolones.</AbstractText>Antimicrobial susceptibility testing and sequence analysis of gyrA, parC, and mtrR loci of 131 N. gonorrhoeae isolates from Japan.</AbstractText>The proportion of N. gonorrhoeae strains resistant and intermediate-resistant to antimicrobials was 25.2% and 48.9% for ciprofloxacin, 25.2% and 30.5% for ofloxacin, 12.2% and 53.4% for penicillin; and 17.6% and 51.1% for tetracycline, respectively. Strains were categorized into 22 mutation profiles, with GyrA-S91F/ParC-D86N/MtrR-G45D being the most predominant profile. The frequency of mutation in gyrA, parC, mtrR, and the mtrR promoter was 71%, 47.3%, 77.1%, and 23.7%, respectively. Seventy-one percent of strains carried mutations in both gyrA and mtrR.</AbstractText>This study reports simultaneous mutations in fluoroquinolone target enzymes and the MtrRCDE efflux system as a fluoroquinolone-resistant mechanism in N. gonorrhoeae.</AbstractText>

Utility of hematological and iron-related screening in elite athletes.

To determine the clinical and performance related utility of hematological and iron-related screening in elite athletes.</AbstractText>Prospective cohort study.</AbstractText>The Department of Sports Medicine at the Australian Institute of Sport.</AbstractText>Male and female elite athletes undergoing routine medical screening over a period of 2 to 3 years.</AbstractText>Blood testing for hematological and iron-related biochemical variables.</AbstractText>White blood cell count, red blood cell count, hemoglobin, hematocrit, mean cell volume, mean cell hemoglobin concentration, platelet count, percent hypochromic red cells, serum iron, ferritin, transferrin, and percent transferrin saturation.</AbstractText>Eight female athletes (4.6%) had clinically relevant abnormal results, 6 with an obvious explanation on clinical history and examination and 1 who was diagnosed with hemochromatosis following genetic testing. Eighty-nine (51.1%) female athletes had abnormal results that were not associated with obvious clinical signs or symptoms. Twenty-seven female athletes had a serum ferritin less than 30 ng/mL and were placed on iron supplementation. In male athletes, 5 cases had screening abnormalities that were associated with illness or other factors identified during the clinical consultations. Nonclinically significant abnormalities in males were generally minor reductions in hemoglobin and/or hematocrit or minor alterations in red cell parameters. Five male athletes had a serum ferritin less than 30 ng/mL and were placed on iron supplementation.</AbstractText>Screening for hematological and iron-related abnormalities in male athletes has a very low yield. Due to the critical nature of the effects of anemia and low serum ferritin on some aspects of performance, it is reasonable to perform a full blood count and a serum ferritin on male athletes entering an elite training program. Further testing should be performed on clinical grounds. In females, the yield is greater. Again, it is reasonable to perform a full blood count and a serum ferritin on female athletes entering an elite training program. In view of their greater risk of iron depletion and to assess the effect of increased training inherent in elite programs, this could be repeated at 6-month intervals, or an isolated measurement of serum ferritin could be performed. Further testing should be performed on clinical grounds.</AbstractText>

Muir-Torre syndrome: role of the dermatopathologist in diagnosis.

Muir-Torre syndrome (MTS) is an autosomal dominantly inherited disorder characterized by sebaceous lesions and visceral malignancies. The defect is thought to be the result of a mutation in mismatch repair genes and associated with microsatellite instability. Two cases whose diagnoses were suggested first by the dermatopathologist are discussed. The first is a 47-year-old white man who over the past 6 years developed multiple sebaceous lesions. Due to the number of sebaceous lesions and their morphology, the possible diagnosis of MTS was suggested by the dermatopathologist. Subsequently, a lesion in the right colon was found during colonoscopy that proved to be a poorly differentiated cecal adenocarcinoma. A pedigree analysis revealed other family members afflicted with multiple malignancies. Genetic testing of the colonic adenocarcinoma showed microsatellite instability. The second patient is a 50-year-old white man who underwent biopsy of a skin lesion that showed features of both a sebaceous hyperplasia and sebaceous adenoma. Because of the mixed, unusual features of the lesion, the dermatopathologist suggested the diagnosis of MTS. It was later confirmed that the patient had a history of malignancies of the colon and kidney as well as a family history significant for multiple malignant neoplasms. These cases demonstrate the important role of the dermatopathologist in alerting the clinician to the possibility of Muir-Torre syndrome when the diagnosis of a sebaceous neoplasm is made, especially when unusual histologic features are observed.

Statistical framework for phylogenomic analysis of gene family expression profiles.

Microarray technology has produced massive expression data that are invaluable for investigating the genome-wide evolutionary pattern of gene expression. To this end, phylogenetic expression analysis is highly desirable. On the basis of the Brownian process, we developed a statistical framework (called the E(0) model), assuming the independent expression of evolution between lineages. Several evolutionary mechanisms are integrated to characterize the pattern of expression diversity after gene duplications, including gradual drift and dramatic shift (punctuated equilibrium). When the phylogeny of a gene family is given, we show that the likelihood function follows a multivariate normal distribution; the variance-covariance matrix is determined by the phylogenetic topology and evolutionary parameters. Maximum-likelihood methods for multiple microarray experiments are developed, and likelihood-ratio tests are designed for testing the evolutionary pattern of gene expression. To reconstruct the evolutionary trace of expression diversity after gene (or genome) duplications, we developed a Bayesian-based method and use the posterior mean as predictors. Potential applications in evolutionary genomics are discussed.

A large-scale screen for mutagen-sensitive loci in Drosophila.

In a screen for new DNA repair mutants, we tested 6275 Drosophila strains bearing homozygous mutagenized autosomes (obtained from C. Zuker) for hypersensitivity to methyl methanesulfonate (MMS) and nitrogen mustard (HN2). Testing of 2585 second-chromosome lines resulted in the recovery of 18 mutants, 8 of which were alleles of known genes. The remaining 10 second-chromosome mutants were solely sensitive to MMS and define 8 new mutagen-sensitive genes (mus212-mus219). Testing of 3690 third chromosomes led to the identification of 60 third-chromosome mutants, 44 of which were alleles of known genes. The remaining 16 mutants define 14 new mutagen-sensitive genes (mus314-mus327). We have initiated efforts to identify these genes at the molecular level and report here the first two identified. The HN2-sensitive mus322 mutant defines the Drosophila ortholog of the yeast snm1 gene, and the MMS- and HN2-sensitive mus301 mutant defines the Drosophila ortholog of the human HEL308 gene. We have also identified a second-chromosome mutant, mus215(ZIII-2059), that uniformly reduces the frequency of meiotic recombination to &lt;3% of that observed in wild type and thus defines a function required for both DNA repair and meiotic recombination. At least one allele of each new gene identified in this study is available at the Bloomington Stock Center.

Chromosomal anomalies in individuals with autism: a strategy towards the identification of genes involved in autism.

We review the different strategies currently used to try to identify susceptibility genes for idiopathic autism. Although identification of genes is usually straightforward in Mendelian disorders, it has proved to be much more difficult to establish in polygenic disorders like autism. Neither genome screens of affected siblings nor the large number of association studies using candidate genes have resulted in finding autism susceptibility genes. We focus on the alternative approach of 'positional cloning' through chromosomal aberrations in individuals with autism. In particular, balanced aberrations such as reciprocal translocations or inversions offer a unique opportunity, since only the genes in the breakpoint regions are candidate genes. This approach, in combination with others, is likely to produce results in the coming years.

Phenotypic expression of a family with multiple endocrine neoplasia type 2A due to a RET mutation at codon 618.

Multiple endocrine neoplasia type 2A (MEN2A) is caused by missense mutations in the RET proto-oncogene on chromosome 10. This paper reports the phenotypic expression of a family with MEN2A, in which serine substitutes for cysteine at codon 618 in exon 10 of the RET gene. It was first claimed that medullary thyroid cancer (MTC) with this rare mutation led to mild disease; this has recently been updated to intermediate-high risk, based on stratified genetic information.</AbstractText>The family was mapped over six generations. In 1971 family members were invited to join a screening programme. Genetic testing was started in 1994.</AbstractText>Twenty-two individuals with MTC were identified, 16 by the screening programme. One screened patient had a phaeochromocytoma and four had hyperparathyroidism. At surgery for MTC 12 patients had local tumour metastases and two young patients also had liver metastases. No screened patient died from MTC during a mean observation time of 19 years. Six other family members were diagnosed with MTC by signs and symptoms, five of whom died from MTC.</AbstractText>Because of the great interindividual differences in tumour aggressiveness within the family it is impossible to predict whether an individual gene carrier will have an aggressive MTC or not. This unpredictability is an additional argument, besides those obtained in stratified genetic studies, for operating on gene carriers at young age.</AbstractText>Copyright 2004 British Journal of Surgery Society Ltd. Published by John Wiley &amp; Sons, Ltd.</CopyrightInformation>

A novel PCR approach for prenatal detection of the common NEMO rearrangement in incontinentia pigmenti.

Incontinentia pigmenti (IP) is a rare X-linked dominant genodermatosis that is usually lethal in males in the prenatal period. Largely 80% of cases are accounted for by a large-scale deletion encompassing exons 4 to 10 of the NEMO gene. The aim of this work was to facilitate prenatal diagnosis of IP by devising a novel test for detection of the prevalent NEMO deletion.</AbstractText>We devised a sensitive and reproducible multiplex PCR test enabling simultaneous amplification of the deleted and wild-type NEMO genes in IP female individuals.</AbstractText>Combination of this DNA test, with Xq28 linkage analysis and X-inactivation pattern study enabled us to offer an IP prenatal diagnosis in 15 of the 16 couples at a 50% risk to have an affected offspring.</AbstractText>A current approach to IP prenatal diagnosis is proposed on the basis of the previously mentioned molecular tools.</AbstractText>Copyright 2004 John Wiley &amp; Sons, Ltd.</CopyrightInformation>

Genetic approach to prenatal diagnosis in urea cycle defects.

To demonstrate the feasibility of prenatal diagnosis by molecular genetics in all urea cycle defects in order to improve and standardize the current approaches.</AbstractText>Deceased index patients who had suffered from a urea cycle disorder were investigated for mutations of the biochemically most likely affected gene. If no material of index patients was available, parental DNA was studied for obligate carrier status. Fetal cells of 15 pregnancies, either chorionic villi or amniotic fluid cells, were used for direct sequence analysis of the respective mutations. Thirteen families were investigated, of which two were affected by N-acetylglutamate synthase deficiency, four by carbamoylphosphate synthetase 1 deficiency, one by ornithine transcarbamylase deficiency, three by argininosuccinate synthetase deficiency, two by argininosuccinate lyase deficiency, and one by arginase deficiency.</AbstractText>Molecular genetics allowed the determination of the fetal status in all cases. Besides 14 known mutations, we detected the novel mutation c.544delC of the N-acetylglutamate synthase gene, the novel missense mutation c.721G&gt;A (E241K) of the argininosuccinate lyase gene, and the novel double mutated allele comprising the known mutation c.703G&gt;A (G235R) and the novel insertion c.712ins[GGACC](2) (254X) of the arginase 1 gene.</AbstractText>Direct genetic analysis of chorionic villi or amniotic fluid cells is feasible, fast, and specific, and can be regarded as the method of choice for prenatal diagnosis in urea cycle disorders.</AbstractText>Copyright 2004 John Wiley &amp; Sons, Ltd.</CopyrightInformation>