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Optimal robust non-unique probe selection using Integer Linear Programming.

Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the presence or absence of biological agents, the targets, in a sample. Given a collection of genetic sequences of targets one faces the challenge of finding short oligonucleotides, the probes, which allow detection of targets in a sample. Each hybridization experiment determines whether the probe binds to its corresponding sequence in the target. Depending on the problem, the experiments are conducted using either unique or non-unique probes and usually assume that only one target is present in the sample. The problem at hand is to compute a design, i.e. a minimal set of probes that allows to infer the targets in the sample from the result of the hybridization experiment. If we allow to test for more than one target in the sample, the design of the probe set becomes difficult in the case of non-unique probes.</AbstractText>Building upon previous work on group testing for microarrays, we describe the first approach to select a minimal probe set for the case of non-unique probes in the presence of a small number of multiple targets in the sample. The approach is based on an ILP formulation and a branch-and-cut algorithm. Our preliminary implementation greatly reduces the number of probes needed while preserving the decoding capabilities.</AbstractText>http://www.inf.fu-berlin.de/inst/ag-bio</AbstractText>

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.

Our understanding of how genes are regulated in a concerted fashion is still limited. Especially, complex phenomena like cell cycle regulation in multicellular organisms are poorly understood. Therefore, we investigated conserved predicted transcription factor binding sites (TFBSs) in man-mouse upstream regions of genes that can be associated to a particular cell cycle phase in HeLa cells. TFBSs were predicted from selected binding site motifs (represented by position weight matrices, PWMs) based on a statistical approach. A regulatory role for a transcription factor is more probable if its predicted TFBSs are enriched in upstream regions of genes, that are associated with a subset of cell cycle phases. We tested for this association by computing exact P-values for the observed phase distributions under the null distribution defined by the relative amount of conserved upstream sequence of genes per cell cycle phase. We considered non-exonic and 5'-untranslated region (5'-UTR) binding sites separately and corrected for multiple testing by taking the false discovery rate into account.</AbstractText>We identified 22 non-exonic and 11 5'-UTR significant PWM phase distributions although expecting one false discovery. Many of the corresponding transcription factors (e.g. members of the thyroid hormone/retinoid receptor subfamily) have already been associated with cell cycle regulation, proliferation and development. It appears that our method is a suitable tool for detecting putative cell cycle regulators in the realm of known human transcription factors.</AbstractText>Further details and supplementary data can be obtained from http://corg.molgen.mpg.de/cellcycle</AbstractText>

Clustering of Parkinson disease: shared cause or coincidence?

The spatial and temporal pattern of excessive disease occurrence, termed clustering, may provide clues about the underlying etiology.</AbstractText>To report the occurrence of 3 clusters of Parkinson disease (PD) in Canada.</AbstractText>We determined the population groups containing the clusters, geographical limits, and duration of exposure to the specific environments. We tested whether there was an excessive presence of Parkinson disease by calculating the probability of the observed cases occurring under the null hypothesis that the disease developed independently and at random in cluster subjects. Results of genetic testing for mutations in the alpha-synuclein, parkin, tau genes, and spinocerebellar ataxia genes (SCA2 and SCA3) were negative.</AbstractText>The probabilities of random occurrence (P values) in the 3 clusters were P = 7.9 x 10 (-7)for cluster 1, P = 2.6 x 10 (-7)for cluster 2, and P = 1.5 x 10 (-7)for cluster 3.</AbstractText>Our findings indicate an important role for environmental causation in Parkinson disease. A possible role exists for environmental factors such as viral infection and toxins in the light of current evidence.</AbstractText>

Molecular biology of primary hyperparathyroidism.

As molecular biology and genetic mapping receive wider application to human disease, genetic alterations have been identified with increased frequency in some patients with primary hyperparathyroidism(HPT). These alterations have been found in molecules related to cellular signaling and growth (RET proto-oncogene)and in tumor suppressors that control cell cycle progression and gene transcription (cyclin D1 and the MEN1 gene product. Although primary HPT can usually be treated surgically without knowledge of which specific genetic alteration has occurred, this information may assist clinicians in identifying which patients will go on to develop multiglandular or recurrent disease. In addition,such an approach would facilitate more appropriate postoperative surveillance, as well as counseling and screening of family members who may be at high risk for HPT.

Eye colour: portals into pigmentation genes and ancestry.

Several recent papers have tried to address the genetic determination of eye colour via microsatellite linkage, testing of pigmentation candidate gene polymorphisms and the genome wide analysis of SNP markers that are informative for ancestry. These studies show that the OCA2 gene on chromosome 15 is the major determinant of brown and/or blue eye colour but also indicate that other loci will be involved in the broad range of hues seen in this trait in Europeans.

Screening for trisomy 21 in Flanders: a 10 years review of 40.490 pregnancies screened by maternal serum.

To evaluate maternal serum screening for trisomy 21 (MSS) in Flanders between 1992 and 2002.</AbstractText>Data of a large database on the results of MSS, nuchal translucency (NT) and pregnancy outcome were analysed retrospectively.</AbstractText>Despite an excellent performance of second trimester MSS at a maternal age &gt; or = 35 years (94.4% detection rate (DR) of trisomy 21 at a false positive rate (FPR) of 22.4%), the proportion of patients above 35 years of age in the study population was significantly lower than in the Flemish general pregnant population (5.5% versus 8.9%, P &lt; 0.001). In the population screened by MSS and NT, the DR of second trimester MSS at a 5% FPR was 44.4%, which was lower than 66.6% in the population screened by MSS without NT. When nine trisomy 21-affected pregnancies were compared to 3265 normal pregnancies, the mean NT-MoM values were not significantly different (1.16 +/- 0.89 versus 1.00 +/- 0.46, P &gt; 0.05). Both the findings comply to a sequential screening practice where second trimester MSS is only performed after a normal measurement of NT in the first trimester.</AbstractText>In Flanders, the uptake of second trimester maternal serum screening is low in women aged 35 years or more. Its screening performance decreased after the introduction of sequential screening.</AbstractText>

High-throughput detection of knockdown resistance in Myzus persicae using allelic discriminating quantitative PCR.

The peach-potato aphid Myzus persicae (Sulzer) has developed resistance to pyrethroid insecticides as a result of a mechanism conferring reduced nervous system sensitivity, termed knockdown resistance (kdr). This reduced sensitivity is caused by two mutations, L1014F (kdr) and M918T (super-kdr), in the para-type voltage-gated sodium channel. We have developed a diagnostic dose bioassay to detect kdr and provide preliminary information on the genotype present. We also developed two allelic discrimination PCR assays to determine precisely the genotypes of the two mutations (L1014F and M918T) in individual M. persicae using fluorescent Taqman MGB probes. In combination with assays for elevated carboxylesterase levels and modified acetylcholinesterase (MACE), this suite of assays allows for rapid high-throughput diagnosis, in individual aphids, of the three main resistance mechanisms of practical importance in the UK.

Mutational analysis of parkin gene by denaturing high-performance liquid chromatography (DHPLC) in essential tremor.

To evaluate the relationship between point mutations within the parkin gene and essential tremor (ET).</AbstractText>Essential tremor, the most common movement disorder, has long been recognised as an autosomal dominant disease. To date the genes involved in ET pathogenesis are still unknown. Several authors reported the association of ET with Parkinson's disease (PD).</AbstractText>One hundred and ten unrelated ET patients were analysed for point mutations within the parkin gene. Experimental conditions for DHPLC mutational analysis of the coding region of the parkin gene were set up.</AbstractText>Neither obvious disruptive mutations, nor mutations previously described in patients with Parkinson's disease were identified in the cohort of patients analysed. DHPLC analysis detected two already reported polymorphisms [c.1138G&gt;C (V380L) and c.1180G&gt;A (D394N)], and four novel rare variants (frequency &lt;1%) [c.645C&gt;A (H215Q); c.847C&gt;T (H279H); c.1393G&gt;A (V465M) and c.2695A&gt;G] located within exonic regions. Four new polymorphisms [c.413-20T&gt;C; c.872-35G&gt;A; c.872-68C&gt;G; c.1286-117A&gt;G], and one rare variant (c.934-3C&gt;T) were also found within intronic regions.</AbstractText>Causative sequence variants in the parkin gene have not been identified in this cohort of Italian ET patients.</AbstractText>

Characterization of ataxias with magnetic resonance imaging and spectroscopy.

A wide variety of autosomal transmitted ataxias exist and their ultimate characterization requires genetic testing. Common clinical characteristics among different ataxia types complicate the choice of the appropriate genetic test. Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) generally show cerebellar or cerebral atrophy and perturbed metabolite levels which differ between ataxias. In order to help the clinician accurately identify the ataxia type, reported MRI and MRS data in different brain regions are summarized for more than 60 different types of autosomal inherited and sporadic ataxias.

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

Autism and familial major mood disorder: are they related?

Family history studies of autism consistently reveal a large subgroup with a high incidence of major mood disorder in family members, suggesting the two entities are related clinically and genetically. This review examines this concept, comparing current clinlical and biological knowledge of autism and major mood disorder, and advances the hypothesis that this subgroup of autism represents an early-life phenotype of major mood disorder. If confirmed, this hypothesis would suggest that the basic biological defects determining major mood disorders may have prominent neurodevelopmental and cognitive dimensions. Testing of the hypothesis will depend on genetic studies.

American Association of Clinical Endocrinologists Medical Guidelines for clinical practice for the evaluation and treatment of hypogonadism in adult male patients--2002 update.

In these clinical practice guidelines, specific recommendations are made for determining the most effective methods of diagnosing and treating hypogonadism in adult male patients. The target populations for these guidelines include the following: (1) men with primary testicular failure requiring testosterone replacement (hypergonadotropic hypogonadism); (2) male patients with gonadotropin deficiency or dysfunction who may have received testosterone replacement therapy or treatment for infertility (hypogonadotropic hypogonadism); and (3) aging men with symptoms relating to testosterone deficiency who could benefit from testosterone replacement therapy. Initial hormonal evaluation generally consists of a testosterone determination, in conjunction with a free testosterone or sex hormone-binding globulin level, inpatients with clear symptoms and signs but normal-range total testosterone, follicle-stimulating hormone, luteinizing hormone, and prolactin levels. Other possible tests include semen analysis, pituitary imaging studies, genetic studies, bone densitometry, testicular ultrasonography,testicular biopsy, and specialized hormonal dynamic testing. Therapeutic options generally consist of testosterone replacement by injections, patches, or topically applied gel in hypergonadotropic patients and in hypogonadotropic patients not interested in fertility. In hypogonadotropic patients interested in fertility, gonadal stimulation option scan be considered, including human chorionic gonadotropin stimulation therapy with or without human menopausal gonadotropin (or follicle-stimulating hormone) or gonadotropin-releasing hormone pump therapy. These therapies may be combined with assisted reproductive technologies such as in vitro fertilization with intracytoplasmic sperm injection, which may allow pregnancy to occur with very low numbers of sperm.

Phenotypic and genetic influences on test-day measures of acetone concentration in milk.

The objectives of this study were to estimate heritability of acetone concentration in milk, based on monthly samples of milk obtained as part of a routine milk testing program, and to evaluate the feasibility of using such data in a genetic evaluation program for selection against ketosis incidence. Milk samples were collected from January to December of 1999 in herds enrolled in the Ontario Dairy Herd Improvement Association, and acetone concentration was measured using an inline chemical procedure. The original data included more than 50,000 records. Because ketosis is generally a problem during early lactation, only the single test with the fewest days in milk was retained. In addition, data were retained only for cows with pedigree information. The final data set included 10,375 records. Among these data, only 6.56% had detectable levels of acetone. Acetone data were log-transformed prior to statistical analysis. Simple ANOVA indicated that herd, parity number, days in milk, and month of test had significant effects on acetone concentration. Acetone levels increased with lactation number and were higher in early lactation. Three approaches were applied for genetic analysis. First, REML was used with a simple linear animal model. Then, a separate procedure used data augmentation and Gibbs Sampling to obtain continuously distributed underlying values for records with zero acetone concentration, and these data were analyzed with both an animal and sire model. Heritability of acetone concentration was less than 1% for all 3 analyses. Herd effects accounted for about 5% of the phenotypic variance. Low estimates of heritability were due either to low actual levels of genetic variance or inability to detect all of the genetic variance present, due to infrequent recording during the early part of the lactation. Genetic evaluation based on recording of acetone concentration on a monthly basis seems of little use as a selection tool to decrease incidence of ketosis.

Thymidylate synthase repeat polymorphisms and risk of neural tube defects in a population from the northern United Kingdom.

A 28-bp repeat polymorphism in the 5'UTR of the thymidylate synthase (TYMS) gene represents a candidate risk factor for neural tube defects (NTDs) due to involvement in folate-dependent homocysteine metabolism. Non-Hispanic, white, U.S. citizens carrying at least one 2x 28-bp repeat allele have recently been shown to be at a four-fold increased risk of spina bifida (SB). We investigated the association between this polymorphism and risk of NTD in families affected by NTDs and controls from the northern United Kingdom (UK).</AbstractText>PCR was performed on genomic DNA extracted from blood or mouth swabs of family members affected by NTDs (mothers, fathers, and cases), and unaffected controls (mothers and infants) to determine the number of 28-bp repeat units within the promoter region of TYMS. Case-control and TDT analyses of the influence of TYMS genotype on risk of NTD, or NTD pregnancy, were conducted.</AbstractText>Odds ratio (OR) analysis indicated that individuals carrying the 2x 28-bp repeat allele either in homozygous or heterozygous form, are not at increased risk of NTDs, or of having an NTD affected pregnancy. Control population allele frequencies are seen to be markedly different between the U.S. controls and those in this study.</AbstractText>TYMS polymorphism appears to be not universally associated with NTD risk across Caucasian samples. The elevated risk of spina bifida in U.S. samples appears to be driven by an unusually low risk allele (2x 28 bp) frequency in control samples. Family based (TDT) testing of U.S. samples is therefore advocated.</AbstractText>

Lack of association between polymorphisms of the toll-like receptor 4 gene and cerebral ischemia.

Toll-like receptor-4 (TLR4), an important mediator of the innate immune response, is expressed in atherosclerotic lesions. The common single nucleotide exchange (Asp299Gly) of the TLR4 gene has been previously reported to impair TLR4 function and to be associated with a decreased risk of carotid atherosclerosis. Therefore, we aimed to detect the potential impact of TLR4 genotypes on the risk of cerebral ischemia. We studied the prevalence of two common polymorphisms of the TLR4 gene (Asp299Gly and Thr399Ile) in 3 independent study populations: (1.) in a cross-sectional study including 769 patients either with type 1 or type 2 diabetes mellitus, of whom 56 (7.2%) had a history of cerebral ischemia (study 1), (2.) a case-control study (study 2) including 128 consecutive patients with cerebral ischemia, mean age 60 +/- 10.9 years and 139 control subjects, and (3.) a case-control study (study 3) including 171 young adults aged &lt; 50 years with cerebral ischemia and 204 control individuals. In all subjects, Asp299Gly and Thr399Ile were detected by restriction length analysis. The prevalence of the TLR4 genotypes was essentially the same between patients with cerebral ischemia and control subjects in all 3 study populations. Furthermore, there was also no association with the subgroup of atherosclerotic stroke in both case-control studies populations. Although TLR4 polymorphisms are associated with a decreased risk of carotid atherosclerotic lesions, our findings indicate that they do not influence the prevalence of cerebral ischemia. This implies that the Asp299Gly TLR4-allele might have a protective role in carotid atherosclerosis, but not in cerebral ischemia.

Familial adolescent-onset scoliosis and later segmental dystonia in an Irish family.

Adolescent-onset scoliosis occurs more frequently than expected in primary adult-onset cervical dystonia and a genetic association between the conditions has been postulated. The authors report a family in which four members have adult-onset cervical and/or brachial dystonia, two of whom have coexistent scoliosis. Four other individuals have isolated childhood- or adolescent-onset scoliosis. Adolescent-onset scoliosis may represent part of the dystonia phenotype in this family.

Two families with autosomal dominant progressive external ophthalmoplegia.

We report here the clinical and genetic features of two new families with autosomal dominant progressive external ophthalmoplegia (adPEO).</AbstractText>The examination of index patients included a detailed clinical characterisation, histological analysis of muscle biopsy specimens, and genetic testing of mitochondrial and nuclear DNA extracted from muscle and leucocytes.</AbstractText>Index patients in both families presented with PEO and developed other clinical disease manifestations, such as myopathy and cardiomyopathy (patient 1) and axonal neuropathy, diabetes mellitus, hearing loss, and myopathy (patient 2), later in the course of illness. Both patients had ragged red fibres on muscle histology. Southern blot of mtDNA from muscle of patient 2 showed multiple deletions. In this case, a novel heterozygous missense mutation F485L was identified in the nuclear encoded putative mitochondrial helicase Twinkle. The mutation co-segregated with the clinical phenotype in the family and was not detected in 150 control chromosomes. In the other index patient, sequencing of ANT1, C10orf2 (encoding for Twinkle), and POLG1 did not reveal pathogenic mutations.</AbstractText>Our cases illustrate the clinical variability of adPEO, add a novel pathogenic mutation in Twinkle (F485L) to the growing list of genetic abnormalities in adPEO, and reinforce the relevance of other yet unidentified genes in mtDNA maintenance and pathogenesis of adPEO.</AbstractText>

Genetic information: a joint account?

Does genetic information belong to the patient from whom it was obtained or to the whole family? The way in which this unavoidable question is answered has profound implications for the future of clinical practice in genetics

Human leukocyte antigen class II alleles and natural history of HPV 2/27/57-induced common warts.

Epidemiological studies have demonstrated an association between HLA-DQB1*03 alleles and the risk of cervical cancer induced by human papillomavirus (HPV). As persistence of HPV infection is required for developing cervical cancer, we wanted to elucidate the role of HLA-class II allele polymorphisms in the persistence of common warts induced by HPV 2, HPV 27 or HPV 57. Therefore, we determined the distribution of HLA-DQA1, -DQB1, and -DRB1 alleles in 71 patients presenting with HPV 2/27/57-induced common warts which had persisted for at least 18 months as well as in 92 individuals who had never suffered from common warts or whose warts had healed in less than 18 months. Among patients with long-lasting warts, the carriership frequencies and allele frequencies of DQA1*0301, DQB1*0301, DRB1*07 and DRB1*09 were higher, and the allele frequencies of DQA1*0501, DQB1*0603, DRB1*01 and DRB1*03 were lower. Statistically significant differences (Bonferroni adjusted Fisher's exact test) were found for carriership frequency of DQA1*0301 (46.5 vs 21.7%, P = 0.013) and for carriership frequency (18.3 vs 1.1%, P = 0.0015) and allele frequency (12 vs 0.5%, P = 0.000013) of DQB1*0301. A greater proportion of patients with long-lasting warts than of subjects without persistent warts were homozygous at the DQA1 (14.1 vs 6.5%) and DQB1 (16.9 vs 8.6%) gene loci. These results suggest that the natural history of cutaneous HPV 2/27/57-induced common warts may be modulated by allele polymorphisms at the HLA-DQA1 and HLA-DQB1 gene loci.

Dimension reduction methods for microarrays with application to censored survival data.

Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes, such as tumor class, drug response and survival time. While there has been extensive studies on tumor classification, there has been less emphasis on other phenotypic features, in particular, patient survival time or time to cancer recurrence, which are subject to right censoring. We consider in this paper an analysis of censored survival time based on microarray gene expression profiles.</AbstractText>We propose a dimension reduction strategy, which combines principal components analysis and sliced inverse regression, to identify linear combinations of genes, that both account for the variability in the gene expression levels and preserve the phenotypic information. The extracted gene combinations are then employed as covariates in a predictive survival model formulation. We apply the proposed method to a large diffuse large-B-cell lymphoma dataset, which consists of 240 patients and 7399 genes, and build a Cox proportional hazards model based on the derived gene expression components. The proposed method is shown to provide a good predictive performance for patient survival, as demonstrated by both the significant survival difference between the predicted risk groups and the receiver operator characteristics analysis.</AbstractText>R programs are available upon request from the authors.</AbstractText>http://dna.ucdavis.edu/~hli/bioinfo-surv-supp.pdf.</AbstractText>

Gene selection using a two-level hierarchical Bayesian model.

The fundamental problem of gene selection via cDNA data is to identify which genes are differentially expressed across different kinds of tissue samples (e.g. normal and cancer). cDNA data contain large number of variables (genes) and usually the sample size is relatively small so the selection process can be unstable. Therefore, models which incorporate sparsity in terms of variables (genes) are desirable for this kind of problem. This paper proposes a two-level hierarchical Bayesian model for variable selection which assumes a prior that favors sparseness. We adopt a Markov chain Monte Carlo (MCMC) based computation technique to simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer.</AbstractText>http://stat.tamu.edu/people/faculty/bmallick.html.</AbstractText>

Limited agreement among three global gene expression methods highlights the requirement for non-global validation.

DNA microarrays have revolutionized biological research, but their reliability and accuracy have not been extensively evaluated. Thorough testing of microarrays through comparison to dissimilar gene expression methods is necessary in order to determine their accuracy.</AbstractText>We have systematically compared three global gene expression methods on all available histologically normal samples from five human organ types. The data included 25 Affymetrix high-density oligonucleotide array experiments, 23 expressed sequence tag based expression (EBE) experiments and 5 SAGE experiments. The reported gene-by-gene expression patterns showed a wide range of correlations between pairs of methods. This level of agreement was sufficient for accurate clustering of datasets from the same tissue and dissimilar methods, but highlights the need for thorough validation of individual gene expression measurements by alternate, non-global methods. Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels.</AbstractText>

Scanning of beta-globin gene for identification of beta-thalassemia mutation in Romanian population.

Beta-thalassemia is uncommon (0.5%) in the Romanian population, but it must be considered in the differential diagnosis of hypochromic anemia. The molecular characterization of beta-thalassemia is absolutely necessary for molecular diagnosis, as well as any genetic epidemiological study in this region. Molecular analyses consist of mutation detection by molecular scanning of beta-globin gene. This gene has 3 exons and 2 introns, involved in beta-thalassemic pathogenesis. Clinical application of DNA analysis on beta-thalassemic chromosomes allowed characterization of 29 persons with different beta-thalassemia mutations among 58 patients with anemia. The experimental strategy was based on sequential PCR amplification of most of the beta-globin gene and running on denaturing gradient gel electrophoresis of amplification products. Definitive characterization of mutations in samples identified with shifted DGGE patterns was performed ARMS-PCR and/or PCR-restriction enzyme analysis methods. Eight different beta-thalassemia alleles were identified, the most common being IVS I-110 (G-A) and cd 39 (C-T). Comparison of overall frequency of mutations in the neighboring countries, shows that these results are in the frame of overall distribution of these mutations in Mediterranean area, especially in Greece and in Bulgaria. Molecular diagnosis is useful for differentiating mild from severe alleles, for genetic counseling, as well as for mutation definition in carriers, identified by hematological analysis necessary for prenatal testing and genetic counseling.

Kirby-Bauer disc approximation to detect inducible third-generation cephalosporin resistance in Enterobacteriaceae.

Resistance to beta-lactam antibiotics in enteric Gram-negative bacilli may be difficult to detect using standard methods of either Kirby-Bauer disc diffusion (KBDD) or broth dilution for minimal inhibitory concentration (MIC). This difficulty is due to genetic differences in resistance determinants, differences in levels of gene expression, and variation in spectra of enzymatic activity against the substrate beta-lactams used for susceptibility testing. We have examined 95 clinical isolates reportedly susceptible to ceftazidime and ceftriaxone, as originally determined by either KBDD or MIC methods. The organisms studied here were isolated in 2002 from two pediatric hospital centers (Seattle, USA and Shanghai, China). They belong to the inducible beta-lactamase producing Gram-negative bacilli, such as Enterobacter spp., Citrobacter spp., Serratia spp., Morganella spp., Providencia spp., and Proteus vulgaris. A Kirby-Bauer disc approximation (KBDA) method identified inducible phenotypes of third-generation cephalosporin resistance in 76% of isolates, which would otherwise be considered susceptible by standard KBDD methods.

Translation repression by an RNA polymerase elongation complex.

Bacteriophage lambda N and bacterial Nus proteins together with a unique site NUT in the leader of the early viral N gene transcript bind RNA polymerase (RNAP) and form a highly processive antitermination complex; N bound at NUT also represses N translation. In this study, we investigate whether N and NUT cause N translation repression as part of the antitermination complex by testing conditions that inhibit the formation of the N-modified transcription complex for their effect on N-mediated translation repression. We show that nus and nut mutations that in combination destabilize multiple interactions in the antitermination complex prevent N-mediated translation repression. Likewise, transcription of the nut-N region by T7 RNAP, which does not lead to the assembly of an effective antitermination complex when N is supplied, eliminates translation repression. We also demonstrate that a unique mutant beta subunit of RNAP reduces N-mediated translation repression, and that overexpression of transcription factor NusA suppresses this defect. We conclude that the N-modified RNAP transcription complex is necessary to repress N translation.

Genetic testing for single gene disorders.

Genetic testing for single gene disorders is becoming available in Sri Lanka. While it offers many benefits, there are concerns about psychological and social problems that can be a consequence of such tests. This article aims to review the potential benefits and disadvantages of genetic testing, and recommends mechanisms that would help minimise problems associated with the inappropriate use of genetic tests.

A longitudinal analysis of reproductive skew in male rhesus macaques.

One of the basic tenets of sexual selection is that male reproductive success should be large in polygynous species. Here, we analysed 6 years of molecular genetic data from a semi-free-ranging population of rhesus macaques (Macaca mulatta), using Nonac's B index, to assess the level of male reproductive skew in the study troop. On average, the top sire in each year produced 24% of the infants, while 71% of troop males sired no offspring at all. Consequently, 74% of infants had at least one paternal half-sibling in their own birth cohort. Reproductive success was greatest for high-ranking males, males who spent the whole mating season in the troop and males of 9-11 years of age. Heterozygosity for major histocompatibility complex (MHC) class II gene DQB1 was the strongest single predictor of male reproductive success. A negative relationship suggestive of female mate choice was noted between the B index and the proportion of extragroup paternities. Reproductive skew was not associated with relatedness among potential sires or with female cycle synchrony. We conclude that reproductive skew in male rhesus macaques is best accounted for by the 'limited-control' model, with multiple factors interacting to regulate individual reproductive output.

Genetic testing for breast and ovarian cancer susceptibility: evaluating direct-to-consumer marketing--Atlanta, Denver, Raleigh-Durham, and Seattle, 2003.

Breast and ovarian cancer are the second and fifth leading causes of cancer death, respectively, among women in the United States. One in eight women will have breast cancer during their lifetimes, and one in 70 will have ovarian cancer. Mutations in two genes, BRCA1 and BRCA2 (BRCA1/2), are associated with predisposition for inherited breast and ovarian cancer and are identified in 5%-10% of women with breast or ovarian cancer (BOC). Since 1996, genetic testing for these mutations has been available clinically; however, population-based screening is not recommended because of the complexity of test interpretation and limited data on clinical validity and utility. Despite the test's limited applicability in the general population, the U.S. provider of clinical BRCA1/2 testing (Myriad Genetic Laboratories, Inc., Salt Lake City, Utah) conducted a pilot direct-to-consumer (DTC) marketing campaign in two cities (Atlanta, Georgia, and Denver, Colorado) during September 2002-February 2003. Although DTC advertisements have been used to raise consumer awareness about pharmaceuticals, this was the first time an established genetic test was marketed to the public. To assess the impact of the campaign on consumer behaviors and health-care provider practices, CDC and the respective state health departments for the pilot cities and two comparison cities (Raleigh-Durham, North Carolina, and Seattle, Washington) surveyed consumers and providers. This report summarizes results of those surveys, which indicated that consumer and provider awareness of BRCA1/2 testing increased in the pilot cities and that providers in these cities perceived an impact on their practice (e.g., more questions asked about testing, more BRCA1/2 tests requested, and more tests ordered). However, in all four cities, providers often lacked knowledge to advise patients about inherited BOC and testing. These findings underscore the need for evidence-based recommendations on appropriate use of genetic tests and education of providers and the public to achieve maximum individual and public health benefit from genetic testing.

Medulloblastoma and retinoblastoma: oncology recapitulates ontogeny.

One major factor hindering progress of pediatric cancers of the nervous system has been the lack of satisfactory model systems for testing novel therapies. A mouse strain, mutant for the Rb1 gene was generated 12 years ago in the hope of producing a model in which to study retinoblastoma. Surprisingly, the Rb(+/-) mice never developed retinoblastoma. Now, Zhang, Schweers and Dyer produce triply deficient Rb, p107 and p53 mutant retinal progenitor cells. All such mice develop intraocular retinoblastoma with invasion of the tumor into the anterior chamber of the eye. This dramatic finding represents the first description of a heritable mouse model of retinoblastoma, which has eluded investigators for the last 12 years. Such models provide an unprecedented opportunity to advance knowledge of tumorigenesis and to develop non-toxic intervention strategies which eradicate disease.

Understanding germ-line mutations in BRCA1.

Germ-line mutations in BRCA1 account for the majority of familial breast and ovarian cancer cases and development of cancer in individuals who carry such mutations requires somatic inactivation of the normal allele. BRCA1 is highly polymorphic with more than 1,200 distinct documented variants. Approximately 70% of reported variants lead to absence of full-length BRCA1 protein, through loss of expression or protein truncation, and are suspected to predispose to cancer. These include regulatory mutations, splice site alterations, large rearrangements, large and small deletions or insertions, and nonsense mutations. However, characterizing the remaining missense alterations as either deleterious (cancer-associated mutations) or neutral variants is more complex, as the functional significance of the respective amino acid substitution is not straightforward to evaluate. In addition, many missense variants have been identified only once in defined ethnic groups and represent alleles with very low frequency. Most often, little information is available about segregation of the variant with disease in families, and assessment of disease risk for low frequency alleles through association studies is problematic, requiring a large number of samples stratified and matched by ethnicity. The fact that a significant proportion of BRCA1 variants remain unclassified represents a gap in risk assessment, such that individuals undergoing genetic testing will receive noninformative test results. An approach for assessing the potential clinical significance of missense variants is to combine available genetic data with functional and structural studies. Here we review the available information on BRCA1 variants and explore ways in which we can analyze unclassified variants.

Genome-wide screening using automated fluorescent genotyping to detect cryptic cytogenetic abnormalities in children with idiopathic syndromic mental retardation.

Mental retardation (MR) is the most common developmental disability, affecting approximately 2% of the population. The causes of MR are diverse and poorly understood, but chromosomal rearrangements account for 4-28% of cases, and duplications/deletions smaller than 5 Mb are known to cause syndromic MR. We have previously developed a strategy based on automated fluorescent microsatellite genotyping to test for telomere integrity. This strategy detected about 10% of cryptic subtelomeric rearrangements in patients with idiopathic syndromic MR. Because telomere screening is a first step toward the goal of analyzing the entire genome for chromosomal rearrangements in MR, we have extended our strategy to 400 markers evenly distributed along the chromosomes to detect interstitial anomalies. Among 97 individuals tested, three anomalies were found: two deletions (one in three siblings) and one parental disomy. These results emphasize the value of a genome-wide microsatellite scan for the detection of interstitial aberrations and demonstrate that automated genotyping is a sensitive method that not only detects small interstitial rearrangements and their parental origin but also provides a unique opportunity to detect uniparental disomies. This study will hopefully contribute to the delineation of new contiguous gene syndromes and the identification of new imprinted regions.

Genetic counseling for familial conditions during pregnancy: an analysis of patient characteristics.

Reproductive genetic counseling for a familial genetic risk factor preferably takes place before conception. However, of the women with a family history of genetic conditions who attend our department of clinical genetics, about 10-20% attend for the first time during a pregnancy. The current study aims to explore patient-related factors that may affect this late timing of reproductive genetic counseling. Consecutive pregnant (n = 100) and non-pregnant (n = 84) women visiting the department of clinical genetics for a genetic risk factor which was not age related completed a questionnaire immediately prior to the consultation. The questionnaire asked for (a) background characteristics, i.e. socio-demographic, obstetric, and disease characteristics (b) cognitive factors, i.e. initiative of referral, knowledge of the risk factor involved, risk perception, worry, child wish, attitudes toward abortion, and preferred participation in decision making, and (c) reasons for the timing of the consultation and for seeking genetic counseling. Pregnant women appeared to be higher educated, considered their children more often as healthy and were less often affected themselves, as compared to non-pregnant women. They also estimated their chance of having an affected child as lower, and they worried less. Furthermore, the initiative for referral was taken less often by the pregnant woman herself and more often by a medical worker. There were no major differences between the two study groups in knowledge, perceived severity of the risk factor, child wish, attitudes toward abortion, desired participation in decision making, and reasons to seek genetic counseling. Women indicated no specific reasons for their timing of referral for reproductive genetic counseling, e.g. during vs before pregnancy. Our data suggest that this timing of referral is not influenced predominantly by the women's level of knowledge. Rather, women's estimation of genetic risks and their degree of worry, which may be in accordance with the actual risk figures, seem to play a role in seeking genetic counseling. Although further studies are required, a more active role of health care providers seems warranted if we want to prevent genetic counseling for familial genetic conditions during pregnancy as much as possible.

Molecular analysis of patients with synostotic frontal plagiocephaly (unilateral coronal synostosis).

Mutations in genes known to be responsible for most of the recognizable syndromes associated with bilateral coronal synostosis can be detected by molecular testing. The genetic alterations that could cause unilateral coronal synostosis are more elusive. It is recognized that FGFR and TWIST mutations can give rise to either bilateral or unilateral coronal synostosis, even in the same family. The authors undertook a prospective study of patients presenting with synostotic frontal plagiocephaly (unilateral coronal synostosis) to Children's Hospital Boston during the period from 1997 to 2000. Mutational analysis was performed on all patients and on selected parents whenever familial transmission was suspected. Intraoperative anthropometry was used in an effort to differentiate those patients in whom a mutation was detected from those in whom it was not. The anthropometric measures included bilateral sagittal orbital-globe distance, inter medial canthal distance, and nasal angulation. Macrocephaly and palpebral angulation were also considered possible determinants. There was a 2:1 female preponderance in 47 patients with synostotic frontal plagiocephaly. Mutations were found in eight of 47 patients: two patients with different single-amino-acid changes in FGFR2, three patients with FGFR3 Pro250Arg, and three patients with TWIST mutations. Another patient had craniofrontonasal syndrome for which a causative locus has been mapped to chromosome X, although molecular testing is not yet available. Two features were strongly associated with a detectable mutation in patients with synostotic frontal plagiocephaly: asymmetrical brachycephaly (retrusion of both supraorbital rims) and orbital hypertelorism. Other abnormalities in the craniofacial region and extremities were clues to a particular mutation in FGFR2, FGFR3, TWIST, or the X-linked mutation. Neither macrocephaly nor degree of nasal angulation nor relative vertical position of the lateral canthi correlated with mutational detection. An additional four patients in this study had either unilateral or bilateral coronal synostosis in an immediate relative and had anthropometric findings that predicted a mutation, and yet no genetic alteration was found. This suggests either that the authors' screening methods were not sufficiently sensitive or that perhaps there are other unknown pathogenic loci. Nevertheless, molecular testing is recommended for infants who have unilateral coronal synostosis, particularly if there are the anthropometric findings highlighted in this study or an otherwise suspicious feature in the child or a parent. Infants with either an identified or a suspected mutation usually need bilateral asymmetric advancement of the bandeau and may be more likely to require frontal revision in childhood.

Feasibility study for a microchip-based approach for noninvasive prenatal diagnosis of genetic diseases.

Fetal DNA in maternal plasma may represent a source of genetic material for prenatal noninvasive diagnosis of genetic diseases. We evaluated a cohort of physiological pregnancies to determine if fetal DNA can be retrieved at any gestational week in sufficient quantity to be analyzed with advanced mutation detection technologies. We performed fetal DNA quantification by real-time polymerase chain reaction (PCR) on the SRY gene in 356 women sampled from 6 to 40 gestational weeks. Fetal DNA was retrieved at any week. All female fetuses were correctly identified. In 5 of 188 (2.6%) male-bearing pregnancies, no amplification was obtained. For noninvasive testing, complete clearance of fetal DNA after delivery is mandatory. Long-term persistence was not detected in women with previous sons or abortions. These findings confirm that maternal plasma may represent the optimal source of fetal genetic material. For noninvasive diagnosis of genetic diseases, we evaluated microchip technology. The detection limit for a minority allele determined by diluting a mutated DNA into a wild-type plasma sample was 5 genome equivalents, indicating that the test might be applied to the identification of paternally inherited fetal alleles in maternal plasma. The addition of peptide nucleic acids (PNAs) to either the PCR reaction or the chip hybridization mixture allowed approximately 50% inhibition of wild-type allele signals.

RET germline mutation in codon 791 in a family representing 3 generations from age 5 to age 70 years: should thyroidectomy be performed?

To describe a kindred with a rare RET germline mutation in codon 791 and discuss potential management strategies.</AbstractText>We present clinical and biochemical data as well as results of mutation analysis in our study subjects and provide an overview of related published reports.</AbstractText>Multiple endocrine neoplasia type 2 (MEN 2) is a familial cancer syndrome characterized by the development of medullary thyroid carcinoma (MTC), pheochromocytoma, and parathyroid hyperplasia or adenoma. Germline mutations in RET are responsible for this autosomal dominant syndrome. Familial MTC is a variant of MEN 2A and can be caused by RET mutations in codon 791. Deaths from gene carriers with mutations in these codons have not yet been reported. In general, gene carriers with these RET mutations have late-onset MTC. Because only a few kindreds with this specific mutation have been identified and no long-term follow-up data are available, management of these patients can be a challenge. We illustrate the difficulties with decisions about not only when to perform thyroidectomy in these patients but also whether thyroidectomy should even be considered in such gene carriers with a benign course. Our reported kindred included four carriers with a codon 791 RET germline mutation, one of whom had the rare concomitant occurrence of acromegaly and MEN 2A. The 70-year-old mother had acromegaly and hyperparathyroidism but normal serum calcitonin levels and normal findings on thyroid ultrasound examination. She refused pentagastrin testing and any surgical intervention. The 37-year-old daughter had hypothyroidism, a small thyroid gland, and negative results of pentagastrin stimulation testing of calcitonin. The 18-year-old grandson also had a negative pentagastrin test result and normal thyroid ultrasound findings. The 5-year-old granddaughter had normal results of thyroid ultrasonography. In all patients, we recommended thyroidectomy.</AbstractText>Prospective studies are needed to clarify which patients with codon 791 RET germline mutation should undergo thyroidectomy.</AbstractText>

Single step high-throughput determination of Toll-like receptor 4 polymorphisms.

Toll-like receptors are central components of host defence in humans, responsible for recognition of pathogen-associated molecular patterns and activation of innate immunity. Toll-like receptor 4 (TLR4) is activated by lipopolysaccharide (LPS) and other microbial components, thereby initiating the expression and release of pro-inflammatory cytokines. The common, frequently co-segregating allelic variants Asp299Gly and Thr399Ile have been related to susceptibility to gram-negative infections and sepsis and may be involved in the development of atherosclerosis. Identification of TLR4 Asp299Gly and Thr399Ile genotypes can be important for examination of genotype/phenotype relationships as well as for individual risk assessment of patients.</AbstractText>TLR4 Asp299Gly and Thr399Ile genotypes were detected by a single tube polymerase chain reaction (PCR), based on exonuclease degradation of dual labelled allele-specific oligonucleotides. The assay results were compared with conventional restriction fragment length polymorphism (RFLP) analysis.</AbstractText>Genotypes of 345 individuals were determined simultaneously in a single PCR assay. Allele frequencies for our population were 6.8% for the TLR4 Asp299Gly polymorphism and 6.4% for the Thr399Ile polymorphism. Validation by RFLP analysis revealed a correct detection of all genotypes.</AbstractText>We have developed a novel method for the detection of the TLR4 Asp299Gly and Thr399Ile mutations, permitting rapid genotyping which should be useful for large-scale population studies as well as applicable for routine clinical testing.</AbstractText>

Creating a stem cell donor: a case study in reproductive genetics.

During the nearly 10 years since its introduction, preimplantation genetic diagnosis (PGD) has been used predominantly to avoid giving birth to a child with identified genetic disease. Recently, PGD was used by a couple not only to test IVF-created embryos for genetic disease, but also to test for a nondisease trait related to immune compatibility with a child in the family in need of an hematropoetic stem cell transplant. This article describes the case, raises some ethical and policy issues, highlights gaps in U.S. policy, and finally makes some recommendations for addressing advancing genetic and reproductive technologies.

A genome scan and follow-up study identify a bipolar disorder susceptibility locus on chromosome 1q42.

In this study, we report a genome scan for psychiatric disease susceptibility loci in 13 Scottish families. We follow up one of the linkage peaks on chromosome 1q in a substantially larger sample of 22 families affected by schizophrenia (SCZ) or bipolar affective disorder (BPAD). To minimise the effect of genetic heterogeneity, we collected mainly large extended families (average family size &gt;18). The families collected were Scottish, carried no chromosomal abnormalities and were unrelated to the large family previously reported as segregating a balanced (1:11) translocation with major psychiatric disease. In the genome scan, we found linkage peaks with logarithm of odds (LOD) scores &gt;1.5 on chromosomes 1q (BPAD), 3p (SCZ), 8p (SCZ), 8q (BPAD), 9q (BPAD) and 19q (SCZ). In the follow-up sample, we obtained most evidence for linkage to 1q42 in bipolar families, with a maximum (parametric) LOD of 2.63 at D1S103. Multipoint variance components linkage gave a maximum LOD of 2.77 (overall maximum LOD 2.47 after correction for multiple tests), 12 cM from the previously identified SCZ susceptibility locus DISC1. Interestingly, there was negligible evidence for linkage to 1q42 in the SCZ families. These results, together with results from a number of other recent studies, stress the importance of the 1q42 region in susceptibility to both BPAD and SCZ.

Early-onset Alzheimer disease: when is genetic testing appropriate?

Alzheimer disease (AD) is a neurodegenerative disease that is currently not preventable or curable. Early-onset AD can be due to mutations in several autosomal dominant genes. Clinical testing is available for presenilin 1 (PS1), which is the most common of these genes. However, many practical and ethical issues must be considered before ordering this test for patients with early-onset AD. In this paper, we present a case that demonstrates the complexities of genetic testing for early-onset AD.

Beta 2-adrenergic receptor polymorphisms and haplotypes are associated with airways hyperresponsiveness among nonsmoking men.

To investigate the relationship of common single nucleotide polymorphisms (SNPs) of the beta(2)-adrenergic receptor (AR) gene at codons 16 and 27, and the intermediate phenotype of airways hyperresponsiveness.</AbstractText>A case-control study in 543 white men (152 case patients and 391 control subjects), who were nested in an ongoing longitudinal cohort.</AbstractText>Subjects were selected from the Normative Aging Study, an ongoing longitudinal cohort of healthy aging.</AbstractText>Case patients were defined as those having a positive response to methacholine challenge testing. Control subjects were selected among those who did not have a diagnosis of asthma and who had no response to methacholine.</AbstractText>There was a trend for an association of the Arg16 SNP genotype with airways hyperresponsiveness (odds ratio, 1.25; 95% confidence interval, 0.96 to 1.64 [in an additive model]). In stratified analyses, the effect of the Arg16 variant was seen mainly among nonsmokers. Smokers had increased risks for airway hyperresponsiveness regardless of genotype at either SNP. Using a program to estimate haplotype frequencies, three common haplotypes were identified. Adjusting for age, baseline FEV(1), serum IgE level, and smoking status, the Gly16/Gln27 haplotype was negatively associated with airways hyperresponsiveness in the full complement of case patients and control subjects (score statistic, - 2.43; p = 0.02). The effect of the beta(2)-AR haplotypes was much stronger among lifelong nonsmokers, among whom the Gly16/Gln27 haplotype remained negatively associated with airways hyperresponsiveness (score statistic, - 3.114; p = 0.002), whereas the Arg16/Gln27 haplotype was positively associated with airways hyperresponsiveness (score statistic, 3.142; p = 0.002). No effects were seen among ever-smokers.</AbstractText>In this cohort of middle-aged to older white men, beta(2)-AR polymorphisms were associated with airways hyperresponsiveness, particularly among lifelong nonsmokers. Our results illustrate an instance in which greater power is obtained by performing haplotype analyses as opposed to single SNP analysis.</AbstractText>

Screening for novel ENU-induced rhythm, entrainment and activity mutants.

Chemical mutagenesis has provided an opportunity to develop and expand the repertoire of behavioural mutants for gene function studies. With this in mind, we have established a screen in mice for mutations affecting circadian rhythms, entrainment to light and other wheel-running parameters. The screen consists of an assessment of mouse wheel-running activity in a 12:12 h light/dark cycle for 7-10 days followed by assessment in constant darkness for up to 20 days. Responses to light are assessed using two protocols; a 15 minute light pulse given at circadian time 16 on the tenth day in constant darkness and an additional 12 h of light upon transition from light/dark conditions to constant darkness. To date, approximately 1300 progeny of chemically mutagenised mice have been screened. Computer-aided assessment of wheel-running parameters has helped in identifying abnormal phenotypes in approximately 5% of all animals screened. Inheritance testing of mice with abnormal phenotypes has confirmed the number of robustly inherited mutant phenotypes to be 1% of the total screened. Confirmed mutants including those affecting free-running period, light-responsiveness and wheel-running endurance have been identified. Thus far, low-resolution map positions have been established for four mutants by completing genome scans in backcross progeny. Mutant loci do not correspond with those previously associated with wheel-running behaviour. This result confirms that phenotype-driven approaches such as this should continue to provide material for mammalian gene function studies.

Polymorphism of the mast cell chymase gene (CMA1) promoter region: lack of association with asthma but association with serum total immunoglobulin E levels in adult atopic dermatitis.

Mast cell chymase has the potential to be an important mediator of inflammation and remodelling in the asthmatic lung. Previous studies have examined association between promoter polymorphism of the chymase gene (CMA1) and allergic phenotypes but the significance of this polymorphism is unclear. We have examined association of a CMA1 variant in relation to asthma in a large UK Caucasian family cohort.</AbstractText>A polymorphism of the CMA1 gene promoter (-1903G/A) was genotyped in 341 asthmatic families and in 184 non-asthmatic adults recruited from the UK PCR-RFLP based genotyping. Association with asthma diagnosis, atopy, specific and total IgE, and atopy and asthma severity was examined.</AbstractText>Case-control studies did not reveal a significant difference in allele frequency between asthmatics and controls. A significant association was found between CMA1 genotypes and total IgE levels in subjects with self-reported eczema that remained significant after correction for multiple testing (median total serum IgE GG 297 kU/L, GA 144 kU/L, AA 48.4 kU/L, Pc=0.0032).</AbstractText>These data suggest that CMA1 promoter polymorphism does not contribute to asthma susceptibility or severity but may be involved in regulating IgE levels in patients with eczema.</AbstractText>

The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer.

Increasing interest in new pattern recognition methods has been motivated by bioinformatics research. The analysis of gene expression data originated from microarrays constitutes an important application area for classification algorithms and illustrates the need for identifying important predictors. We show that the Goodman-Kruskal coefficient can be used for constructing minimal classifiers for tabular data, and we give an algorithm that can construct such classifiers.

Association between HLA class II genes and autoantibodies to cyclic citrullinated peptides (CCPs) influences the severity of rheumatoid arthritis.

The functional role of HLA class II molecules in the pathogenesis of rheumatoid arthritis (RA) is unclear. HLA class II molecules are involved in the interaction between T and B lymphocytes required for long-lived B cell responses and generation of high-affinity IgG antibodies. We undertook this study to investigate the relationship between HLA class II gene polymorphisms and RA-specific IgG antibodies against cyclic citrullinated peptides (anti-CCP antibodies).</AbstractText>High-resolution HLA-DR and DQ typing and anti-CCP-2 antibody testing were performed on 268 RA patients from the Early Arthritis Clinic cohort at the Department of Rheumatology of the Leiden University Medical Center. The presence of anti-CCP antibodies was analyzed in carriers of the different DR and DQ alleles. Disease progression was measured over a period of 4 years by scoring radiographs of the hands and feet using the Sharp/van der Heijde method.</AbstractText>Carriership of the individual alleles HLA-DRB1*0401, DRB1*1001, DQB1*0302, and DQB1*0501 was associated with the presence of anti-CCP antibodies. Carriers of DQ-DR genotypes containing proposed RA susceptibility alleles were significantly more often anti-CCP antibody positive. Carriership of one or two HLA-DRB1 shared epitope (SE) alleles was significantly associated with production of anti-CCP antibodies (odds ratio [OR] 3.3, 95% confidence interval [95% CI] 1.8-6.0 and OR 13.3, 95% CI 4.6-40.4, respectively). An increased rate of joint destruction was observed in SE+, anti-CCP+ patients (mean Sharp score 7.6 points per year) compared with that in SE-, anti-CCP+ patients (2.4 points per year) (P = 0.04), SE+, anti-CCP- patients (1.6 points per year) (P &lt; 0.001), and SE-, anti-CCP- patients (1.6 points per year) (P &lt; 0.001).</AbstractText>HLA class II RA susceptibility alleles are associated with production of anti-CCP antibodies. Moreover, more severe disease progression is found in RA patients with both anti-CCP antibodies and SE alleles.</AbstractText>

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

The predictability of factor V Leiden (FV:Q(506)) gene mutation via clotting-based diagnosis of activated protein C resistance.

After the discovery of activated protein C resistance (APCR) due to factor V Leiden mutation and the causal relationship of the phenomenon with clinical thromboembolism, a wide variety of functional clotting-based assays were developed for testing of APCR in relation to the specific DNA-based analysis of FV:Q(506) Leiden. The aim of this study is to assess a clotting-based APCR assay using procoagulant crotalidae snake venom with respect to the sensitivity, specificity, and predictability for the presence of the factor V Leiden mutation. APCR testing and factor V DNA analyses have been performed concurrently on 319 patient specimens. APCR values of the patients with homozygous factor V Leiden mutation (70.4+/-13.5 s) were significantly lower (p&lt;0.001) in comparison to the subjects with the heterozygous mutation (87.6+/-13.4 s). The assay is highly sensitive (98.7%) and specific (91.9%) for the screening of factor V Leiden mutation. The sensitivity and specificity of the APCR testing reached to 100% below the cut-off value of 120 s among the patients with homozygous factor V Leiden mutation. Therefore, this method could help the desired effective optimal screening strategy for the laboratory search of hereditary thrombophilia focusing on the diagnosis of APCR due to FV:Q(506).

Cost-effectiveness analysis of HLA B*5701 genotyping in preventing abacavir hypersensitivity.

Abacavir, a human immunodeficiency virus-1 (HIV-1) nucleoside-analogue reverse transcriptase inhibitor, causes severe hypersensitivity in 4-8% of patients. HLA B*5701 is a known genetic risk factor for abacavir hypersensitivity in Caucasians. Our aim was to confirm the presence of this genetic factor in our patients, and to determine whether genotyping for HLA B*5701 would be a cost-effective use of healthcare resources.</AbstractText>Patients with and without abacavir hypersensitivity were identified from a UK HIV clinic. Patients were genotyped for HLA B*5701, and pooled data used for calculation of test characteristics. The cost-effectiveness analysis incorporated the cost of testing, cost of treating abacavir hypersensitivity, and the cost and selection of alternative antiretroviral regimens. A probabilistic decision analytic model (comparing testing versus no testing) was formulated and Monte Carlo simulations performed.</AbstractText>Of the abacavir hypersensitive patients, six (46%) were HLA B*5701 positive, compared to five (10%) of the non-hypersensitive patients (odds ratio 7.9 [95% confidence intervals 1.5-41.4], P = 0.006). Pooling of our data on HLA B*5701 with published data resulted in a pooled odds ratio of 29 (95% CI 6.4-132.3; P &lt; 0.0001). The cost-effectiveness model demonstrated that depending on the choice of comparator, routine testing for HLA B*5701 ranged from being a dominant strategy (less expensive and more beneficial than not testing) to an incremental cost-effectiveness ratio (versus no testing) of Euro 22,811 per hypersensitivity reaction avoided.</AbstractText>Abacavir hypersensitivity is associated with HLA B*5701, and pre-prescription pharmacogenetic testing for this appears to be a cost-effective use of healthcare resources.</AbstractText>

MS analysis of single-nucleotide differences in circulating nucleic acids: Application to noninvasive prenatal diagnosis.

The analysis of circulating nucleic acids has revealed applications in the noninvasive diagnosis, monitoring, and prognostication of many clinical conditions. Circulating fetal-specific sequences have been detected and constitute a fraction of the total DNA in maternal plasma. The diagnostic reliability of circulating DNA analysis depends on the fractional concentration of the targeted sequence, the analytical sensitivity, and the specificity. The robust discrimination of single-nucleotide differences between circulating DNA species is technically challenging and demands the adoption of highly sensitive and specific analytical systems. We have developed a method based on single-allele base extension reaction and MS, which allows for the reliable detection of fetal-specific alleles, including point mutations and single-nucleotide polymorphisms, in maternal plasma. The approach was applied to exclude the fetal inheritance of the four most common Southeast Asian beta-thalassemia mutations in at-risk pregnancies between weeks 7 and 21 of gestation. Fetal genotypes were correctly predicted in all cases studied. Fetal haplotype analysis based on a single-nucleotide polymorphism linked to the beta-globin locus, HBB, in maternal plasma also was achieved. Consequently, noninvasive prenatal diagnosis in a mother and father carrying identical beta-thalassemia mutations was accomplished. These advances will help in catalyzing the clinical applications of fetal nucleic acids in maternal plasma. This analytical approach also will have implications for many other applications of circulating nucleic acids in areas such as oncology and transplantation.

Preliminary evaluation of DNA damage related with the smoking habit measured by the comet assay in whole blood cells.

The alkaline single-cell gel electrophoresis (SCGE) assay, also called the comet assay, is a rapid and simple method for the detection of DNA damage in individual cells. The objective of this study was to establish if the alkaline SCGE assay in whole blood cells gives similar results as the same method in isolated lymphocytes, because whole blood cells are simpler and more economical to use, specifically in human genotoxic biomonitoring. To validate the method, we first used mouse blood cells, because mouse is one of the most commonly used animals in genetic toxicology testing. Groups of seven CF1 male mice were given i.p. injections of relatively low doses of methyl methanesulfonate (25 mg/kg body weight), a direct acting genotoxic agent, or cyclophosphamide (50 mg/kg body weight), which requires metabolic activation. Three, 6, 8, 12, 16, 20, and 65 hours after treatment, 5 microL of blood were collected from each animal and were processed for the alkaline SCGE assay. On the basis of an analysis of tail moment, the results showed that this assay can detect DNA damage induced by both kinds of alkylating mutagens. We then did a preliminary study to assess the status of DNA damage in a young (19 to 23 years old) healthy population of male smokers (n = 6) and nonsmokers (n = 6) using the comet assay in whole blood cells. A significant difference was observed between the two groups, showing that the method is able to detect DNA damage in the smoking group despite the short time that the volunteers had actually been smoking.

Haplotype associations of the MHC with psoriasis vulgaris in Chinese Hans.

Summary Haplotype associations of the major histocompatibility complex (MHC) with psoriasis vulgaris (PV) have been demonstrated in different racial or ethnic populations. The objective of this study was to demonstrate the different haplotype associations of the MHC in Chinese patients with psoriasis according to the type of onset and their sex. One hundred and thirty-eight patients with PV and 149 normal control subjects without psoriasis were typed for HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 by using the PCR with sequence-specific primers. The results showed: (i) HLA-A*26 (26.1% vs. 12.1%, Pc &lt; 1 x 10(-5)), -B*27 (17.03% vs. 1.01%, Pc &lt; 1 x 10(-7)), -Cw*0602 (15.58% vs. 5.03%, Pc &lt; 1 x 10(-2)), -DQA1*0104 (19.93% vs. 9.40%, Pc &lt; 1 x 10(-3)), -DQA1*0201 (22.40% vs. 10.74%, Pc &lt; 1 x 10(-3)), -DQB1*0303 (18.12% vs. 9.73%, Pc &lt; 1 x 10(-7)), and -DRB1*0701/02 (26.09% vs. 9.73%, Pc &lt; 1 x 10(-7)) were significantly increased in PV patients, while HLA-B*57, -DQB1*0201 were slightly increased in PV patients. HLA-Cw*0304 (5.07% vs. 14.43%, Pc &lt; 1 x 10(-3)), -DQA1*0501 (5.79% vs. 14.09%, Pc &lt; 0.05) were found to be negatively associated with PV, but HLA-A*2 (2.54% vs. 6.38%, Pc &lt; 0.5) was decreased in PV patients without statistical significance. (ii) HLA-A*26-B*27 [P &lt; 0.0001, odds ratio (OR) = 48.38], -A*26-Cw*0602 (P &lt; 0.0001, OR = 11.84), -B*27-Cw*0602 (P &lt; 0.0001, OR = undefined), -DRB1*0701/02-B*27 (P &lt; 0.0001, OR = 22.62), -DRB1*0701/02-DQA1*0104 (P &lt; 0.0002, OR = 3.59), -DRB1*0701/02-DQB1*0303 (P &lt; 0.0001, OR = 5.63), -DQA1*0201-DQB1*0303 (P &lt; 0.0002, OR = 7.77), -A*26-B*27-Cw*0602 (P &lt; 0.0004, OR = undefined), -A*26-DRB1*0701/02-DQA1*0201-DQB1*0303 (P &lt; 0.01, OR = undefined) were identified as risk haplotypes for patients with PV in China. (iii) HLA-A*26 -B*27 (P &lt; 0.0001, OR = 58.47), -DQA1*0201-DQB1*0303 (P &lt; 0.0001, OR = 8.62), -DRB1*0701/02 -DQA1*0104 (P &lt; 0.0002, OR = 4.13), -DRB1*0701/02-DQB1*0303 (P &lt; 0.0001, OR = 6.68) and -A*26-DRB1*0701-DQA1*0201 -DQB1*0303 (P &lt; 0.006, OR = undefined) were only significantly associated with type I psoriasis compared with controls, while others showed no differences in either type I or type II psoriasis. (iv) These associated haplotypes with PV were not different by sex, except that the frequency of DRB1*0701/02-DQB1*0303 (P &lt; 0.0001, OR = 10.14) was higher in male patients with psoriasis. To summarize, this study demonstrated a differential association of HLA and identified some special risk haplotypes in Chinese patients with PV compared with other ethnic or racial populations.

World-wide survey of an Accord insertion and its association with DDT resistance in Drosophila melanogaster.

Previous work showed that insecticide resistance in Drosophila melanogaster is correlated with the insertion of an Accord-like element into the 5' region of the cytochrome P450 gene, Cyp6g1. Here, we study the distribution of the Accord-like element in 673 recently collected D. melanogaster lines from 34 world-wide populations. We also examine the extent of microsatellite variability along a 180-kilobase (kb) genomic region of chromosome II encompassing the resistance gene. We confirm a 100% correlation of the Accord insertion with insecticide resistance and a significant reduction in variability extending at least 20 kb downstream of the Cyp6g1 gene. The frequency of the Accord insertion differs significantly between East African (32-55%) and nonAfrican (85-100%) populations. This pattern is consistent with a selective sweep driving the Accord insertion close to fixation in nonAfrican populations as a result of the insecticide resistance phenotype it confers. This study confirms that hitchhiking mapping can be used to identify beneficial mutations in natural populations.

No evidence of an MHC-based female mating preference in great reed warblers.

Female mate-choice based on genetic compatibility is an area of growing interest. The major histocompatibility complex (MHC) genes are likely candidates for such mate-choice since these highly polymorphic genes may both increase offspring viability and also provide direct cues for mate-choice. In great reed warblers, females actively choose a breeding partner out of a handful of males that they visit and evaluate; thus, female preference for compatible or heterozygous MHC genes could have evolved. Here, I investigate whether great reed warbler females preferentially mate with males with dissimilar MHC class I alleles or with males that are heterozygous at MHC class I. Despite favourable conditions, a thorough screening method and a large sample size, there was no evidence of an MHC-based female mating preference based on either genetic compatibility or heterozygosity in this population. Power analyses of the data sets revealed that relatively small differences (15% and 8%, respectively) between true and random pairs should have been detected.

Population genetics after fragmentation: the case of the endangered Spanish imperial eagle (Aquila adalberti).

The highly endangered Spanish imperial eagle, Aquila adalberti, has suffered from both population decline and fragmentation during the last century. Here we describe the current genetic status of the population using an extensive sampling of its current distribution range and both mitochondrial control region sequences and nuclear microsatellite markers. Results were evaluated in comparison to those obtained for the Eastern imperial eagle, Aquila heliaca, its nearest extant relative. Mitochondrial haplotype diversity was lower in the Spanish than in the Eastern species whereas microsatellite allelic richness and expected heterozygosity did not differ. Both allelic richness and expected heterozygosity were lower in the small Parque Nacional de Do&#xf1;ana breeding nucleus compared to the remaining nuclei. A signal for a recent genetic bottleneck was not detected in the current Spanish imperial eagle population. We obtained low but significant pairwise FST values that were congruent with a model of isolation by distance. FST and exact tests showed differentiation among the peripheral and small Parque Nacional de Do&#xf1;ana population and the remaining breeding subgroups. The centrally located Montes de Toledo population did not differ from the surrounding Centro, Extremadura and Sierra Morena populations whereas the latter were significantly differentiated. On the other hand, a Bayesian approach identified two groups, Parque Nacional de Do&#xf1;ana and the rest of breeding nuclei. Recent migration rates into and from Parque Nacional de Do&#xf1;ana and the rest of breeding nuclei were detected by assignment methods and estimated as 2.4 and 5.7 individuals per generation, respectively, by a Bayesian approach. We discuss how management strategies should aim at the maintenance of current genetic variability levels and the avoidance of inbreeding depression through the connection of the different nuclei.

Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas.

The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations.

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore.

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Retinoblastoma in Karachi, Pakistan.

The objective was to assess epidemiologic aspects of retinoblastoma development in Karachi, Pakistan. Incident cases, diagnosed clinically or microscopically and registered at Karachi Cancer Registry (KCR) during 1(st)January 1998 to 31(st) December 2002 were reabstracted, rechecked and reanalyzed for this purpose. One hundred and one cases of retinoblastoma were reported to KCR over the 5 years (1998-2002). Fifty-seven were residents of Karachi, 34 (59.6%) males and 23 (40.4%) females. The gender ratio (M:F) was 1.5. The mean age at diagnosis was 3.96 years (95% CI 2.92; 4.99) and 3.85 years (95% CI 2.72; 4.98) in males and females respectively. The annual crude incidence of retinoblastomas in Karachi was 4.0/100,000 and 2.4/100,000 in children under the age of 5 and 10 years respectively, the corresponding age standardized rates being 5.3/100,000 and 4.8/100,000. The age groups at risk of developing retinoblastoma, associated morbidity and possibility of almost 100% 5-year survival with available treatments, calls for ophthalmologic screening of all infants below 1 year, and high-risk children until the age of 7 years. In order to detect retinoblastoma, as early as possible, health education for parents and health providers, and improved training of ophthalmologists is essential. Genetic testing for siblings and children of retinoblastoma cases and identification of high-risk children would be helpful, but lacks financial feasibility in developing countries at present. Future health care planning should focus on capacity building for neonatal ophthalmologic screening, handling of parents'and children'emotional reactions and opportunities for education, occupational training and cosmetic rehabilitation for surviving retinoblastoma patients.

[The right to be born and the need to be born healthy... questions in medical ethics].

Science, thanks to the commitment of huge amount of human capitals, in many cases supported even by enormous fund investment, gain continuously ground reaching new position and spreading out the borders on human chances in a sphere so delicate like birth. New genetic screening tests, new contraceptive drugs using even more sophisticated features, comply with the new law on assisted insemination, put up new challenges involving all the scientific-social environments and necessitate precise answers on ethical side, but even concrete commitment on vocational training.</AbstractText>In this case we take working examples distinguished only on perception, as the pre-implant diagnosis, the morning after pill, and certain about the recent legislation on assisted insemination, to highlight their common scientific and cultural milieu. These problems call for an unquestionable and unique response, to restore clarity about choices involving the need and ability on human being to look for and find answers about existential matter as the beginning of life. Human being value and its significance need to be relentlessly restated, just because they are endlessly debated by a synergy of the emotional point of view, even impressive, and new stand out techniques.</AbstractText>in that sense vocational training is undeniable goal, even more, but not only, in a Faculty of Medicine. A student needs to learn to reflect on the relations between scientific forthcoming and their ethical and bioethical repercussion.</AbstractText>

Carrier screening for Canavan disease in Australia.

This study reports, for the first time, the carrier frequency of Canavan disease in the Ashkenazi Jewish population in Australia, and the identification of a novel mutation in the ASPA gene.

HIV RNA testing in the context of nonoccupational postexposure prophylaxis.

The specificity and positive predictive value of human immunodeficiency virus (HIV) RNA assays have not been evaluated in the setting of postexposure prophylaxis (PEP).</AbstractText>Plasma from subjects enrolled in a nonoccupational PEP study was tested with 2 branched-chain DNA (bDNA) assays, 2 polymerase chain reaction (PCR) assays, and a transcription-mediated amplification (TMA) assay. Assay specificity and positive predictive value were determined for subjects who remained negative for HIV antibody for &gt;or=3 months.</AbstractText>In 329 subjects examined, the lowest specificities (90.1%-93.7%) were seen for bDNA testing performed in real time. The highest specificities were seen with batched bDNA version 3.0 (99.1%), standard PCR (99.4%), ultrasensitive PCR (100%), and TMA (99.6%) testing. Only the 2 assays with the highest specificities had positive predictive values &gt;40%. For the bDNA assays, increasing the cutoff point at which a test is called positive (e.g., from 50 copies/mL to 500 copies/mL for version 3.0) increased both specificity and positive predictive values to 100%.</AbstractText>The positive predictive value of HIV RNA assays in individuals presenting for PEP is unacceptably low for bDNA-based testing and possibly acceptable for PCR- and TMA-based testing. Routine use of HIV RNA assays in such individuals is not recommended.</AbstractText>

Association of human-leukocyte-antigen class I (B*0703) and class II (DRB1*0301) genotypes with susceptibility and resistance to the development of severe acute respiratory syndrome.

Severe acute respiratory syndrome (SARS) is a public health concern worldwide. By studying the human leukocyte antigen (HLA) types A, B, DR, and DQ alleles in 90 Chinese patients with serologically confirmed SARS infections, we identified a strong association between HLA-B*0703 (OR, 4.08; 95% CI, 2.03-8.18; P=.00072 [Bonferroni-corrected P value, P(c) &lt;.0022]) and -DRB1*0301 (OR, 0.06; 95%, 0.01-0.47; P=.00008 [after Bonferroni correction, P&lt;.0042]) and the development of SARS. Moreover, the frequency of B*0703 and B60 coinheritance (9.6%; 95% CI, 4.6%-19.0%) in our SARS group was significantly higher (P=3x10(-9)) than that expected in the general population (0.4%). These genetic data will critically affect both the study of the pathogenesis of SARS and the design of vaccination programs.

[A psychodynamic approach in counselling vulnerable persons for Chorea Huntington -- a case report].

The availability of predictive testing for neurodegenerative diseases such as Chorea Huntington has far-reaching consequences on psychological, ethical, and legal issues. The special situation of persons vulnerable for the disease requires a comprehensive counselling including psychotherapeutic measures. On the basis of a case report, the authors outline a psychodynamic practice, which intends not only the identification of deliberate arguments and development of coping strategies, but also a clarification of unconscious backgrounds and expectations. In the discussion, the necessity of sufficient time is stressed that allows the reflection of repressed motives in respect of the genetic testing.

Identification of the severe acute respiratory syndrome coronavirus by simultaneous multigene DNA sequencing.

The recent severe acute respiratory syndrome (SARS) outbreak resulted in calls for an accurate diagnostic test that can be used not only for routine testing but also for generating nucleotide sequences to monitor the epidemic. Although the identity of the SARS coronavirus (SARS-CoV) genome was confirmed by DNA sequencing, it is impractical to sequence the entire 29-kb SARS-CoV genome on a routine basis. Therefore, alternative assay methods such as the enzyme-linked immunosorbent assay and PCR have been pursued for routine testing, primarily to resolve probable cases. We report here a modification of standard DNA sequencing technology for accurate identification of SARS-CoV in routine testing. Instead of requiring the sequencing of the whole SARS-CoV genome, our modification enables the simultaneous sequencing of three regions of the SARS-CoV genome, the spike protein-encoding gene (35 nucleotides), gene M (43 nucleotides), and gene N (45 nucleotides), in a single electropherogram. Comparing these nucleotide sequences to DNA databank entries (National Institutes of Health) conclusively identified them as SARS-CoV sequences.

Detection of human immunodeficiency virus type 1 antiretroviral resistance mutations by high-density DNA probe arrays.

Genotypic resistance testing has become an important tool in the clinical management of patients infected with human immunodeficiency virus type 1 (HIV-1). Standard sequencing methodology and hybridization-based technology are the two principal methods used for HIV-1 genotyping. This report describes an evaluation of a new hybridization-based HIV-1 genotypic test of 99 clinical samples from patients infected mostly with HIV-1 subtype B and receiving treatment. This test combines RNA extraction with magnetic silica particles, amplification by nested reverse transcriptase PCR, and detection with high-density probe arrays designed to detect 204 antiretroviral resistance mutations simultaneously in Gag cleavage sites, protease, reverse transcriptase, integrase, and gp41. The nested reverse transcriptase PCR success rates at viral loads exceeding 1,000 copies/ml were 98% for the 2.1-kb amplicon that covers the Gag cleavage sites and the protease and reverse transcriptase genes, 92% for the gp41 amplicon, and 100% for the integrase amplicon. We analyzed 4,465 relevant codons with the HIV-1 DNA chip genotyping assay and the classic sequence-based method. Key resistance mutations in protease and reverse transcriptase were identified correctly 95 and 92% of the time, respectively. This test should be a valuable alternative to the standard sequence-based system for HIV-1 drug resistance monitoring and a useful diagnostic tool for simultaneous multiple genetic analyses.

Eucaryotic expression of the nucleocapsid protein gene of porcine circovirus type 2 and use of the protein in an indirect immunofluorescence assay for serological diagnosis of postweaning multisystemic wasting syndrome in pigs.

The purpose of this study was to develop a sensitive, rapid, and inexpensive immunofluorescence assay (IFA) using a recombinant porcine circovirus type 2 (PCV2) nucleocapsid protein for the serological detection of PCV2-specific antibodies in pig sera. The viral nucleocapsid protein encoded by the PCV2 ORF2 gene has recently been identified as the most immunoreactive viral protein that carries type-specific antigenic determinants. The ORF2 sequence of the IAF-2897 strain of PCV2 has been cloned into a pCEP5 eucaryotic expression vector under the control of the cytomegalovirus promoter, downstream of a polyhistidine sequence tag. The recombinant plasmid was used in transfection experiments with human epithelial kidney 293 cells that were further tested, and positive expression of the viral nucleocapsid protein was confirmed by IFA and Western blotting. Strong, specific fluorescence was observed in the nuclei of transfected cells. Test specificity to PCV2 was verified with several related infectious agents. Sensitivity was compared to that of standard IFA using PCV2-infected cells by evaluating the reactivities of 44 field serum samples from pigs on farms with a porcine population suffering from postweaning multisystemic wasting syndrome. The recombinant nucleocapsid-based test was able to detect 15 more positive-testing pigs than the PCV2-based IFA. Therefore, the relative sensitivity of the latter test was estimated at only 57.1% compared to that of the recombinant nucleocapsid-based test. The recombinant fusion protein has been purified by affinity chromatography and is being used to develop further sensitive serological tests.

The phenotype of motor neuropathies associated with BSCL2 mutations is broader than Silver syndrome and distal HMN type V.

Silver syndrome is a rare autosomal dominant neurodegenerative disorder characterized by marked amyotrophy and weakness of small hand muscles and spasticity in the lower limbs. The locus for Silver syndrome (SPG17) was assigned to a 13 cM region on chromosome 11q12-q14 in a single large pedigree. We recently found heterozygous mutations in the Berardinelli-Seip congenital lipodystrophy (BSCL2, seipin) gene causing SPG17 and distal hereditary motor neuropathy type V (distal HMN V). Here we report the clinical features of two families with heterozygous BSCL2 mutations. Interestingly, both families show a clinical phenotype different from classical Silver syndrome, and in some patients the phenotype is also different from distal HMN V. Patients in the first family had marked spasticity in the lower limbs and very striking distal amyotrophy that always started in the legs. Patients in the second family had distal amyotrophy sometimes starting and predominating in the legs, but no pyramidal tract signs. These observations broaden the clinical phenotype of disorders associated with BSCL2 mutations, having consequences for molecular genetic testing.

Multiprotein HIV type 1 clade B DNA/MVA vaccine: construction, safety, and immunogenicity in Macaques.

Recently, a simian/human immunodeficiency virus (SHIV) vaccine consisting of priming with a Gag-Pol-Env-expressing DNA and boosting with a Gag-Pol-Env-expressing recombinant modified vaccinia Ankara (rMVA) has successfully controlled a virulent SHIV challenge in a macaque model. In this, and the accompanying paper, we report on the construction and testing of a Gag-Pol-Env DNA/MVA vaccine for HIV-1/AIDS. The DNA vaccine, pGA2/JS2, expresses aggregates of Gag proteins and includes safety mutations that render it integration, reverse transcription, and packaging defective. The rMVA vaccine, MVA/HIV 48, is integration and reverse transcription defective and has a truncated Env to enhance expression on the plasma membrane. In a study in rhesus macaques, priming with pGA2/JS2 and boosting with MVA/HIV 48 raised high frequencies of T cells for Gag and Env and lower frequencies of T cells for PR, RT, and Tat. Stimulations with five peptide pools for Gag and seven peptide pools for Env revealed epitopes for cellular immune responses throughout Gag and Env. On average, CD4 T cells from the vaccinated animals recognized 7.1 peptide pools and CD8 T cells, 3.2 peptide pools. Both the height and the breadth of the elicited cellular response provide hope that this multiprotein DNA/MVA vaccine will successfully control clade B isolates of HIV-1, as well as contribute to the control of other clades and recombinant forms of HIV-1/AIDS.

[Identification and management of HNPCC syndrome (hereditary non polyposis colon cancer), hereditary predisposition to colorectal and endometrial adenocarcinomas].

The HNPCC syndrome (hereditary non polyposis colon cancer) is an inherited condition defined by clinical and genealogical information, known as Amsterdam criteria. In about 70% of cases, HNPCC syndrome is caused by germline mutations in MMR genes, leading to microsatellite instability of tumor DNA (MSI phenotype). Patients affected by the disease are at high risk for colorectal and endometrial carcinomas, but also for small intestine, urothelial, ovary, stomach and biliary tract carcinomas. HNPCC syndrome is responsible for 5% of colorectal cancers. Identification and management of this disease are part of a multidisciplinary procedure.</AbstractText>12 experts have been mandated by the French Health Ministry to analyze and synthesize their consensus position, and the resulting document has been reviewed by an additional group of 4 independent experts.</AbstractText>The lack of sensitivity of Amsterdam criteria in recognizing patients carrying a MMR germline mutation led to an enlargement of these criteria for the recruitment of possible HNPCC patients, and to a 2-steps strategy, asking first for a tumor characterization according to MSI phenotype, especially in case of early-onset sporadic cases. The identification of germline MMR mutations has no major consequence on the cancer treatments, but influences markedly the long-term follow-up and the management of at-risk relatives. Gene carriers will enter a follow-up program regarding their colorectal and endometrial cancer risks, but other organs being at low lifetime risk, no specific surveillance will be proposed.</AbstractText>

Fecal-based DNA assays: a new, noninvasive approach to colorectal cancer screening.

Stool-based DNA testing is a new, noninvasive method of colorectal cancer screening. Because it is easier to use and more sensitive than fecal occult blood testing, physicians may be more likely to recommend it, and patients may be more apt to comply. Although it is expensive, initial assessments show it to be cost-effective.

Psychologic distress after disclosure of genetic test results regarding hereditary nonpolyposis colorectal carcinoma.

To the authors' knowledge, there have been few studies of the psychologic distress after disclosure of genetic test results for hereditary nonpolyposis colorectal carcinoma (HNPCC). The objectives of this study were to identify the prevalence rates and predictors of psychologic distress and to evaluate the feelings of guilt after disclosure of the test results in Japanese probands and unaffected relatives.</AbstractText>Probands and unaffected relatives were interviewed immediately after the first genetic counseling session for HNPCC and again 1 month after disclosure of the genetic test results. The prevalence of major and minor depression, acute stress disorder (ASD), posttraumatic stress disorder (PTSD), and posttraumatic stress symptoms (PTSS) were assessed using the Structured Clinical Interview based on the Diagnostic and Statistical Manual of Mental Disorders, 3rd edition revised (DSM-III-R) or the DSM-IV; feelings of guilt were investigated using a numeric scale and a semistructured interview.</AbstractText>Among 47 participants who completed the baseline interview, 42 participants (89%) completed the 1-month follow-up interview. Although none of the participants met the criteria for major depression, ASD, or PTSD at the follow-up interview, 3 of 42 participants (7%) met the criteria for minor depression and 2 participants (5%) had PTSS. The only predictor of psychologic distress found was the presence of a history of major or minor depression (odds ratio, 19.41; 95% confidence interval, 1.42-264.95; P &lt; 0.05). Five of 42 participants (12%) had feelings of guilt.</AbstractText>Disclosure of genetic test results for HNPCC may not cause significant psychologic distress in Japanese probands or relatives. However, healthcare providers should not neglect to assess these individuals for psychologic responses, such as minor depression and PTSS.</AbstractText>Copyright 2004 American Cancer Society.</CopyrightInformation>

Establishing the multidisciplinary care of patients with cancer in the state of Delaware.

Delaware has the fifth highest cancer death rate in the U.S. As part of a comprehensive program to decrease the cancer mortality and incidence in the state, an infrastructure to establish the multidisciplinary care of patients with cancer was established. In May 2002, Christiana Care Health Services opened the Helen F. Graham Cancer Center to meet the specific need for coordinated and centralized comprehensive cancer care. This effort took the cooperation of many individuals in a community-based teaching hospital, the largest of six acute care hospitals in the state. These efforts have led to a 13% accrual rate to the Community Clinical Oncology Program funded by the National Cancer Institute. The effort also led to the establishment of multidisciplinary disease site centers with representation from the three major physician disciplines of surgery, medical oncology, and radiation oncology. In addition, translational research projects, a tissue procurement center, and genetic counseling and testing with the establishment of a high-risk family cancer registry and collaborative efforts with hospitals across the state were established. The current article reviewed the continued success of this program in the state of Delaware in the effort to reduce the cancer incidence and mortality.

Real-time quantitative PCR as a routine method for screening large rearrangements in Rett syndrome: Report of one case of MECP2 deletion and one case of MECP2 duplication.

Mutations in the X-linked methyl-CpG-binding protein 2 gene (MECP2) are found in 70-80% of cases of classical Rett syndrome (RTT) and in about 50% of cases of preserved speech variant (PSV). This high percentage of MECP2 mutations, especially in classical RTT cases, suggests that another major RTT locus is unlikely. Missed mutations may be due to the limited sensitivity of the methodology used for mutation scanning and/or the presence of intronic mutations. In a double-copy gene, such as MECP2 in females, current methodologies (e.g., DGGE, SSCP, DHPLC, direct sequencing) are prone to miss gross rearrangements. Three previous reports during 2001-2003 have shown the presence of large deletions in a fraction of MECP2-negative classical RTT patients. We developed a reliable, single tube, quantitative PCR assay for rapid determination of MECP2 gene dosage. This method involves a multiplex reaction using a FAM labeled TaqMan probe with a TAMRA quencher derived from MECP2 exon 4 and two primers derived from the same exon and RNAaseP as an internal reference. The copy number of the MECP2 gene was determined by the comparative threshold cycle method (ddCt). Each sample was run in quadruplicate. We validated this assay through the analysis of 30 healthy controls (15 female and 15 male) and we then applied this method to eight classical RTT and six PSV patients, all negative for MECP2 mutations. We identified gross rearrangements in two patients: a deletion in a classical RTT patient and a duplication in a PSV patient. Our results confirm that a fraction of MECP2-negative RTT cases have MECP2 gross rearrangements and we propose real-time quantitative PCR as a simple and reliable method for routine screening of MECP2 in addition to DHPLC analysis.

Improved testing for CMT1A and HNPP using multiplex ligation-dependent probe amplification (MLPA) with rapid DNA preparations: comparison with the interphase FISH method.

Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP) are the two most common peripheral neuropathies, with incidences of about 1 in 2,500. Several techniques can be used to detect the typical 1.5-Mb duplication or deletion associated with these respective conditions, but none combines simplicity with high sensitivity. MLPA is a new technique for measuring sequence dosage. We have assessed its performance for the detection of the specific 1.5-Mb duplication/deletion by prospectively testing 50 patients referred with differential diagnoses of CMT or HNPP. Probes were designed to evaluate the TEKT3, PMP22, and COX10 genes within the CMT1A/HNPP region. We have compared the results with our existing fluorescence in situ hybridization (FISH) assay, which was performed in parallel. There was concordance of results for 49 patients. Of note, one patient showed an intermediate multiplex ligation-dependent probe amplification (MLPA) result with an abnormal FISH result, which is consistent with mosaicism. The assay works equally well with either purified DNA or rapid DNA preparations made by direct cell lysis. The use of the latter significantly reduces the cost of the assay. MLPA is a sensitive, specific, robust, and cost-effective technique suitable for fast, high-throughput testing and offers distinct advantages over other testing methods.

The role of common single-nucleotide polymorphisms on exon 9 and exon 12 skipping in nonmutated CFTR alleles.

Classic cystic fibrosis (CF) is caused by two loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, whereas patients with nonclassic CF have at least one copy of a mutant gene that retains partial function of the CFTR protein. In addition, there are several other phenotypes associated with CFTR gene mutations, such as idiopathic chronic pancreatitis. In CFTR-associated disorders and in nonclassic CF, often only one CFTR mutation or no CFTR mutations can be detected. In this study, we screened 23 patients with CFTR-associated disorders for CFTR mutations by complete gene testing and quantitative transcript analysis. Mutations were found in 10 patients. In cells from respiratory epithelium, we detected aberrant splicing of CFTR mRNA in all investigated individuals. We observed a highly significant association between the presence of coding single-nucleotide polymorphisms (coding SNPs, or cSNPs) and increased skipping of exon 9 and 12. This association was found both in patients and in normal individuals carrying the same cSNPs. The cSNPs c.1540A&gt;G, c.2694T&gt;G, and c.4521G&gt;A may have affected pre-mRNA splicing by changing regulatory sequence motifs of exonic splice enhancers, leading to lower amounts of normal transcripts. The analysis of CFTR exons indicated that less frequent and weak exonic splicing enhancer (ESE) motifs make exon 12 vulnerable to skipping. The number of splice variants in individuals with cSNPs was similar to previously reported values for the T5 allele, suggesting that cSNPs may enhance susceptibility to CFTR related diseases. In addition, cSNPs may be responsible for variation in the phenotypic expression of CFTR mutations. Quantitative approaches rather than conventional genomic analysis are required to interpret the role of cSNPs.

Genetic pathways and new progression markers for prostate cancer defined by microsatellite allelotyping.

A prospective study was carried out on a large cohort of males undergoing radical retropubic prostatectomy in order to identify genetic marker regions significantly associated with tumor formation. By comprehensive allotyping of chromosomes known to be associated with prostate carcinogenesis, an algorithm could be formulated for the genetic pathway and a method of discrimination between aggressive and less aggressive forms could be identified.

[Mitochondrial hearing impairment. Background, genetic predisposition and possibilities for diagnosis].

Hearing impairment (HI) is one of the most common neurosensory disorders, with sensorineural hereditary HI being the most common form. Mitochondrial maternally inherited HI appears to be increasing in frequency. The incidence of mitochondrial defects causing HI is estimated to be between 6 and 33% of all hearing deficiencies, with an even higher percentage for some syndromic cases. This review summarises the syndromic and non-syndromic characteristics of sensorineural HI based on mutations in mitochondrially encoded genes, the relationship to aminoglycoside-induced HI and related diagnostic tools.

[The genetic revolution-impact on therapy and prevention].

After the successful sequencing of the human genome the genetic variation between individuals will be worked out in the near future. The genetic differences are the basis for different predispositions to diseases. The next goal is to correlate the host of genetic variants with phenotypes. This endeavor has already been successful for monogenic diseases; however, it will also be possible in genetically complex diseases. If a trait follows a monogenic mode of inheritance, a phenotype results nearly completely from a single mutation; in genetically complex diseases there exists only a statistical relationship. Predictive genetic diagnostics should only be considered after genetic counseling; it makes sense, if there exists efficient prevention or therapy, respectively. This applies e. g. to various familial cancer predispositions. In the future, medical doctors should be able to apply genetic risk figures and to convey them to their patients.

Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers.

The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic level.

Motivation and ability to walk for a food reward in fast- and slow-growing broilers to 12 weeks of age.

Poor physical abilities of broilers may prevent them from performing behaviours for which they are motivated. The aim of this study was to measure the influence of physical ability and motivation on the performance of broilers in short physical tasks. We tested birds from a fast- and a slow-growing broiler strain in a runway to 12 weeks of age. To manipulate motivation, half of the birds of each strain was feed deprived for 3h and the other half for 24h before testing. Each bird was tested in a control and a slalom runway test once a week. With a similar motivation, slow growers had a shorter latency to start walking and walked faster through the runway than fast growers in both tests. In fast growers walking speed decreased faster with age than in slow growers. Slow growers vocalised more in both tests. In the slalom test, 24h deprived birds vocalised more than 3h deprived birds. Although the fast and slow growers have a different genetic background, the results indicated that motivation is the dominant determinative factor for walking in birds with a low body weight, while physical ability is the dominant determinative factor for walking in birds with a high body weight.

Polyphasic study of the genetic diversity of lactobacilli associated with 'Almagro' eggplants spontaneous fermentation, based on combined numerical analysis of randomly amplified polymorphic DNA and pulsed-field gel electrophoresis patterns.

The goal of this study was to assess the genetic diversity of lactic acid bacteria (LAB) from the complex natural ecosystem present in the spontaneous fermentation of 'Almagro' eggplants by a polyphasic approach based on molecular techniques.</AbstractText>Randomly amplified polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) were applied to 149 Lactobacillus isolates obtained from that fermentation process. Two random primers, OPL-05 and ArgDei-For, and two rare-cutting enzymes, SfiI and SmaI, chosen after preliminary testing on the basis of band intensity and distribution, were used. RAPD and PFGE generated electrophoretic patterns suitable for strain discrimination, but further discrimination was achieved when combined numerical analysis of the results from both methods and the results previously obtained by SDS-PAGE whole cell protein analysis, was carried out. The findings indicated a considerable degree of genomic diversity in the LAB microbiota studied and especially in the Lactobacillus plantarum isolates. In terms of species assignment, the polyphasic study allowed a definite and well-founded identification of 98.7% of the isolates.</AbstractText>The combined numerical analysis of RAPD and PFGE patterns represented a useful tool to discriminate the diversity of the Lactobacillus strains responsible for the spontaneous fermentation of this pickle. The species identification and strain typing results from the polyphasic study were regarded as the most exact compromise yielding the fewest contradictions based on the available data.</AbstractText>Combined numerical analysis of RAPD-PCR and PFGE patterns has not yet been employed to study the genetic diversity of LAB from an ecosystem like that found in fermenting vegetables.</AbstractText>

[Validation of the Diagnostic Interview for Genetic Studies (DIGS) in Colombia].

An interview tool, Diagnostic Interview for Genetic Studies (DIGS 3.0), was translated into Spanish for application in studies of psychiatric disorders in Colombia. Two Spanish translations of the original English version of DIGS were prepared and back-translated into English. A review committee verified the linguistic and cultural equivalence of the translations. The evaluator and test-retest reliability were assessed calculating Cohen's kappa for samples of 65 and 91 patients respectively. DIGS proved valid in both appearance and content. The confidence interval (C.I.) was excellent for schizophrenia (kappa = 0.81, C.I. 95% = 0.68-0.93), bipolar disorder (kappa = 0.87, C.I. 95% = 0.75-0.99), major depressive disorder (kappa = 0.86, C.I. 95% = 0.70-1.00), and for a normal diagnosis (kappa = 0.65, C.I. 95% = 0.41-0.89); it was good for other psychiatric diagnosis (kappa = 0.65, C.I. 95% = 0.41-0.89) and poor for schizoaffective disorder (kappa = 0.37, C.I. 95% = -0.02-0.76). Test-retest reliability was excellent for all diagnoses (kappa &gt; 0.8), except for "other psychiatric diagnoses" (kappa = 0.64, C.I. 95% = 0.31-0.96). The Spanish translation of the DIGS was comprehensible, with face and content validity, and good test-retest and evaluator reliability. This translation will be a useful tool for genetic studies of psychiatric disorders in Latin America, particularly where schizophrenia and affective disorders are involved.

A physician's duty to warn family members of genetic risks: limiting the importance of Tarasoff.

This paper addresses whether a physician should be held liable for failing to warn family members of potential risks of genetic disease. Resolution of this complex issue requires consideration of physician-patient responsibility, the psychological impact of the warning, the efficacy of genetic testing, and the need to protect the physical well being of family members. The paper concludes that application of the Tarasoff factors, which focus primarily on the foreseeable aspect of the threat and the identifiable nature of the third parties, is an insufficient means for determining whether this duty to disclose exists. Instead, in addition to the Tarasoff factors, a physician must consider a number of case-specific factors in deciding whether the benefits of disclosure outweigh the psychological effects of knowing of the disease and the public policy reasons behind physician-patient confidentiality. Likewise, a court should consider these same factors as applied to a hypothetical "reasonable physician" before concluding that a specific physician has a duty to warn family members potential of genetic threats.

A multistage testing strategy for detection of quantitative trait Loci affecting disease resistance in Atlantic salmon.

A multistage testing strategy to detect QTL for resistance to infectious salmon anemia (ISA) in Atlantic salmon is proposed. First, genotyping of amplified fragment length polymorphisms (AFLP) and a transmission disequilibrium test (TDT) were carried out using dead offspring from a disease resistance challenge test. Second, AFLP genotyping among survivors followed by a Mendelian segregation test was performed. Third, within-family survival analyses using all offspring were developed and applied to significant TDT markers with Mendelian inheritance. Maximum-likelihood methodology was developed for TDT with dominant markers to exploit linkage disequilibrium within families. The strategy was tested with two full-sib families of Atlantic salmon sired by the same male and consisting of 79 offspring in total. All dead offspring from the two families were typed for 64 primer combinations, resulting in 340 scored markers. There were 26 significant results out of 401 TDTs using dead offspring. In the second stage, only 17 marker families showed Mendelian segregation and were tested in survival analysis. A permutation test was performed for all survival analyses to compute experimentwise P-values. Two markers, aaccac356 and agccta150, were significant at P &lt; 0.05 when accounting for multiple testing in the survival analyses. The proposed strategy might be more powerful than current mapping strategies because it reduces the number of tests to be performed in the last testing stage.

Ordered subset linkage analysis supports a susceptibility locus for age-related macular degeneration on chromosome 16p12.

Age-related macular degeneration (AMD) is a complex disorder that is responsible for the majority of central vision loss in older adults living in developed countries. Phenotypic and genetic heterogeneity complicate the analysis of genome-wide scans for AMD susceptibility loci. The ordered subset analysis (OSA) method is an approach for reducing heterogeneity, increasing statistical power for detecting linkage, and helping to define the most informative data set for follow-up analysis. OSA assesses the linkage evidence in subsets of potentially more homogeneous families by rank-ordering family-specific lod scores with respect to trait-associated covariates or phenotypic features. Here, we present results of incorporating five continuous covariates into our genome-wide linkage analysis of 389 microsatellite markers in 62 multiplex families: Body mass index (BMI), systolic (SBP) and diastolic (DBP) blood pressure, intraocular pressure (IOP), and pack-years of cigarette smoking. Chromosome-wide significance of increases in nonparametric multipoint lod scores in covariate-defined subsets relative to the overall sample was assessed by permutation.</AbstractText>Using a correction for testing multiple covariates, statistically significant lod score increases were observed for two chromosomal regions: 14q13 with a lod score of 3.2 in 28 families with average IOP &lt;/= 15.5 (p = 0.002), and 6q14 with a lod score of 1.6 in eight families with average BMI &gt;/= 30.1 (p = 0.0004). On chromosome 16p12, nominally significant lod score increases (p &lt;/= 0.05), up to a lod score of 2.9 in 32 families, were observed with several covariate orderings. While less significant, this was the only region where linkage evidence was associated with multiple clinically meaningful covariates and the only nominally significant finding when analysis was restricted to advanced forms of AMD. Families with linkage to 16p12 had higher averages of SBP, IOP and BMI and were primarily affected with neovascular AMD. For all three regions, linkage signals at or very near the peak marker have previously been reported.</AbstractText>Our results suggest that a susceptibility gene on chromosome 16p12 may predispose to AMD, particularly to the neovascular form, and that further research into the previously suggested association of neovascular AMD and systemic hypertension is warranted.</AbstractText>

Fanconi anaemia and leukaemia - clinical and molecular aspects.

Fanconi anaemia (FA) is an autosomal recessive chromosomal instability disorder, which is characterized by congenital abnormalities, defective haemopoiesis and a high risk of developing acute myeloid leukaemia and certain solid tumours. It can be caused by mutations in at least eight different genes. Molecular studies have established that a common pathway exists, both between the FA proteins and other proteins involved in DNA damage repair such as NBS1, ATM, BRCA1 and BRCA2. This review summarizes the general clinical and specific haematological features and the current management of FA. Recent molecular advances will also be discussed in the context of the cellular and clinical FA phenotype, with particular emphasis on the haematological aspects of the condition.

How should preconceptional cystic fibrosis carrier screening be provided? Opinions of potential providers and the target population.

Since the identification of the cystic fibrosis (CF) gene, large-scale CF carrier screening has become possible. One possible target group is couples planning a pregnancy (preconceptional screening), providing a maximum number of reproductive options and a minimum of time constraints.</AbstractText>To identify obstacles in the implementation of a preconceptional CF carrier screening programme, to find out how potential providers and the target population think the screening should be implemented, and to determine whether potential providers think they are able to provide the screening programme.</AbstractText>A survey was conducted among 200 general practitioners (GPs), 134 Municipal Health Service (MHS) workers and 303 recently married couples.</AbstractText>52% (102/197) of the eligible GPs participated, 84% (113/134) of the MHS workers and 70% (380/544) of the individuals planning a pregnancy. In general, potential providers and the target population had a positive attitude towards CF screening. Preferred methods of informing the target population were: in leaflets, during a GP consultation for those people seeking advice before pregnancy, and sending a personal invitation to all people of reproductive age. Potential providers believed that they would be able to provide the screening programme. Important perceived obstacles were the absence of a preconceptional care setting, high workload, and lack of financial resources.</AbstractText>Different intervention strategies will be necessary to overcome the obstacles in the implementation. The positive attitude towards CF carrier screening in combination with the willingness of the potential providers to participate in the screening programme will make it easier to overcome the obstacles.</AbstractText>Copyright 2003 S. Karger AG, Basel</CopyrightInformation>

Awareness of genetic testing for increased cancer risk in the year 2000 National Health Interview Survey.

This study explores factors associated with differential awareness of genetic tests for increased cancer risk in the US.</AbstractText>27,405 respondents from the 2000 National Health Interview Survey, ages 25+, were asked if they had heard of these tests.</AbstractText>44.4% said 'yes', including 49.9% of whites, 32.9% of African-Americans, 32.3% of American Indians/Alaskan Natives, 28.0% of Asian/Pacific Islanders, and 20.6% of Hispanics. In multivariate analysis, test awareness was significantly associated with higher education, white race, age &lt;60 years, female gender, private health insurance, personal or parent's history of certain cancers, physical activity, and vitamin/supplement use, among other factors.</AbstractText>The survey showed which population subgroups may lack access to cancer genetics information and may therefore benefit from targeted strategies to ensure risk-appropriate utilization of genetic counseling and testing.</AbstractText>Copyright 2003 S. Karger AG, Basel</CopyrightInformation>

Ethical aspects of genetic testing in the workplace.

The European Group on Ethics and New Technologies, which advises the European Commission, has published an opinion paper on ethical aspects of genetic testing in the workplace. The paper goes well beyond the usual ethical issues, presenting a summary of genetic testing in the workplace in the United States and Europe and criteria for appropriate testing. Unlike many other documents on ethics, it pays close attention to the problem of false-positive and false-negative test results. Although no genetic tests are currently appropriate for screening workers or applicants for jobs in which occupational hazards exist, inappropriate testing has occurred and regulations are needed to ensure that only appropriate testing is used in the future. Workers or their representatives should be involved in deciding when and how genetic testing in the workplace is done.

Mucolipidosis type IV a rare genetic disorder: new addition to the Ashkenazi Jewish panel.

Mucolipidosis type IV (MLIV) is a rare genetic disorder that primarily affects persons of Ashkenazi Jewish descent. Current information available about testing options and the Ashkenazi Jewish Screening panel, including the addition of screening for MLIV, is presented. The importance of genetic screening and counseling is emphasized.

Development of the AmpFISTR SEfiler PCR amplification kit: a new multiplex containing the highly discriminating ACTBP2 (SE33) locus.

The AmpFISTR SEfiler kit co-amplifies 11 short tandem repeat loci including SE33 in a single multiplex. After establishing the optimum in primer titration studies, the primer concentrations of all loci in the multiplex were chosen such that the heterozygote peak height ratios of each of the loci were balanced. The combined primer set was then tested to determine the robustness of the multiplex under various conditions. Different MgCl(2) concentrations were evaluated to establish the optimum concentration for the multiplex. The amplification of the various loci in the multiplex was tested at several annealing temperatures (55-63 degrees C). Additionally, DNA from primates, non-primates and microorganisms were amplified to investigate the specificity of the kit. The stability of the AmpFISTR SEfiler kit was determined by addition of hematin, to simulate inhibition, and the use of degraded DNA. Population studies revealed a probability of identity of 6.47x10(-15) for African Americans and 7.46x10(-14) for US Caucasians. To assess the ability of the multiplex to analyze forensic samples, testing on blood, oral swabs and mixtures was performed. Based on the various studies, it was determined that the AmpFISTR SEfiler PCR amplification kit can be used to successfully analyze a variety of forensic, databasing and paternity samples.

Single nucleotide polymorphisms of protein tyrosine phosphatase 1B gene are associated with obesity in morbidly obese French subjects.

<AbstractText Label="AIMS/HYPOTHESIS" NlmCategory="OBJECTIVE">The development of insulin resistance may contribute to the occurrence and progression of the metabolic syndrome associated with obesity. Components contributing to the insulin pathway and its regulation are good candidates for the molecular study of metabolic syndrome pathogenesis. Protein tyrosine phosphatase 1B (PTP 1B) is an important negative regulator of insulin. We investigated whether PTP 1B SNPs are associated with obesity and obesity-related traits as well as global metabolic syndrome in morbidly obese subjects.</AbstractText>Untranslated and coding regions of the PTP 1B gene were screened in groups of non-diabetic and diabetic obese subjects and in non-obese subjects. Unrelated morbidly obese ( n=711) and non-obese ( n=427) French Caucasian subjects were genotyped for a case-control study.</AbstractText>Six SNPs were identified: two rare variants were located in 5'UTR (-109 C&gt;T and -69 C&gt;T), two in the intronic regions (IVS3+38 G&gt;T and IVS5+3666delT) and two have been described previously (P303P in exon 8 and P387L in exon 9). A case-control study showed an association between the frequent IVS5+3666delT SNP and obesity ( p=0.02). In the obese group, associations between PTP 1B SNPs and features of dyslipidaemia were found. P303P was associated with lower apolipoprotein A1 levels ( p=0.05) whereas P387L was associated with higher triglyceride ( p=0.0003), apolipoprotein B ( p=0.09) and lipoprotein a concentrations ( p=0.006).</AbstractText><AbstractText Label="CONCLUSIONS/INTERPRETATION" NlmCategory="CONCLUSIONS">Our results support the hypothesis that the PTP 1B gene contributes to the polygenic basis of obesity. PTP 1B SNPs may interact with environmental factors to induce more severe phenotypes, e.g. atherogenic dyslipidaemia, in morbidly obese subjects.</AbstractText>

Mutation detection of GJB2 using IsoCode and real-time quantitative polymerase chain reaction with SYBR green I dye for newborn hearing screening.

<AbstractText Label="OBJECTIVES/HYPOTHESIS" NlmCategory="OBJECTIVE">Recent developments in molecular genetics have opened a new era in genetic analysis accompanied by new concepts concerning genetic disorders. Although 30 genes responsible for nonsyndromic deafness have been discovered as of March 27, 2003, the connexin 26 gene (GJB2) is commonly found in cases of deafness of unknown origins. The GJB2 contains a predicted open reading frame of 785 base pairs, which makes it relatively easy to detect mutations. Accordingly, mutation analysis of GJB2 should be suitable for the screening of congenital deafness.</AbstractText>Prospective study.</AbstractText>IsoCode Stix is a useful device to isolate DNA from small samples of blood, which can be delivered from remote areas. To apply the detection of common mutations of GJB2 to hearing screening, DNA was extracted from several droplets of blood applied to the IsoCode device, and an allele-specific amplification method with real-time quantitative polymerase chain reaction was performed using GeneAmp 7700 with SYBR Green I dye.</AbstractText>DNA extracted from IsoCode was purified within 45 minutes, which was sufficient to detect the full sequence of GJB2. Four types of common GJB2 mutations were reliably detected within 2.5 hours.</AbstractText>IsoCode and real-time quantitative polymerase chain reaction will be promising tools for newborn screening of deafness genes in the future in DNA-based deafness screening, allowing early diagnosis of deafness and prompt training for language development.</AbstractText>

Partial trisomy 13 with features similar to C syndrome.

We report a case of partial trisomy 13 with trigonocephaly, upslant eyes, long smooth philtrum, polydactyly, agenesis of right kidney and mild developmental delay. In this family phenotypically normal mother had pericentric inversion of chromosome 13 and the child (proband) received recombinant 13 from the mother. Genetic counselling of the family for reproductive risks and testing siblings of the mother for detection of balanced carriers is essential.

Methodology in longitudinal studies on psychological effects of predictive DNA testing: a review.

In the last two decades predictive testing programs have become available for various hereditary diseases, often accompanied by follow-up studies on the psychological effects of test outcomes. The aim of this systematic literature review is to describe and evaluate the statistical methods that were used in these follow-up studies. A literature search revealed 40 longitudinal quantitative studies that met the selection criteria for the review. Fifteen studies (38%) applied adequate statistical methods. The majority, 25 studies, applied less suitable statistical techniques. Nine studies (23%) did not report on dropout rate, and 18 studies provided no characteristics of the dropouts. Thirteen out of 22 studies that should have provided data on missing values, actually reported on the missing values. It is concluded that many studies could have yielded more and better results if more appropriate methodology had been used.

Germline E-cadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria.

Mutations in the E-cadherin (CDH1) gene are a well documented cause of hereditary diffuse gastric cancer (HDGC). Development of evidence based guidelines for CDH1 screening for HDGC have been complicated by its rarity, variable penetrance, and lack of founder mutations.</AbstractText>Forty three new gastric cancer (GC) families were ascertained from multiple sources. In 42 of these families at least one gastric cancer was pathologically confirmed to be a diffuse gastric cancer (DGC); the other family had intestinal type gastric cancers. Screening of the entire coding region of the CDH1 gene and all intron/exon boundaries was performed by bi-directional sequencing.</AbstractText>Novel mutations were found in 13 of the 42 DGC families (31% overall). Twelve of these mutations occur among the 25 families with multiple cases of gastric cancer and with pathologic confirmation of diffuse gastric cancer phenotype in at least one individual under the age of 50 years. The mutations found include small insertions and deletions, splice site mutations, and three non-conservative amino acid substitutions (A298T, W409R, and R732Q). All three missense mutations conferred loss of E-cadherin function in in vitro assays. Multiple cases of breast cancers including pathologically confirmed lobular breast cancers were observed both in mutation positive and negative families.</AbstractText>Germline truncating CDH1 mutations are found in 48% of families with multiple cases of gastric cancer and at least one documented case of DGC in an individual under 50 years of age. We recommend that these criteria be used for selecting families for CDH1 mutational analysis.</AbstractText>

Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation.

Interpretation of results from mutation screening of tumour suppressor genes known to harbour high risk susceptibility mutations, such as APC, BRCA1, BRCA2, MLH1, MSH2, TP53, and PTEN, is becoming an increasingly important part of clinical practice. Interpretation of truncating mutations, gene rearrangements, and obvious splice junction mutations, is generally straightforward. However, classification of missense variants often presents a difficult problem. From a series of 20,000 full sequence tests of BRCA1 carried out at Myriad Genetic Laboratories, a total of 314 different missense changes and eight in-frame deletions were observed. Before this study, only 21 of these missense changes were classified as deleterious or suspected deleterious and 14 as neutral or of little clinical significance.</AbstractText>We have used a combination of a multiple sequence alignment of orthologous BRCA1 sequences and a measure of the chemical difference between the amino acids present at individual residues in the sequence alignment to classify missense variants and in-frame deletions detected during mutation screening of BRCA1.</AbstractText>In the present analysis we were able to classify an additional 50 missense variants and two in-frame deletions as probably deleterious and 92 missense variants as probably neutral. Thus we have tentatively classified about 50% of the unclassified missense variants observed during clinical testing of BRCA1.</AbstractText>An internal test of the analysis is consistent with our classification of the variants designated probably deleterious; however, we must stress that this classification is tentative and does not have sufficient independent confirmation to serve as a clinically applicable stand alone method.</AbstractText>

Analysis of European mitochondrial haplogroups with Alzheimer disease risk.

We examined the association of mtDNA variation with Alzheimer disease (AD) risk in Caucasians (989 cases and 328 controls) testing the effect of individual haplogroups and single nucleotide polymorphisms (SNPs). Logistic regression analyses were used to assess risk of haplogroups and SNPs with AD in both main effects and interaction models. Males classified as haplogroup U showed an increase in risk (OR = 2.30; 95% CI, 1.03-5.11; P = 0.04) of AD relative to the most common haplogroup H, while females demonstrated a significant decrease in risk with haplogroup U (OR = 0.44 ; 95% CI, 0.24-0.80; P = 0.007). Our results were independent of APOE genotype, demonstrating that the effect of mt variation is not confounded by APOE4 carrier status. We suggest that variations within haplogroup U may be involved in AD expression in combination with environmental exposures or nuclear proteins other than APOE.

Searching for genomic variants in IGF2 and CDKN1C in Silver-Russell syndrome patients.

Silver-Russell syndrome (SRS) is a heterogeneous syndrome with evidence for a substantial role of genetic factors in its etiology. Apart from other specific clinical features, severe intrauterine and postnatal growth retardation are the dominant characteristics of SRS. Therefore, studies on the genetic basis of the disease focus on genes involved in growth and its regulation. Another key for the identification of (a) SRS gene(s) is the finding of chromosomal disturbances in SRS patients: recently, four growth retarded patients carrying duplications in 11p15 of maternal origin have been described, two of these cases presented SRS-like features. The same region includes IGF2 and CDKN1C and is well known to harbour alterations in patients suffering from Beckwith-Wiedemann syndrome. We therefore decided to perform an extensive search for variants in the IGF2 and CDKN1C genes; mutations in these genes cause growth disturbances. More than 40 SRS patients were screened for mutations by different detection strategies, allele frequencies were compared between patients and controls. In both genes, we did not detect any obvious pathogenic mutation. In case of IGF2, slight differences in the allelic distribution of specific polymorphisms between SRS patients and controls were observed. In CDKN1C, several variants could be identified in both cohorts with similar frequencies, but only one patient showed a so far unknown variant not detectable in controls.

Ocular features of the congenital cataracts facial dysmorphism neuropathy syndrome.

To determine the nature and course of ophthalmologic abnormalities in congenital cataracts facial dysmorphism neuropathy (CCFDN) syndrome in a genetically verified group of 9 patients.</AbstractText>Observational case series.</AbstractText>Nine affected male individuals of 5 pedigrees aged 1.3 to 16.8 years were examined. Four individuals were recruited during an ongoing prospective study of congenital cataracts; 5 individuals could be assigned to the CCFDN group on the basis of our retrospective data.</AbstractText>Linkage and haplotype analysis, neurologic examinations, bilateral cataracts, axial length, corneal diameter, pupil diameter and pupillary reactions, intraoperative and postoperative complications, lid changes, aphakic correction problems, refractive results, and visual function.</AbstractText>All families originated from the eastern part of Serbia, close to the border with Romania. The 8 tested individuals were homozygous for the conserved ancestral CCFDN haplotype in the telomeric region of chromosome 18q. All patients showed a peripheral, demyelinating neuropathy and varying degrees of ataxia. In the older patients, muscular atrophy in distal muscles and facial dysmorphism was evident. Early-onset bilateral congenital cataracts associated with microcornea, microphthalmos, and micropupil could be found in all patients. All children had floppy eyelid syndrome and pseudoptosis. An increased inflammatory reaction to contact lenses and intraocular lenses could be documented in all. All patients had syndrome-associated nystagmus and congenital esotropia. Distant visual acuity could be classified as severe to moderate impairment, whereas near visual acuity was much better (mild to moderate impairment).</AbstractText>Early-onset congenital cataracts associated with microcornea, microphthalmos, and micropupil are essential ocular features of the CCFDN syndrome and are the first recognizable signs during early infancy. Awareness of this syndrome by pediatric ophthalmologists is important, because these typical findings, combined with information on ethnic origin, may lead to very early diagnosis at an age when the nature and severity of nonophthalmologic features are not apparent. Affected individuals may benefit from careful ophthalmologic treatment and follow-up, as well as from early management of the neurologic problems and developmental delay. Affected families will benefit from genetic counseling and predictive testing.</AbstractText>

The usefulness of buccal swabs for mutation screening in patients with suspected corneal dystrophies.

To make ophthalmologists aware of the usefulness of buccal swabs for the collection of cells from which DNA may be extracted to be used in genetic screening of patients with known or suspected inherited ocular disorders, such as corneal dystrophies.</AbstractText>Illustrative interventional case report.</AbstractText>Buccal epithelial swabs were collected from a 3-year-old boy with a presumed corneal dystrophy and his unaffected parents. Swabs were mailed to a laboratory where transforming growth factor-beta-induced gene (TGFBI) mutation screening was performed.</AbstractText>Results of sequencing TGFBI exons 4 and 12.</AbstractText>Transforming growth factor-beta-induced gene mutation screening in a child with bilateral anterior corneal stromal opacification revealed the following changes in exon 12: 1667T&gt;C (Phe540Phe), 1684C&gt;A (Ala546Asp), and 1699C&gt;A (Pro551Gln). The child's father demonstrated the 1667T&gt;C nucleotide substitution, but neither parent demonstrated the 1684T&gt;C or the 1699C&gt;A changes.</AbstractText>Buccal swabs provide the ophthalmologist with a simple, inexpensive means of collecting and transporting cells from which DNA may be extracted to be used to either confirm or refute diagnoses solely on the basis of clinical features. In this case, the diagnosis of an atypical variant of lattice corneal dystrophy was made on the basis of the identification of previously reported mutations in TGFBI.</AbstractText>

Prolonged biologically active transgene expression driven by HSV LAP2 in brain in vivo.

Herpes simplex virus (HSV) naturally establishes a life-long latent state in neurons, characterized by the expression of latency-associated transcripts (LATs) in the absence of viral lytic functions, and the latency-associated promoter (LAP2) has been identified as a moveable element responsible for the expression of LATs from latent HSV genomes. Prolonged transgene expression will be required for the treatment of chronic diseases of the CNS using HSV vectors. We therefore examined the ability of LAP2 to drive prolonged expression of a biologically active transgene from latent HSV vector genomes in brain in vivo using the 6-hydroxydopamine (6-OHDA) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) models of Parkinson disease. A replication-incompetent HSV vector containing the glial cell-derived neurotrophic factor (GDNF) under the control of LAP2 was injected into the substantia nigra and 5 and a half months later 6-OHDA was injected into the striatum. GDNF expression from the vector preserved dopaminergic function measured by histology and behavior 6 months after vector inoculation. Mice inoculated with the LAP2-GDNF replication-incompetent HSV vector followed by 3 months of daily low-dose MPTP injections were substantially protected against the consequences of that treatment measured by weekly behavioral testing and histologic measures at the conclusion of the experiment. These studies using subacute and chronic models of neurodegeneration demonstrate that the HSV LAP2 promoter element provides prolonged expression of relevant amounts of a transgene to produce significant biological effects in brain in vivo over the course of many months.