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PubMed2006

Generation Scotland: the Scottish Family Health Study; a new resource for researching genes and heritability.

BACKGROUND: Generation Scotland: the Scottish Family Health Study aims to identify genetic variants accounting for variation in levels of quantitative traits underlying the major common complex diseases (such as cardiovascular disease, cognitive decline, mental illness) in Scotland. METHODS/DESIGN: Generation Scotland will recruit a family-based cohort of up to 50,000 individuals (comprising siblings and parent-offspring groups) across Scotland. It will be a six-year programme, beginning in Glasgow and Tayside in the first two years (Phase 1) before extending to other parts of Scotland in the remaining four years (Phase 2). In Phase 1, individuals aged between 35 and 55 years, living in the East and West of Scotland will be invited to participate, along with at least one (and preferably more) siblings and any other first degree relatives aged 18 or over. The total initial sample size will be 15,000 and it is planned that this will increase to 50,000 in Phase 2. All participants will be asked to contribute blood samples from which DNA will be extracted and stored for future investigation. The information from the DNA, along with answers to a life-style and medical history questionnaire, clinical and biochemical measurements taken at the time of donation, and subsequent health developments over the life course (traced through electronic health records) will be stored and used for research purposes. In addition, a detailed public consultation process will begin that will allow respondents' views to shape and develop the study. This is an important aspect to the research, and forms the continuation of a long-term parallel engagement process. DISCUSSION: As well as gene identification, the family-based study design will allow measurement of the heritability and familial aggregation of relevant quantitative traits, and the study of how genetic effects may vary by parent-of-origin. Long-term potential outcomes of this research include the targeting of disease prevention and treatment, and the development of screening tools based on the new genetic information. This study approach is complementary to other population-based genetic epidemiology studies, such as UK Biobank, which are established primarily to characterise genes and genetic risk in the population.

Adolescent↗
PubMed2006

Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

BACKGROUND: The aetiology of the autoimmune disease type 1 diabetes (T1D) involves many genetic and environmental factors. Evidence suggests that innate immune responses, including the action of interferons, may also play a role in the initiation and/or pathogenic process of autoimmunity. In the present report, we have adopted a linkage disequilibrium (LD) mapping approach to test for an association between T1D and three regions encompassing 13 interferon alpha (IFNA) genes, interferon omega-1 (IFNW1), interferon beta-1 (IFNB1), interferon gamma (IFNG) and the interferon consensus-sequence binding protein 1 (ICSBP1). RESULTS: We identified 238 variants, most, single nucleotide polymorphisms (SNPs), by sequencing IFNA, IFNB1, IFNW1 and ICSBP1, 98 of which where novel when compared to dbSNP build 124. We used polymorphisms identified in the SeattleSNP database for INFG. A set of tag SNPs was selected for each of the interferon and interferon-related genes to test for an association between T1D and this complex gene family. A total of 45 tag SNPs were selected and genotyped in a collection of 472 multiplex families. CONCLUSION: We have developed informative sets of SNPs for the interferon and interferon related genes. No statistical evidence of a major association between T1D and any of the interferon and interferon related genes tested was found.

Autoimmune Diseases↗
PubMed2005

CONCOR, an initiative towards a national registry and DNA-bank of patients with congenital heart disease in the Netherlands: rationale, design, and first results.

INTRODUCTION: Survival of patients with congenital heart disease has dramatically improved after surgical repair became available 40 years ago. Instead of a mortality of 85% during childhood following the natural course, over 85% of these infants are now expected to reach adulthood. However, data on long-term outcome is scarce due to the lack of large, national registries. Moreover, little is known about the genetic basis of congenital heart defects. In 2000, the Interuniversity Cardiology Institute of the Netherlands and the Netherlands Heart Foundation have taken the initiative to develop a national registry and DNA-bank of patients with congenital heart disease in the Netherlands named CONCOR. OBJECTIVES: The aims of the CONCOR project are to facilitate investigation of the prevalence and long-term outcome of specific congenital heart defects and their treatment, to develop an efficient organisational structure for the improvement of healthcare for patients with congenital heart disease, and to allow investigation of the molecular basis of congenital heart defects. METHODS: After informed consent, research nurses enter data of participating patients into the CONCOR database using a web application. Data is transferred over the Internet via a secure connection. About 20 ml blood is withdrawn from the patient, and the DNA is isolated and stored. From each participating patient family history on congenital heart disease is obtained. RESULTS: Within two and a half years more than 4200 patients have agreed to participate. More than 99% of the patients that were asked have given their consent to participate in CONCOR. From 60% of these patients DNA has already been obtained. Mean age of the patients included is 34 years; more than 85% of the patients are younger than 45 years. Late complications occur frequently and the incidence increases with advancing age. 18% of the patients are known with supraventricular or ventricular arrhythmias. 2% of the included patients suffered a cerebrovascular accident, 139 (3%) had endocarditis. 6% of the patients has pulmonary hypertension or Eisenmenger syndrome. More than 15% of the patients reported an affected family member with congenital heart disease in the first, second, or third degree. 6% has an affected first-degree relative, and 4% a second-degree relative. Already 10 research projects have started using the CONCOR data and DNA. CONCLUSION: The population of patients with congenital heart disease is young and rapidly growing. Late complications occur frequently and the incidence increases with advances age. The CONCOR registry and DNA-bank facilitates research on prevalence and long-term outcome and allows investigation of the molecular basis of congenital heart disease.

Academies and Institutes↗
PubMed2006

Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data.

BACKGROUND: Several genes underlying rare monogenic forms of Parkinson's disease have been identified over the past decade. Despite evidence for a role for genetics in sporadic Parkinson's disease, few common genetic variants have been unequivocally linked to this disorder. We sought to identify any common genetic variability exerting a large effect in risk for Parkinson's disease in a population cohort and to produce publicly available genome-wide genotype data that can be openly mined by interested researchers and readily augmented by genotyping of additional repository subjects. METHODS: We did genome-wide, single-nucleotide-polymorphism (SNP) genotyping of publicly available samples from a cohort of Parkinson's disease patients (n=267) and neurologically normal controls (n=270). More than 408,000 unique SNPs were used from the Illumina Infinium I and HumanHap300 assays. FINDINGS: We have produced around 220 million genotypes in 537 participants. This raw genotype data has been and as such is the first publicly accessible high-density SNP data outside of the International HapMap Project. We also provide here the results of genotype and allele association tests. INTERPRETATION: We generated publicly available genotype data for Parkinson's disease patients and controls so that these data can be mined and augmented by other researchers to identify common genetic variability that results in minor and moderate risk for disease.

Aged↗
PubMed2005

Exopolysaccharide biosynthesis genes required for social motility in Myxococcus xanthus.

Social (S)-motility in Myxococcus xanthus is a flagellum-independent gliding motility system that allows bacteria to move in groups on solid surfaces. S-motility has been shown to require type IV pili (TFP), exopolysaccharide (EPS; a component of fibrils) and lipopolysaccharide (LPS). Previously, information concerning EPS biogenesis in M. xanthus was lacking. In this study, we screened 5000 randomly mutagenized colonies for defects in S-motility and EPS and identified two genetic regions essential for EPS biogenesis: the EPS synthesis (eps) region and the EPS-associated (eas) region. Mutants with insertions in the eps and eas regions were defective in S-motility and fruiting body formation. These mutants failed to bind the dye calcofluor white, indicating that they lacked EPS; however, they retained normal TFP and LPS. Analysis of the eps locus showed several open reading frames (ORFs) that encode homologues to glycosyltransferases, glucanases and EPS transporters as well as regulatory proteins; the eas locus contains two ORFs: one exhibits homology to hypothetical proteins with a conserved domain of unknown function and the other displays no apparent homology to other proteins in the database. Further genetic mutagenesis analysis indicates that the whole eps region is involved in the biosynthesis of fibrils and fibril EPS. The operon at the proximal end of the eps region was analysed by generating in-frame deletion mutations. These mutants showed varying degrees of defects in the bacterium's ability to produce EPS or perform EPS-related functions, confirming the involvement of these genes in M. xanthus EPS biogenesis.

DNA, Bacterial↗
PubMed2005

Development of a functional genomics platform for Sinorhizobium meliloti: construction of an ORFeome.

The nitrogen-fixing, symbiotic bacterium Sinorhizobium meliloti reduces molecular dinitrogen to ammonia in a specific symbiotic context, supporting the nitrogen requirements of various forage legumes, including alfalfa. Determining the DNA sequence of the S. meliloti genome was an important step in plant-microbe interaction research, adding to the considerable information already available about this bacterium by suggesting possible functions for many of the >6,200 annotated open reading frames (ORFs). However, the predictive power of bioinformatic analysis is limited, and putting the role of these genes into a biological context will require more definitive functional approaches. We present here a strategy for genetic analysis of S. meliloti on a genomic scale and report the successful implementation of the first step of this strategy by constructing a set of plasmids representing 100% of the 6,317 annotated ORFs cloned into a mobilizable plasmid by using efficient PCR and recombination protocols. By using integrase recombination to insert these ORFs into other plasmids in vitro or in vivo (B. L. House et al., Appl. Environ. Microbiol. 70:2806-2815, 2004), this ORFeome can be used to generate various specialized genetic materials for functional analysis of S. meliloti, such as operon fusions, mutants, and protein expression plasmids. The strategy can be generalized to many other genome projects, and the S. meliloti clones should be useful for investigators wanting an accessible source of cloned genes encoding specific enzymes.

Bacterial Proteins↗
PubMed2006

The Type 1 Diabetes Genetics Consortium.

The Type 1 Diabetes Genetics Consortium (T1DGC) is an international, multicenter program organized to promote research to identify genes and their alleles that determine an individual's risk for type 1 diabetes (T1D). The primary goal of the T1DGC is to establish resources and data that can be used by, and that is fully accessible to, the research community in the study of T1D. All the information on T1DGC can be accessed at the following web address: http://www.t1dgc.org. A resource base of well-characterized families is being assembled that will facilitate the localization and characterization of T1D susceptibility genes. From these families, the T1DGC is establishing banks of DNA, serum, plasma, and cell lines, as well as useful databases. The T1DGC also sponsors training opportunities (bioinformatics) and technology transfer (HLA genotyping).

Alleles↗
PubMed2003

A gene recommender algorithm to identify coexpressed genes in C. elegans.

One of the most important uses of whole-genome expression data is for the discovery of new genes with similar function to a given list of genes (the query) already known to have closely related function. We have developed an algorithm, called the gene recommender, that ranks genes according to how strongly they correlate with a set of query genes in those experiments for which the query genes are most strongly coregulated. We used the gene recommender to find other genes coexpressed with several sets of query genes, including genes known to function in the retinoblastoma complex. Genetic experiments confirmed that one gene (JC8.6) identified by the gene recommender acts with lin-35 Rb to regulate vulval cell fates, and that another gene (wrm-1) acts antagonistically. We find that the gene recommender returns lists of genes with better precision, for fixed levels of recall, than lists generated using the C. elegans expression topomap.

Algorithms↗
PubMed1964

SOVIET NEUROLOGICAL SCIENCE TODAY.

Neurological sciences in the U.S.S.R. are healthy but have middle-age spread, as judged from an intensive personal tour of facilities as a guest of the Soviet Academy of Sciences during the autumn of 1963. Many of the recent Western enthusiasms in ultrastructure, cytogenetics and molecular genetics appear not to have inflamed many imaginations. However, Soviet neurologists are contributing to the same types of electrophysiological research as are current in the West. The full realization of the talents of many well-trained young investigators is hindered by the strong emphasis on Pavlovian theory and technique, the rigid multi-layered structure of research institutes, and the relative isolation from undergraduate medical schools of most research.

Academies and Institutes↗
PubMed2002

Quantitative structure/property relationship analysis of Caco-2 permeability using a genetic algorithm-based partial least squares method.

Caco-2 cell monolayers are widely used systems for predicting human intestinal absorption. This study was carried out to develop a quantitative structure-property relationship (QSPR) model of Caco-2 permeability using a novel genetic algorithm-based partial least squares (GA-PLS) method. The Caco-2 permeability data for 73 compounds were taken from the literature. Molconn-Z descriptors of these compounds were calculated as molecular descriptors, and the optimal subset of the descriptors was explored by GA-PLS analysis. A fitness function considering both goodness-of-fit to the training data and predictability of the testing data was adopted throughout the genetic algorithm-driven optimization procedure. The final PLS model consisting of 24 descriptors gave a correlation coefficient (r) of 0.886 for the entire dataset and a predictive correlation coefficient (r(pred)) of 0.825 that was evaluated by a leave-some-out cross-validation procedure. Thus, the GA-PLS analysis proved to be a reasonable QSPR modeling approach for predicting Caco-2 permeability.

Algorithms↗
PubMed2005

An information-driven approach to pharmacogenomics.

Effective information management of the pharmacogenomics discipline presents many unique challenges. Genetic and genomic data generated via high-throughput methods need to be integrated with phenotypic data which are defined at multiscale levels, ranging from the molecular to the clinical level. Repositories storing these data are distributed and vary in terms of syntax and semantics which result in issues concerning data exchange and integration. The application of the emerging semantic web offers a promising solution to these interoperability issues.

Animals↗
PubMed2003

Secure communication and management of clinical and genomic data: the use of pseudonymisation as privacy enhancing technique.

The growing need of managing both clinical and genetic data raises important legal and ethical challenges. This article introduces some of the privacy protection problems related to genomic medicine and highlights the relevance of Trusted Third Parties and of Privacy Enhancing Techniques (PETs) in the context of e.g. research. Practical approaches based on two pseudonymisation models, for both batch and interactive data collection and exchange, are presented.

Access to Information↗
PubMed2006

Experimental approaches to identify genetic networks.

Systems biology offers the promise of a fully integrated view of cellular physiology. To realize this potential requires the analysis of diverse genome-wide datasets and the incorporation of these analyses into integrated networks. In the past decade, the budding yeast Saccharomyces cerevisiae has provided the benchmark for the design of such large-scale experiments. Many of these experimental approaches have been adopted and adapted to study other systems, including worm, fly, fish and mammalian cultured cells, using an ingenious set of molecular tools.

Animals↗
PubMed2005

Genetic variants of Anaplasma phagocytophilum infecting dogs in Western Washington State.

Eight dogs from western Washington State suspected of being infected with Anaplasma phagocytophilum because of the finding of morulae in peripheral blood neutrophils were studied for determination of the etiologic agent of disease. All cases were diagnosed between April 2003 and April 2004. Six of the eight dogs had no travel history during the 6 months prior to presentation. Two dogs had traveled within the Northwest United States and Canada. Fever, lethargy, and anorexia were the most common clinical signs in the dogs. Lymphopenia, thrombocytopenia, and an elevated activity of alkaline phosphatase in the serum were the most common laboratory findings. All dogs tested during the acute phase of clinical signs were seropositive for A. phagocytophilum antibodies but negative for Ehrlichia canis antibodies. PCR amplification and direct sequencing of portions of the 16S rRNA gene from the whole blood of all seven dogs that were tested yielded A. phagocytophilum after a comparison to bacterial sequences available in the GenBank database. Five genetic variants were identified based on one or two nucleotide differences in the 16S rRNA gene sequences at nucleotide positions 54, 84, 86, and 120. Individual dogs were infected with more than one variant. Treatment with doxycycline or tetracycline resulted in a rapid resolution of clinical signs. The occurrence of canine granulocytic anaplasmosis in western Washington State suggests that A. phagocytophilum infection should be considered in differential diagnoses of dogs presenting with lethargy, anorexia, fever, and lameness, particularly in the context of lymphopenia, thrombocytopenia, and increased serum alkaline phosphatase. The zoonotic importance of A. phagocytophilum should support an increase in surveillance for horses and people residing in this area.

Anaplasma phagocytophilum↗
PubMed2006

The genetic basis of the Pierre Robin Sequence.

OBJECTIVE: The Pierre Robin Sequence (PRS) is subgroup of the cleft palate population. As with the etiology of cleft lip or palate, the etiology of PRS is generally unknown. Some factors are suggestive of a genetic basis for PRS. The purpose of this study was to compare genetic information on PRS available in the literature and in a cytogenetic database to facilitate focused genetic studies of PRS. DESIGN: After searching Medline for "pierre robin and genetics," the Mendelian Cytogenetics Network database for "robin" and "pierre robin," and two reviews from the Human Cytogenetics Database for "cleft palate" and "micrognathia," a comparison of the data and a search in Online Mendelian Inheritance in Man (OMIM) Gene Map was performed to identify relevant candidate genes. RESULTS: The findings revealed consistency to a certain degree to loci 2q24.1-33.3, 4q32-qter, 11q21-23.1, and 17q21-24.3. A search in the OMIM Gene Map provided many candidate genes for PRS in these regions. The GAD67 on 2q31, the PVRL1 on 11q23-q24, and the SOX9 gene on 17q24.3-q25.1 are suggested to be of particular importance. CONCLUSION: Candidate loci and a few potential candidate genes for PRS are proposed from the present study. This may enable researchers to focus their effort in the studies of PRS.

Cleft Lip↗
PubMed2004

Sir2-independent life span extension by calorie restriction in yeast.

Calorie restriction slows aging and increases life span in many organisms. In yeast, a mechanistic explanation has been proposed whereby calorie restriction slows aging by activating Sir2. Here we report the identification of a Sir2-independent pathway responsible for a majority of the longevity benefit associated with calorie restriction. Deletion of FOB1 and overexpression of SIR2 have been previously found to increase life span by reducing the levels of toxic rDNA circles in aged mother cells. We find that combining calorie restriction with either of these genetic interventions dramatically enhances longevity, resulting in the longest-lived yeast strain reported thus far. Further, calorie restriction results in a greater life span extension in cells lacking both Sir2 and Fob1 than in cells where Sir2 is present. These findings indicate that Sir2 and calorie restriction act in parallel pathways to promote longevity in yeast and, perhaps, higher eukaryotes.

Caloric Restriction↗
PubMed2004

Genetic association studies: web-based resources for effective screening and assessment of candidate genes and pathways.

The increased availability of polymorphism resources for humans and high-throughput genotyping technologies account for the large number of genetic associations published every month. Resources that allow one to synthesise published data quickly and effectively are needed to keep up to date with such information. In addition, the full exploitation of data from the HapMap project will depend on the availability of tools for the analysis of clinical and phenotypic information at the genome-wide level. Here, web resources created to aid access to such data, starting from a gene, disease or pathway of interest, are reviewed.

Databases, Genetic↗
PubMed2006

AFLP analysis of genetic variation within the two economically important Anatolian grapevine (Vitis vinifera L.) varietal groups.

The Anatolian region of modern-day Turkey is believed to have played an important role in the history of grapevine (Vitis vinifera L.) domestication and spread. Despite this, the rich grape germplasm of this region is virtually uncharacterized genetically. In this study, the amplified fragment length polymorphisms (AFLP)-based genetic relations of the grapevine accessions belonging to the 2 economically important Anatolian table grape varietal groups known as V. vinifera 'Misket' (Muscat) and V. vinifera 'Parmak' were studied. Thirteen AFLP primer combinations used in the analyses revealed a total of 1495 (35.5% polymorphic) and 1567 (34.6% polymorphic) DNA fragments for the 'Misket' and 'Parmak' varietal groups, respectively. The unweighted pair-group method with arthimetic averaging (UPGMA) cluster analysis and principal coordinate analysis (PCA) conducted on polymorphic AFLP markers showed that both varietal groups contain a number of synonymous (similar genotypes known by different names) as well as homony mous (genetically different genotypes known by the same name) accessions. Our results also showed that 6 of the Anatolian 'Misket' genotypes were genetically very similar to V. vinifera 'Muscat of Alexandria', implying that these genotypes might have played some role in the formation of this universally known grape cultivar. Finally, the close genetic similarities found here between 'Muscat of Alexandria' and V. vinifera 'Muscat of Hamburg' support the recent suggestion that 'Muscat of Hamburg' probably originated from 'Muscat of Alexandria' through spontaneous hybridizations. Overall, the results of this study have implications for not only preservation and use of the Anatolian grape germplasm, but also better understanding of the historical role that this region has played during the domestication of grapes.

Cluster Analysis↗