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PubMed2004

GeneLink: a database to facilitate genetic studies of complex traits.

BACKGROUND: In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of these projects. To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database. RESULTS: GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data. Specifically designed to facilitate large-scale (multi-center) genetic linkage or association studies, GeneLink securely and efficiently handles large amounts of data and provides additional features to facilitate data analysis by existing software packages and quality control. These include the ability to download chromosome-specific data files containing marker data in map order in various formats appropriate for downstream analyses (e.g., GAS and LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. CONCLUSIONS: GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC). GeneLink is freely available at http://research.nhgri.nih.gov/genelink.

Alleles↗
PubMed1999

Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis.

We have generated Dissociation (Ds) element insertions throughout the Arabidopsis genome as a means of random mutagenesis. Here, we present the molecular analysis of genomic sequences that flank the Ds insertions of 931 independent transposant lines. Flanking sequences from 511 lines proved to be identical or homologous to DNA or protein sequences in public databases, and disruptions within known or putative genes were indicated for 354 lines. Because a significant portion (45%) of the insertions occurred within sequences defined by GenBank BAC and P1 clones, we were able to assess the distribution of Ds insertions throughout the genome. We discovered a significant preference for Ds transposition to the regions adjacent to nucleolus organizer regions on chromosomes 2 and 4. Otherwise, the mapped insertions appeared to be evenly dispersed throughout the genome. For any given gene, insertions preferentially occurred at the 5' end, although disruption was clearly possible at any intragenic position. The insertion sites of >500 lines that could be characterized by reference to public databases are presented in a tabular format at http://www.plantcell. org/cgi/content/full/11/12/2263/DC1. This database should be of value to researchers using reverse genetics approaches to determine gene function.

Arabidopsis↗
PubMed1995

A Rosetta stone of mammalian genetics.

The Mammalian Comparative Database provides genetic maps of mammalian species. Comparative maps are valuable aids for predicting linkages, developing animal models and studying genome organization and evolution.

Animals↗
PubMed1999

Reference database of hypervariable genetic markers of Argentina: application for molecular anthropology and forensic casework.

The population of Argentina is mostly composed of people of European ancestry. Aboriginal communities are at present very reduced in number and restricted to small geographically isolated patches. Three aboriginal communities, the Mapuche, Tehuelche and Wichi, were selected for short tandem repeat (STR) investigation. The metropolitan population of the city of Buenos Aires was analyzed, with both micro- and minisatellites. The minisatellite loci D1S7, D2S44, D4S139, D5S110, D8S358, D10S28, and D17S26 were typed on HaeIII-digested DNA obtained from unrelated individuals. D1S80 was typed by polymerase chain reaction (PCR). The autosomal STRs THO1, FABP, D6S366, CSF1PO, TPOX, F13A1, FES/FPS, vWA, MBPA/B, D16S539, D7S820, D13S317, and RENA4 and the sex chromosome STRs HPRTB, DYS385, DYS3891, DYS38911, DYS19, DYS390, DYS391, DYS392, DYS393 and YCAII were also investigated. As a by-product of our investigations, a reference database was created that is routinely used in forensic casework and paternity testing. STR allele frequency distributions are characterized by significant differences within and also between different populations. In contrast, the minisatellite bin distribution of the metropolitan population is not significantly different from other Caucasian populations.

Alleles↗
PubMedDate not supplied

Cardiac genes and gene databases for cardiovascular disease genetics.

Genes play a very important role in the etiology of hypertension. This paper reviews the current pool of candidate genes for human hypertension. Some of the genes studied in rat models of hypertension are also discussed. The methods for studying the genetics of hypertension are reviewed. A discussion of the role of cardiac gene libraries and gene databases in the characterization of cardiovascular disease is also included. This review is concluded by a discussion on the future role of genomics and cardiovascular gene databases in medical research.

Animals↗
PubMed2002

A database on alternative splice forms on the integrated genetic map service (IGMS).

UNLABELLED: The IGMS is a comprehensive information system that combines the knowledge from genomic sequence, genetic map and genetic disorders databases. This system is updated weekly and focuses on the analysis of EST data. The IGMS identifies UniGene clusters that are differentially expressed in different types of cancer with respect to different reference tissues. The results can be combined with clinical data to asses the potential relevance of specific genes for patient survival or metastatic spread. The second application maps EST with a specific expression profile. Our third application generates a database of alternative splice forms for nine organisms from EST and mRNA sequence data. The results can be used to find splicing patterns specific for certain tissues or tumour types. AVAILABILITY: http://www.bioinf.mdc-berlin.de/igms/.

Alternative Splicing↗
PubMed2002

Environmental and heritable causes of cancer among 9.6 million individuals in the Swedish Family-Cancer Database.

The genetic and environmental components in 15 common cancers were estimated using the nationwide Swedish Family-Cancer Database. Tetrachoric correlations were used to describe similarity in cancer liability among family members. Structural equation modeling was used to derive estimates of the importance of genetic and environmental effects. Statistically significant estimates of proportion of cancer susceptibility, accounted for by genetic effects, were obtained for all studied cancers except for leukemia. The estimate was highest in thyroid cancer (53%), followed by tumors at endocrine glands (28%), testis (25%), breast (25%), cervix (22%), melanoma (21%), colon (13%), nervous system (12%), rectum (12%), non-Hodgkin lymphoma (10%), lung (8%), kidney (8%), urinary bladder (7%), stomach (1%) and leukemia (1%). The estimates of shared environmental effects ranged from 0% (cervix) to 15% (stomach). The childhood shared environmental effects were most important in testicular cancer (17%), stomach cancer (13%) and cervix in situ (13%). Our results indicate that environment has a principal causative role in cancer at all studied sites except for thyroid. The relatively large effect of heritability in cancer at some sites, on the other hand, indicates that even though susceptibility genes have been described at many cancer sites, they are likely to explain only part of the genetic effects.

Breast Neoplasms↗
PubMed2002

Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease.

The inclusion of a mutation in a pathology-based database such as the Human Gene Mutation Database (HGMD) is a two-stage process: first, the mutation must occur at the DNA level, then it must cause a clinically detectable disease state. The likelihood of the latter step, termed the relative clinical observation likelihood (RCOL), can be regarded as a function of the structural/functional consequences of a mutation at the protein level. Following this paradigm, we modeled in silico all amino acid replacements that could potentially have arisen from an inherited single base pair substitution in five human genes encoding arylsulphatase A (ARSA), antithrombin III (SERPINC1), protein C (PROC), phenylalanine hydroxylase (PAH), and transthyretin (TTR). These proteins were chosen on the basis of 1) the availability of a crystallographic structure, and 2) a sufficiently large number of amino acid replacements being logged in HGMD. A total of 9,795 possible mutant structures were modeled and 20 different biophysical parameters assessed. Together with the HGMD-derived spectra of clinically detected mutations, these data allowed maximum likelihood estimation of RCOL profiles for the 20 parameters studied. Nine parameters (including energy difference between wild-type and mutant structures, accessibility of the mutated residue, and distance from the binding/active site) exhibited statistically significant variability in their RCOL profiles, indicating that mutation-associated changes affected protein function. As yet, however, a biological meaning could only be attributed to the RCOL profiles of solvent accessibility and, for three proteins, local energy change, disturbed geometry, and distance from the active center. The limited ability of the biophysical properties of mutations to explain clinical consequences is probably due to our current lack of understanding as to which amino acid residues are critical for protein folding. However, since the proteins examined here were unrelated, and our findings consistent, it may nevertheless prove possible to extrapolate to other proteins whose dysfunction underlies inherited disease.

Amino Acid Substitution↗
PubMed1987

Rapid prototyping of database systems in human genetics data collection.

This work examines some of the problems encountered in developing small and large database application systems involving human genetics data collection efforts that include data on individuals as well as family pedigree data. Rapid prototyping of a database application requires software tools to produce the application with little or no programming. Features of MEGADATS-4 that provide for rapid prototyping and for producing stand-alone applications are examined.

Data Collection↗
PubMed1997

An on-line database for zebrafish development and genetics research

We have built a relational database of zebrafish developmental and genetic research information accessible via the World Wide Web. Our team of biologists and computer scientists employed a user-centered design process, using input from the research community to tailor the contents and usability of the database. The database supports the broad range of data types generated by zebrafish research including text, images and graphical information about mutations, gene expression patterns and the genetic map. Data are entered both by the database staff and directly by authorized users. The database also maintains links among data, scientists and laboratories, thus facilitating information exchange within the research community.Copyright 1997 Academic Press Limited Copyright 1997Academic Press Limited

Journal Article↗
PubMed1991

Recombinant inbreds for molecular mapping in maize: theoretical and practical considerations.

Molecular mapping is rapidly being extended to more species as one result of the current emphasis on genome initiatives. The choice of the population used for mapping can have important consequences on the efficiency and accessibility of the mapping information. Recombinant inbred lines offer certain advantages over other mapping populations for many species. These more or less permanent populations permit many geneticists to contribute to the mapping effort and to profit from each other's work. Recombinant inbred lines are used extensively in mouse genetics and have been used in maize to compile a detailed molecular map.

Chromosome Mapping↗
PubMed2024

Estimation of carrier frequencies of autosomal and X-linked recessive genetic conditions based on gnomAD v4.0 data in different ancestries.

PURPOSE: Monogenic rare diseases contribute significantly to infant deaths and pediatric hospitalizations and cause burden to the patients and their families. The American College of Medical Genetics and Genomics recommended in 2021 that carrier screening of autosomal recessive and X-linked conditions with a carrier frequency of ≥1/200 and a severe or moderate phenotype should be offered when planning or during pregnancy. In November 2023 gnomAD v4.0 was released. It contains in total 807,162 individuals, being nearly 5× larger than previous versions, which have been used to estimate gene carrier frequencies (GCF). METHODS: We utilized gnomAD v4.0 (GRCh38) to calculate the GCFs for available genetic ancestry groups for variants having pathogenic or likely pathogenic classification (>80% of submissions) in ClinVar. We calculated GCF separately for exomes and genomes, combined data, and at-risk couple frequencies (ACF) per genetic ancestry group. RESULTS: In total, 324 genes had a GCF ≥1/200 in at least 1 ancestry subgroup. The number of genes with GCF ≥1/200 varied greatly between subgroups. ACFs were more similar, Ashkenazi Jewish having the highest ACF of 6.11%. CONCLUSION: Improved understanding of carrier risks and updated carrier screening content would allow patients to make more informed reproductive decisions.

Humans↗
PubMed1998

A high-resolution microsatellite map of the mouse genome.

The European Collaborative Interspecific Backcross (EUCIB) resource was constructed for the purposes of high-resolution genetic mapping of the mouse genome (). The large Mus spretus/C57BL/6 backcross of 982 progeny has a genetic resolution of 0.3 cM at the 95% confidence level ( approximately 500 kb in the mouse genome). We have used the EUCIB mapping resource to develop a genome-wide high-resolution genetic map incorporating 3368 microsatellites. The microsatellites are distributed among 2302 genetically separated bins with 1.46 markers per bin on average. Average bin separation is 0.61 cM. This high-resolution genetic map will aid the construction of a robust physical map of the mouse genome.

Animals↗