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At least 793 records · Page 44Linked to original sources
PubMed2005

Smoothing of the bivariate LOD score for non-normal quantitative traits.

Variance component analysis provides an efficient method for performing linkage analysis for quantitative traits. However, type I error of variance components-based likelihood ratio testing may be affected when phenotypic data are non-normally distributed (especially with high values of kurtosis). This results in inflated LOD scores when the normality assumption does not hold. Even though different solutions have been proposed to deal with this problem with univariate phenotypes, little work has been done in the multivariate case. We present an empirical approach to adjust the inflated LOD scores obtained from a bivariate phenotype that violates the assumption of normality. Using the Collaborative Study on the Genetics of Alcoholism data available for the Genetic Analysis Workshop 14, we show how bivariate linkage analysis with leptokurtotic traits gives an inflated type I error. We perform a novel correction that achieves acceptable levels of type I error.

Alcoholism↗
PubMed2005

The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history.

Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the "floral state" by contributing to floral organ and meristem identity. SEP genes have not been detected in gymnosperms and seem to have originated since the lineage leading to extant angiosperms diverged from extant gymnosperms. Therefore, both functional and evolutionary studies suggest that SEP genes may have been critical for the origin of the flower. To gain insights into the evolution of SEP genes, we isolated nine genes from plants that occupy phylogenetically important positions. Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily, providing potential opportunities for functional divergence. The first duplication occurred prior to the origin of the extant angiosperms, resulting in the AGL2/3/4 and AGL9 clades. Subsequent duplications occurred within these clades in the eudicots and monocots. The timing of the first SEP duplication approximately coincides with duplications in the DEFICIENS/GLOBOSA and AGAMOUS MADS-box subfamilies, which may have resulted from either a proposed genome-wide duplication in the ancestor of extant angiosperms or multiple independent duplication events. Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower.

Algorithms↗
PubMedDate not supplied

A first study of cytokine genomic polymorphisms in CFS: Positive association of TNF-857 and IFNgamma 874 rare alleles.

OBJECTIVE: In the past two years we have developed a biological bank of genomic DNA, cDNA, serum and red blood cells of Italian patients with certified CFS from the two Italian referral centers for the syndrome. Recent studies have shown an imbalance in cytokine production in disease states similar to Chronic Fatigue Syndrome (CFS), such as sickness behavior, both in animals and in humans. However we notice that serum cytokine concentrations are often inconstant and degrade rapidly. With this in mind, we investigated cytokine gene polymorphisms in 80 Italian patients with CFS in order to ascertain whether in this group of patients it is possible to describe a genetic predisposition to an inflammatory response. METHODS: We analyzed the promoter polymorphisms of IL-10, IL-6 and the IFNgamma 874 T/A polymorphism in intron 1 with a PCR-SSP method (Cytogen One Lambda Inc. Canoga Park, CA, U.S.A) in 54 patients and TNF-308 G/A and -857 C/T promoter polymorphisms with a PCR-RFLP method (in 54 and 80 patients respectively). RESULTS: There is a highly significant increase of TNF -857 TT and CT genotypes (p = 0.002) among patients with respect to controls and a significant decrease of IFN gamma low producers (A/A) (p = 0.04) among patients with respect to controls. CONCLUSIONS: We hypothesize that CFS patients can have a genetic predisposition to an immunomodulatory response of an inflammatory nature probably secondary to one or more environmental insults of unknown nature.

Adolescent↗
PubMed2003

The ERGO genome analysis and discovery system.

The ERGO (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.

Animals↗
PubMed2006

Analysing the developing brain transcriptome with the GenePaint platform.

We discuss technical means by which the complexity of gene and protein signalling cascades can be projected onto the complex structure of the mammalian brain. We argue that this requires both robotics and novel computational tools to register images of gene expression, annotate expression patterns and quantify gene expression. When sufficiently enriched and detailed, such gene expression/neuroanatomical atlases are hypothesis-generating tools and contain in themselves much of the information needed to investigate function in normal and genetically or otherwise modified brains. To be successful and useful, data-rich and comprehensive gene expression/neuroanatomical atlases have to be web accessible and structured in a way that allows the application of data exploration and mining tools.

Animals↗
PubMed2006

Genome-wide prediction of C. elegans genetic interactions.

To obtain a global view of functional interactions among genes in a metazoan genome, we computationally integrated interactome data, gene expression data, phenotype data, and functional annotation data from three model organisms-Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster-and predicted genome-wide genetic interactions in C. elegans. The resulting genetic interaction network (consisting of 18,183 interactions) provides a framework for system-level understanding of gene functions. We experimentally tested the predicted interactions for two human disease-related genes and identified 14 new modifiers.

Algorithms↗
PubMed2003

Informatics center for mouse genomics: the dissection of complex traits of the nervous system.

In recent years, there has been an explosion in the number of tools and techniques available to researchers interested in exploring the genetic basis of all aspects of central nervous system (CNS) development and function. Here, we exploit a powerful new reductionist approach to explore the genetic basis of the very significant structural and molecular differences between the brains of different strains of mice, called either complex trait or quantitative trait loci (QTL) analysis. Our specific focus has been to provide universal access over the web to tools for the genetic dissection of complex traits of the CNS--tools that allow researchers to map genes that modulate phenotypes at a variety of levels ranging from the molecular all the way to the anatomy of the entire brain. Our website, The Mouse Brain Library (MBL; http://mbl.org) is comprised of four interrelated components that are designed to support this goal: The Brain Library, iScope, Neurocartographer, and WebQTL. The centerpiece of the MBL is an image database of histologically prepared museum-quality slides representing nearly 2000 mice from over 120 strains--a library suitable for stereologic analysis of regional volume. The iScope provides fast access to the entire slide collection using streaming video technology, enabling neuroscientists to acquire high-magnification images of any CNS region for any of the mice in the MBL. Neurocartographer provides automatic segmentation of images from the MBL by warping precisely delineated boundaries from a 3D atlas of the mouse brain. Finally, WebQTL provides statistical and graphical analysis of linkage between phenotypes and genotypes.

Analysis of Variance↗
PubMed1999

Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database.

FlyNets (http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.++ +html) is a WWW database describing molecular interactions (protein-DNA, protein-RNA and protein-protein) in the fly Drosophila melanogaster. It is composed of two parts, as follows. (i) FlyNets-base is a specialized database which focuses on molecular interactions involved in Drosophila development. The information content of FlyNets-base is distributed among several specific lines arranged according to a GenBank-like format and grouped into five thematic zones to improve human readability. The FlyNets database achieves a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. (ii) FlyNets-list is a very simple and more general databank, the long-term goal of which is to report on any published molecular interaction occuring in the fly, giving direct web access to corresponding s in Medline and in FlyBase. In the context of genome projects, databases describing molecular interactions and genetic networks will provide a link at the functional level between the genome, the proteome and the transcriptome worlds of different organisms. Interaction databases therefore aim at describing the contents, structure, function and behaviour of what we herein define as the interactome world.

Animals↗
PubMedDate not supplied

Attitudes toward genetic testing: gender, role, and discipline.

As a result of the Human Genome Project, genetic testing could result in the availability of detailed genetic information (presence of disease, genetic risk or predisposition to disease, and characteristics or traits) that can ultimately be used for healthcare-related decisions. This study explored whether gender, role, and professional discipline would influence attitudes toward genetic testing when making reproductive decisions, as interpreted by 2 roles--as a parent making decisions or as a professional giving advice. An original research instrument was administered to masters and doctoral genetics students, pediatric residents, and masters-level ministry students. Statistical analyses revealed that discipline strongly influenced decision making while gender rarely did. In addition, differences in attitudes were also found based on parental and professional roles.

Adult↗
PubMed2005

Simulation-based homozygosity mapping with the GAW14 COGA dataset on alcoholism.

BACKGROUND: We have developed a simulation-based approach to the analysis of shared homozygous chromosomal segments and have applied it to data on allele sharing among alcoholics in a single Collaborative Study on the Genetics of Alcoholism pedigree. Our assessment of sharing involved the use of a single-nucleotide polymorphism (SNP) marker map provided by Affymetrix. RESULTS: All 11 affected individuals in the selected pedigree shared 2 copies of an allele at 4 adjacent SNPs in a region on chromosome 5. Via simulation, we determined that the probability that such sharing is caused by mere chance is less than 0.0000001. After correcting for undocumented inbreeding, this probability rose to 0.0016. The probability that the shared segment emanates from a single ancestor and is unrelated to the affection status is less than 0.0000001 in the corrected pedigree. Haplotype association analysis and a search for a protective locus using unaffected individuals yielded no significant results. CONCLUSION: Homozygosity mapping results on chromosome 5 provide suggestive evidence of the region's role as one that may harbor a genetic determinant of alcoholism. Furthermore, the probabilities of chance homozygous allele sharing for the original and for the inbreeding-corrected pedigree provide insight into the impact that inbreeding can have on such calculations.

Alcoholism↗
PubMed2005

A genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking.

Genetic mechanisms underlying alcoholism are complex. Understanding the etiology of alcohol dependence and its comorbid conditions such as smoking is important because of the significant health concerns. In this report, we describe a method based on classification trees and deterministic forests for association studies to perform a genome-wide joint association analysis of alcoholism and smoking. This approach is used to analyze the single-nucleotide polymorphism data from the Collaborative Study on the Genetics of Alcoholism in the Genetic Analysis Workshop 14. Our analysis reaffirmed the importance of sex difference in alcoholism. Our analysis also identified genes that were reported in other studies of alcoholism and identified new genes or single-nucleotide polymorphisms that can be useful candidates for future studies.

Alcoholism↗
PubMed2006

PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways.

The PUMA2 system (available at http://compbio.mcs.anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and metabolic reconstructions from sequence data. PUMA2 provides a framework for comparative and evolutionary analysis of genomic data and metabolic networks in the context of taxonomic and phenotypic information. Grid infrastructure is used to perform computationally intensive tasks. PUMA2 currently contains precomputed analysis of 213 prokaryotic, 22 eukaryotic, 650 mitochondrial and 1493 viral genomes and automated metabolic reconstructions for >200 organisms. Genomic data is annotated with information integrated from >20 sequence, structural and metabolic databases and ontologies. PUMA2 supports both automated and interactive expert-driven annotation of genomes, using a variety of publicly available bioinformatics tools. It also contains a suite of unique PUMA2 tools for automated assignment of gene function, evolutionary analysis of protein families and comparative analysis of metabolic pathways. PUMA2 allows users to submit batch sequence data for automated functional analysis and construction of metabolic models. The results of these analyses are made available to the users in the PUMA2 environment for further interactive sequence analysis and annotation.

Computational Biology↗
PubMed1997

NEXUS: an extensible file format for systematic information.

NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.

Animals↗
PubMed2006

Developments in medical law in the United Kingdom in 2005 and 2006.

This article highlights and summarises the key developments in medical law in the jurisdictions of the United Kingdom in 2005 and to April 2006. Topics are mental health and mental capacity, data protection, freedom of information and the impact on health data, the Human Tissue Act, genetic research databanks, Human Fertilisation and Embryology Act--Review of the legislation, consultations and related case law, developments in embryo and embryonic stem cell research, clinical trials and human subject research, medical futility, and physician assisted dying.

Commitment of Persons with Psychiatric Disorders↗
PubMed2005

Mycobacterium tuberculosis molecular evolution in western Mediterranean Islands of Sicily and Sardinia.

In this study, a total of 204 Mycobacterium tuberculosis DNAs from Sicily (n = 144) and Sardinia (n = 60) were studied by three genotyping methods. Results were analyzed both within and across islands, to define the phylogeographical specificities of the genotypes, look for their diversity and infer a molecular evolutionary scenario. A strong link between geography and tuberculosis genotypes was observed in Sardinia. The results were also matched against a world-wide genetic diversity database to compare the population structure of the tubercle bacilli in the islands. Eight common genotypes between Sicily, Sardinia and continental Italy were found which underlines the influences of the Italian mainland on the population structure on the islands and vice versa. A unified evolutionary scenario of M. tuberculosis evolution was built using numerical taxonomy and maximum parsimony (MP) methods. The finding of multiple families of M. tuberculosis strains (S, T, LAM, Haarlem), their presumed links with the major genetic groups (MGG) of M. tuberculosis complex, supports the view of independent introduction of several ancestral genotypes in Sicily and in Sardinia. We conclude that the two PCR-based genotyping combination (spoligotyping-VNTR) is an excellent tool to reconstruct M. tuberculosis phylogeny, that may be used to construct global and local evolutionary scenarios of the M. tuberculosis complex. The results obtained are paradigmatic of the complex interplay that exists between epidemic dynamics and evolutionary genetics of M. tuberculosis.

DNA, Bacterial↗
PubMed2005

A high-resolution survey of deletion polymorphism in the human genome.

Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes. Here we report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. Notably, we estimate that typical individuals are hemizygous for roughly 30-50 deletions larger than 5 kb, totaling around 550-750 kb of euchromatic sequence across their genomes. The detected deletions span a total of 267 known and predicted genes. Overall, however, the deleted regions are relatively gene-poor, consistent with the action of purifying selection against deletions. Deletion polymorphisms may well have an important role in the genetics of complex traits; however, they are not directly observed in most current gene mapping studies. Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.

Databases, Genetic↗
PubMed2004

HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data.

BACKGROUND: Human immunodeficiency virus (HIV) research involves ongoing, repetitious sequencing of the HIV genome and the massive accumulation of associated investigational data. As a result, the storage of annotated DNA and/or protein sequences, as well as information retrieval, have become increasingly difficult tasks, with scientists extracting less information from their collected data than they should. OBJECTIVES: Our objective was to design and develop a software package to aid researchers in the storage, analysis and exploration of their HIV-associated data. RESULTS: HIVbase contains familiar, easy-to-use interfaces and functionality for integrating many types of disparate data. The software contains tools that allow for the mass import of raw genetic data, eliminate repetitious sequence translations, have the ability to identify automatically and store HIV regions of interest from nucleic acid or protein sequences, allow for the export of data in commonly used analysis-ready formats, and for unique querying approaches.

Algorithms↗