Advertisement

Topics

GCTA: A Tool for Genome-wide Complex Trait Analysis.

Summary of "GCTA: A Tool for Genome-wide Complex Trait Analysis."

For most human complex diseases and traits, SNPs identified by genome-wide association studies (GWAS) explain only a small fraction of the heritability. Here we report a user-friendly software tool called genome-wide complex trait analysis (GCTA), which was developed based on a method we recently developed to address the "missing heritability" problem. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait rather than testing the association of any particular SNP to the trait. We introduce GCTA's five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. We focus on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation. The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets.

Affiliation

Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia.

Journal Details

This article was published in the following journal.

Name: American journal of human genetics
ISSN: 1537-6605
Pages: 76-82

Links

DeepDyve research library

PubMed Articles [24588 Associated PubMed Articles listed on BioPortfolio]

Abstract: Genome-Wide Complex Trait Analysis of Shared Genetic Effects Between Brain Electrophysiology Measures and Alcohol Dependence.

GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs.

A computationally efficient tool is required for a genome-wide gene-gene interaction analysis that tests an extremely large number of single-nucleotide polymorphism (SNP) interaction pairs in genome-w...

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium.

Extraversion is a relatively stable and heritable personality trait associated with numerous psychosocial, lifestyle and health outcomes. Despite its substantial heritability, no genetic variants have...

Genome-wide association study of generalized anxiety symptoms in the Hispanic Community Health Study/Study of Latinos.

Although generalized anxiety disorder (GAD) is heritable and aggregates in families, no genomic loci associated with GAD have been reported. We aimed to discover potential loci by conducting a genome-...

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.

Genome-wide association studies (GWASs) have successfully identified many sequence variants that are significantly associated with common diseases and traits. Tens of thousands of such trait-associate...

Clinical Trials [2659 Associated Clinical Trials listed on BioPortfolio]

A Genome-Wide Scan For Quantitative Trait Loci of Serum Bilirubin - A Framingham Study

Studies have shown that there is a significant association between serum bilirubin concentrations and risk of coronary artery disease (CAD). So far, no linkage analysis in humans between ...

Genome-Wide Association Study in Patients With Nontuberculous Mycobacterial Lung Disease

The aim of this study was to elucidate genetic susceptibility of patients with nontuberculous mycobacterial lung disease using genome-wide association study.

Mitral Valve Prolapse (MVP) - France Study

This prospective nation-wide (France) study aims to search for susceptibility genes in MVP using a genome wide analysis and comparing results obtained in 1000 patients with MVP and 1000 n...

Evaluation of the Physiodoloris Pain Monitor in Patients With Complex Regional Pain Syndrome

A French University team (M. Jeanne, MD, and M. LOGIER, Ph D) have developed a pain assessment tool based on the analysis of the variability heart rate which evaluates the Analgesia Nocice...

Analysis of Genomic DNA Alterations in Familial Schizophrenia

Persons with schizophrenia experience imaginary voices, visions and disorganized thoughts, and are handicapped when it comes to social life, which is detrimental to the affected individual...

Medical and Biotech [MESH] Definitions

Locations, on the GENOME, of GENES or other genetic elements that encode or control the expression of a quantitative trait (QUANTITATIVE TRAIT, HERITABLE).

An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.

A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.

The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.

Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.

Quick Search
Advertisement
 


DeepDyve research library

Relevant Topic

Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...


Searches Linking to this Article