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.
Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia.
This article was published in the following journal.
Name: American journal of human genetics
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/21167468
- DOI: http://dx.doi.org/10.1016/j.ajhg.2010.11.011
Twin studies suggest that expressive vocabulary at ~24 months is modestly heritable. However, the genes influencing this early linguistic phenotype are unknown. Here we conduct a genome-wide screen an...
Genome-wide association studies (GWAS) have revealed 74 single nucleotide polymorphisms (SNPs) associated with high-density lipoprotein cholesterol (HDL) blood levels. This study is, to our knowledge,...
DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensi...
The discovery and prioritization of heritable phenotypes is a computational challenge in a variety of settings, including neuroimaging genetics and analyses of the vast phenotypic repositories in elec...
Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during...
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 ...
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...
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...
Genome-wide Pharmacogenetic Candidate Gene Single Nucleotide Polymorphism (SNP) Array-based Approach to Predict Chemoresponse and Survival in Patients With Acute Myeloid Leukemia With Normal Karyotype
The most reliable prognostic marker of acute myeloid leukemia(AML) is cytogenetics by karyotyping. According to cytogenetic results, the patients with AML are classified as better, interme...
To reveal the genetic determinants of the treatment outcome of escitalopram in depressed patients (by using candidate gene approach and whole genome scanning).
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.