GCTA: a Tool for Genome-wide Complex Trait Analysis

Overview

Journal Am J Hum Genet

Publisher Cell Press

Specialty Genetics

Date 2010 Dec 21

PMID 21167468

Citations 3874

Authors

Jian Yang

S Hong Lee

Michael E Goddard

Peter M Visscher

Affiliations

Soon will be listed here.

Abstract

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.

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