GCTA: a tool for genome-wide complex trait analysis.

doi:10.1016/J.AJHG.2010.11.011

Open AccessJournal ArticleDOI

GCTA: a tool for genome-wide complex trait analysis.

Jian Yang, +3 more

- 07 Jan 2011 -

American Journal of Human Genetics

- Vol. 88, Iss: 1, pp 76-82

TLDR

The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets and focuses on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation.

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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Christopher C. Chang, +5 more

- 25 Feb 2015 -

GigaScience

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Brendan Bulik-Sullivan, +8 more

- 02 Feb 2015 -

Nature Genetics

TL;DR: It is found that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size, and the LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control.

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Christopher C. Chang, +5 more

- 17 Oct 2014 -

arXiv: Genomics

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Glgc, +2 more

- 12 Feb 2015 -

Nature

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Brendan Bulik-Sullivan, +20 more

- 28 Sep 2015 -

Nature Genetics

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Nature

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