LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

Bulik-Sullivan, Brendan K. and Loh, Po-Ru and Finucane, Hilary K. and Ripke, Stephan and Yang, Jian and Patterson, Nick and Daly, Mark J. and Price, Alkes L. and Neale, Benjamin M. and Knight, Jo (2015) LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nature Genetics, 47 (3). pp. 291-295. ISSN 1061-4036

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Abstract

Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size.

Item Type: Journal Article
Journal or Publication Title: Nature Genetics
Uncontrolled Keywords: /dk/atira/pure/subjectarea/asjc/1300/1311
Subjects:
Departments: Faculty of Health and Medicine > Medicine
ID Code: 80068
Deposited By: ep_importer_pure
Deposited On: 15 Jun 2016 13:40
Refereed?: Yes
Published?: Published
Last Modified: 26 Feb 2020 03:19
URI: https://eprints.lancs.ac.uk/id/eprint/80068

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