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

Bulik-Sullivan, Brendan K.; Albus, M; Alexander, M; Amin, F; Bacanu, SA; Begemann, M; Belliveau, RA; Bene, J; Bergen, SE; Bruggeman, R; Bevilacqua, E; Bigdeli, TB; Black, DW; Buccola, NG; Buckner, RL; Byerley, W; Cahn, W; Cai, G; Cairns, MJ; Campion, D; Cantor, RM; Carr, VJ; Carrera, N; Catts, SV; Chambert, KD; Chan, RCK; Chen, RYL; Cohen, D; Chen, EYH; Cheng, W; Cheung, EFC; Chong, SA; Cloninger, CR; Cohen, N; Cormican, P; Craddock, N; Crespo-Facorro, B; Crowley, JJ; Curtis, D; Davidson, M; Davis, KL; Degenhardt, F; Del Favero, J; Loh, Po-Ru; Michie, Patricia T.; Schall, Ulrich; Scott, Rodney J.; Tooney, Paul A.; Wu, Jing Qin; Patterson, Nick; Daly, Mark J.; Price, Alkes L.; Neale, Benjamin M.; Finucane, Hilary K.; Ripke, Stephan; Yang, Jian; Schizophrenia Working Group of the Psychiatric Genomics Consortium,; Cairns, Murray J.; Henskens, Frans A.; Kelly, Brian J.; Loughland, Carmel M.

Title: LD score regression distinguishes confounding from polygenicity in genome-wide association studies
Creator: Bulik-Sullivan, Brendan K.; Albus, M; Alexander, M; Amin, F; Bacanu, SA; Begemann, M; Belliveau, RA; Bene, J; Bergen, SE; Bruggeman, R; Bevilacqua, E; Bigdeli, TB; Black, DW; Buccola, NG; Buckner, RL; Byerley, W; Cahn, W; Cai, G; Cairns, MJ; Campion, D; Cantor, RM; Carr, VJ; Carrera, N; Catts, SV; Chambert, KD; Chan, RCK; Chen, RYL; Cohen, D; Chen, EYH; Cheng, W; Cheung, EFC; Chong, SA; Cloninger, CR; Cohen, N; Cormican, P; Craddock, N; Crespo-Facorro, B; Crowley, JJ; Curtis, D; Davidson, M; Davis, KL; Degenhardt, F; Del Favero, J; Loh, Po-Ru; Michie, Patricia T.; Schall, Ulrich; Scott, Rodney J.; Tooney, Paul A.; Wu, Jing Qin; Patterson, Nick; Daly, Mark J.; Price, Alkes L.; Neale, Benjamin M.; Finucane, Hilary K.; Ripke, Stephan; Yang, Jian; Schizophrenia Working Group of the Psychiatric Genomics Consortium,; Cairns, Murray J.; Henskens, Frans A.; Kelly, Brian J.; Loughland, Carmel M.
Relation: Nature Genetics Vol. 47, Issue 3, p. 291-295
Publisher Link: http://dx.doi.org/10.1038/ng.3211
Publisher: Nature Publishing Group
Resource Type: journal article
Date: 2015
Description: 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.
Subject: genome-wide association studies; LD score regression; polygenicity; statistics
Identifier: http://hdl.handle.net/1959.13/1339677
Identifier: uon:28311
Identifier: ISSN:1061-4036
Language: eng
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