Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies

Peter Joshi, James Prendergast, Ross M Fraser, Jennifer E Huffman, Veronique Vitart, Caroline Hayward, Ruth McQuillan, Dominik Glodzik, Ozren Polašek, Nicholas D Hastie, Igor Rudan, Harry Campbell, Alan F Wright, Chris S Haley, James F Wilson, Pau Navarro

Research output: Contribution to journal › Article › peer-review

Abstract

The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10%) in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%.
Original languageEnglish
Article numbere68604
Number of pages6
JournalPLoS ONE
Volume8
Issue number7
DOIs
Publication statusPublished - 16 Jul 2013

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    • CROATIA PROGRAMME

      Wright, A. (Principal Investigator), Adams, I. (Co-investigator), Aligianis, I. (Co-investigator), Baldock, R. (Co-investigator), Bickmore, W. (Co-investigator), Caceres, J. (Co-investigator), Dorin, J. (Co-investigator), Dunlop, M. (Co-investigator), FitzPatrick, D. (Co-investigator), Haley, C. (Co-investigator), Hastie, N. (Co-investigator), Hill, B. (Co-investigator), Jackson, I. (Co-investigator), Jackson, A. (Co-investigator), Kudla, G. (Co-investigator), Meehan, R. (Co-investigator), O'Connell, M. (Co-investigator), Overton, I. (Co-investigator), Patton, E. (Co-investigator), Taylor, M. (Co-investigator), Tenesa, A. (Co-investigator) & Van Heyningen, V. (Co-investigator)

      MRC

      1/04/12 → 31/07/13

      Project: Research

    • CORE FUNDS

      Haley, C. (Principal Investigator), Cabrera-Cardenas, C. (Researcher), Navarro, P. (Researcher) & Wei, W. (Researcher)

      MRC

      1/10/11 → 31/03/12

      Project: Research

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