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 journalArticlepeer-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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