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Public Library of Science, PLoS ONE, 7(8), p. e68604, 2013

DOI: 10.1371/journal.pone.0068604

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Local Exome Sequences Facilitate Imputation of Less Common Variants and Increase Power of Genome Wide Association Studies

Journal article published in 2013 by Peter K. Joshi ORCID, James Prendergast, Ross M. Fraser, Jennifer E. Huffman, Veronique Vitart, Caroline Hayward, Ruth McQuillan, Dominik Glodzik, Ozren Polasek, Nicholas D. Hastie, Igor Rudan, Harry Campbell, Alan F. Wright, Chris S. Haley, James F. Wilson and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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%.