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

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    Rights statement: Copyright: © 2013 Joshi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Original languageEnglish
Article numbere68604
Number of pages6
JournalPLoS ONE
Issue number7
Publication statusPublished - 16 Jul 2013


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%.

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