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

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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%. © 2013 Joshi et al.

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Joshi, P. K., Prendergast, J., Fraser, R. M., Huffman, J. E., Vitart, V., Hayward, C., … Navarro, P. (2013). Local Exome Sequences Facilitate Imputation of Less Common Variants and Increase Power of Genome Wide Association Studies. PLoS ONE, 8(7). https://doi.org/10.1371/journal.pone.0068604

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