The effect of genome-wide association scan quality control on imputation outcome for common variants

Lorraine Southam, Kalliope Panoutsopoulou, N. William Rayner, Kay Chapman, Caroline Durrant, Teresa Ferreira, Nigel Arden, Andrew Carr, Panos Deloukas, Michael Doherty, John Loughlin, Andrew McCaskie, William E R Ollier, Stuart Ralston, Timothy D. Spector, Ana M. Valdes, Gillian A. Wallis, J. Mark Wilkinson, Jonathan Marchini, Eleftheria Zeggini

    Research output: Contribution to journalArticlepeer-review


    Imputation is an extremely valuable tool in conducting and synthesising genome-wide association studies (GWASs). Directly typed SNP quality control (QC) is thought to affect imputation quality. It is, therefore, common practise to use quality-controlled (QCed) data as an input for imputing genotypes. This study aims to determine the effect of commonly applied QC steps on imputation outcomes. We performed several iterations of imputing SNPs across chromosome 22 in a dataset consisting of 3177 samples with Illumina 610k (Illumina, San Diego, CA, USA) GWAS data, applying different QC steps each time. The imputed genotypes were compared with the directly typed genotypes. In addition, we investigated the correlation between alternatively QCed data. We also applied a series of post-imputation QC steps balancing elimination of poorly imputed SNPs and information loss. We found that the difference between the unQCed data and the fully QCed data on imputation outcome was minimal. Our study shows that imputation of common variants is generally very accurate and robust to GWAS QC, which is not a major factor affecting imputation outcome. A minority of common-frequency SNPs with particular properties cannot be accurately imputed regardless of QC stringency. These findings may not generalise to the imputation of low frequency and rare variants. © 2011 Macmillan Publishers Limited All rights reserved. © 2011 Macmillan Publishers Limited.
    Original languageEnglish
    Pages (from-to)610-614
    Number of pages4
    JournalEuropean Journal of Human Genetics
    Issue number5
    Publication statusPublished - May 2011


    • Genome-wide association study
    • Imputation
    • Quality control
    • Single nucleotide polymorphism


    Dive into the research topics of 'The effect of genome-wide association scan quality control on imputation outcome for common variants'. Together they form a unique fingerprint.

    Cite this