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Genetic Variation pp 341–372Cite as

Quality Control for Genome-Wide Association Studies

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 628))

Abstract

This chapter is a comprehensive review of quality control (QC) methods for SNP-based genotyping panels used in genome-wide association studies. These include QC on individuals for missingness, gender checks, duplicates and cryptic relatedness, population outliers, heterozygosity and inbreeding, and QC on SNPs for missingness, minor allele frequency and Hardy-Weinberg equilibrium. The emphasis is on the reasons behind each QC step and on the use of intelligent approaches rather than arbitrary QC thresholds. Scripts and code for performing these QC steps are available at www.kcl.ac.uk/mmg/gwascode/.

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Author information

Authors and Affiliations

  1. Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London, UK

    Michael E. Weale

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  1. Michael E. Weale
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Correspondence to Michael E. Weale .

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Editors and Affiliations

  1. Medicines Research Centre, GlaxoSmithKline R&D Limited, Gunnels Wood Road, Stevenage, Hertfordshire, SG12NY, United Kingdom

    Michael R. Barnes

  2. Institute of Psychiatry, Social, Genetic & Developmental, King's College, Denmark Hill 111, London, SE58AF, United Kingdom

    Gerome Breen

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Weale, M.E. (2010). Quality Control for Genome-Wide Association Studies. In: Barnes, M., Breen, G. (eds) Genetic Variation. Methods in Molecular Biology, vol 628. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-367-1_19

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  • DOI: https://doi.org/10.1007/978-1-60327-367-1_19

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-366-4

  • Online ISBN: 978-1-60327-367-1

  • eBook Packages: Springer Protocols

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