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Nat Protoc. 2010 Sep;5(9):1564-73. doi: 10.1038/nprot.2010.116. Epub 2010 Aug 26.

Data quality control in genetic case-control association studies.

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1
Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. carl.anderson@sanger.ac.uk

Abstract

This protocol details the steps for data quality assessment and control that are typically carried out during case-control association studies. The steps described involve the identification and removal of DNA samples and markers that introduce bias. These critical steps are paramount to the success of a case-control study and are necessary before statistically testing for association. We describe how to use PLINK, a tool for handling SNP data, to perform assessments of failure rate per individual and per SNP and to assess the degree of relatedness between individuals. We also detail other quality-control procedures, including the use of SMARTPCA software for the identification of ancestral outliers. These platforms were selected because they are user-friendly, widely used and computationally efficient. Steps needed to detect and establish a disease association using case-control data are not discussed here. Issues concerning study design and marker selection in case-control studies have been discussed in our earlier protocols. This protocol, which is routinely used in our labs, should take approximately 8 h to complete.

PMID:
21085122
PMCID:
PMC3025522
DOI:
10.1038/nprot.2010.116
[Indexed for MEDLINE]
Free PMC Article
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