title: Data quality control in genetic case-control association studies.
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.
authors.affiliation: Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. carl.anderson@sanger.ac.uk
authors.forename: Carl A
authors.initials: CA
authors.lastname: Anderson
authors.forename: Fredrik H
authors.initials: FH
authors.lastname: Pettersson
authors.forename: Geraldine M
authors.initials: GM
authors.lastname: Clarke
authors.forename: Lon R
authors.initials: LR
authors.lastname: Cardon
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Morris
authors.forename: Krina T
authors.initials: KT
authors.lastname: Zondervan
mesh_terms: D000818:Animals; D016022:Case-Control Studies; D019295:Computational Biology / Q000379:methods*; D005260:Female; D005821:Genetic Techniques; D055106:Genome-Wide Association Study / Q000379:methods; D006801:Humans; D008297:Male; D011786:Quality Control