Data quality control in genetic case-control association studies

被引：943

作者：

Anderson, Carl A. ^{[1
,2
]}

Pettersson, Fredrik H. ^{[1
]}

Clarke, Geraldine M. ^{[1
]}

Cardon, Lon R. ^{[3
]}

Morris, Andrew P. ^{[1
]}

Zondervan, Krina T. ^{[1
]}

机构：

[1] Univ Oxford, Wellcome Trust Ctr Human Genet, Genet & Genom Epidemiol Unit, Oxford, England

[2] Wellcome Trust Sanger Inst, Cambridge, England

[3] GlaxoSmithKline, King Of Prussia, PA USA

来源：

NATURE PROTOCOLS | 2010年 / 5卷 / 09期

基金：

英国惠康基金;

关键词：

GENOME-WIDE ASSOCIATION; RISK LOCI; STRATIFICATION; TOOL;

D O I：

10.1038/nprot.2010.116

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：1564 / 1573

页数：10

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