Quality Control for Genome-Wide Association Studies
- 8 February 2010
- book chapter
- Published by Springer Nature
- Vol. 628, 341-372
- https://doi.org/10.1007/978-1-60327-367-1_19
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/.Keywords
This publication has 32 references indexed in Scilit:
- Accounting for ancestry: population substructure and genome-wide association studiesHuman Molecular Genetics, 2008
- Smarter clustering methods for SNP genotype callingBioinformatics, 2008
- Evaluating the Effects of Imputation on the Power, Coverage, and Cost Efficiency of Genome-wide SNP PlatformsAmerican Journal of Human Genetics, 2008
- Long-Range LD Can Confound Genome Scans in Admixed PopulationsAmerican Journal of Human Genetics, 2008
- A Statistical Method for Predicting Classical HLA Alleles from SNP DataAmerican Journal of Human Genetics, 2008
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- Successful design and conduct of genome-wide association studiesHuman Molecular Genetics, 2007
- Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controlsNature, 2007
- Principal components analysis corrects for stratification in genome-wide association studiesNature Genetics, 2006
- Estimation of individual admixture: Analytical and study design considerationsGenetic Epidemiology, 2005