Quality Control, Imputation and Analysis of Genome-wide Genotyping Data from the Illumina HumanCoreExome Microarray

Overview

Journal Brief Funct Genomics

Publisher Oxford University Press

Date 2015 Oct 8

PMID 26443613

Citations 39

Authors

Jonathan R I Coleman

Jack Euesden

Hamel Patel

Amos A Folarin

Stephen Newhouse

Gerome Breen

Affiliations

Soon will be listed here.

Abstract

The decreasing cost of performing genome-wide association studies has made genomics widely accessible. However, there is a paucity of guidance for best practice in conducting such analyses. For the results of a study to be valid and replicable, multiple biases must be addressed in the course of data preparation and analysis. In addition, standardizing methods across small, independent studies would increase comparability and the potential for effective meta-analysis. This article provides a discussion of important aspects of quality control, imputation and analysis of genome-wide data from a low-coverage microarray, as well as a straight-forward guide to performing a genome-wide association study. A detailed protocol is provided online, with example scripts available at https://github.com/JoniColeman/gwas_scripts.

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