Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray

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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.
Original languageEnglish
Pages (from-to)298-304
Number of pages7
JournalBriefings In Functional Genomics
Volume15
Issue number4
Early online date5 Oct 2015
DOIs
Publication statusPublished - Jul 2016

Keywords

  • GWAS
  • Methods
  • Low-coverage microarray
  • Imputation
  • Analysis

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