Quality Control for Genome-Wide Association Studies
Quality Control for Genome-Wide Association Studies
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DOI：
10.1007/978-1-60327-367-1_19
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发表时间：
2010-01-01
期刊：
影响因子：
--
通讯作者：
Weale, Michael E.
中科院分区：
文献类型：
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作者：
Weale, Michael E.
本章是一个全面的审查质量控制（QC）方法的SNP为基础的基因分型面板用于全基因组关联研究。这些包括对缺失、性别检查、重复和隐性相关性、群体离群值、杂合性和近亲繁殖的个体的QC，以及对缺失、次要等位基因频率和Hardy-Weinberg平衡的SNP的QC。重点是每个QC步骤背后的原因，以及使用智能方法而不是任意的QC阈值。可在www.kcl.ac.uk/mmg/gwascode/上获得执行这些QC步骤的方法和代码。
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/.