Weale Michael E
Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, UK
Methods Mol Biol. 2010;628:341-72. doi: 10.1007/978-1-60327-367-1_19.
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/ .
本章全面综述了全基因组关联研究中基于单核苷酸多态性（SNP）的基因分型芯片的质量控制（QC）方法。这些方法包括对个体进行缺失数据、性别检查、重复样本和隐秘亲缘关系、群体离群值、杂合性和近亲繁殖的质量控制，以及对SNP进行缺失数据、次要等位基因频率和哈迪-温伯格平衡的质量控制。重点在于每个质量控制步骤背后的原因以及智能方法的使用，而非任意的质量控制阈值。执行这些质量控制步骤的脚本和代码可在www.kcl.ac.uk/mmg/gwascode/获取。
