Van Asselt Austin J, Ehli Erik A
Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA.
Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA.
Methods Mol Biol. 2022;2418:269-287. doi: 10.1007/978-1-0716-1920-9_16.
The field of population genetics has exploded in the last two decades following the sequencing of the human genome in 2001 (Green et al. Nature 526:29-31, 2015). Tools to measure genetic variation have matured significantly throughout this advancement in knowledge (Lenoir and Giannella. J Biomed Discov Collab 1:11, 2006; Marzancola et al. Methods Mol Biol 1368:161-178, 2016). In this chapter, the focus is on the laboratory methods developed to perform genome-wide genotyping utilizing DNA microarrays, which is one of the most commonly used molecular techniques to assess global genetic variation (Heller MJ, Annu Rev Biomed Eng 4:129-153, 2002). DNA microarrays allow for the interrogation of hundreds of thousands of SNPs (single nucleotide polymorphisms) at once utilizing array-based technology in conjunction with fluorescent molecular labels in a process referred to as genotyping (Marzancola et al. Methods Mol Biol 1368:161-178, 2016). Genotype data can be utilized to associate certain phenotypes in relation with specific genetic variants within a population in a process known as genome-wide association studies or GWAS (Charlesworth and Charlesworth. Heredity (Edinb) 118(1):2-9, 2017; Casillas and Barbadilla. Genetics 205(3):1003-1035, 2017). This experimental technique is a multiple-day process involving the combination of DNA extraction, amplification, fragmentation, binding, and staining (Illumina Infinium HTS Assay Protocol Guide, 2013). Many vendors supply platforms and products to assess global genetic variation using DNA microarrays (Illumina Infinium HTS Assay Protocol Guide, 2013). In this chapter, the focus is on the methods utilized to generate high-quality genotype data with the Illumina Infinium Global Screening Array. Although data analysis and quality control are not the focus for this chapter, they are also briefly addressed.
自2001年人类基因组测序完成以来（格林等人，《自然》526:29 - 31，2015年），群体遗传学领域在过去二十年中得到了迅猛发展。在这一知识进步过程中，用于测量遗传变异的工具已经显著成熟（勒努瓦和詹内拉，《生物医学发现与合作杂志》1:11，2006年；马尔赞科拉等人，《分子生物学方法》1368:161 - 178，2016年）。在本章中，重点是为利用DNA微阵列进行全基因组基因分型而开发的实验室方法，DNA微阵列是评估全球遗传变异最常用的分子技术之一（海勒·M·J，《生物医学工程年度评论》4:129 - 153，2002年）。DNA微阵列允许在一个称为基因分型的过程中，利用基于阵列的技术结合荧光分子标记一次性检测数十万单核苷酸多态性（SNPs）（马尔赞科拉等人，《分子生物学方法》1368:161 - 178，2016年）。基因型数据可用于在一个称为全基因组关联研究或GWAS的过程中，将某些表型与群体内特定的遗传变异联系起来（查尔斯沃思和查尔斯沃思，《遗传学（爱丁堡）》118(1):2 - 9，2017年；卡西利亚斯和巴尔巴迪拉，《遗传学》205(3):1003 - 1035，2017年）。这种实验技术是一个需要多天的过程，涉及DNA提取、扩增、片段化、结合和染色（Illumina Infinium HTS分析协议指南，2013年）。许多供应商提供使用DNA微阵列评估全球遗传变异的平台和产品（Illumina Infinium HTS分析协议指南，2013年）。在本章中，重点是利用Illumina Infinium全球筛选阵列生成高质量基因型数据的方法。虽然数据分析和质量控制不是本章的重点，但也会简要提及。
