Gunderson Kevin L
Illumina, Inc, San Diego, CA, USA.
Methods Mol Biol. 2009;529:197-213. doi: 10.1007/978-1-59745-538-1_13.
In this review, we describe the laboratory implementation of Infinium whole genome genotyping (WGG) technology for whole genome association studies and copy number studies. Briefly, the Infinium WGG assay employs a single tube whole genome amplification reaction to amplify the entire genome; genomic loci of interest are captured on an array by specific hybridization of picomolar concentrations amplified gDNA. After target capture, single nucleotide polymorphisms (SNPs) are genotyped on the array by a primer extension reaction using hapten-labeled nucleotides. The resultant hapten signal is amplified by immunhistochemical sandwich staining and the array is read out on a high resolution confocal scanner. We have combined this Infinium assay with high-density BeadChips to create the first array platform capable of genotyping over 1 million SNPs per slide. Additionally, the complete Infinium assay is automated using Tecan GenePaint slide processing system. Hybridization, washing, array-based primer extension and staining are performed directly in the Tecan capillary gap Te-Flow Through chambers. This automation process greatly increases assay robustness and throughput while enabling Laboratory Information Management System (LIMS) control of sample tracking. Finally, we give several examples of how this advance in genotyping technology is being applied in whole genome association and copy number studies.
在本综述中，我们描述了用于全基因组关联研究和拷贝数研究的Infinium全基因组基因分型（WGG）技术在实验室中的应用。简而言之，Infinium WGG检测采用单管全基因组扩增反应来扩增整个基因组；通过皮摩尔浓度的扩增基因组DNA（gDNA）的特异性杂交，将感兴趣的基因组位点捕获到芯片上。目标捕获后，通过使用半抗原标记核苷酸的引物延伸反应在芯片上对单核苷酸多态性（SNP）进行基因分型。产生的半抗原信号通过免疫组织化学夹心染色进行扩增，并在高分辨率共聚焦扫描仪上读取芯片。我们将这种Infinium检测与高密度BeadChips相结合，创建了第一个能够在每张载玻片上对超过100万个SNP进行基因分型的芯片平台。此外，完整的Infinium检测使用Tecan GenePaint载玻片处理系统实现自动化。杂交、洗涤、基于芯片的引物延伸和染色直接在Tecan毛细管间隙Te-Flow Through腔室中进行。这种自动化过程极大地提高了检测的稳健性和通量，同时实现了实验室信息管理系统（LIMS）对样品追踪的控制。最后，我们给出了几个关于这种基因分型技术进展如何应用于全基因组关联研究和拷贝数研究的例子。
