Gochi Leo, Kawai Yosuke, Fujimoto Akihiro
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0003, Japan.
Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan.
Hum Genet. 2023 Jan;142(1):45-57. doi: 10.1007/s00439-022-02484-3. Epub 2022 Sep 1.
Microsatellites (MS) are tandem repeats of short units, and have been used for population genetics, individual identification, and medical genetics. However, studies of MS on a whole-genome level are limited, and genotyping methods for MS have yet to be established. Here, we analyzed approximately 8.5 million MS regions using a previously developed MS caller for short reads (MIVcall method) for three large publicly available human genome sequencing data sets: the Korean Personal Genome Project, Simons Genome Diversity Project, and Human Genome Diversity Project. Our analysis identified 253,114 polymorphic MS. A comparison among different populations suggests that MS in the coding region evolved by random genetic drift and natural selection. In an analysis of genetic structures, MS clearly revealed population structures as SNPs and detected clusters that were not found by SNPs in African and Oceanian populations. Based on the MS polymorphisms, we selected MS marker candidates for individual identification. Finally, we applied our method to a deep sequenced ancient DNA sample. This study provides a comprehensive picture of MS polymorphisms and application to human population studies.
微卫星（MS）是短单元的串联重复序列，已被用于群体遗传学、个体识别和医学遗传学研究。然而，全基因组水平上的微卫星研究有限，且微卫星的基因分型方法尚未建立。在此，我们使用先前开发的用于短读长的微卫星检测方法（MIVcall方法），对三个公开可用的大型人类基因组测序数据集进行分析，这些数据集分别是韩国个人基因组计划、西蒙斯基因组多样性计划和人类基因组多样性计划，共分析了约850万个微卫星区域。我们的分析鉴定出253,114个多态性微卫星。不同人群之间的比较表明，编码区的微卫星是通过随机遗传漂变和自然选择进化而来的。在遗传结构分析中，微卫星与单核苷酸多态性（SNP）一样，清晰地揭示了群体结构，并在非洲和大洋洲人群中检测到了SNP未发现的聚类。基于微卫星多态性，我们选择了用于个体识别的微卫星标记候选物。最后，我们将我们的方法应用于深度测序的古代DNA样本。这项研究提供了微卫星多态性的全面图景及其在人类群体研究中的应用。
