Hai Dang Thanh, Thanh Nguyen Dai, Trang Pham Thi Minh, Quang Le Si, Hang Phan Thi Thu, Cuong Dang Cao, Phuc Hoang Kim, Duc Nguyen Huu, Dong Do Duc, Minh Bui Quang, Son Pham Bao, Vinh Le Sy
University of Engineering and Technology, Vietnam National University Hanoi, Hanoi, Vietnam.
J Biosci. 2015 Mar;40(1):113-24. doi: 10.1007/s12038-015-9501-0.
We here present the first whole genome analysis of an anonymous Kinh Vietnamese (KHV) trio whose genomes were deeply sequenced to 30-fold average coverage. The resulting short reads covered 99.91 percent of the human reference genome (GRCh37d5). We identified 4,719,412 SNPs and 827,385 short indels that satisfied the Mendelian inheritance law. Among them, 109,914 (2.3 percent) SNPs and 59,119 (7.1 percent) short indels were novel. We also detected 30,171 structural variants of which 27,604 (91.5 percent) were large indels. There were 6,681 large indels in the range 0.1-100 kbp occurring in the child genome that were also confirmed in either the father or mother genome. We compared these large indels against the DGV database and found that 1,499 (22.44 percent) were KHV specific. De novo assembly of high-quality unmapped reads yielded 789 contigs with the length greater than or equal to 300 bp. There were 235 contigs from the child genome of which 199 (84.7 percent) were significantly matched with at least one contig from the father or mother genome. Blasting these 199 contigs against other alternative human genomes revealed 4 novel contigs. The novel variants identified from our study demonstrated the necessity of conducting more genome-wide studies not only for Kinh but also for other ethnic groups in Vietnam.
我们在此展示了对一个匿名的京族越南人（KHV）三人组的首次全基因组分析，其基因组深度测序至平均覆盖度为30倍。所得短读长覆盖了人类参考基因组（GRCh37d5）的99.91%。我们鉴定出4,719,412个单核苷酸多态性（SNP）和827,385个短插入缺失突变，这些均符合孟德尔遗传定律。其中，109,914个（2.3%）SNP和59,119个（7.1%）短插入缺失突变是新发现的。我们还检测到30,171个结构变异，其中27,604个（91.5%）是大的插入缺失突变。在儿童基因组中出现的0.1 - 100 kbp范围内有6,681个大插入缺失突变，在父亲或母亲基因组中也得到了证实。我们将这些大插入缺失突变与DGV数据库进行比较，发现1,499个（22.44%）是KHV特有的。对高质量未映射读长进行从头组装产生了789个长度大于或等于300 bp的重叠群。来自儿童基因组的有235个重叠群，其中199个（84.7%）与来自父亲或母亲基因组的至少一个重叠群有显著匹配。将这199个重叠群与其他替代人类基因组进行比对，发现了4个新的重叠群。我们研究中鉴定出的新变异表明，不仅对京族，而且对越南的其他民族进行更多全基因组研究是必要的。
