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Whole Genome Analysis of a Vietnamese Trio

Dang, Thanh Hai and Nguyen, Dai Thanh and Pham, Thi Minh Trang and Le, Si Quang and Phan, Thi Thu Hang and Dang, Cao Cuong and Hoang, Kim Phuc and Nguyen, Huu Duc and Do, Duc Dong and Bui, Quang Minh and Pham, Bao Son and Le, Sy Vinh (2015) Whole Genome Analysis of a Vietnamese Trio. Journal of Bioscience, 40 (1). pp. 114-123. ISSN 0250-5991

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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% 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%) SNPs and 59,119 (7.1%) short indels were novel. We also detected 30,171 structural variants of which 27,604 (91.5%) 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%) were KHV specific. De novo assembly of high-quality unmapped reads yielded 789 contigs with the length ≥300 bp. There were 235 contigs from the child genome of which 199 (84.7%) 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.

Item Type: Article
Subjects: Information Technology (IT)
ISI-indexed journals
Depositing User: Prof. Xuan-Tu Tran
Date Deposited: 10 Jan 2016 14:45
Last Modified: 10 Jan 2016 14:45

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