eprintid: 1476
rev_number: 8
eprint_status: archive
userid: 4
dir: disk0/00/00/14/76
datestamp: 2016-01-10 14:45:58
lastmod: 2016-01-10 14:45:58
status_changed: 2016-01-10 14:45:58
type: article
metadata_visibility: show
creators_name: Dang, Thanh Hai
creators_name: Nguyen, Dai Thanh
creators_name: Pham, Thi Minh Trang
creators_name: Le, Si Quang
creators_name: Phan, Thi Thu Hang
creators_name: Dang, Cao Cuong
creators_name: Hoang, Kim Phuc
creators_name: Nguyen, Huu Duc
creators_name: Do, Duc Dong
creators_name: Bui, Quang Minh
creators_name: Pham, Bao Son
creators_name: Le, Sy Vinh
creators_id: ducnh@soict.hust.edu.vn
creators_id: sonpb@vnu.edu.vn
title: Whole Genome Analysis of a Vietnamese Trio
ispublished: pub
subjects: IT
subjects: isi
abstract: 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.
date: 2015-03-01
date_type: published
publisher: Springer
official_url: http://www.springer.com/life+sciences/journal/12038
id_number: 10.​1007/​s12038-015-9501-0
full_text_status: none
publication: Journal of Bioscience
volume: 40
number: 1
pagerange: 114-123
refereed: TRUE
issn: 0250-5991
citation:   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