TY  - JOUR
ID  - SisLab1476
UR  - http://www.springer.com/life+sciences/journal/12038
IS  - 1
A1  - Dang, Thanh Hai
A1  - Nguyen, Dai Thanh
A1  - Pham, Thi Minh Trang
A1  - Le, Si Quang
A1  - Phan, Thi Thu Hang
A1  - Dang, Cao Cuong
A1  - Hoang, Kim Phuc
A1  - Nguyen, Huu Duc
A1  - Do, Duc Dong
A1  - Bui, Quang Minh
A1  - Pham, Bao Son
A1  - Le, Sy Vinh
Y1  - 2015/03/01/
N2  - 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.
PB  - Springer
JF  - Journal of Bioscience
VL  - 40
SN  - 0250-5991
TI  - Whole Genome Analysis of a Vietnamese Trio
SP  - 114
AV  - none
EP  - 123
ER  -