Whole genome analysis of a Vietnamese trio
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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.
KeywordsGenomic variant analysis Vietnamese human genome Whole genome sequencing data analysis
We would like to express our special thanks to Prof Nguyen Huu Duc from Vietnam National University, Hanoi, for his constant encouragement and support. We thank Prof Jean Daniel Zucker, Dr Zamin Iqbal and Prof Arndt von Haeseler for providing useful inputs to our manuscript. This project is partly financially supported by the Science and Technology Foundation of Vietnam National University, Hanoi (grant no. QKHCN.13.01). We also would like to thank the Center for Integrative Bioinformatics Vienna for providing computational resources. BQM acknowledges financial support by the Austrian Science Fund - FWF (grant no. I760-B17).
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