Whole genome analysis of a Vietnamese trio

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 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.

Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations

“…Compared with SNVs, the de novo mutation events for indels occurred less frequently. The mutation rate was estimated to be 1.0 × 10 − 9 -2.9 × 10 − 9 per site per generation according to the 4-10 de novo indels identified in each offspring (Table 2; Additional file 1: Table S12), in accordance with previous reports [14,52]. We did not observe any direct physical or functional attribution between the de novo indels and de novo SNVs in each samplethey were located distant from each other (> 1 Mb) and in different genes.…”

“…To date, most trio-based sequencing studies are disease-related [11][12][13]. Wholegenome sequencing studies of healthy trios are less biased than those of the disease-based ones, but publications on these are rather limited, except for the one Vietnamese trio and 10 Danish trios that were sequenced to high coverage in recent years [14,15].…”

A Vietnamese human genetic variation database

“…Vietnam has about 95 million people (the 14th largest country by population in the world) of which more than 86% are Kinh people. We started the first Vietnamese human genome project with a Kinh Vietnamese (KHV) trio and discovered a considerable number of novel variants (Hai et al, ). Phase 3 of the 1KG project sequenced 99 unrelated KHV people in Ho Chi Minh City, Vietnam at the low coverage level.…”

“…We started the first Vietnamese human genome project with a Kinh Vietnamese (KHV) trio and discovered a considerable number of novel variants (Hai et al, 2015). Phase 3 of the 1KG project sequenced 99 unrelated KHV people in Ho Chi Minh City, Vietnam at the low coverage level.…”

A computational framework to analyze human genomes

“…This allows us to perform large-scale human genome projects to study genotype-phenotype relationships; personalized medicines; the evolutionary and diversity of human populations [1,2,3,4]. Various human genome projects have been conducted for different Asian populations such as 100 Malay genomes project to detect low-frequency and rare variants [2]; 35 Korean genomes project to decipher the genetic architecture of the Korean population [5]; 90 Han Chinese genomes project to investigate Han Chinese human genomes [6]; Vietnamese genomes project to build Vietnamese variation database [7,8].…”