Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing.
We report the analysis of a Japanese male using high-throughput sequencing to × 40 coverage. More than 99% of the sequence reads were mapped to the reference human genome. Using a Bayesian decision method, we identified 3,132,608 single nucleotide variations (SNVs). Comparison with six previously reported genomes revealed an excess of singleton nonsense and nonsynonymous SNVs, as well as singleton SNVs in conserved non-coding regions. We also identified 5,319 deletions smaller than 10 kb with high accuracy, in addition to copy number variations and rearrangements. De novo assembly of the unmapped sequence reads generated around 3 Mb of novel sequence, which showed high similarity to non-reference human genomes and the human herpesvirus 4 genome. Our analysis suggests that considerable variation remains undiscovered in the human genome and that whole-genome sequencing is an invaluable tool for obtaining a complete understanding of human genetic variation.
Center for Genomic Medicine, RIKEN, Tsurumi, Yokohama, Japan.
Akihiro
A
Fujimoto
Hidewaki
H
Nakagawa
Naoya
N
Hosono
Kaoru
K
Nakano
Tetsuo
T
Abe
Keith A
KA
Boroevich
Masao
M
Nagasaki
Rui
R
Yamaguchi
Tetsuo
T
Shibuya
Michiaki
M
Kubo
Satoru
S
Miyano
Yusuke
Y
Nakamura
Tatsuhiko
T
Tsunoda
D044466:Asian People / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D030342:Genetic Diseases, Inborn / Q000235:genetics; D014644:Genetic Variation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide; D014178:Translocation, Genetic