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Nat Commun. 2015 Aug 21;6:8018. doi: 10.1038/ncomms9018.

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals.

Author information

1
Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.
2
Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
3
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan.
4
International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan.
5
Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, USA.
6
Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.

Abstract

The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.

PMID:
26292667
PMCID:
PMC4560751
DOI:
10.1038/ncomms9018
[Indexed for MEDLINE]
Free PMC Article

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