IJGVD


27081555	iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. [PMID: 27081555] Yamaguchi-Kabata Y, Nariai N, Kawai Y, Sato Y, Kojima K, Tateno M, Katsuoka F, Yasuda J, Yamamoto M, Nagasaki M. Abstract The integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides genomic variation data detected by whole-genome sequencing (WGS) of Japanese individuals. Specifically, the database contains variants detected by WGS of 1,070 individuals who participated in a genome cohort study of the Tohoku Medical Megabank Project. In the first release, iJGVD includes >4,300,000 autosomal single nucleotide variants (SNVs) whose minor allele frequencies are >5.0%. Hum Genome Var. 2015:2() \| 69 Citations (from Europe PMC, 2025-03-15)
26292667	Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. [PMID: 26292667] Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Douglas Engel J, Kinoshita K, Kure S, Yaegashi N, ToMMo Japanese Reference Panel Project, Yamamoto M. 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. Nat Commun. 2015:6() \| 239 Citations (from Europe PMC, 2025-03-15)

iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. [PMID: 27081555]

Yamaguchi-Kabata Y, Nariai N, Kawai Y, Sato Y, Kojima K, Tateno M, Katsuoka F, Yasuda J, Yamamoto M, Nagasaki M.

The integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides genomic variation data detected by whole-genome sequencing (WGS) of Japanese individuals. Specifically, the database contains variants detected by WGS of 1,070 individuals who participated in a genome cohort study of the Tohoku Medical Megabank Project. In the first release, iJGVD includes >4,300,000 autosomal single nucleotide variants (SNVs) whose minor allele frequencies are >5.0%.

Hum Genome Var. 2015:2() | 69 Citations (from Europe PMC, 2025-03-15)

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. [PMID: 26292667]

Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Douglas Engel J, Kinoshita K, Kure S, Yaegashi N, ToMMo Japanese Reference Panel Project, Yamamoto M.

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.

Nat Commun. 2015:6() | 239 Citations (from Europe PMC, 2025-03-15)

URL:	http://ijgvd.megabank.tohoku.ac.jp
Full name:	Integrative Japanese Genome Variation
Description:	Integrative Japanese Genome Variation (iJGVD) provides data of genomic variations obtained by whole-genome sequencing of Japanese individuals, who participate in the genome cohort study by ToMMo, IMM and other cohort projects in Japan. This initial database contained data of single nucleotide variations (SNVs) and their frequencies among the 1,070 Japanese individuals (1KJPN) from the ToMMo cohort. The genome browser provides an intuitive view of SNV information along with the reference human genome sequence using hg19/GRCh37 coordinate system.
Year founded:	2015
Last update:	2018/3/19
Version:
Accessibility:	Accessible
Country/Region:	Japan

Data type:	DNA
Data object:	Animal
Database category:	Gene genome and annotation
Major species:	Homo sapiens
Keywords:	gene regulation genetic interaction

University/Institution:	Tohoku University
Address:	Group of Genome Information Analysis Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University Tohoku Mediacl Megabank Building Tohoku University 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, JAPAN
City:
Province/State:
Country/Region:	Japan
Contact name (PI/Team):	Group of Genome Information Analysis
Contact email (PI/Helpdesk):	insilico-support@is.megabank.tohoku.ac.jp

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