iJGVD statistics

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Protocols

iJGVD specifications

Information


Unique identifier OMICS_21852
Name iJGVD
Alternative name Integrative Japanese Genome Variation Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Masao Nagasaki
  • person_outline Yumi Yamaguchi-Kabata

Publication for Integrative Japanese Genome Variation Database

iJGVD citations

 (9)
library_books

TP53 and OSBPL10 alterations in diffuse large B cell lymphoma: prognostic markers identified via exome analysis of cases with extreme prognosis

2018
Oncotarget
PMCID: 5929408
PMID: 29731965
DOI: 10.18632/oncotarget.24656

[…] 1000 Genomes Project; frequently observed variants (≥ 5%) in NHLBI Exome Sequencing Project esp6500siv2; frequently observed variants (≥ five samples) in HGVD; frequently observed variants (≥ 5%) in iJGVD; and somatic variants called by more than one analysis tool. Copy number variation (CNV) and tumor content analyses were performed using ExomeCNV []. CNV was plotted with CIRCOS version 0.69-2, […]

library_books

Whole exome sequencing and gene based rare variant association tests suggest that PLA2G4E might be a risk gene for panic disorder

2018
PMCID: 5804028
PMID: 29391400
DOI: 10.1038/s41398-017-0088-0

[…] mic Variation Database (HGVD) exome data of 1208 individuals collected in Japan; SNV allele frequency collected from whole-genome sequencing data of 2049 healthy Japanese individuals (2KJPN) (https://ijgvd.megabank.tohoku.ac.jp); and (3) mutations not included in the UCSC segmental duplication region. […]

call_split

Rare loss of function mutations in N methyl d aspartate glutamate receptors and their contributions to schizophrenia susceptibility

2018
PMCID: 5802496
PMID: 29317596
DOI: 10.1038/s41398-017-0061-y
call_split See protocol

[…] cbi.nlm.nih.gov/SNP/), the Exome Aggregation Consortium (http://evs.gs.washington.edu/EVS/), the 1000 Genomes Project (http://www.1000genomes.org/), the Integrative Japanese Genome Variation (https://ijgvd.megabank.tohoku.ac.jp/), or the Human Genetic Variation Database (http://www.hgvd.genome.med.kyoto-u.ac.jp/index.html); (2) we looked for a possible impact of amino acid substitutions as predict […]

call_split

Prevalence of TECTA mutation in patients with mid frequency sensorineural hearing loss

2017
Orphanet J Rare Dis
PMCID: 5613382
PMID: 28946916
DOI: 10.1186/s13023-017-0708-z
call_split See protocol

[…] frequency < 1% in all public databases, including 1000 GENOMES [], NHLBI Exome Sequencing Project (ESP6500) [], Exome Aggregation Consortium (ExAC) [], Human Genetic Variation Database (HGVD) [], and integrative Japanese Genome Variation Database (iJGVD) []; 3) high amino acid conservation (>90% in primates and mammals, >50% in vertebrates) among up to 12 primate, 50 mammal, and 38 vertebrate spec […]

library_books

Deep sequencing reveals variations in somatic cell mosaic mutations between monozygotic twins with discordant psychiatric disease

2017
Hum Genome Var
PMCID: 5529667
DOI: 10.1038/hgv.2017.32

[…] ta; Human Genomic Variation Database exome data of 1,208 individuals collected in Japan; SNV allele frequency collected from whole-genome sequencing data of 2,049 healthy Japanese population (https://ijgvd.megabank.tohoku.ac.jp) and (3) mutations not included in the UCSC segmental duplication region. To find genomic differences in discordant MZ twins, SNVs and indels were selected based on the fol […]

library_books

Novel human mutation and CRISPR/Cas genome edited mice reveal the importance of C terminal domain of MSX1 in tooth and palate development

2016
Sci Rep
PMCID: 5137164
PMID: 27917906
DOI: 10.1038/srep38398

[…] resent in human genome variation databases [i.e., 1000 Genomes Project database (http://www.1000genomes.org/), NHLBI GO Exome Sequencing Project (ESP6500, http://evs.gs.washington.edu/EVS/), HGVD and integrative Japanese Genome Variation Database (iJGVD, https://ijgvd.megabank.tohoku.ac.jp/)] nor in disease-causing mutation databases [i.e., Human Gene Mutation Database Professional 2016.1 (HGMD, h […]

Citations

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iJGVD institution(s)
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Graduate School of Medicine, Tohoku University, Sendai, Japan; Department of Cohort Genome Information Analysis, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Graduate School of Information Sciences, Tohoku University, Sendai, Japan
iJGVD funding source(s)
Supported in part by the Tohoku Medical Megabank Project (Special Account for Reconstruction from the Great East Japan Earthquake; by the Center of Innovation Program from Japan Science and Technology Agency, JST.

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