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Protocols

HGVD specifications

Information


Unique identifier OMICS_11833
Name HGVD
Alternative name Human Genetic Variation Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Yoichi Matsubara

Publication for Human Genetic Variation Database

HGVD citations

 (41)
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

[…] n 131; frequently observed variants (≥ 5%) in 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 []. […]

call_split

Genomic analysis identifies masqueraders of full‐term cerebral palsy

2018
PMCID: 5945967
PMID: 29761117
DOI: 10.1002/acn3.551
call_split See protocol

[…] abase, the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP6500), the Exome Aggregation Consortium (ExAC) database version 0.3 (all and East Asian populations), and the Human Genetic Variation Database (HGVD), to discover rare de novo variants. For the autosomal recessive and X‐linked models, we excluded variants with an allele frequency equal to or greater than 1% […]

call_split

Novel Variants in Individuals with RYR1 Related Congenital Myopathies: Genetic, Laboratory, and Clinical Findings

2018
PMCID: 5845096
PMID: 29556213
DOI: 10.3389/fneur.2018.00118
call_split See protocol

[…] with standards outlined by the American College of Medical Genetics regarding interpretation of sequence variants (). Variants were considered novel if they were not previously reported in ExAC, ESP, HGVD, ClinVar, 1000 Genomes, or HGMD databases and not published in the scientific literature to date. Software tools (SIFT and PolyPhen-2) were also used to predict whether novel variants were likely […]

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

[…] lyses (CMC, Madsen–Browning, and SKAT-O). We removed common variants using the following criteria: alternative allele frequency of more than 0.005 in any public database (ExAC, ESP6500, 1000 Genomes, HGVD, and ToMMo 2KJPN) or more than 0.005 in control samples in this study; call rate of less than 90% in the study samples; and genotyping quality score of less than 99. In German samples, GFRA4 was […]

library_books

Novel rare variations in genes that regulate developmental change in N methyl d aspartate receptor in patients with schizophrenia

2018
Hum Genome Var
PMCID: 5794673
PMID: 29423241
DOI: 10.1038/hgv.2017.56

[…] sed to validate all genetic variants using a 3130XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) after removal of the variants detected in a healthy database cohort of Japanese origin (Human Genetic Variation Database: http://www.genome.med.kyoto-u.ac.jp/SnpDB/index.html; HGVD). The primers were designed using Primer 3 software (http://bioinfo.ut.ee/primer3-0.4.0/primer3/). Primer p […]

library_books

Genetic basis of cardiomyopathy and the genotypes involved in prognosis and left ventricular reverse remodeling

2018
Sci Rep
PMCID: 5792481
PMID: 29386531
DOI: 10.1038/s41598-018-20114-9

[…] ed variants with an alternative allele frequency greater than 0.01% in any freely accessible population database in the ethnically matched 1000 Genomes database, Exome Aggregation Consortium Browser, Human Genetic Variation Database (HGVD, http://www.genome.med.kyoto-u.ac.jp/SnpDB), and ToMMo database. All variants were predicted in silico using CADD scores and were excluded if CADD scores were le […]

Citations

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HGVD institution(s)
Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Pediatrics, St Marianna University School of Medicine, Kanagawa, Japan; Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan; Bits Co., Ltd., Tokyo, Japan; Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
HGVD funding source(s)
This work was supported by the Practical Research Project for Rare/Intractable Diseases (201238002A) from the Ministry of Health, Labour and Welfare of Japan.

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