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IGSR / International Genome Sample Resource

Expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups.

PanSNPdb / Pan-Asian SNP Consortium

Offers genome structural information pertaining to Asian populations in a familiar graphical comparative view. PanSNPdb offers pre-computed information of linkage disequilibrium (LD) blocks and their haplotypes on each chromosome. The comprehensive information in this database can be considered as worldwide data collection, but with special emphasis on Asian populations. The Haploview tool is also integrated into the PanSNPdb website: users can adjust the haplotype inferencing parameters in order to recalculate haplotype blocks ‘‘on-the-fly’’.

Taiwan View

Provides access to the annotations and summary statistics of The Taiwan Biobank (TWB). Taiwan View is a database that contains chromosome, position, single nucleotide polymorphism (SNP) ID, reference allele, alternative allele, counts of three genotypes, and call rate. It also provides an online query webpage for SNP information and an online genome-wide association study (GWAS) platform that allows users to upload their genotype data and perform GWASs using the Cochran–Armitage trend test.

SISu / Sequencing Initiative Suomi

Offers a way to search for data on sequence variants in Finns. SISu provides valuable summary data for researchers and clinicians as well as other people having an interest in genetics in Finland. With SISu, users can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map. Users can search for summary data on single nucleotide variants (SNVs) and indels from exomes of over 10 000 individuals sequenced in disease-specific and population genetic studies. The SISu project is an international collaboration between multiple research groups aiming to build tools for genomic medicine. The first version of the SISu search engine was released in 2014. The project is coordinated in the Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki.

TPMD / Taiwan Polymorphic Marker Database

Offers experimental details and marker information allelotyped in population of Taiwan. TPMD is a shared database and resources for genotyping with microsatellite markers that reduces cost and errors of genotyping and facilitates disease gene mapping in human populations. This resource contains two major sections including the database for sharing useful microsatellite marker information and the resources for supporting consistent genotyping experiments.

iJGVD / Integrative Japanese Genome Variation Database

Provides allele frequency data for more than 4 000 000 autosomal single nucleotide variants (SNVs). iJGVD contains SNV alleles, genomic positions based on the GRCh37/hg19 coordinates, allele frequencies, the corresponding dbSNP IDs, P values for the Hardy–Weinberg equilibrium test, gene annotations and so on. It provides functions to explore the region surrounding an SNV based on chromosome coordinates. The database can be requested with gene symbol, rsSNP ID, or genomic position.

KoVariome

Provides access to single nucleotide polymorphism (SNP) data for Korean population. KoVariome is a comprehensive database of genomic variations and corresponding metadata, constructed based on whole genome sequencing (WGS) data from 50 unrelated Korean individuals who responded to questionnaires detailing body characteristics, habits, allergies, family histories, and physical conditions related to 19 disease classes. It was used to predict candidate loci, inheritance patterns, and genetic risk for several diseases. The database can be useful for biomedical researchers and health practitioners.

CAAPA / Consortium on Asthma among African-ancestry Populations in the Americas

Hosts whole genome sequences available on 883 individuals from 19 case-control studies of asthma. CAAPA uses these data to summarize the genomic contributions to individuals of African ancestry. The original selection criteria were (i) self-reported African ancestry; (ii) a physician’s diagnosis of asthma for cases or a negative history of asthma symptoms and asthma medication usage for controls. Recruitment sites included 9 cities in the US (Atlanta, Baltimore/Washington, Chicago, Detroit, Nashville, New York City, San Francisco, Jackson, MS, and Winston-Salem NC), 4 populations in the Caribbean (Barbados, Dominican Republic, Jamaica, and Puerto Rico), 4 in Central/South America (Brazil, Honduras, and 2 in Colombia) and 2 populations representing West Africa (Nigeria and Gabon), from which most ancestral founders of the African diaspora originated.

HGVD / Human Genetic Variation Database

A reference database of genetic variations in the Japanese population. We collected exomic sequencing data of 1208 Japanese individuals from five institutes and a data set of common variants determined by Illumina’s BeadArray technology from 3248 individuals of Japanese cohorts. Although several sequencing projects are going on for the East Asian population including Japanese for East Asian-specific genetic diversity information, our data sets currently provide the largest catalog of genetic diversity on the protein coding regions in the Japanese population. We centralized these data sets into a newly developed public database—human genetic variation database (HGVD). HGDV will serve as a useful resource sharing system, which will be required for research in genetic profiling in the future as well as for the development of genetic tests to screen for clinically relevant variants in personal genomes.

MFMD / Mediterranean Founder Mutation Database

A comprehensive database established to offer a web-based access to founder mutation data in Mediterranean population. The database provides an overview about the spectrum of founder mutations found in Mediterranean population to the scientific community. Furthermore, MFMD will help scientists to design more efficient diagnostic tests and provides beneficial information to understand the history and the migration events of the Mediterranean population.

JG-SNP / Japanese Single Nucleotide Polymorphism for Geriatric Research

Collects information about genetic polymorphisms topic. JG-SNP is an online resource that informs about allele frequencies of single nucleotide polymorphisms (SNPs) of candidate genes and associations between SNPs and geriatric diseases. It provides an explanation on the significance of genetic polymorphisms and brief explanations on each geriatric disease. Comparison can be made between researchers’ data on SNPs of the candidate genes to obtain the allele frequencies in the elderly population.

SweGen

A database which hosts whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project. SweGen is intended to be used as a resource for the research community and clinical genetics laboratories. Individual positions in the genome can be viewed using the Data Beacon or ExAC Browser. Please note that the 1000 individuals included in the SweGen project represent a cross-section of the Swedish population and that no disease information has been used for the selection. The frequency data may therefore include genetic variants that are associated with, or causative of, disease.

Amish, Mennonite, and Hutterite Genetic Disorders Database

Assists in research and diagnosis of genetic conditions in Anabaptist groups. The Amish, Mennonite, and Hutterite Genetic Disorders Database focuses on single-gene Mendelian disorders and the specific mutations that have been reported. To navigate the database, user can search by disorder, mutation, clinical signs, symptoms, and can input either the OMIM number or the name of disorder, and is directed to the corresponding page.

ThaiSNPdb / Thailand SNP database

Determines Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) in Thai population by using 5th generation Affymetrix SNP genotyping array, each array contains approximately 500,000 known SNP genotyping positions. ThaiSNPdb allows easy browsing and comparisons of genetic polymorphism data from Thai populations as well as others, which were retrieved from several public variation databases including NCBI dbSNP, HapMap3, JSNP and Database of Genomic Variant (DGV).

TMC-SNPdb / Tata Memorial Centre-SNP database

A database of ‘normal’ germline variants derived from Indian (nonEuropean Caucasian population). TMC-SNPdb is the first open source, flexible, upgradable, and freely available single nucleotide polymorphism (SNP) database, not yet included in the public databases with predominant Caucasian representations. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. This database is flexible to accommodate the need for customization by allowing inclusion of similar datasets from additional individuals.

MyHVPDb / Malaysian Node of the Human Variome Project database

A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. MyHVPDb provides only information about the genetic variations and mutations found in the Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based on diseases or genetic mutation types which have three main subcategories: single nucleotide polymorphism (SNP), copy number variation (CNV) followed by the mutations which code for the common diseases among Malaysians.

ThaiMUT / Thailand Mutation and Variation database

Offers a web-based access to genetic mutation and variation information in Thai population. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches.

IGVBrowser

Provides allele and genotype frequency data generated in the Indian Genome Variation Consortium (IGVC) project. The database harbors 4,229 SNPs from more than 900 candidate genes in contrasting Indian populations. Analysis shows that most of the markers are from genic regions. Further, a large fraction of genes are implicated in cardiovascular, metabolic, cancer and immune system-related diseases. Thus, the IGVC data provide a basal level variation data in Indian population to study genetic diseases and pharmacology.

Polymorphix

Obsolete
Provides access to information about sequence polymorphism. Polymorphix is a database, dedicated to within-species sequence polymorphism, that organizes GenBank/EMBL sequences into within-species sequence ‘families’, using both nucleotide similarity and bibliographic criteria. It contains more than 200 million bases, 200 000 sequences and 18 000 bibliographic references and allows simple or elaborate queries on EMBL/GenBank fields (species names, keywords, etc.), and a blast-assisted selection of families.

KGVDB / Korean Genomic Variant Database

Obsolete
Provides multi-class CNV regions and well-tagged SNP information. The data were obtained from 4694 individuals using two different genotyping platforms and publicly available CNV data. The major features of KGVDB that are different from others include the following: (i) polymorphic CNV regions identified under strict quality controls and manual curation; (ii) CNV information from Korean populations to supplement currently biased ethnic information; (iii) large dataset of CNVs tagged with SNPs from 4694 individuals using two different genotyping platforms (SNP array and CGH array); (iv) rich information on tagging SNPs, including frequencies in HapMap populations; and (v) copy number states of the reference sample using log2 ratios from two kinds of CGH data and the depth of coverage from whole-genome sequencing data. The large dataset of KGVDB will provide a rich public resource for the study of CNV and SNP.