VarSome
| Content | |
|---|---|
| Description | Search engine and aggregator for all human genome-related data. |
| Contact | |
| Primary citation | Kopanos et al. (2018) |
| Access | |
| Website | http://www.varsome.com |
VarSome is an open access search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants[1]. It renders and displays a detailed annotation of the queried variant, including multiple notations, predicted pathogenicity status from a variety of tools, genomic context, as well as information from 35+ public genomic databases. It allows users to mark the pathogenicity of variants and to link variants to specific phenotypes, diseases and publications. Finally, it provides an automated pathogenicity assessment consistent with the widely accepted ACMG guidelines. It therefore provides a powerful analysis resource as well as a repository for the accumulated global knowledge of the genomics community. From a technical point of view, it allows convenient application programming interface for accessing all its data.
Features
35+ Genomics Databases
VarSome offers a cross-referenced knowledge base consisting of 35+ public genomic databases, representing over 33 billion variant annotations. Whenever a public database is updated, VarSome downloads the update, processes it and makes it available for annotation and classification to the whole genomic community.
Following genomic databases have been integrated in VarSome: ClinVar, RefSeq, UniProt, GnomAD, COSMIC, 1000Genomes, dbSNP, Mutation Taster, Sift, CGD, Pubmed, Unigene, DGI, Clinical Trials, HPO, Orphanet, ICGC, CIViC, DECIPHER, Genecards, KEGG, BioGPS, Reactome, Genetests, HGNC, Wikigenes, Ensembl, Vega, UCSC.
Search Functionality
You can search VarSome by gene name, transcript symbol, genomic location, variant ID or HGVS nomenclature. VarSome can also parse single lines from VCF files to look up the variant they describe. The results are not limited to known variants, any variant of any length may be entered.
VarSome full text search functions pretty much like Google search with one important difference. The search query returns only entries in relation to the VarSome internal aggregated knowledge base. Full search expands the regular search functionality of VarSome, enabling you to search not only for variants, but also to perform word searches over the entire contents of VarSome, such as articles, diseases, phenotypes, genes, ClinVar & UniProt variants. Importantly, this includes content provided by VarSome user community.
ACMG Classification
Apart from regular ClinVar and RefSeq pathogenicity classification, VarSome displays also the classification according to the ACMG guidelines[2]. Every ACMG rule is explained, along with information why it has been triggered, or not. In cases you have some additional evidence, you can manually trigger additional ACMG rules and reach easily the final verdict for your variant.
Community
Although backed by expertise of its core team, VarSome is a community-driven project aiming at sharing global expertise on human variants. You can classify any variant, comment on it or link a publication and thus give something back to the whole VarSome community. As of 2018, VarSome has a community of over 80,000 clinical geneticists, health care professionals and researchers worldwide.
API
VarSome provides a powerful REST API interface which allows you to integrate VarSome knowledge base into your own in-house built bioinformatic pipeline for variant annotation and classification purposes.
References
- ↑ Kopanos, Christos; Tsiolkas, Vasilis; Kouris, Alexandros; Chapple, Charles E.; Aguilera, Monica Albarca; Meyer, Richard; Massouras, Andreas (2018-07-13). "VarSome: The Human Genomic Variant Search Engine". bioRxiv 367359.
- ↑ Richards, Sue; Aziz, Nazneen; Bale, Sherri; Bick, David; Das, Soma; Gastier-Foster, Julie; Grody, Wayne W.; Hegde, Madhuri; Lyon, Elaine (2015-03-05). "Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology". Genetics in Medicine. 17 (5): 405–423. doi:10.1038/gim.2015.30. ISSN 1098-3600. PMC 4544753. PMID 25741868.
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