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HGVA: the Human Genome Variation Archive.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Lopez, Javier 
Coll, Jacobo 
Kandasamy, Swaathi 
Tarraga, Joaquin 

Abstract

High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets.

Description

Keywords

Genetic Variation, Genome, Human, Humans, Internet, Software, User-Computer Interface

Journal Title

Nucleic Acids Res

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

45

Publisher

Oxford University Press (OUP)
Sponsorship
Cambridge University Hospitals NHS Foundation Trust (CUH) (unknown)