Medical Research

University of California, Santa Cruz

David Haussler, Benedict Paten
Santa Cruz, CA
$2,000,000
June 2015

Since the sequencing of the human genome was announced in 2000, much has been learned about the remarkable level of genomic variations in diverse human populations.  However there is no framework to reliably compare these variations to understand their role in health and disease.  This project, led by University of California, Santa Cruz researchers, aims to construct a new representation of the human reference genome, the Human Genome Variation Map (HGVM), which will accommodate all common human genomic variations using a new mathematical platform.  This graph-based structure will augment the existing human reference genome, providing a means to name, identify, and analyze all common variations precisely and reproducibly.  The HGVM data model will integrate into the standard application programming interface (API) for representing genomic variation being developed by the Global Alliance for Genomics and Health, placing it at the center of a burgeoning set of standards for sharing genomic data.  The HGVM will be progressively scaled from prototypes for pilot regions to a complete resource that incorporates data from all major public sources of genetic variation, including common, complex structural variations and satellite DNA.  It will include tools necessary for working with this rich structure to gain a deeper understanding of human genetic variation and its association with phenotypes relevant to health and disease.  The HGVM will be public and freely available to all.

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