MyGene2 and Geno2MP
MyGene2 is a web-based platform that enables families, clinicians, and researchers to share genetic information such as candidate genes/variants and phenotypic data publicly with the goal of facilitating rare disease research such as novel disease gene discovery and genotype/phenotype relationship studies. Families can share their own identifiable health and genetic information and clinicians and researchers can use MyGene2 to share de-identified health and candidate gene/variant information on behalf of families with Mendelian conditions. Information about each family is organized into a “Profile.” All profiles are publicly searchable, and all stakeholders have the same level of access to the data shared through the site. To help families share their data and make matches with others interested in the same candidate genes or Mendelian conditions, MyGene2 uses concept recognition software to automatically extract structured phenotype terms from narratives submitted by families and variant validation software to assist families in submitting their candidate variants to the site. MyGene2 currently hosts ~5000 family profiles that share candidate gene/variant and reported clinical findings and shares all variants through Beacon Network, a search engine across the global network of Beacons enabling discovery of genetic variants of interest around the world (Fiume et al. 2019). Beacon Network users can visit the MyGene2 profiles for any variant identified through a search of the Network.
Geno2MP is a web-accessible, searchable database containing rare variant genotypes linked to phenotypic information developed by the University of Washington Center for Mendelian Genomics to publicly share all rare (<2.5% alternate allele frequency in gnomAD v2.1 or v3.0) sequence variants identified in individuals affected by suspected Mendelian conditions and/or in their putatively unaffected relatives alongside de-identified phenotype data describing the affected status and original phenotype of interest for which each family was ascertained. As of October 1, 2021, Geno2MP shares variant zygosity and phenotype data from 19,344 individuals sequenced by one of the University of Washington, Broad, or Yale Centers for Mendelian Genomics. Geno2MP can be searched by gene, chromosomal coordinates, or HPO term, and a bulk sites-only VCF is available for download. The Geno2MP dataset will eventually be integrated into MyGene2 in order to make its data available for matchmaking/querying via the future variant-level Matchmaker Exchange and the Beacon Network. This will also enable users to sign up to be notified about future variant matches.