Collaborators are expected to provide high quality, appropriately consented DNA samples from patients and family members. The consent form signed by subjects must include language regarding secondary use, data sharing, and deposition into controlled access databases.
Matchmaker Exchange
The Matchmaker Exchange (MME) is a federated network of genomic centers that share their cases with candidate genes to help find the underlying genetic changes that cause rare disease. The goal of this network is to help aggregate data of patients with similar disorders from around the world. These centers connect to each other through a common application programming interface (API) that uses a mutually agreed upon data format.
We built the matchbox software application to serve as a primary bridge to the MME. Matchbox shares both genotype and phenotype data with other nodes within MME. Building a MME server is a resource intensive process, and a limiting factor to a new center interested in joining this data-sharing network. To help such an institution, we made matchbox open source and free to use.
More information can be found on www.matchmakerexchange.org and in a special issue of Human Mutation (https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23655). You can download matchbox from GitHub. Please contact matchmaker@broadinstitute.org for any questions.
ClinVar
ClinVar is a publicly available database of genomic variation and its relationship to human health, maintained by the National Center for Biotechnology Information (NCBI) and funded by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine. ClinVar catalogs and aggregates variant submissions from external groups with their reported clinical significance and supporting information, when available. ClinVar adds value to submitted interpretations by standardizing descriptions of variants, conditions, and terms for clinical significance. This information is made publicly available through ClinVar for use in research and healthcare communities. More information about ClinVar is available at https://www.ncbi.nlm.nih.gov/clinvar/.
Our submissions can be found under the name “Broad Center for Mendelian Genomics; Broad Institute of MIT and Harvard.”
AnVIL
The Genomic Analysis, Visualization, and Informatics Lab-space, or ‘AnVIL,’ is NHGRI’s genomic data resource that leverages a cloud-based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic-related data sets. In addition to downloading copies of data to local computers and servers, users will have the option to work with data in a secure cloud environment, where they can also use common bioinformatics tools and packages and develop and share their own software tools. Terra is the compute engine and analysis unit of AnVIL where biomedical researchers can access data, run analysis tools, and collaborate easily with others.
Broad CMG data are deposited into dbGaP under study ID phs001272 (CMG) or phs003047 (GREGoR). Researchers can apply to gain access to these data directly via dbGaP.