seqr: an open-source rare disease genomic analysis platform on the AnVIL

seqr is a one-of-a-kind platform designed to support the analysis and visualization of genomic and transcriptomic data for rare disease families, while enabling data sharing and collaboration among researchers, clinicians and clinical laboratories.

Security and Functionality

The seqr platform is Federal Information Security Management Act (FISMA)-compliant and is fully integrated into the cloud-based AnVIL on the Terra ecosystem since 2021. Since then, seqr has been used in the analysis of >70,000 samples (45% Broad Institute Center for Mendelian Genomics data and 55% from external data owners loading through AnVIL).

seqr's analysis functionality includes predefined searches and customizable search parameters resulting in the filtration and display of richly annotated variants (A); Project management tools facilitate tracking of case and project-level metadata, including data type(s), pedigree, structured phenotype information, and analysis status (B); Data sharing functionality includes the integration of Matchmaker Exchange and Variant-Level Matching to facilitate novel disease discovery and phenotype expansions (C).

Using seqr on AnVIL

Any AnVIL-registered user can submit a request to import data directly from their AnVIL workspace into a private seqr project for analysis. The entire pipeline is fully automated, with quality checks and error messages surfaced directly to the user throughout the process.

Support resources for seqr include tutorials and a comprehensive FAQ page, which provide a useful starting point for learning more about the platform.

Users can also reach out directly to the seqr team with additional questions or to collaborate on new features.

Visit https://seqr.broadinstitute.org/faq/ to learn more.