Conversation

Daniel MacArthur
@dgmacarthur
After nearly a decade (!) of iterative development on the seqr platform for management and analysis of rare disease genomic data, we have a preprint up describing this critical piece of our rare disease infrastructure:
medrxiv.org
seqr : a web-based analysis and collaboration tool for rare disease genomics
Exome and genome sequencing have become the tools of choice for rare disease diagnosis, leading to large amounts of data available for analyses. To identify causal variants in these datasets,...
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Daniel MacArthur
@dgmacarthur
seqr has been our workhorse platform for collaborations with groups around the world through the
@broadinstitute
Center for Mendelian Genomics; to date it's been used to study more than 10,000 families, to make more than 3,800 diagnoses, and find >300 new disease genes.
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Daniel MacArthur
@dgmacarthur
It's been critical for our approach to rare disease research, because (1) it scales to massive numbers of families with WGS data, (2) it's accessible to any collaborator through a web browser, and (3) it facilitates collaboration and data sharing.
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Daniel MacArthur
@dgmacarthur
seqr has always been open-source, and is under very active development (e.g. recently added support for structural variants and RNA-seq data). There are now deployments in Australia, Bahrain, Estonia, UK, and multiple US labs. Code here:
github.com
GitHub - broadinstitute/seqr: web-based analysis tool for rare disease genomics
web-based analysis tool for rare disease genomics - GitHub - broadinstitute/seqr: web-based analysis tool for rare disease genomics
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Daniel MacArthur
@dgmacarthur
Replying to
@dgmacarthur
At seqr's heart is the analysis interface, which makes it easy to filter variants by inheritance, frequency, functional impact, known pathogenicity, and quality; review read data and external evidence; and tag variants with shared notes.
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