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griffithlab / civic-meeting

Repo for advertising and organizing CIViC unconference/meeting activities
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Best practices in annotating CNVs and fusions alongside variants in knowledgebases #39

Closed bpitel12 closed 2 years ago

bpitel12 commented 5 years ago

One noted gap in many well-known knowledgebases is the coverage and searchability of copy number variants and fusions/structural variants. Many our our in-house tools are attempting to employ segment/coordinate based searches to link to relevant data/knowledge for clinical reporting of copy number variants. Fusions are another beast for us - each assay seems to annotate things a little differently. For example, are the fusion partners always listed 5' --> 3'? How do we document structural rearrangements (translocations/inversions/CNVs) that result in over/under expression by position effect (i.e. they don't result in a fusion product)?

anna-tanska commented 5 years ago

That's a great topic. CNVs curation hasn't been well defined so far. Reporting and clinical actionability of CN poses many questions in our lab especially the ones that don't create a functional fusion but may still affect gene expression.

bpitel12 commented 5 years ago

CNV-SV.pptx