Assume there is a patient or patients for which you have WGS or genotyping results. What are the most commonly used databases where you can get reliable clinical annotations (clinical impact) of each observed short variant.
Examples are HGMD (Human Genome Mutations database), dbSNP (limited clinical annotations), ClinVar (not yet fully deployed) or PharmGKB (only pharmacogenomics domain). (is there one for cancer only?)
But there are probably many more. What would be a good overview of the most commonly used? (open or commercial, tag those as such)
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user56
1 answer
GeneInsight - I cannot vouch for the quality of the data, but our lab did recently have a live demo of this software, and it seems to perform exactly what you are describing. I believe it is designed for genetic counselors, and so is focused on conservative and manually curated annotations. It's also commercial.
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