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Old 01-29-2014, 04:26 PM   #1
cmccabe
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Location: chicago

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Default variant database

Is there a publically avaliable database of clinically known variants? What we do is upload a list of genes and get the known pathogenic variants in this gene. Currently we do this manually every 3 moths with HGMD, but that is getting too dificult and I would like to automate that process. Thank you.
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Old 01-30-2014, 05:05 AM   #2
TiborNagy
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The dbSNP contains information about pathogenic variations.
There is a tool Genes2FANS which do the same task (upload genes and see connections with known disease).
This tool is based on OMIM.
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Old 01-31-2014, 06:47 AM   #3
Factor
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Well, HGMD Professional is still the best source of data on germline mutations. Similar type of information could be found in OMIM and ClinVar as well, however HGMD is manually curated and just comparing numbers it has about 150k mutations while OMIM has 22k and ClinVar 67k. It could take a lot of effort to regularly extract information in bulk from online version of HGMD as you do with gene panels, but that's what download version is for. It comes as simple relational database (MySQL) and querying it is very easy.
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