Incorporate emerging measures for Gene intolerance to Variation

[arq5x]

For example, the RVIS measure from Petrovski et al [1] assesses a gene's intolerance to genetic variation based on the ESP project. I also recall a poster from Mark Daly's lab at Biology of Genomes that introduces a similar statistic. These may be useful in interpreting / prioritizing genes based on observed variants.

[1] http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003709

[chapmanb]

Awesome, I had this on my list of things to do. Dataset S2 has the gene names and Residual Variation Intolerance Score Percentile that could be extracted into a BED file after retrieving coordinates. Generalizing the gene to coordinate mapping would be nice, but is a hard one.

[arq5x]

Yep, S2 is what we are using currently for another project. Biggest issue is the darn gene naming problem. GENCODE gene names may not always map to their CCDS names (which I think use HGNC). We will need to "explode" Dataset S2 to include gene synonyms.

[tanglingfung]

I was told that you can handle the mapping issue with bridgedb webservice: http://bridgedb.org/wiki/BridgeWebservice to standardize everything to one gene name, hope it makes the gene->coordinate issue easier to resolve

Paul

On Tue, Sep 3, 2013 at 11:53 AM, Aaron Quinlan notifications@github.comwrote:

Yep, S2 is what we are using currently for another project. Biggest issue is the darn gene naming problem. GENCODE gene names may not always map to their CCDS names (which I think use HGNC). We will need to "explode" Dataset S2 to include gene synonyms.

— Reply to this email directly or view it on GitHubhttps://github.com/arq5x/gemini/issues/208#issuecomment-23737503 .

[TonyRoscioli]

Hi

We think RVIS is pretty good too - it would be a great addition with the PROVEAN score to GEMINI if possible! See the following link: http://provean.jcvi.org/genome_submit.php

thanks

Tony