[GET-dev] PharmGKB & SNPs in get-evidence

Madeleine Price Ball meprice at gmail.com
Sat May 8 14:01:10 EDT 2010

We'd like to get the paper rewritten & submitted ASAP, but it would
really help the paper if we could reduce the emphasis on nsSNPs. (One
of the criticisms from the negative review was that we only look at
exon, so it's silly to sell it as "whole genome analysis".)

To do this, I propose getting these two things done:
(1) Fix PharmGKB analysis so it matches against all SNPs, not just the
nsSNPs. (Was this a bug in processing at our end?)
(2) Add SNP variants to get-evidence. I know this is not easy, but if
we do it we'll really have fixed this criticism.

If both of these are done, I imagine we could make a figure or
something with the an analysis of presence of well-established
pharmacogenetic warfarin-affecting variants in the genomes: CYP2C9*2
and CYP2C9*3 (we both have already) and VKORC1 -1639 G>A (we don't
have because it's not a nsSNP) -- as I understand it these are the
three FDA approved ones. This figure would make two points: (1)
healthy people have genetic variants with clinical impact, and (2) we
aren't limited to covering nsSNPs.

A lot of this depends on what Tom can do. I don't want to hold up the
paper for this, but I think it would really help.

  - Madeleine

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