[GET-dev] Interesting tidbit: genomes on GET variant pages and dbSNP

Kimberly Robasky krobasky at gmail.com
Tue May 25 10:14:01 EDT 2010

After clicking through to dbSNP, I erroneously thought the GET variant
pages were linking to the wrong genomes.  So that others will avoid my
mistake, here was the thought process:

Take as example: http://evidence.personalgenomes.org/PARP4-L1550P

Click the dbSNP link:

Scroll down about 1/4-way to 'GeneView' table, and see the codons that
represent the SNPs at this locus:

CTG to CAG corresponds to L to Q mutation
CTG to CCG "                 "   L to P "
CTG to CGG "                 "  L to R  "

So I expected the L to P mutation to pull genomes that are het/hom for
C, as in CTG->CCG above.
But the PARP4-L155P GET page has genomes that are het/hom for G.

I missed the fact that dbSNP states that it reports the  CTG->CCG
sequences as mRNA.  I'm still unsure why they didn't use CUG->CCG,
wouldn't it be more correct to state it's reported as cDNA?  Anyway,
the corresponding DNA in the genome is GAC->GGC, in which case, you'd
want to pull the het G genomes, which is exactly what GET does.

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