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