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

[Kimberly Robasky]

I stand corrected once again (thanks Madeleine!):

The key is to notice the reported sequence on dbSNP is '- strand', so
I needed to take the reverse complement to find the genomic sequence:

CTG->CCG becomes CAG->CGG

So for '+ strand', the sequence would be the same as genomic dna.

Incidently, this also clears up my confusion below over why the dbSNP
sequence uses T instead of U :)

-Kim


On Tue, May 25, 2010 at 10:14 AM, Kimberly Robasky <krobasky at gmail.com> wrote:
> 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:
> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs1822135
>
> 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.
>