Question: Allele discrepancy between Database and Publication
0
gravatar for snp_guy
9 months ago by
snp_guy0
snp_guy0 wrote:

Dear community,

I'm interested in to genotype the SNP rs679620, however in Ensembl (and the Lab Kit Provider) the reference/alternative alleles for the forward strand are T/C, whereas in the publication the alleles are A/G.

How may I interpret this discrepancy? Should I expect to look for the C allele, which in the reverse strand is actually a G?

Thanks in advance for your suggestions,

snp genotype dbsnp ensembl • 170 views
ADD COMMENTlink modified 9 months ago by Emily_Ensembl21k • written 9 months ago by snp_guy0
4
gravatar for Emily_Ensembl
9 months ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

Strand. The databases will always quote the forward strand alleles, papers quote either, often the strand that the gene they're interested in is on, and no, they often won't tell you which one.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Emily_Ensembl21k

Thanks for your quick reply Emily.

So this assumption is correct: "Should I expect to look for the C allele, which in the reverse strand is actually a G?"

ADD REPLYlink written 9 months ago by snp_guy0
1

In your genotyping results, yes.

ADD REPLYlink written 9 months ago by Emily_Ensembl21k
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