What Is The Meaning Of Snp Strand
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12.9 years ago
Jonathan Hsu ▴ 60

I noticed that the SNP in dbSNP have the attribute 'strand', I was wondering what's the meaning of the strand because the DNA is complementary, the SNP in Watson strand can also be observed in Crick strand. And if one SNP is labeled in plus strand, can I map this SNP to the gene in minus strand when the chromosome location is proper?

snp mapping strand • 9.7k views
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I'm just a touch confused.

How can a SNP be on the antisense / -ve strand? If the opposite strand's base is to be complementary and therefore also a SNP, it seems redundant to label a strand..? I read that were are occasionally mismatch errors across the DNA helix in that A binds opposite C or G..? Is that the reason?

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The SNP is of course on both strands, but was mapped to one strand or the other because one strand of DNA is sequenced against a template of the other strand. In other words, strand A was sequenced and a SNP was found and hence mapped to a position on strand A and incorporated into a chromosome map also on that same strand. It could be that there is a gene in that same region but on strand B and so the SNP appears to be on the opposite strand of the gene.

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12.9 years ago
Adrian Cortes ▴ 550

Eg. An A/T SNP:

ATGTAC[A/T]CGTCT

TACATG[T/A]GCAGA

Its important to know if you are given the SNP in the Watson or the Crick strand so that you can compare MAF or odds ratios reported elsewhere.

If the SNP is a A/G or A/C then its not that problematic as you can just flip the SNP to be in the right strand to compare.

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12.9 years ago

Yes, if one SNP is labeled or mapped to the plus strand, you can indeed map that SNP to a gene located on the minus strand. Adrian's answer is good - the A/T and G/C SNPs can be problematic due to strand mapping. Often, it can be difficult or impossible to know which strand actually has been genotyped, but you would still know which SNP was genotyped and that may override any strand concerns.

So, the gene really maps to both strands because a gene is double-stranded. The reading frame of the gene may map to the minus strand of the chromosome and some SNP assays or reported SNPs map to the plus strand. If this assignment needs to be confirmed, then use a simple alignment tool or sequence similarity search (BLASTN) to find where and which strand of the gene and SNP match each other. With the hundreds of SNPs that I analyze in close detail, I need to perform this only once or twice per 100 SNPs. In other words, strand designation of the SNPs is not critical for most work on genetic variation and association studies.

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6 weeks ago
Ömer An ▴ 260

No more such confusion as it is now always reported according to forward strand:

https://www.ncbi.nlm.nih.gov/core/assets/snp/docs/RefSNP_orientation_updates.pdf

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