Question: Determining genome build in dbSNP restults
2
gravatar for sbrown8
2.8 years ago by
sbrown820
Canada
sbrown820 wrote:

We are trying to search for variants in dbSNP but running into difficulties where dbSNP uses a human genome build other than hg19. We have a large number of variants we are examining, and this process needs to be fully automated. We have the chromosome, hg19 base position, and allele. Is there a way to determine the genome build used in dbSNP from results, we are using the entrez eutils docsum.

For example, searching '1[Chromosome] AND 69511[Base Position] AND snp[SNP_CLASS]' gives us this docsum for rs75062661.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=75062661

However, searching '1[Chromosome] AND 906272[Base Position] AND snp[SNP_CLASS]' doesn't give us rs28507236, but using the GRCH38 position '1[Chromosome] AND 970893[Base Position] AND snp[SNP_CLASS]' does

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=28507236

The CHRPOS field in the first link is related to the GRCh37 genome build, while the CHRPOS field in the second link is related to GRCh38. Is there a way to tell which genome build that field is referring to? We need to search by genomic coordinate, however, right now the only way we can think of to search dbSNP by genomic coordinate it to lift over the coordinates to GRCh38 from GRCH37 and try them both. Even then, we wouldn't know for sure which genome build the resulting SNP is part of. Is there a way to search by build in dbSNP? Or even just to determine which genome build the CHRPOS field is referring to in the dbSNP results?

entrez snp genome builds dbsnp • 776 views
ADD COMMENTlink modified 2.8 years ago by Sean Davis24k • written 2.8 years ago by sbrown820
3
gravatar for Sean Davis
2.8 years ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k wrote:

dbSNP is using GRCh38 positions in both cases.  However, in your first example, the coordinates for GRCh37 and GRCh38 happen to be identical.  You can see that by looking on this page. Note that the HGVS notation for both the NT accessions (which represent chromosome 1 versions) are identical.  

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Sean Davis24k
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