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Why no SNPs are at chr6:13650971-13954632 (based on hg19) in Affy 6.0 snp array

Perhaps many regions in human genome are absent in Affy 6.0 array due to the limited sampling in human genome.

However, I want to know why no SNPs are at exact chr6:13650971-13954632 (based on hg19) in Affy 6.0 snp array?

Could anyone help? Best regards,

snp genome snp array
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updated by Biostar Biostar • written by Jie Ping • Jie Ping

1 answer

I am guessing, but it could be due differences between genome builds. The Affy 6.0 array design was submitted to GEO on Apr 30, 2008 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801). The design thus cannot have been based on hg19.

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written by Lars Juhl Jensen Lars Juhl Jensen

Thank you for reply. You are correct. I also noted that Affy 6.0 do not have genomic position based on hg19. But for the purpose of keeping the consistent positions with my whole genome seq data, I turned positions to build hg19 using liftover from UCSC browser.

I am wondering that whether SNPs at chr6:13650971-13954632 were excluded by some reason? If yes, I am curious about the reason?

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written by Jie Ping • Jie Ping

I think you are missing my point: I suspect the region chr6:13650971-13954632 in hg19 simply did not exist in the genome build that was used to design the chip, for which reasons no probes were designed against it.

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written by Lars Juhl Jensen Lars Juhl Jensen

Yes! I agree with you. Well, I still want to confirm whether some other reason exists, cause I am doing some job in this region. What would you suggest me to do to figure it out?

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written by Jie Ping • Jie Ping

You could compare the assemblies and see if this region of hg19 is indeed missing in earlier assemblies, if so, then I'd argue you have the answer. Other than that, I cannot think of anything but contacting Affy and asking them.

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written by Lars Juhl Jensen Lars Juhl Jensen

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