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

Question

[Jie Ping]

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,

Answer 1

[Lars Juhl Jensen]

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.

[Jie Ping]

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?

[Lars Juhl Jensen]

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.

[Jie Ping]

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?

[Lars Juhl Jensen]

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.