List of SNPs per sequencer (company/chip)

Question

[Danielson]

Biology is not my expertise, which makes it harder to find specific stuff since I lack the terminology. But I do possess some basic information.

Nonetheless, I am looking for a site where I can download the list of SNPs (plain-text) that are sequenced for different machines. Preferable also for RNA and epi-genetics.

Could someone guide me in the right direction?

[sentausa]

What do you mean by SNPs sequenced for different machines? You are referring to Single Nucleotide Polymorphisms, right? It's a biological phenomenon and doesn't depend on the machine you use to sequence it.

[Danielson]

We have a couple of SNPs (Single Nucleo...) indeed. But the Illumnia CytoSnp 12 sequences 298K SNPs, whereas another Illumnia sequences 730K, 3M - same principle for other brands. Different kinds of chips can be inserted into a sequencing machine - all with different price-cards. The 2 examples given (Illumnia) covers +- 200K same SNPs, the other are different

[sentausa]

Ah, so you're looking for the list of SNPs (in human genome) on which these kinds of (microarray) chips are based? I suppose this is a proprietary information, but I'm not an expert in this domain.

Answer 1

[Devon Ryan]

You're not using sequencing, you're using genotyping microarrays from a variety of vendors. The best way to find out what they cover is to simply ask the manufacturers (in reality, they'll have downloadable annotation file specifying what's being covered by each probe). You can typically get similar information from GEO or R annotation packages, assuming appropriate entries exist for your array of choice.

[Danielson]

The problem is that I don't know which assay on-forehand. And to get information from, lets say affymetrix, you need to login. I know that after the read you get the list of RS/SS ids from the vendor, but I want to decide which Chip is best before we buy them. Which is dependent on what SNPs are read, what RNAs are probed and what methylation is checked. (It looks like UCSC might have answers)

[Devon Ryan]

The accounts from affymetrix are free, you don't have to buy anything beforehand. I also wouldn't be surprised if you can get this information elsewhere (like I said, GEO, Bioconductor, etc.) for many arrays.