Commercial Snp Panels

Question

[ngsgene]

I am looking to get my hands on the SNP panels for some of the commercial arrays from Illumina and Affymetrix. Wanting to compare the different arrays these companies offer, surprisingly it is not as easy to get my hands on these panels as I had thought. As a starting point I am looking at myillumina account and their downloads and trying to figure out the illumina SNP panels... Any words of wisdom?

Update: LD Mapper in Affymatrix looks helpful .. still investigating

Update: SNAP from Broad Institute comes the closest for the comparison - the probes per say for Illumina chips are still not accessible but one can compare probes to see which one of these arrays has them. So something there..

[Giovanni M Dall'Olio]

I remember that the Illumina 650K SNP arrays used to genotype the Human Genome Diversity Panel (HGDP) overlapped very poorly with the equivalent Affymetrix panels of the time, a few years ago. Unfortunately, I don't know what is the situation now.

[ngsgene]

Thats what I am interested in finding out - only if I could get my hands on their SNP Panels

Answer 1

[Abdel]

Try Ensembl's Biomart database:

http://www.ensembl.org/biomart/martview/

Choose the Ensembl Variation 67 -> Homo Sapiens Variation (dbSNP) database.

If you then go to "Filters", and then to "General Variation Filters", you can choose several chip sets under "Variation Source".

Choose what information you want for these SNPs under "Attributes", and then click on "Results".

Good luck!