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Genome-Wide Human SNP Array 5.0
What is the content of the SNP5.0 array?
The SNP 5.0 array contains all 500,568 SNPs from the original two chip Mapping 500K product. Using the current version of the algorithm (BRLMM), we are currently able to demonstrate that a set of 440,794 SNPs meet the specified performance criteria (see below). Advanced users can analyze the full set of 500,568 SNPs using an alternative library file (CDF) that reveals all the SNP content on the array. This advanced workflow can only be performed with the command-line “snp5-probeset-genotype” software.
In addition, there are 420.000 non-polymorphic probes, with great promise for copy number analysis.
Note: We have been collaborating with the Broad to develop the SNP 5.0 array, which combines the 500K SNPs on a single chip to decrease array processing time and improve ease of use. The single chip product was enabled by reducing the number of probes per SNP from 12 PM/MM (24 probes in total) to only 8 probes (2 PM with 4 replicates each).