The Microarray Core at Dana-Farber Cancer Institute offers several SNP analysis options. 

The Mapping 500K Set is comprised of two chips, Mapping Nsp and Mapping Sty, that may be analyzed together (500K) or separately (250K Nsp or 250K Sty).  Each of the two arrays is designed to discriminate alleles at approximately 250,000 dimorphic positions in the human genome.  These microarrays have been particularly useful in cancer research for carrying out genome-wide analysis of allelic changes (including deletions, amplifications, and gene conversions) in tumors. They are also useful in linkage analysis. At this time, only DNA from a fresh or frozen source can be analyzed on the SNP microarrays.

The SNP 6.0 array is a single array that contains probes for SNP discrimination at over 900,000 loci plus approximately 940,000 probes at non-SNP loci.  It therefore provides a higher resolution analysis of both SNP genotypes and copy number variations than can be obtained with the 250K arrays either singly or in combination.    

The sample processing procedures for the 500K set, 250K assay, and the SNP 6.0 assay are similar in that all use restriction digestion, adapter ligation, PCR, fragmentation and biotinylation.  Details of each procedure can be found below.