What’s the difference between v1 and v2?
Two array versions exist and have some different features. Version 1 has ~27,000 high quality SNPs tiled as PM/MM probes, making this a very robust and easy to use array for disease gene mapping. Version 2 has a larger number of high-quality SNPs (~50,000), but are tiled as PM probes only which means that a “feature effects” file is needed to run the genotyping algorithm. Alternatively, projects with a large number of unrelated, diverse samples (such that all genotypes are represented multiple times) can be analyzed without such a file. The version 2 array should be useful for trait mapping and also perhaps for identification of selective sweeps and copy number polymorphisms. Version 1 details: The version 1 array (part number 520170) is a 5um, 100-format, PM/MM probe strategy (20 probe pairs/SNP), Whole Genome Sampling Assay (WGSA) design which can detect a total of 66K canine SNPs. These SNPs were chosen from the 2.5 million SNP map generated as part of the dog genome project. A “v1
