A-AFFY-195 - Affymetrix rat genotyping array [RATDIVm520813]

Rattus norvegicus
The Rat Genome Sequencing and Mapping Consortium designed a high density SNP array for the genotyping of the rat heterogenous stock (HS) samples. The consortium focused on the whole genome sampling analysis where genomic complexity is reduced with the selective amplification of restriction fragments. This targeted subset of the genome is used for labeling and hybridization. For the design of the RATDIV array, the consortium chose a two phase approach with a pilot array to test candidate SNPs in phase I and a final array (RATDIV) with selected high quality SNPs in phase II. Several criteria were assigned for the primary selection of 2.1 million candidate SNPs for the pilot array: SNPs need to reside on a 200- 600bp StyI or NspI restriction fragment, the relevant SNP should be within the fragment no closer than 16bp to the cutting sites, no other SNP within 10bp is allowed and the 25mer SNP probe set must be unique in the rat genome. Only biallelic SNPs were chosen. For the final RATDIV array, the consortium obtained 803,485 SNPs for which they selected the optimal probe sets for the final array. In total, the RATDIV array consists of almost 6 million probes evenly spaced throughout the rat genome. SNPs are interrogated with one probe set per SNP in 3 or 4 replicates, depending on their FLD. Final cleaning retrieved a ultimate set of 556,358 SNPs with a maximum density of 15 SNPs in a 10kb window. Maximum gap size shown is 1Mb, minimum gap size shown is 50kb. There are 19 larger gaps (1-3.8Mb) on chr1 to chr20 and 12 on chrX, with a maximum of 4.8 Mb. Additionally, 1 million (1,046,070) copy number (CN) probes have been selected to interrogate known and potential copy number variation (CNV) sites. These probes are located in known CNV in the rat genome12 and in addition in all constitutively expressed rat exons on basis of ENSEMBL release 56 (ENS56). For more information, please see supplementary information in this Nature Genetics publication:
. The Affymetrix array design library files have also been provided as additional files (
Amelie Baud (abaud@ebi.ac.uk)
Experiment E-MTAB-2332
Array DesignA-AFFY-195.adf.txt