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Method Detail
Submitter Method Handle: KRIBB_YJKIM
Submitter Method ID: AFFYMETRIX
Submitted method description:
The Mapping 500K Array Set is comprised of two arrays, each capable of genotyping on average 250,000 SNPs.
One array uses the Nsp I restriction enzyme (~262,000 SNPs), while the second uses Sty I (~238,000 SNPs).
Total genomic DNA (250 ng) is digested with a restriction enzyme (Nsp I or Sty I) and ligated to adaptors that recognize the cohesive four base-pair(bp) overhangs.
All fragments resulting from restriction enzyme digestion, regardless of size, are substrates for adaptor ligation.
A generic primer that recognizes the adaptor sequence is used to amplify adaptor-ligated DNA fragments.
PCR conditions have been optimized to preferentially amplify fragments in the 200 to 1,100 bp size range.
The amplified DNA is then fragmented, labeled, and hybridize to a GeneChip Human Mapping 250K Array.
Each consisting of more than one milion copies of a 25-bp oligonucleotide probe of a defined sequence.
Two reagent kits were developed and validated for use in conjunction with the Mapping 500K Array Set.
One kit is specific to the Nsp I restriction enzyme while the other is designed for the Sty I restriction enzyme.
Both kits contain validated and qualified reagents for the most critical steps in the GeneChip Mapping Array.
This includes the PCR primer and adaptor necessary to selectively amplify a portion of the human genome, reagents to fragment and label the PCR product, and several control reagents.
Kits are available for either 30 or 100 reactions.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
KRIBB_YJKIM Assay KHB2007_1_AFFYMETRIX 129
KRIBB_YJKIM Assay KHB2008_2_AFFYMETRIX 130