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Paul De Bakker's HLA tag SNPs are listed here:
Paul De Bakker's HLA tag SNPs are listed here:
http://www.broadinstitute.org/~debakker/hla_tags_exome.txt
http://www.broadinstitute.org/~debakker/hla_tags_exome.txt
= Illumina Exome Arrays =
== Coding Variants ==
Design criteria included a requirement for an assay design score >= 0.50, a primer that didn't overlap a nearby variant with minor allele count >100, a primer that didn't map with 0, 1 or 2 mismatches to other genomic locations. Assay design failures appeared to be largely independent of frequency.
In the Illumina platform, 243,094 of the original set of 275,165 coding variants (non-synonymous, stop and splice) passed assay design criteria. We expect that 80-90% of the variants that pass design criteria will ultimately be included in genotyping arrays.
