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I'm following up a GWAS association with some fine mapping in a 150kb region in African-Americans. I've done some sequencing on pooled samples and used 1000 Genomes to get a sense of what SNPs should be polymorphic in my sample.
I was hoping to design a 768-SNP OPA using Illumina's GoldenGate system. The problem is - I have too many SNPs within 60bp of each other, which causes problems on hybridization-based OPA genotyping platforms (GoldenGate, OpenArray). I don't have the money to resequence thousands of samples. Any recommendation for another genotyping platform that doesn't have the problems with dense SNPs?
I was hoping to design a 768-SNP OPA using Illumina's GoldenGate system. The problem is - I have too many SNPs within 60bp of each other, which causes problems on hybridization-based OPA genotyping platforms (GoldenGate, OpenArray). I don't have the money to resequence thousands of samples. Any recommendation for another genotyping platform that doesn't have the problems with dense SNPs?