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We have developed a systematic, single-tube assay approach to reduce the chance of SNP genotyping error due to otherwise unidentifiable allelic drop-out during PCR amplification. Allelic drop-out in such cases would normally be caused by additional and rare genetic variation within the PCR primer site sequence itself. Our method is novel in that it does not require prior knowledge of the additional “hidden” genetic variation. The method has been tested in multiplex using a microarray-based SNP genotyping chip and results in the rescue of previously reported false genotype calls.