I'm trying to genotype a SNP for which I have to design custom primers and probes. The problem with this SNP is that it is in the middle of a large area masked as non-specific using RepeatMasker. Is there any way to identify this SNP using qPCR, or even any other genotyping system?
Another problem I have with another SNP is that the probe is in a highly G-C concentrated area, making self-annealing a large possibility. Is there any way to genotype this SNP in spite of its location?
Thanks for the help!