Performing PCR using primers that overlie single nucleotide polymorphism (SNP) sites can have a dramatic impact on the reaction and can undermine obtaining accurate data. The presence of SNPs can influence primer and probe Tm, polymerase extension, and target specificity. Because the number of identified SNPs is increasing exponentially, manually checking whether your primers contain SNPs (e.g., using the NCBI SNP database: www.ncbi.nlm.nih.gov/snp) can be cumbersome.
An alternative is to select assays from IDT that are developed using a sophisticated qPCR assay design engine. Design of our PrimeTime® Predesigned qPCR Assays is performed using frequently updated information from new RefSeq releases from NCBI. All designs are checked against up-to-date databases for SNPs and intron/exon junctions. While it is not possible to avoid all SNPs due to their ever-increasing numbers, it is possible to screen target regions to better manage SNPs and to avoid possible sequences that are repeated elsewhere in the genome. Because each assay from IDT is synthesized only after it is ordered, you will receive up-to-date assays.
For more information, see the DECODED article, When Designing PCR Assays, ALWAYS Check For SNPs, at www.idtdna.com/decoded.