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How can I avoid designing my qPCR primers/probes over SNPs?

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, efficient polymerase extension, and even target specificity; and the number of identified SNPs is increasing exponentially! Thus, having to manually check 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 where SNP screening is done for you. IDT has developed a sophisticated qPCR assay design engine that checks all designs against up-to-date information on locations of SNPs and intron/ exon junctions. Design of PrimeTime® Predesigned qPCR Assays is performed using frequently updated information from new RefSeq releases from NCBI. Target regions are screened to avoid SNPs and sequences that are repeated elsewhere in the genome. Because each assay is synthesized only after it is ordered, there is never a stock of outdated assays that may omit recently identified SNPs. For more information, see the DECODED 3.3 Core Concepts article, When Designing PCR Assays, ALWAYS Check For SNPs, at www.idtdna.com/decoded.
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  • SNP
  • primetime
  • predesign
  • polymorphism
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