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Frequently asked questions

Our Scientific Applications Support team has assembled a list of frequently asked questions to help you find answers quickly. Filter using one or more categories to focus on specific topics, or use the search bar to perform a text search.

How can SNPs affect my qPCR?

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: 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.


*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.