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Researchers often look for genetic variations to better understand phenotypic traits, such as plant fruit production or human disease incidence. One individual’s genome may differ from others in numerous ways, including single nucleotide polymorphisms (SNPs), insertions or deletions (indels), or copy number variations (CNV).

Polymerase chain reaction (PCR) is a commonly used genotyping technique. Often employing a primer-pair and target-specific fluorescent probe, quantitative PCR (qPCR) can be a sensitive and specific way to detect SNPs. IDT offers a complete SNP-typing solution with predesigned assays, as well as complementary easy- and ready-to-use reagent mixes. For other applications, modified probes are available that can be incorporated into custom qPCR assays.

rhAmp® SNP Genotyping System »

The rhAmp SNP Genotyping System is a fully integrated genotyping solution that includes an extensive predesigned assay collection, a custom design tool, optimized reagent mixes, and optional synthetic control templates. SNP detection may be performed on any commonly available qPCR instrument.

Precise and easy-to-use, the rhAmp SNP Genotyping System offers an out-of-the-box solution for SNP genotyping studies for small discovery or large screening projects.

Affinity Plus qPCR Probes

Use Affinity Plus qPCR Probes for SNP genotyping, transcript variant identification, and more sensitive target detection in challenging samples (FFPE tissue, biofluids). The Affinity Plus bases used in these qPCR probes are locked nucleic acid monomers. When incorporated into a probe, they impart heightened structural stability, leading to increased hybridization melt temperature (Tm).

PrimeTime® LNA® qPCR Probes »

PrimeTime LNA qPCR Probes are 5′ nuclease probes that incorporate one or more LNAs into the sequence design. An LNA is a modified nucleic acid monomer whose structure is “locked” into the 3′-endo conformation, thereby promoting base-stacking and increasing probe Tm.

LNAs can improve specificity and assay sensitivity. Incorporation of LNA bases allows increased discrimination of single base pair differences or address complex sequence regions with shortened probes. Some common applications are transcript variant detection or differential detection of microbial species.

MGB Eclipse® Probes »

(available through our GMP services)

MGB (minor groove binder) Eclipse Probes are dual-labeled, 5′ nuclease probes incorporating a 5′ conjugated MGB ligand, which stabilizes its complementary sequence duplex, thereby increasing Tm of the probe. Use MGB Eclipse Probes to create shortened probes with high specificity. Pair with primers manufactured under GMP regulations for a complete qPCR assay.

MGB Eclipse is a registered trademark of ELITech Group.

PACE™ SNP Genotyping Assays »

PACE™ SNP genotyping uses competitive, allele-specific PCR and a simple, easily detected fluorescent readout for bi-allelic genotyping. Obtain primer sets from IDT for cost-effective, high-throughput assays.