rhAmp™ SNP Assays

Genotyping assays with enhanced precision and flexible design

rhAmp SNP Assays are a core component of a complete genotyping solution that offers precision, performance, and a wide variety of design options. Choose your target SNPs from a predesigned library containing >10 million assays, including 330,000 common human SNPs (minor allele frequencies >1%) found in RefSeq. Custom assays for other human SNPs or SNPs in other species can also be created using the rhAmp Genotyping Design Tool. Use rhAmp SNP Assays with rhAmp Genotyping Master Mix and rhAmp Reporter Mix (with or without reference dye) to form a complete amplification and reporting reaction chemistry.

  • Generate the highest level of performance with >99.5% call accuracy for over 90% of assays tested
  • Validate markers affordably using the smallest size pack commercially available
  • Get started quickly with delivery in fewer than 5 business days
  • Interrogate SNPs in difficult sequence regions with amplicon sizes as small as 40 bp
  • Ensure confidence in your data using gBlocks® Gene Fragments as control templates

 

The rhAmp SNP Genotyping System is a complete solution requiring the following 3 components:

  • rhAmp SNP Assays, or rhAmp ADME SNP Assays
  • rhAmp Genotyping Master Mix, required for activation and PCR amplification of all rhAmp SNP Assays
  • rhAmp Reporter Mix, available with or without reference dye for compatibility with all common qPCR instruments

rhAmp SNP Genotyping technology

rhAmp SNP Genotyping is a quick, easy to use, single-tube assay chemistry that allows for routine automation and delivers genotypes after only 90 min PCR cycling time. rhAmp SNP Genotyping can be either performed directly on a real-time PCR instrument, or performed in a benchtop thermal cycler and transferred to a fluorescence detection platform for end-point analysis.

  • rhAmp technology delivers increased specificity and amplification without primer-dimers
  • Novel, dual-enzyme system increases mismatch discrimination
  • Universal probe reporter system enables low cost per genotype
rhAmp SNP Gentotyping reaction

Figure 1. Schematic representation of a rhAmp™ SNP Genotyping PCR cycle. All components needed to measure both alleles are combined in a single reaction before cycling. 1) Both allele-specific primers query the SNP locus. 2) RNase H2 enzyme cleaves the primers that are perfectly annealed to the target sequence, removing the RNA base and 3′ blocking modification, which allows extension by the Taq Polymerase. 3) During the first two amplification cycles, a tail sequence is incorporated into the amplicon that is subsequently recognized by a universal, probe-based reporter system. 4) Polymerase extension leads to degradation of the probe and signal generation. 

rhAmp SNP Assays 

The rhAmp SNP Assay library contains designs for human SNPs with a minor allele frequency >1%. The database currently contains >10 million predesigned SNP assays and continues to grow. rhAmp SNP Assays demonstrate consistently high performance with >99.5% call accuracy on over 90% of tested assays. All human predesigned assays are guaranteed to work, or IDT will replace them at no additional charge.

Search human predesigned rhAmp SNP Assays

rhAmp ADME SNP Assays

rhAmp ADME SNP Assays target SNPs in human genes that are responsible for the absorption, distribution, metabolism, and excretion (ADME) of pharmaceutical compounds. These target SNPs are important biomarkers in pharmacogenetic studies. Each rhAmp ADME SNP Assay is experimentally validated to ensure optimized performance and signal generation. 

Search for human rhAmp ADME SNP Assays

Click here to download an Excel file of available rhAmp ADME SNP Assays

Custom rhAmp SNP Assays

The rhAmp Genotyping Design Tool can be used to design rhAmp SNP assays for newly discovered SNPs that are not currently included in the predesigned human assay library, and for SNPs in any other species. The custom assay tool delivers a high design rate by accommodating short amplicons (as short as 40 bp) for maximum design flexibility. 

For newly discovered human SNPs that are not currently in the predesign database, the design algorithm will perform BLAST and other sequence analyses to generate the best design. Custom design is easily performed by submitting target SNP sequences for any genome in FASTA format.

Click here for custom rhAmp SNP Assay design

  • All rhAmp SNP Assays are manufactured on demand and consist of 2 allele-specific forward primers, and a locus-specific reverse primer. 
  • Each assay is available in 2 mL tubes or matrix racks (96-well format). Assays are formulated and normalized to 20X or 80X concentration, in IDTE pH 7.5 (1X TE Solution).
  •  rhAmp SNP Assays in tubes are shipped in fewer than 5 business days, and assays in plates are shipped in fewer than 7 business days.

Product

Package size

Reactions*

Concentration

rhAmp SNP Assay
or
rhAmp ADME SNP Assay

XS

100

20X

S

750

20X

M

2500

80X

L

6000

80X

* Reaction size is for a 10 μL reaction volume.


Related protocols


Storage conditions

  • Store rhAmp™ SNP Assays at –20°C for up to 2 years.
  • Store rhAmp™ Genotyping Master Mix and rhAmp™ Reporter Mix at –20°C for up to 1 year.
  • Store rhAmp™ Reporter Mix protected from light. 
  • Alternatively, you can store rhAmp™ SNP Assays, Genotyping Master Mix, and Reporter Mix at 4°C for 2 weeks.


Brochure


Related IDT publications

  1. Dobosy JR, Rose SD, Beltz KR, Rupp SM, Powers KM, Behlke MA, Walder JA. (2011) RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers. BMC Biotechnol, 11(80):1–18.

rhAmp SNP Assays provide excellent genotyping performance

More than 90% of rhAmp SNP Assays provide a ≥90% call rate and ≥99.5% call accuracy for reliable data generation in your genotyping experiments (Figure 1).

rhAMP PCR GT Call Rate and Accuracy (V2)

Figure 1. rhAmp™ SNP Genotyping assays provide a 90% call rate and 99.5% call accuracy. Genotyping was performed on 213 assays in 5 µL reactions using 3 ng of human gDNA from 46 individuals (Coriell Institute). Analysis was performed using QuantStudio™ 7 Flex Real-Time PCR System software (Thermo Fisher).

High quality genotyping performance using gDNA from whole blood

rhAmp SNP Genotyping offers reliable genotyping performance across sample types. We have tested our assays and enzyme mixes across samples, including commercially available, purified genomic DNA and DNA isolated from whole blood, that all perform similarly to synthetic, gBlocks® Gene Fragment templates (Figure 2).

Whole blood composite figure

Figure 2. rhAmp™ SNP Assays provide consistent performance across sample types. Assays for were designed for SNPs in genes (A) SLCO1B1 and (B) ABCC2. These assays were used to assess SNPs in 3 different sample types: synthetic gBlocks® Gene Fragments (*), purified genomic DNA (Coriell Institute; ∆) and genomic DNA isolated from whole blood using the Qiagen QIAamp DNA Blood Mini Kit (prepared by BioChain Institute; ○). Assay performance is similar across sample types, as shown by overlapping symbols. Analysis was performed using QuantStudio™ 7 Flex Real-Time PCR System software (Thermo Fisher).

rhAmp primer technology virtually eliminates primer-dimer artifacts

rhAmp SNP Genotyping technology uses activation of RNA-DNA hybrid primers by the RNase H2 enzyme from Pyrococcus abyssi (see overview tab). The primers are only activated upon precise annealing to the correct target, and this RNase H2 activation mechanism nearly eliminates primer-dimers and other amplification artifacts that can affect experimental results. Figure 3 shows how effective RNase H2 activation is for eliminating primer-dimer artifacts, even when 96 primer pairs are multiplexed together in a single PCR reaction. 

rhAmp amplification gel

Figure 3. rhAmp™ primers virtually eliminate primer-dimers and nonspecific amplification artifacts in multiplex applications. In multiplex PCR amplification of 96 targets from human genomic DNA (NA12878, Coriell Institute), two sets of multiplex primers for the 96 assays (192 individual primers) were synthesized either as standard PCR primers or as RNase H2-activated, rhAmp primer pairs. The results show tight control of primer-dimer artifacts, even in highly multiplexed assays. Total reaction volumes were 50 µL, with 10 ng of genomic DNA template or no template controls. RNase H2 was present in all reactions but has no functional role in PCRs with standard primers.

Greater signal-to-noise ratio for higher confidence calls

rhAmp SNP Assays deliver an increased signal-to-noise ratio over traditional 5′-nuclease chemistry. In rhAmp technology, RNA-DNA hybrid primers are blocked at the 3’ end to prevent primer-dimer formation and non-specific amplification, mitigating the unbalanced consumption of reaction components. More robust signal provides improved cluster separation for higher confidence automated genotyping calls (Figures 4 and 5).

18 assays cluster separation

Figure 4. rhAmp SNP genotyping assays deliver consistently higher genotype cluster signal and greater cluster angle separation in comparison to genotyping assays from Supplier T. rhAmp SNP Assays targeting 18 SNPs were evaluated against 5′-nuclease SNP assays from Supplier T targeting the same 18 SNPs. 3 ng genomic DNA samples from 46 individuals (Coriell Institute) were tested in 5 µL reactions, with all 3 possible genotypes represented. 2 no-template, negative control (NTC) reactions were run for each assay. Post-PCR analysis of normalized reporter dyes (Rn) was used to generate allelic discrimination plots of (A) combined data for all 18 rhAmp SNP Assays, and (B) combined data for all 18 SNP assays from Supplier T.  The universal reporter system utilized in rhAmp SNP genotyping contributes to high normalized signal for all gDNA samples, consistent signal from the negative control reactions, and consistent cluster angles across all 18 SNP assays.

Cluster to NTC distances

Figure 5. rhAmp SNP assays result in higher average cluster to NTC distance than SNP assays from Supplier T.  rhAmp SNP Assays targeting 18 SNPs were evaluated against 5’-nuclease SNP assays from Supplier T targeting the same 18 SNPs. 3 ng genomic DNA samples from 46 individuals (Coriell Institute) were tested in 5 µL reactions, with all 3 possible genotypes represented.  (A)  The average cluster to NTC distance describes the distance of a straight line between the homozygous cluster and NTC for each assay.  The maximum average distance achieved for rhAmp assays was 5.3 for Allele 1 and 4.0 for Allele 2, while the maximum distance for Supplier T assays was 2.3 for Allele 1 and 2.7 for Allele 2.  (B) The average homozygous cluster to NTC distance and standard deviation is shown across all 18 assays.  The rhAmp SNP genotyping assays consistently produced high cluster signal, with a 2.5-fold higher average cluster to NTC distance than assays from Supplier T.

R System (Thermo Fisher). 

 

rhAmp SNP Assays and reagents are made using the highest quality oligonucleotides

Consistent synthesis quality ensures that when you or another researcher orders a rhAmp™ SNP Assay for the same SNP ID, the results will not change (Figure 6).

Synthesis Reproducibility-01

Figure 6. Consistent synthesis quality ensures reproducibility of data with rhAmp™ SNP Assays. Three independent lots of rhAmp SNP Genotyping assays targeting SNP ID (A) rs3825505 and (B) rs2289221 were synthesized and formulated (Synthesis A, B, and C). Genotyping was performed in 5 µL reactions, using 3 ng human gDNA from 46 individuals (Coriell Institute). Data was analyzed using CFX Manager™ Software (Bio-Rad). Yakima Yellow® signal was detected using the VIC® channel without calibration.

rhAmp SNP Genotyping is compatible with commonly available real-time qPCR platforms

rhAmp SNP Assays are compatible with all common real-time qPCR platforms (Figure 7). Universal probes are part of the rhAmp Reporter Mix, available with or without reference dye to ensure compatibility.

Instrument Comparison ADME SNP Assays 35 and 36

Figure 7. rhAmp™ SNP Genotyping assays deliver high precision and performance regardless of qPCR instrument used. Allelic discrimination plots for SNPs located in genes (A and B) SMARCD1 (rs3782323) and (C and D) LINC00111 (rs3850713) show consistent performance of rhAmp SNP Assays analyzed using QuantStudio™ Real-Time PCR Software (Thermo Fisher) or the CFX Real-Time PCR Software (Bio-Rad). Genotyping was performed in 5 µL reactions, using 3 ng human gDNA from 46 individuals (Coriell Institute). Yakima Yellow® signal was detected using the VIC® channel without calibration. More than 90% of rhAmp SNP Assays demonstrate a call rate >95% and call accuracy of 99.5% regardless of qPCR instrument.