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Custom rhAmpSeq Panels

Achieve deep, targeted amplicon sequencing with highly multiplexed panels

Custom rhAmpSeq Panels consist of rhAmp primer pairs designed to minimize primer dimers and maximize multiplexing capability for high quality amplicon libraries. This combination of robust, uniform coverage and efficient library prep allows you to confidently analyze more samples, faster. The bioinformatics experts in our Custom rhAmpSeq Design Service will work with you 1-on-1 to create a panel tailored to your research goals.

  • Design custom panels for a wide range of plant and animal species, including human, macaque, mouse, tomato, corn, and grape
  • Multiplex up to 5000-plex in a single pool for efficient amplicon library prep
  • Choose from 3 delivery scales and formats for unparalleled flexibility to meet your project goals

Ordering

Custom rhAmpSeq Panels

Create custom NGS amplicon panels. Prices shown are per primer pair.

To complete your rhAmpSeq workflow, you will also need the rhAmpSeq Library Kit and rhAmpSeq Index Primers. Additional details about the rhAmpSeq workflow can be found on the overview page.

Custom rhAmpSeq Panels are highly multiplexed primer sets for targeted sequencing. Panels have been designed for and successfully tested in a wide range of animal and plant species, including human, macaque, mouse, tomato, corn, and grape.

Custom rhAmpSeq Panels are well suited for diverse targeted NGS applications, including:

  • Marker-assisted selection and genomic selection in agricultural genetics and breeding
  • Confirmation of on-target and off-target CRISPR gene editing experiments
  • Hotspot panels for oncology, rare and inherited diseases, and other disease research

Design custom panels tailored to your research

Our expert bioinformatics team will help you design a custom, targeted sequencing panel optimized for your targets in your plant or animal species of interest.

We provide a detailed summary report for your custom panel design so you can review the results and, if necessary, iterate your design with the Design Service before ordering your Custom rhAmpSeq Panel.

Figure 1. Overview of the Custom rhAmpSeq Design Service process.

Custom rhAmpSeq Panels are designed for hotspot target SNPs and indels. We do not currently offer gene scanning or tiling panels, but we expect to offer panel design services for those applications in future product releases.

Custom rhAmpSeq Design Service

The 2 key steps in our custom design bioinformatics pipeline provide performance and workflow advantages over other amplicon sequencing systems.

  • Assay design involves extensive target site review and rhAmp primer design for each target, followed by comprehensive QC of each rhAmp primer to mitigate off-target effects, such as primer-dimer formation and non-specific genomic hybridization.
  • Virtual assay pooling is a unique multiplex primer QC feature that further enhances the specificity of rhAmp PCR technology. It allows us to more accurately predict potential primer-dimer amplification products that could lower overall reaction efficiency and decrease the percentage of correctly mapped reads.

Technical details

Custom rhAmpSeq Panels are available in 3 convenient scales to fit your experimental needs: 0.4 nmol, 4 nmol, and 8 nmol. As shown in Table 1, we recommend adjusting rhAmp primer concentrations in the first amplification reaction (Targeted rhAmp PCR 1) depending on your panel size (plexity). Table 1 shows the approximate number of reactions for each scale based on panel size and scale.

Table 1. Number of rhAmp primer reactions based on scale and panel size.

Panel sizerhAmp primer concentration in 10X panel*Number of reactions per rhAmp primer orderExample
Panel sizeNumber of reactions
0.4 nmol primer (x)4 nmol primer (x)8 nmol primer (x)
≥500-plex50 µM total primersx nmol of primer/(0.1 nmol total/panel size)1000400040,00080,000
750300030,00060,000
500200020,00040,000
101-499–plex100 nM each primerx nmol of primer/0.0002 nmol per rxn400200020,00040,000
200200020,00040,000
≤100-plex250 nM each primerx nmol of primer/0.0005 nmol per rxn100800800016,000
50800800016,000
25800800016,000

* Important: When creating rhAmpSeq primer pools, do not to combine forward and reverse primers for long term storage. The primer concentrations in the 10X panel stocks assume making a separate forward pool of primers and a separate reverse pool of primers. Refer to the protocols in the Resources section for details.

High quality sequencing data

The data shown in Figure 2 are representative of performance from 3 different custom rhAmpSeq panels using random SNP markers in the human genome with initial (non-optimized) rhAmpSeq panel designs. Performance of your custom panel may depend on several factors, including the quality of the input sequences and the reference genome in the case of non-human species.

Figure 2. High quality sequencing data across a range of non-optimized panel sizes and DNA input quantities. Coriell DNA samples were used to evaluate the performance of non-optimized rhAmpSeq panels of varying sizes (20, 282, and 994 amplicons) following the high-throughput (HT) protocol using 10 and 50 ng of DNA input. The largest panel (994 amplicons) was evaluated following the regular (Reg) protocol with 10 and 100 ng of DNA input. Coverage uniformity is the percent of targets with coverage ≥0.2X of the mean. Error bars = standard deviation from the mean.