rhAmpSeq Library Kit

Prepare amplicon sequencing libraries quickly and cost-effectively

Use the rhAmpSeq Library Kit with rhAmpSeq panels and rhAmpSeq Index Primers to quickly prepare amplicon libraries for sequencing on Illumina platforms. Our proprietary rhAmp PCR technology enables a simple, elegant workflow with only 2 PCR master mixes for optimum specificity and high multiplex amplification capability.

  • Rapidly generate sequencing-ready amplicon libraries, even from difficult sample types or low-input DNA amounts, with this efficient 2-mix system
  • Obtain robust, uniform amplification across thousands of target sites with a single panel
  • Study larger sample sizes with a more economical solution


To complete your rhAmpSeq workflow, you will also need a rhAmpSeq primer panel—either a Custom rhAmpSeq Panel or the predesigned rhAmpSeq Sample ID Panel—and rhAmpSeq Index Primers.

The rhAmpSeq Library Kit contains 2 amplification mixes optimized for rapid preparation of highly specific, sequencing-ready amplicon libraries.

  • rhAmpSeq Library Mix 1—optimized for high specificity and multiplexing capability. This mix is for Targeted rhAmp PCR 1 in the rhAmpSeq workflow (Figure 1).
  • rhAmpSeq Library Mix 2—optimized for high-efficiency amplification. This mix is for Indexing PCR 2 in the rhAmpSeq workflow. In this universal PCR step, rhAmpSeq Index Primers add index barcodes and Illumina P5/P7 adapter sequences to the library (Figure 1).

Harnessing the power of rhAmp PCR

Our proprietary rhAmp PCR technology drives the rhAmpSeq system. This technology harnesses the intrinsic properties of the RNase H2 enzyme and RNA-base–containing blocked primers (rhAmp primers), minimizing primer dimers and enabling rhAmpSeq panels to be highly multiplexed.

Those 2 advantages—minimal primer dimers and high multiplexing capabilities—allowed us to develop the high-performance rhAmpSeq system, whose fast, easy workflow requires only 2 PCR amplification steps (Figure 1) to generate amplicon libraries for Illumina platform sequencing.

To learn more about rhAmp PCR technology, visit this page.

Figure 1. Detail of amplification steps in the rhAmpSeq workflow. RNase H2 activates rhAmp primers by target-specific cleavage of the RNA base within the DNA:RNA duplex, removing a 3′ blocker. RNase H2 activity is highly specific, thus reducing the amount of amplification from non-specific hybridization and primer dimers. Only activated rhAmp primers can be extended to generate target amplicons.

Illumina sample barcodes and P5/P7 sequences are incorporated during Indexing PCR 2.

Technical details

Because all rhAmpSeq reagents are compatible with both our regular and high-throughput library preparation protocols, you can choose the best workflow for each experiment without having to buy different reagents. Table 1 shows the features and specifications common to both rhAmpSeq system protocols.

Table 1. rhAmpSeq system features and specifications.

Supported protocolsRegular library preparation (10–100 ng)
High-throughput library preparation (10–50 ng)
Sample typeTissue, FFPE, cfDNA
Insert sizeFlexible (50–200 nt)
Custom panel sizeUp to 5000 amplicons per panel
Sample indexing capability96 index sequences (up to 9216 combinations)
Compatible platformsIllumina

When multiplexing many samples in a single NGS run, we have observed slightly better sample-level coverage uniformity with the regular rhAmpSeq library preparation protocol. Nevertheless, the high-throughput protocol also offers effective genotype calling, and performs best when read coverage is not limiting (e.g., >500X per target).

In contrast to the regular protocol, the high-throughput protocol saves both overall time and reagent costs by removing a cleanup step and the need to quantify and normalize libraries before combining libraries onto a flow cell. However, your results may vary—please contact Application Support for more information.

Table 2. Choose the best rhAmpSeq library preparation protocol for your needs.

ConsiderationsRegular protocolHigh-throughput protocol
Better sample-to-sample coverage uniformity 
Better performance with challenging sample types (e.g., FFPE, cfDNA) 
Ideal for high-throughput screening labs 
No library quantification and normalization required 
Hands-on time*2.5–4.5 hr1–1.5 hr
Total workflow time*4–6 hr4–4.5 hr
* Estimated time to process 12–96 samples using manual pipetting, including reaction setup, cleanup, library quantification, and normalization steps

Consistent performance

Your sequencing data can only be as good as your amplicon libraries. High quality amplicon library preparation reagents are therefore essential for obtaining excellent and reproducible performance. The data in Figure 2 show typical consistency and performance of the rhAmpSeq Library Kit.

Figure 2. Multiple rhAmpSeq Library Mix lots demonstrate consistent performance. We evaluated the performance of 3 lots of rhAmpSeq Library Mix. Each lot was evaluated with multiple Coriell samples (10 and 50 ng input DNA) using the rhAmpSeq Sample ID Panel following the high-throughput rhAmpSeq library preparation protocol (32 replicates per input quantity per lot). Performance was consistent across lots. Coverage uniformity is the percent of targets with coverage ≥0.2X of the mean.