1. Roche Sequencing
  2. Target Enrichment
  3. Primer Extension
  4. KAPA HyperPETE

KAPA HyperPETE

Primer Extension Target Enrichment

woman scientist in front of a DNA strand.

The performance of hybrid-capture target enrichment with the speed and simplicity of amplicon workflows

KAPA HyperPETE (Primer Extension Target Enrichment) is a novel hybridization capture technology designed to employ primer extension reactions to specifically capture and release target library molecules for sequencing. 

This target enrichment technology preserves the performance of conventional hybridization while enabling a more efficient workflow.  It has been specifically designed and optimized for small design sizes and validated to detect all major somatic variants in cfDNA, FFPE, and RNA samples, including SNVs, short indels, CNVs, MSI, and fusion transcripts (novel and known) and is especially suited for small panel oncology research applications. 

The KAPA HyperPETE Portfolio includes readily available fixed-design panels for hereditary oncology, oncology hotspots, pan-cancer variants (with an MSI module), and lung cancer fusion variants. In addition, custom panels can be designed using HyperDesign, our easy-to-use online design tool.

 

Save valuable time with an efficient, single-day, automatable workflow

  • Take hours off of total workflow time compared to typical hybridization capture, with time requirements similar to anchored multiplex methods (Figure 1)
  • Enrich for long contiguous regions with fewer tubes per sample compared to amplicon technologies

 

Figure 1. The turnaround time (TAT) for KAPA HyperPETE target enrichment is similar to the TAT for amplicon-based workflows.

(A) While most hybridization-based workflows take two days to complete, KAPA HyperPETE workflows can be completed in one day. (B) Differences in the TAT for various applications of KAPA HyperPETE are dependent on the library preparation kit used, as each kit requires slightly different completion times. However, once the libraries are created, the enrichment workflow is the same across applications.

Achieve superior performance and coverage uniformity

  • Obtain more uniform coverage compared to anchored multiplex PCR (Figure 2)
  • Avoid over- or under-representation of PCR-based target regions; KAPA HyperPETE technology uses primers to capture the regions of interest, rather than amplify them, greatly reducing amplification bias
  • Streamline bioinformatics pipelines and increase your sequencing efficiency by eliminating the need to remove primer binding site sequences from your sequencing data

Figure 1. KAPA HyperPETE coverage across the APC gene compared to anchored multiplex PCR.

Uncover critical genomic information from difficult sample types

Tissue RNA (FFPET)

  • Achieve highly specific enrichment from a broad range of FFPET RNA input amounts (Figure 3)
  • Detect all fusions present in reference cell line samples (Table 1)

Figure 3. The KAPA HyperPETE Lung Cancer Fusion Panel achieved 92%-97% reads on-target from 10 ng and 50 ng of all FFPET samples tested.

Plasma cfDNA

  • Achieve high % reads on-target and high exon coverage (at ≥1000X) for a range of cfDNA input amounts (Figure 4)
  • Detect variants with high sensitivity, from a range of plasma input cfDNA amounts (Table 2)

Figure 4. The KAPA HyperPETE Hot Spot Panel and KAPA HyperPETE Pan Cancer Panel provide high-quality results for plasma cfDNA (10 ng and 50 ng input). 

Table 3. Overview of additional sample types compatible with KAPA HyperPETE

KAPA HyperPETE Panel FFPET Plasma cfDNA Human cell-line gDNA High-quality human gDNA High-quality human RNA
  DNA RNA     Blood Fresh Tissue Blood Fresh Tissue
KAPA HyperPETE Choice / Explore ✓   ✓ ✓ ✓ ✓    
KAPA HyperPETE Choice / Explore RNA   ✓         ✓ ✓
KAPA HyperPETE Pan Cancer Panel ✓   ✓ ✓ ✓ ✓    
KAPA HyperPETE Hot Spot Panel ✓   ✓ ✓ ✓ ✓    
KAPA HyperPETE Hereditary Oncology Panel       ✓ ✓ ✓    
KAPA HyperPETE Lung Cancer Fusion Panel   ✓         ✓ ✓

KAPA HyperPETE Catalog Panels

Leverage over a decade of probe-design experience with KAPA HyperPETE fixed design panels. When ordered, these readily available designs are delivered the next business day.

Contact us to request Panel Gene List, Data Data Proof of Principle, or Design Files.

The KAPA HyperPETE Pan Cancer Panel is a 302 Kb capture target panel covering 1324 target regions, 86 cancer related genes and 190 MSI loci relevant to somatic oncology research applications.The panel’s been optimized to deliver high uniformity and specificity from low quality, low quantity FFPET DNA and cfDNA samples.

The KAPA HyperPETE Hot Spot Panel is a 40 Kb capture target panel covering 37 targets from the genomic 'hot spot' regions that are frequently mutated in human cancer genes. It is optimized to deliver high uniformity and specificity from low quality, low quantity FFPET DNA and cfDNA samples.

The KAPA HyperPETE Hereditary Oncology Panel is a 200 Kb capture target panel focusing on hereditary breast and ovarian cancer research (including BRCA1 and BRCA2) as well as hereditary colorectal cancer research. It covers 47 related genes in these cancer types and has been optimized to deliver high uniformity and specificity in germline variant research with the pre-capture multiplexing capacity of 8 samples.

The KAPA HyperPETE Lung Cancer Fusion Panel is a 18 Kb capture target panel also using the novel KAPA HyperPETE technology to detect the known fusions and unknown fusion partners including 17 lung cancer fusion genes and 4 housekeeping genes (as internal controls). 

The design and analysis (supported by NAVIFY® Mutation Caller) covers fusions, but the design also covers other variants near the capture region through alternative analysis solutions.

KAPA HyperPETE Custom Panels (human)

Use HyperDesign, a user-friendly online tool, that builds on two decades of in silico design experience to select probe panels that achieve deeper, more uniform downstream sequencing coverage with fewer sequencing reads—even across difficult-to-capture regions.

KAPA HyperPETE Choice designed by customers using HyperDesign
KAPA HyperPETE Explore designed by the Roche Expert Designer Service

Project: KAPA HyperPETE, Pleasanton, CA 2021.

Research Use Only. Not for use in diagnostic procedures.

HYPERPETE, and KAPA are trademarks of Roche. All other product names and trademarks are the property of their respective owner.