KAPA HyperPETE Choice and KAPA HyperPETE Explore Panels

Overview

KAPA HyperPETE Panels for custom regions  

Roche introduces its target enrichment custom panels, KAPA HyperPETE Choice Panels and KAPA HyperPETE Explore Panels, for DNA or RNA. KAPA HyperPETE Choice Panels and KAPA HyperPETE Explore Panels enable custom designs up to 250Kb for DNA inputs and 50Kb for RNA inputs.

Features and Benefits of KAPA HyperPETE Custom Panels
 

• Better by design, using Roche's renowned oligo design and selection algorithms, enable access to challenging genomic regions
• Seamless online generated designs in the HyperDesign Tool either with a few clicks or through an expert designer-assisted process
  
• High uniformity for better sequencing efficiency with less optimization

Product highlights

• Quickly and efficiently cover your custom regions with the high-performing KAPA HyperPETE Custom Panels
  • Rely on Roche’s proven design and primer selection expertise to improve your desired target coverage and maximize the data return from your research. Use the HyperDesign Tool to prepare your custom design in four (4) simple steps, include an optimized MSI (Microsatellite Instability) target set into your design or consult with Roche’s expert designers team for your special design needs.

• Take fewer steps to optimal performance and sequencing efficiency

  • Experience high performance from your very first panel design iteration as a result of Roche’s design expertise and extensive KAPA HyperPETE Workflow optimization.

• Achieve confident variant detection for all major mutation classes
  • Detect Single Nucleotide Variants (SNVs), insertions or deletions (Indels), Copy Number Variants (CNVs), Fusions and Microsatellite Instability (MSI) in your regions of interest, using an optimized workflow.

Figure 2. Performance using tissue RNA (FFPET).  High specificity was demonstrated by the high percent of reads on-target when starting from 10 ng of various quality (low, medium, high) input FFPE RNA. On-target rate was 94.6% to 97.9% (includes housekeeping and fusion targets) with good performance across all sample input qualities, and types. The on-target rate was calculated following rRNA read removal (0.5% to 3.5% of all reads). One reference cell-line sample (in duplicates), 3 reference FFPET samples (in duplicates) and 8 normal adjacent FFPET samples were used to assess performance.
 

RNA was extracted with the Roche High Pure FFPET RNA Isolation Kit and quality was determined with the DV200 score using the Agilent RNA 6000 Pico Assay on the Bioanalyzer. The KAPA HyperPETE Workflow for Tissue RNA Fusion Transcript Preparation using a KAPA HyperPETE Choice RNA Panel (capture target size ~13 Kb) was followed. Libraries were generated using the KAPA RNA HyperPrep kit in combination with the KAPA Universal UMI Adapters and 10ng of RNA while adjusting PCR cycles based on the DV200 score. Libraries were captured using the KAPA HyperPETE Reagent Kit and sequenced on an Illumina NextSeq™ 550 system. Total read pairs (2x150 bp) per sample ranged from 2.4M to 3.5M, and data was analyzed using an internal Roche secondary analysis pipeline to assess enrichment and variant detection performance.