KAPA HyperPETE Catalog Panels and Kits

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 has 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 an 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 cover fusions, but the design also covers other variants near the capture region through alternative analysis solutions.

The KAPA HyperPETE Newborn Screening Panel is a 290 Kb capture target panel covering 89 related genes. It is optimized to deliver high uniformity and specificity in germline variant research with the pre-capture multiplexing capacity of 8 samples.

Figure 1: Performance using FFPE RNA with the KAPA HyperPETE LC Fusion Panel.

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

High specificity was demonstrated by the high percentage of reads on-target when starting from 10 ng or 50 ng of various quality (low, medium, high) input FFPE RNA. On-target rate was 92% to 97% (includes housekeeping and fusion targets) with good performance across all sample input amounts, qualities, and types. The on-target rate was calculated following rRNA read removal (0.8% to 11% of all reads). Two (2) cell-line samples (in duplicates) and fourteen (14) 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 the KAPA HyperPETE LC Fusion Panel was followed. Libraries were generated using the KAPA RNA HyperPrep Kit in combination with the KAPA Universal UMI Adapter and either 10 ng or 50 ng of RNA, while adjusting PCR cycles based on the input amount and DV200 score. Libraries were captured using the KAPA HyperPETE Reagent Kit and sequenced on an Illumina NextSeq™ 550 System. Total read pairs (2 x 150 bp) per sample ranged from 3.6M to 17M, and data was analyzed with an internal Roche secondary analysis pipeline.

Figure 2: Performance metrics using cfDNA.

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).

High specificity with deep and broad unique target coverage was demonstrated using the KAPA HyperPETE Workflow for Somatic Plasma cfDNA Preparation across all sample input amounts and types. On-target rate was 65% – 73% for the KAPA HyperPETE Hot Spot Panel and 70% – 73% for the KAPA HyperPETE Pan Cancer Panel. At 50 ng cfDNA input, the percent of panel exon bases covered at ≥1000X of unique depth (PCR duplicates removed) was >99% for the KAPA HyperPETE Hot Spot Panel and 97% – 98% for the KAPA HyperPETE Pan Cancer Panel. The respective percentages at ≥3000X unique depth were 80% – 94% and 67% – 85%. At 10 ng of cfDNA input, the unique depth was concordant with the available unique genome equivalents (~3300 in 10 ng of DNA), and the percentages at ≥1000X unique depth were 83% – 99% and 80% – 94% per panel, respectively.

Libraries were generated using the KAPA HyperPrep Kit and the KAPA Universal UMI Adapter from either 10 ng or 50 ng of plasma cfDNA or fragmented reference cell-line DNA as input, and individually captured using the KAPA HyperPETE Reagent Kit and the respective panel. Final libraries were sequenced on an Illumina NextSeq™ 550 System with 6M – 14M (median: 8M) high-quality read pairs (2 x 150 bp) allocated per sample for the KAPA HyperPETE Hot Spot Panel, and 55M – 81M (median: 66M) high-quality read pairs allocated per sample for the KAPA HyperPETE Pan Cancer Panel. Two (2) Seraseq® ctDNA Mutation Mix samples in duplicates and sixteen (16) healthy donor plasma cfDNA samples were used to assess the performance. Data was analyzed with an internal Roche secondary analysis pipeline.