KAPA HyperPETE Catalog Panels

Overview

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.

KAPA HyperPETE Pan Cancer Panel

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.

KAPA HyperPETE Hot Spot Panel

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.

KAPA HyperPETE Hereditary Oncology Panel

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.

KAPA HyperPETE Lung Cancer Fusion Panel

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

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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 1)
Detect all fusions present in reference cell line samples (Table 1)

(Figure 1) High specificity was demonstrated by the high percent 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 using navify^® Mutation Caller* to assess enrichment and variant detection performance.

Figure 1. The KAPA HyperPETE Lung Cancer Fusion Panel achieved 92%-97% reads on-target from 10 ng and 50 ng of all FFPET samples tested.

Table 1. Fusion detection performance using tissue RNA (FFPET).

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Table 1. Fusion detection performance using tissue RNA (FFPET).

All fusions (100%) were detected in the reference cell line samples at both 10 ng and 50 ng RNA input amounts. Two (2) Seraseq^® RNA Fusion FFPE samples and one (1) Horizon Discovery RNA Fusion FFPE sample, each run in duplicate, were used to assess fusion detection performance. The EGFR-SEPT14 variant in Seraseq^® Fusion RNA Mix v4 was manually curated as the fusion caller in navify^® Mutation Caller* identified an EGFR partner that has a homologous sequence to SEPT14. Comparable variant detection results were achieved when down-sampling to 1M read pairs (data not shown).

Variant Type	RNA Input Amount (ng)	Total replicates	Expected Variants	True Positive Rate
Fusion	10	6	60	100%
Fusion	50	6	60	100%

Plasma cfDNA

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

(Figure 2) 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 using the navify^® Mutation Caller*.

Figure 2. 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 2. Variant detection performance using reference cell-line cfDNA.

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Table 2. Variant detection performance using reference cell-line cfDNA.

High true positive detection rates were demonstrated for short variants (Single Nucleotide Variants - SNVs, and Indels) at low variant allele expected frequencies across all reference cell line samples (2 Seraseq^® ctDNA Mutation Mix samples in duplicates). From both input amounts (10 ng and 50 ng) 100% of short variants (SNVs and Indels) were detected at 1% allele frequency using either of the two KAPA HyperPETE Panels. At 0.5% allele frequency from 10 ng input, the true positive detection rate was 94% and 96.9% using the KAPA HyperPETE Hot Spot Panel and the KAPA HyperPETE Pan Cancer Panel, respectively. At 0.5% allele frequency from 50 ng input, the true positive detection rate was 100% and 98.4% using the KAPA HyperPETE Hot Spot Panel and the KAPA HyperPETE Pan Cancer Panel, respectively. * Variants were present but not included in the true positive rate calculation as read support was lower than the cutoff used in the analysis pipeline.

Panel	Input (ng)	Allele Frequency	Expected Variants	Detected Variants	True Positive Rate
KAPA HyperPETE Hot Spot Panel	10	1.0%	56	56	100%
	50	1.0%	56	56	100%
	10	0.5%	50	47*	94%
	50	0.5%	50	50	100%
KAPA HyperPETE Pan Cancer Panel	10	1.0%	70	70	100%
	5	1.0%	70	70	100%
	10	0.5%	64	62*	96.9%
	50	0.5%	64	63*	98.4%

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

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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		✓					✓	✓

*navify® Mutation Caller is not available in the United States of America

Roche Catalog #	Description	Pack size	How to buy
09329161001	KAPA HyperPETE Pan Cancer Panel	24 reactions	Login for pricing
09329196001		96 reactions	Login for pricing
09329226001		384 reactions	Login for pricing
09329234001	KAPA HyperPETE Hot Spot Panel	24 reactions	Login for pricing
09329277001		96 reactions	Login for pricing
09329307001		384 reactions	Login for pricing
09329315001	KAPA HyperPETE Hereditary Oncology Panel	24 reactions	Login for pricing
09329340001		96 reactions	Login for pricing
09329374001		384 reactions	Login for pricing
09329471001	KAPA HyperPETE LC Fusion Panel	24 reactions	Login for pricing
09329501001		96 reactions	Login for pricing
09329536001		384 reactions	Login for pricing

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KAPA HyperPETE Catalog Panels

Overview

Uncover critical genomic information from difficult sample types

Tissue RNA (FFPET)

Table 1. Fusion detection performance using tissue RNA (FFPET).

Table 1. Fusion detection performance using tissue RNA (FFPET).

Plasma cfDNA

Table 2. Variant detection performance using reference cell-line cfDNA.

Table 2. Variant detection performance using reference cell-line cfDNA.

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

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

Ordering information for KAPA HyperPETE Catalog Panels

Ordering information for KAPA HyperPETE Catalog Panels

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KAPA HyperPETE Catalog Panels

Overview

Resources

Technical documents

Download Design Files

Uncover critical genomic information from difficult sample types

Tissue RNA (FFPET)

Table 1. Fusion detection performance using tissue RNA (FFPET).

Table 1. Fusion detection performance using tissue RNA (FFPET).

Plasma cfDNA

Table 2. Variant detection performance using reference cell-line cfDNA.

Table 2. Variant detection performance using reference cell-line cfDNA.

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

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

Ordering information for KAPA HyperPETE Catalog Panels

Ordering information for KAPA HyperPETE Catalog Panels