KAPA HyperPETE Choice and KAPA HyperPETE Explore Panels

Overview

KAPA HyperPETE Custom Panels for Human Genomic Regions of Interest (≤250 Kb)

Leverage over a decade of probe-design experience with HyperDesign, a user-friendly online panel-design tool, to create custom KAPA HyperPETE custom panels. Panels created with HyperDesign achieve deeper, more uniform downstream sequencing coverage with fewer sequencing reads—even across difficult-to-capture regions.

Choose the design approach that best suits your needs: either use HyperDesign to create your KAPA HyperPETE Choice Panels on your own in four simple steps, or request assistance from a Roche Expert Designer to help design your unique KAPA HyperPETE Explore Panels.

Whichever approach you choose, HyperPETE panels provide the ability to:

Uncover critical genomic information from a variety of sample types, including FFPET and cfDNA
Detect all major somatic variant types, including SNVs, short indels, CNVs, MSI, and fusion transcripts (known and unknown)
Achieve superior performance and coverage uniformity in fewer optimization steps

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Tissue DNA (FFPET): Variant Detection and Performance Data

Figure 1. Performance metrics using tissue DNA (FFPET). High specificity with deep and broad target coverage were demonstrated using a KAPA HyperPETE Choice Panel (capture target of 88 Kb plus 25 Kb of the Roche preset MSI targets). Percent of reads on-target ranged from 77.1% to 87.7% (median 84.4%), percent of bases covered at > 300X ranged from 97.2% to 98.7% (median 98.4%), and percent of bases covered at > 500X ranged from 94.4% to 98.3% (median 97.4%).

Eight (8) FFPET DNA samples and eight (8) control FFPET DNA samples of varying quality were tested in duplicates by following the KAPA HyperPETE Workflow for Somatic Tissue DNA Preparation. High quality DNA samples had a normalized Q score > 0.4 with input range of 20 ng to 34.4 ng, medium quality > 0.22 with input range of 37 ng to 55.5 ng, and low quality > 0.09 with input range of 62.6 ng to 121.1 ng. Final libraries were sequenced on an Illumina NextSeq™ 550 system. Total read pairs (2x150 bp) per sample ranged from 12.5M to 20.4M and data was analyzed using navify® Mutation Caller* to assess enrichment and variant detection performance.

Table 1 (a, b, c, d). Highly confident detection of SNVs, Indels, CNV and MSI using Horizon Discovery FFPET control and CrownBio FFPET xenograft samples. Performance was demonstrated using a KAPA HyperPETE Choice Panel (capture target of 88 Kb plus 25 Kb of the Roche preset MSI targets). True positive detection rates were 100% for SNVs, or Indels (Table 1a), CNVs (Table 1b) and MSI (Table 1c), without any false negatives. False positive rate was 0% for microsatellite stable samples (Table 1d). Final libraries were sequenced on an Illumina NextSeq™ 550 system. Total read pairs (2x150 bp) per sample ranged from 12.5M to 20.4M and data was analyzed using navify® Mutation Caller* to assess the variant detection.

* 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.

Table 1a. Performance in SNV and Indel detection

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Sample	Input (ng)	Expected allele frequency	Total replicates	Expected variants	True Positive Rate
HD200	20	5%	4	24 SNVs	100%
HD200	20	5%	4	4 Indels	100%
HD789	20	5%	4	8 Indels	100%

Table 1b. Performance in CNV detection

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Sample	Input (ng)	Gene	Expected copies	Total replicates	False negatives	True Positive Rate
HD789	20	MET	4.5	4	0	100%

Table 1c. Performance in MSI detection (true positive rate)

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Sample (xenografts)	Input (ng)	Expected status	Total replicates	Reported status (≥40% = MSI)	True Positive Rate
DU145	62.6 - 343.3	MSI	2	MSI: 83.1% - 84.3%	100%
SW48	41.3 - 45.7	MSI	2	MSI: 97.1% - 98.3%	100%

Table 1d. Performance in MSI detection (false positive rate)

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**Table 1d. Performance in MSI detection (false positive rate)**
Sample (xenografts)	Input (ng)	Expected status	Total replicates	Reported status (<40% = MSS)	False Positive Rate
BT474	40.3 - 51.7	MSS (Microsatellite stable)	2	MSI: 23.4% - 29.2%	0%
MDA-MB-453	72.5	MSS (Microsatellite stable)	1	MSI: 28.5%	0%

Tissue RNA (FFPET): Fusion detection and performance data

KAPA HyperPETE Choice RNA Panel enables confident fusion detection from RNA samples

Single-day from RNA to the sequencer, optimized and low hands-on time workflow
Sequencing efficiency by high on-target rates
Confident fusion detection with high true positive rates
KAPA HyperPETE technology allows detection of unknown fusion partners

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 navify^® Mutation Caller* to assess enrichment and variant detection performance.

Table 2. Fusion detection performance using tissue RNA (FFPET).

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Table 2. Fusion detection performance using tissue RNA (FFPET).

All fusions (100%) were detected in the reference cell line sample at 10 ng RNA input amount. The data of the reference cell-line was used to assess fusion detection performance. Data analysis was performed using the navify^® Mutation Caller*.

Variant	RNA Input Amount (ng)	Total replicates	Expected Fusions	True Positive Rate
Fusion	10	2	6	100%

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

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		✓					✓	✓

Roche Catalog #	Description	Pack size
09418741001	KAPA HyperPETE Choice 75Kb	96 reactions
09418776001		384 reactions
09418784001		1536 reactions
09418792001		10000 reactions
09418806001	KAPA HyperPETE Choice 150Kb	96 reactions
09418849001		384 reactions
09418857001		1536 reactions
09418865001		10000 reactions
09418873001	KAPA HyperPETE Choice 250Kb	96 reactions
09418903001		384 reactions
09418911001		1536 reactions
09418920001		10000 reactions
09418938001	KAPA HyperPETE Choice RNA 50Kb	96 reactions
09418962001		384 reactions
09418989001		1536 reactions

Roche Catalog #	Description	Pack size
09419004001	KAPA HyperPETE Explore 75Kb	96 reactions
09419047001		384 reactions
09419055001		1536 reactions
09419063001		10000 reactions
09419071001	KAPA HyperPETE Explore 150Kb	96 reactions
09419101001		384 reactions
09419110001		1536 reactions
09419128001		10000 reactions
09419136001	KAPA HyperPETE Explore 250Kb	96 reactions
09419179001		384 reactions
09419187001		1536 reactions
09419195001		10000 reactions
09419209001	KAPA HyperPETE Explore RNA 50Kb	96 reactions
09419233001		384 reactions
09419241001		1536 reactions

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KAPA HyperPETE Choice and KAPA HyperPETE Explore Panels

KAPA HyperPETE Custom Panels for Human Genomic Regions of Interest (≤250 Kb)

Tissue DNA (FFPET): Variant Detection and Performance Data

Table 1a. Performance in SNV and Indel detection

Table 1a. Performance in SNV and Indel detection

Table 1b. Performance in CNV detection

Table 1b. Performance in CNV detection

Table 1c. Performance in MSI detection (true positive rate)

Table 1c. Performance in MSI detection (true positive rate)

Table 1d. Performance in MSI detection (false positive rate)

Table 1d. Performance in MSI detection (false positive rate)

Tissue RNA (FFPET): Fusion detection and performance data

Table 2. Fusion detection performance using tissue RNA (FFPET).

Table 2. Fusion detection performance using tissue RNA (FFPET).

Overview of additional sample types compatible with KAPA HyperPETE

Overview of additional sample types compatible with KAPA HyperPETE

Ordering information for KAPA HyperPETE Choice Panels

Ordering information for KAPA HyperPETE Choice Panels

Ordering information for KAPA HyperPETE Explore Panels

Ordering information for KAPA HyperPETE Explore Panels

rdoe_persona_userprofile

rdoe_persona_select_up

KAPA HyperPETE Choice and KAPA HyperPETE Explore Panels

KAPA HyperPETE Custom Panels for Human Genomic Regions of Interest (≤250 Kb)

Resources

Technical documents

Tissue DNA (FFPET): Variant Detection and Performance Data

Table 1a. Performance in SNV and Indel detection

Table 1a. Performance in SNV and Indel detection

Table 1b. Performance in CNV detection

Table 1b. Performance in CNV detection

Table 1c. Performance in MSI detection (true positive rate)

Table 1c. Performance in MSI detection (true positive rate)

Table 1d. Performance in MSI detection (false positive rate)

Table 1d. Performance in MSI detection (false positive rate)

Tissue RNA (FFPET): Fusion detection and performance data

Table 2. Fusion detection performance using tissue RNA (FFPET).

Table 2. Fusion detection performance using tissue RNA (FFPET).

Overview of additional sample types compatible with KAPA HyperPETE

Overview of additional sample types compatible with KAPA HyperPETE

Ordering information for KAPA HyperPETE Choice Panels

Ordering information for KAPA HyperPETE Choice Panels

Ordering information for KAPA HyperPETE Explore Panels

Ordering information for KAPA HyperPETE Explore Panels