KAPA HyperExome V2 Probes

For research use only. Not for use in diagnostic procedure.

Efficient whole-exome sequencing (WES) begins with expertly designed probes that effectively capture challenging genomic regions.

KAPA HyperExome V2 Probes, the latest Roche WES design, delivers superior coverage of recent versions of ACMGv3.1, RefSeq, CCDS, ClinVar, Ensembl, and COSMIC genomic databases. This design also reduces sequencing requirements, with a compact capture target of 43.2 Mb covering 37.5 Mb of key content.

Leverage the most relevant genomic databases
Unlock unique insights in translational research by capturing more content from key genomic databases
Achieve higher uniformity across the entire range of %GC content
Sequence with confidence with an improved whole-exome workflow
Streamline targeted sequencing with the HyperCap Workflow, driven by KAPA HyperPrep, KAPA HyperPlus, and KAPA EvoPlus Library Prep Kits

Fully automated whole-exome sequencing (WES) on the AVENIO Edge Liquid Handling System

No prior NGS and/or automation experience required
As little as 20 minutes of deck setup time for the entire WES workflow
Automated quantification, normalization and pooling
Complementary support team to help you along the way

Start here

Performance data

Leverage the most relevant databases

Build confidence by using a design featuring updated ClinVar, RefSeq & Ensembl content*
Achieve exceptional coverage of ACMGv3.1, CCDS, ClinVar, COSMIC, Ensembl, HGMD, & RefSeq databases
Balance specificity & coverage with probes designed using the telomere-to-telomere genome assembly CHM13

Exceptional content coverage

Cover your bases, see what others may find difficult to see
Add more value and confidence in your results with superior database regions’ coverage
Eliminate “blind” spots - Leave fewer unknowns

Figure 1. Percent bases covered by at least 30x across some of the key genomic databases such as Ensembl, RefSeq and CCDS, based on a January 2024 snapshot. KAPA HyperExome V2 Probes deliver better database coverage compared to vendors I, A and T that are leaving more “blind” spots, which may lead to repeats or need for spike-in probes. Vendor sample prep protocols were followed with singleplex 4h hybridizations for vendor I (3 replicates, NA12878), 8-plex o/n hybridizations for vendor A (48 data points from 6 replicate captures of 16 coriell DNAs), 8- plex o/n hybridizations for vendor T (72 data points from 16 coriell and 24 blood extracted DNAs). For KAPA HyperExome V2 Probes the KAPA HyperCap Evolved Workflow v4 was followed. A total of 40 libraries were prepared with the KAPA EvoPrep Kit and 40 libraries with the KAPA EvoPlus V2 Kit starting from 100 ng of blood extracted DNA samples (in 2 x 16-plex hybridizations) and from 100 ng of NA12878 DNA samples (in 4 x 1-plex hybridization and 4 replicates from an 8-plex hybridization). KAPA HyperExome V2 Probes enriched libraries were sequenced on a NovaSeq^TM 6000 System at 2 x 100 bp and 60 M high-quality reads were analyzed per library. Vendor-enriched libraries were sequenced proportionally to their capture target size.

Design advantage

Maximize your sequencing coverage starting from a better exome design
Deliver higher quality results by covering more regions from the key genomic databases

Figure 2. Percent bases covered by at least 30X across some key genomic databases. KAPA HyperExome V2 Probes deliver better database coverage compared to Suppliers I, A, and T, which leave more “blind” spots and may thus require repeated experiments and/or the addition of supplemental probes. Supplier sample prep protocols were followed with singleplex 4h hybridizations for Supplier I (3 replicates, NA12878), 8-plex O/N hybridizations for Supplier A (48 data points from 6 replicate captures of 16 coriell DNAs), 8-plex O/N hybridizations for Supplier T (72 data points from 16 coriell and 24 blood-extracted DNAs) and 16-plex O/N hybridizations for the KAPA HyperExome V2 Probes (48 data points from 16 blood-extracted DNAs in 3 captures) with the KAPA EvoPlus Kit, KAPA HyperPlus Kit, and KAPA HyperPrep Kit (48 data points from 16 coriell DNAs in 3 captures). KAPA HyperExome V2 Probes-enriched libraries were sequenced on a NovaSeq™ 6000 System at 2 x 100 bp and 60 M high-quality reads were analyzed per library. Supplier-enriched libraries were sequenced proportionally to their capture target size.³

Achieve higher uniformity across the entire %GC range

Achieve exceptionally uniform coverage even through the extremes of the GC% spectrum
Eliminate GC bias and cover equally well low and high GC regions with an optimized design and uniform library amplification using the KAPA EvoPrep or KAPA EvoPlus V2 Kits

Figure 3. Exceptional uniformity of normalized capture coverage across the extremes of the GC% spectrum. Vendor sample prep protocols were followed with 8-plex o/n hybridizations for vendor A (48 data points from 6 replicate captures of 16 coriell DNAs), 8-plex o/n hybridizations for vendor T (72 data points from 16 coriell and 24 blood extracted DNAs). For KAPA HyperExome V2 Probes the KAPA HyperCap Evolved Workflow v4 was followed. A total of 32 libraries were prepared with the KAPA EvoPrep Kit or the KAPA EvoPlus V2 Kit starting from 100 ng of blood extracted DNA samples and were hybridized by 2 x 16-plex captures for each kit workflow. Final libraries were sequenced on a NovaSeq^TM 6000 System at 2 x 100 bp and 60 M high-quality reads were analyzed per library and proportionally to the capture target for the other vendor exomes.

Unlock unique insights in translational research

Cover more bases and reduce “blind” spots, leaving fewer unknowns
Increase value and confidence in the results with superior coverage of database content

Streamline targeted sequencing with the KAPA HyperCap Workflow

KAPA HyperCap Workflow delivers uniform libraries by combining the high conversion rate of KAPA HyperPrep, KAPA HyperPlus, KAPA EvoPrep, and KAPA EvoPlus Kits with KAPA HyperCap probes (such as KAPA HyperExome V2 Probes), creating a streamlined, single-vendor supported workflow.

Multiplex up to 16 samples in the same capture, and potentially post-capture multiplex more samples in the same sequencing lane, with KAPA UDI Primer Mixes,1-384
Reduce workflow complexity and hands-on time with KAPA Universal Enhancing Oligos, eliminating the need for adapter-matched blocking oligos
Automate the entire KAPA HyperCap Workflow without the need for a SpeedVac—now with all hybridization and bead wash steps at 55ºC

KAPA HyperExome V2 Design Files

The design and annotation files provide information about genomic regions covered by the capture probes and the genes included in these regions.

The KAPA HyperExome V2 panel was designed to cover coding exon sequence from the following annotation sources: RefSeq (June 29, 2022), ClinVar (June 29, 2022) and Ensembl release v106. The panel covers 529 sample tracking SNPs to facilitate sample identity tracking in the workflow. A set of 96 probes, composed of non-naturally occurring sequences, are included in the design. These probes may be used to capture exogenous synthetic DNA fragments, potentially used as process controls.

The total design size is 43.2 Mb of capture target space; the capture targets BED file shows the capture probe footprint. The UCSC Browser BED files are provided for upload as a custom track. All design files are provided in the original hg38 genome assembly and also converted to hg19 genome assembly. Conversion was performed using the NCBI Genome Remapping Service.

Download hg38 Design Files for the KAPA HyperExome V2 Probes

Download hg19 Design Files for the KAPA HyperExome V2 Probes

*Databases reviewed June 2022

1. A SNP profiling panel for sample tracking in whole-exome sequencing studies. Pengelly RJ, et al. Genome Med. 2013 Sep 27;5(9):89. doi: 10.1186/gm492. eCollection 2013

2. A SNP panel for identification of DNA and RNA specimens. Yousefi S, et al. BMC Genomics. 2018 Jan 25;19(1):90. doi: 10.1186/s12864-018-4482-7.

3. Project: Roche KAPA HyperExome V2 Launch Data, Pleasanton, CA, Mar. 2023

Thinking of automating library prep on your existing liquid handler?

Roche’s NGS Automation Support Team, in collaboration with non-Roche liquid handling vendors, creates menus of automated methods for KAPA library prep reagents. Let’s talk about the next steps to get you up and running with automating your NGS library prep protocols. Visit support for non-Roche liquid handlers to learn more.

Support for automating KAPA reagents on non-Roche liquid handlers

AVENIO Edge reagents and workflows are for Research Use Only. They are not intended for diagnostic applications.

View Full Table

Demo data files are available. Please contact a local Roche representative.

Product Name	Capture reactions	Catalog No.
KAPA HyperExome V2 Prep Kit Complete KAPA HyperCap Workflow NGS sample prep kit for 192 8-plex reaction samples Includes: KAPA HyperPrep Kit, Universal Adapters, HyperBeads, Probes Resuspension Buffer, HyperExome V2 Probes, HyperCapture Reagent Kit, and Hypercapture Bead Kit	192 8-plex rxn	9983759001
KAPA HyperExome V2 Plus Kit Complete KAPA HyperCap Workflow NGS sample prep kit for 192 8-plex reaction samples Includes: KAPA HyperPlus Kit, Universal Adapters, HyperBeads, Probes Resuspension Buffer, HyperExome V2 Probes, HyperCapture Reagent Kit, and Hypercapture Bead Kit	192 8-plex rxn	9983775001
KAPA HyperExome V2 Evo Kit Complete KAPA HyperCap Workflow NGS sample prep kit for 192 8-plex reaction samples Includes: KAPA EvoPlus Kit, Universal Adapters, HyperBeads, Probes Resuspension Buffer, HyperExome V2 Probes, HyperCapture Reagent Kit, and Hypercapture Bead Kit	192 8-plex rxn	9983783001
KAPA HyperExome V2 Probes	12	9718630001
	24	9718648001
	48	9718656001
	96	9718664001
	192	9718672001
	384	9718699001
	768	9718702001
	1152	9718729001
	1536	9718737001

AVENIO Edge reagents and workflows are for Research Use Only. They are not intended for diagnostic applications.

Fully automated whole-exome sequencing (WES) on the AVENIO Edge Liquid Handling System

No prior NGS and/or automation experience required
As little as 20 minutes of deck setup time for the entire WES workflow
Automated quantification, normalization and pooling
Complementary support team to help you along the way

From sample to sequencing, with automation and support at every step

KAPA HyperExome V2 Probes deliver superior whole-exome sequencing (WES) coverage of recent versions of ACMGv3.1, RefSeq, CCDS, ClinVar, Ensembl, and COSMIC genomic databases. This design reduces sequencing requirements, with a compact capture target of 43.2 Mb covering 37.5 Mb of key content.

Figure 1. High sequencing efficiency delivered by the KAPA HyperExome V2 Probes when used on the AVENIO Edge System, delivering low PCR duplication (mean 1.76%), with high specificity (mean 80.5% reads on-target) and high uniformity (mean 1.46 Fold-80 base penalty). Library Preparation and Target Enrichment based on 8-plex pre-capture pooling (n=24, NA12878 100 ng input in the AVENIO Edge HyperPrep Kit) – 60 M high-quality reads 2 x 150bp analyzed from a NovaSeq^TM 6000 System. The AVENIO Edge System is a Class 1 US IVD and a Class A CE-IVDR.

Thinking of automating library prep on your existing liquid handler?

Support for automating KAPA reagents on non-Roche liquid handlers

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KAPA HyperExome V2 Probes

Efficient whole-exome sequencing (WES) begins with expertly designed probes that effectively capture challenging genomic regions.

Fully automated whole-exome sequencing (WES) on the AVENIO Edge Liquid Handling System