The KAPA HyperExome V2 Probes are Roche’s brand new Whole Exome Sequencing solution delivering superior coverage of the recent versions of ACMGv3.1, RefSeq, CCDS, ClinVar, Ensembl and COSMIC genomic databases within a compact capture target of 43.2 Mb with low sequencing requirements. The new T2T (telomere-to- telomere) genome assembly was utilized as part of the design process to identify potentially problematic regions not apparent in the GRCh38 genome assembly.
This new version is extensively optimized using real-world samples in the streamlined KAPA HyperCap Workflow including the KAPA EvoPrep and KAPA EvoPlus V2 Kits, to efficiently cover hard-to-capture regions.
When automating using the AVENIO Edge System you can focus on your clinical research based on a high-performing and reproducible walk-away whole-exome sequencing workflow from DNA to confident variant calling.
Figure 1. Superior probe database coverage by the KAPA HyperExome V2 design compared to other vendors’ designs across important genomic databases (even up to 17% better). Database data retrieved in Jan 2023, unpadded capture target used to compare across vendors.
Figure 2. 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 NovaSeqTM 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.
Figure 3. 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 NovaSeqTM 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.
Figure 4. 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 NovaSeqTM 6000 System. The AVENIO Edge System is a Class 1 US IVD and a Class A CE-IVDR. The AVENIO Design Software and the AVENIO Edge System reagents are for research use only, not for use in diagnostic procedures.
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
Demo data is available for evaluation. Contact us using the form below to submit a question or schedule a sales or demo call.
Unless otherwise indicated all data is on file with Roche.
Purchase convenient all-in-one kits or simply the KAPA HyperExome V2 Probes in convenient reaction pack sizes, from 12 reactions up to 1536 reactions.
| Roche Cat. No | Description | Kit Size (reactions) |
|---|---|---|
| 10212225702 | KAPA HyperExome V2 EvoPrep Kit - 192 samples | Convenient all-in-one package for 192 samples – all kits provided except the KAPA UDI Primer Mixes – For Covaris sonicated DNA input with the KAPA EvoPrep Kit - Talk to your Roche representative today |
| 9983783001 | KAPA HyperExome V2 EvoPlus Kit - 192 samples | Convenient all-in-one package for 192 samples – all kits provided except the KAPA UDI Primer Mixes – Integrated enzymaticDNAshearing with the KAPA EvoPlus V2 Kit- Talk to your Roche representative today |
| 9718630001 | KAPA HyperExome V2 Probes, 12 rxn | 12 reactions |
| 9718648001 | KAPA HyperExome V2 Probes, 24 rxn | 24 reactions |
| 9718656001 | KAPA HyperExome V2 Probes, 48 rxn | 48 reactions |
| 9718664001 | KAPA HyperExome V2 Probes, 96 rxn | 96 reactions |
| 9718672001 | KAPA HyperExome V2 Probes, 192 rxn | 192 reactions |
| 9718699001 | KAPA HyperExome V2 Probes, 384 rxn | 384 reactions |
| 9718702001 | KAPA HyperExome V2 Probes, 768 rxn | 768 reactions |
| 9718729001 | KAPA HyperExome V2 Probes, 1152 rxn | 1152 reactions |
| 9718737001 | KAPA HyperExome V2 Probes, 1536 rxn | 1536 reactions |
