KAPA HyperExome Probes

The KAPA HyperExome Probes are Roche’s brand new Whole Exome Sequencing solution, based on the next generation KAPA Target Enrichment Probe’s technology. Their design and technology provide broad, relevant database coverage and high sequencing efficiency.

The product has been extensively optimized through design and manufacturing processes to increase coverage in hard-to-sequence regions for a more uniform and complete exome. Based on customer feedback, Roche Sequencing scientists created the KAPA HyperExome Probes, a sequencing efficient design with actionable and well-annotated content.

KAPA HyperExome Probes are targeting the GRCh38/hg38 genome assembly (coordinates for hg19 annotation are also provided) by covering the CCDS, RefSeq, Ensembl, GENCODE and ClinVar genomic databases in an efficient ~43 Mb capture target size, including 387 sample tracking SNPs to streamline sample identity tracking throughout the WES workflow.

Sequencing data generated with the KAPA HyperExome Probes can be analyzed with Roche's cloud-based secondary analysis solution - NAVIFY® Mutation Caller - for accurate detection of variants.


Features and benefits of KAPA HyperExome Probes

  • Better by design - Uncover difficult regions and access more content from important genomic databases
  • Validated with the KAPA HyperCap Workflow v3.0 for high sequencing efficiency by superior uniformity and low duplication rates
  • Higher result confidence with >98.7% sensitivity and >99.7% specificity of SNP detection
  • Stronger enrichment by high fidelity probes that are manufactured with KAPA HiFi DNA Polymerase and target both DNA strands
  • Streamline your sample identity tracking to new levels of result confidence by intrinsically targeting 387 sample tracking SNPs 
  • Experience consistent quality and efficiency with NGS probe pool QC and larger reaction pack sizes
  • Simplify your secondary data analysis with confident germline SNV and Indel calling using NAVIFY® Mutation Caller.

Performance data


Better by design for higher result confidence

  • Utilize a whole exome solution with exceptional exon coverage of genes and variants from CCDS, RefSeq, Ensembl, GENCODE, ClinVar for maximal coverage of regions of medical research relevance in an efficient capture target size of just 43 Mb
  • Achieve better sequencing coverage of the important medical research content for less repeats and higher result confidence

KAPA HyperExome 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 Probes were designed to cover coding exons sequence from the following annotation sources: CCDS release 20, RefSeq (July 30, 2018), Ensembl release 93, and GENCODE release 28. It is also covering ClinVar variants (pathogenic, likely pathogenic, variants of unknown significance – as of July 29, 2018), the TERT promoter and 387 sample tracking SNPs. The genome assembly coordinates are based on the UCSC human genome build hg38, though hg19 files are also provided.

The total design size is 43 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.


Demo Data

Demo data is available for evaluation. Please contact your local Roche representative

The KAPA HyperExome Probes replace SeqCap EZ MedExome Probes, which will be supported until the end of March 2022.

All graphic data is on file, unless otherwise noted.