KAPA HyperCap Custom Probes

KAPA HyperChoice and KAPA HyperExplore
For Research Use Only. Not for use in diagnostic procedures.
KAPA HyperCap custom probes
KAPA HyperCap Target Enrichment Probes for custom regions

Hybridization or capture-based target enrichment enables researchers to enrich specific target regions for next-generation sequencing (NGS).

With its renowned probe design algorithm, Roche introduces KAPA HyperCap Target Enrichment custom probes with the new HyperDesign online custom design tool for higher probe fidelity and improved target capture NGS. Our custom portfolio of KAPA HyperChoice and KAPA HyperExplore probes along with our other reagents and accessory products helps scientists enhance their target enrichment workflow and save on sequencing costs.

Features and Benefits of KAPA HyperCap Target Enrichment Probes

KAPA HyperChoice and KAPA HyperExplore Probes*: 

  • Better by design, using Roche's renowned probe design and selection algorithms, enable access to challenging genomic regions
  • Seamless on-line generated designs in HyperDesign either with a few clicks or through an expert designer-assisted process
  • Stronger enrichment with high fidelity probes manufactured using KAPA HiFi DNA Polymerase
  • Consistent quality and performance with probe presence and concentration QC by NGS
  • High uniformity and low duplication for better sequencing efficiency with less optimization


*KAPA HyperExplore Probes enable enrichment of up to 200 Mb of genomic regions for non-human genomes and for unconventional human designs.

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Product highlights

High uniformity in coverage and low PCR duplicates with KAPA HyperChoice Probes

  • High uniformity in coverage and very low PCR duplicates
  • High % of reads on-target provide better target coverage
  • Higher sequencing efficiency with less iterations saves on cost and optimization time

 

The KAPA HyperChoice version of the SeqCap EZ Neurodegenerative design is delivering very low PCR duplicates and even better uniformity even by the first iteration, in contrast to the SeqCap EZ version that was empirically rebalanced. KAPA HyperChoice probes offer the same high % reads on target and better target coverage.

[Experimental details]: For KAPA HyperChoice Probes and SeqCap EZ Choice Probes, we followed the respective version of the KAPA HyperCap Workflow protocol starting from coriell control DNA. We have multiplexed 8 DNA libraries in each capture and we sequenced proportionally to the capture target size, at 2 x 101 bp on an MiSeq system.

Figure 1

Specificity and uniformity

Table 1: Performance of two KAPA HyperChoice designs

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Table 1: Performance of two KAPA HyperChoice designs

Design Genes Target size (capture) HQ reads System % total duplicates Fold 80 (uniformity) % bases ≥30X
Neurodegenerative > 98 335 Kb 1.75 M NovaSeq 6000 2.78 1.38 99.83
Hereditary disease > 4100 12.3 Mb 20.00 M NovaSeq 6000 1.62 1.43 97.22
First iteration designs, showing very low PCR duplication with high uniformity (low Fold80 base penalty) and broad target coverage (% of bases covered at ≥30X) when run on a NovaSeq 6000 system. For both designs, we followed the KAPA HyperCap Workflow v3.0 starting from 100 ng of NA12891 DNA. Metrics are average of six replicates of single captures per design.
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KAPA HyperChoice Probes by maximum target size Rxn size range
KAPA HyperChoice MAX 0.5Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000
KAPA HyperChoice MAX 3Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperChoice MAX 5Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperChoice MAX 20Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperChoice MAX 40Mb 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperChoice MAX 60Mb 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperChoice MAX 200Mb 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
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KAPA HyperExplore Probes by maximum target size Rxn size range
KAPA HyperExplore MAX 0.5Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000
KAPA HyperExplore MAX 3Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperExplore MAX 5Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperExplore MAX 20Mb 12, 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperExplore MAX 40Mb 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperExplore MAX 60Mb 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
KAPA HyperExplore MAX 200Mb 24, 96, 192, 384, 768, 1152, 1536, 4000, 10000, 20000, 50000, 100000
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