Targeted Sequencing

Even with reductions in the cost-per-base of DNA sequencing, routine sequencing of large numbers of whole eukaryotic genomes is not always economically feasible. Enrichment of specific genomic regions, prior to sequencing, is an effective method for reducing sequencing costs and simplifying analysis. Targeted sequencing of large cohorts of samples is a powerful tool for the discovery and detection of disease-causing variants associated with many inherited diseases and cancers.

Hybrid capture and PCR-based methods are currently the most common methods for target-enrichment. Hybrid capture involves pools of oligonucleotide probes designed to target specific regions of interest within a fragment library. Non-specific hybrids are removed, resulting in a library enriched for the targeted DNA. Highly multiplexed PCR can also be used to generate amplicon pools for targeted sequencing. Each method has strengths and weaknesses, and the optimal strategy is often determined by the factors such as specificity, sensitivity, sample type and input, throughput, target size, turnaround time, sequencing platform and cost.

The construction of libraries with maximum molecular complexity and minimal bias is critical for targeted sequencing applications. KAPA library preparation and amplification kits utilize optimally-formulated and evolved enzymes, including KAPA HiFi DNA Polymerase, and optimized protocols to achieve superior library yields and limit amplification bias. KAPA Library Preparation and KAPA Hyper Prep Kits are compatible with the Roche® NimbleGen™ SeqCap™ EZ System, SureSelect® Target Enrichment systems from Agilent Technologies, and xGen® Lockdown® probes from IDT.

See how the KAPA Stranded RNA-Seq Kit is being used in targeted RNA-seq workflows


For Research Use Only. Not for use in diagnostic procedures.


  • FFPE Sample

    Sample QC

  • Library Preparation

    Library Preparation

  • Library Amplification

    Library Amplification

  • Hybridization

    Hybrid Capture

  • Library Amplification

    Library Amplification

  • Library Quantification


Available Products by Workflow

FFPE Sample

Sample QC

KAPA Human Genomic DNA Quantification and QC Kit

  • Reliably quantify and assess quality of low-input or FFPE samples to optimize library construction yields and workflows
Library Preparation

DNA Library Preparation

KAPA Hyper Prep Kit (Illumina®)

  • Construct high-quality libraries from FFPE and challenging samples in less than 3 hours

KAPA Library Preparation Kit (Illumina)

  • Construct high-quality libraries using an optimized “with bead” protocol to minimize bias, resulting in superior sequencing coverage and uniformity
See how the KAPA Library Preparation Kit is being used in hybridization workflows:
Roche NimbleGen SeqCap EZ and SeqCap Epi Systems
Kapa Biosystems and Roche NimbleGen have partnered to provide a best-in-class, complete workflow solution for targeted sequencing.* KAPA Library Preparation Kits improve performance for low inputs by achieving greater molecular complexity and improved sequencing results due to more uniform coverage.

*Data on file

Library Amplification

Library Amplification

KAPA Library Amplification Kits

  • Minimize PCR-induced bias of AT- and GC-rich library molecules during pre- and post-capture amplification
Library Quantification

Library Quantification

KAPA Library Quantification Kits

  • Accurately quantify adapter-ligated molecules prior to sample pooling and cluster generation for optimal sequencing results