|   Application Note, Article

Improving data quality and turnaround times

High-quality capture libraries from FFPE samples.

Formalin-fixed paraffin-embedded (FFPE) tissue is an important source of DNA for cancer genomic studies and clinical diagnostics. High-throughput targeted next-generation sequencing (NGS) of FFPE DNA can help optimise patient care to a great extent. A major challenge however, is the ability to process samples of variable quality with predictable success rates and within competitive turnaround times.1

To improve success rates and turnaround times, the Centre for Molecular Pathology at the Royal Marsden Hospital in the UK adopted the KAPA HyperPlus Kit in their targeted sequencing workflows. This kit, with integrated enzymatic fragmentation, streamlines the SeqCap EZ Target Enrichment workflow, yielding high-quality libraries.2,3,4

After the implementation of the KAPA HyperPlus Kit, the Centre for Molecular Pathology evaluated its experiences. Researchers found that by using the KAPA HyperPlus Kit in targeted sequencing assays, employing a small, custom SeqCap EZ Choice target enrichment panel, they could significantly improve both the turnaround time and the FFPE library quality.

  • Their most important results of the HyperPlus workflow were:
    It outperformed the existing workflow in all evaluation metrics, and there were notable improvements for the FFPE samples.
  • It eliminated the process bottleneck of mechanical fragmentation of DNA, which was previously time consuming and labor intensive.
  • The HyperPlus Kit enabled a significant increase in coverage depth for FFPE samples. This is critical for the accurate detection of rare somatic variations.
  • It produced libraries that were functionally equivalent to those produced with the previous results.

Would you like to read the full report of this evaluation? You can download it here.

For research use only. Not for use in diagnostics procedures.

References

Miller B, et al. (2015). KAPA HyperPlus—A Single-tube NGS Library Prep Workflow Integrating Enzymatic Fragmentation Results in High Yields and Low Sequencing Bias. Kapa Biosystems Poster A064.

Walker B (2015). Covaris Targeted Capture of DNA Using KAPA HyperPrep Kit and NimbleGenTM Baits, version 1.0. Royal Marsden index number SMD72.

Walker B (2015). Targeted Capture of DNA Using KAPA HyperPlus Kit and NimbleGen Baits, version 2.0. Royal Marsden index number SMD74.

KAPA HyperPlus Technical Data Sheet. Kapa Biosystems document number KR1145.

Burgess D, et al. (2012). Double Capture: An Alternative Protocol for Sequence Capture of Difficult Targets. Roche® NimbleGen Technical Note 06870406 001.

SeqCap EZ Library SR User’s Guide, v5.0 (2014). Roche NimbleGen document number 06588786 001.