A novel, end-to-end target enrichment Workflow for high-performance somatic variant analysis
Cancers are genetically complex and heterogeneous. Whilst germline (inherited) variants play a major role in 5 – 10% of all cancers, it is the somatic (acquired) variants that drive disease progression and response
to therapeutic intervention.
Targeted next-generation sequencing (NGS) is an established tool for studying the genetic basis of cancer, offering the ability to survey large numbers of targets in parallel, at high sensitivity (variant allele frequencies of 5% or less).
NGS pipelines for the analysis of somatic variants require :
- Efficient methods for the preparation of enriched libraries including cell-free/circulating tumor DNA (cf/ctDNA), formalin-fixed paraffin-embedded (FFPE) tissue samples, and total RNA.
- Relevant, optimized enrichment panels(content).
- Advanced bioinformatic tools.
In this Application Note, we demonstrate the performance and versatility of the KAPA HyperPETE technology for somatic variant analysis, achieving true positive rates of 97.9 – 100% for all major variant classes, across >450 libraries prepared from cfDNA, FFPE DNA, FFPE RNA, and reference cell line DNA and RNA samples.
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References
National Cancer Institute. The Genetics of Cancer. https://www.cancer.gov/about-cancer/causes-prevention/genetics. Accessed 22 October 2021.
Bewicke-Copley F, Arjun Kumar E, Palladino G, et al. Applications and analysis of targeted genomic sequencing in cancer studies.Comput. Struct. Biotechnol. J. 2019;17(1348–1359). doi:10.1016/j.csbj.2019.10.004.
Roche Sequencing Solutions. KAPA HyperPETE Brochure. https://sequencing.roche.com/content/dam/rochesequence/worldwide/resources/KAPA-HyperPETE-Brochure-MC–08217.pdf.
Roche Sequencing Solutions. KAPA HyperPETE Somatic Tissue DNA Workflow; Instructions for use, Version 1.0.
https://pim-eservices.roche.com/eLD/api/downloads/124d7ceb-5033-ec11-0d91-005056a71a5d?countryIsoCode=pi.
Roche Diagnostics GmbH. High Pure FFPET RNA Isolation Kit Instructions for Use, Version 06 (Content version: October 2020).
Agilent Technologies. Simplified DV200 Evaluation with the Agilent 2100 Bioanalyzer System. https://www.agilent.com/cs/library/technicaloverviews/public/5991-8287EN.pdf. Accesed 22 October 2021.
Roche Sequencing Solutions. KAPA HyperPETE Somatic Plasma cfDNA Workflow; Instructions for use, Version 1.0.
https://pim-eservices.roche.com/eLD/web/pi/en/documents/download/b616daab-a841-ec11-0d91-005056a71a5d
Roche Sequencing Solutions. KAPA HyperPETE Tissue RNA Fusion Transcript Workflow; Instructions for use, Version 1.0.
https://pim-eservices.roche.com/eLD/web/pi/en/documents/download/737ff2ff-b941-ec11-0b91-005056a772fd.
Roche Sequencing Solutions. NAVIFY® Mutation Caller, User Assistance version 1.0, Software version 1.0.
https://github.com/tidyverse/ggplot2. Accesed 22 October 2021