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Updated: Jan 22, 2026

Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
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Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors

Published on: September 20, 2016

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Detection of mutational patterns in cell-free DNA of colorectal cancer by custom amplicon sequencing

Simon Herrmann1,2,3, Tianzuo Zhan1,2,3, Johannes Betge1,2,3

  • 1Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Molecular Oncology
|June 30, 2019
PubMed

Insights

Monitoring cancer mutations using cell-free DNA (cfDNA) is challenging. This study presents a new workflow for analyzing cfDNA mutations, aiding in cancer therapy and resistance detection.

Area of Science:

  • Oncology
  • Genomics
  • Molecular Biology

Background:

  • Monitoring solid tumor mutations during cancer therapy is crucial but challenging.
  • Cell-free DNA (cfDNA) analysis offers a noninvasive method for detecting prognostic and predictive mutations.
  • The diverse mutational landscape of cancer presents a significant hurdle for cfDNA diagnostics.

Purpose of the Study:

  • To develop a flexible, end-to-end workflow for analyzing cfDNA mutations using custom amplicon sequencing.
  • To create a robust bioinformatic pipeline for identifying genetic alterations in cfDNA.
  • To apply the workflow to detect mutations in colorectal cancer patients and understand treatment resistance.

Main Methods:

  • Developed an experimental and bioinformatic workflow for cfDNA mutation analysis.
  • Utilized open-software tools for primer selection and multiplex PCR with minimal cfDNA input.
  • Designed a custom amplicon panel for hotspot mutations in colorectal cancer and analyzed serial cfDNA samples from 34 patients.

Main Results:

  • Successfully detected recurrent and patient-specific mutational patterns in the majority of advanced colorectal cancer patients.
  • Demonstrated that dynamic changes in mutant allele frequencies in cfDNA correlate with disease progression.
  • Showed that cfDNA sequencing can identify mechanisms of resistance to anti-Epidermal Growth Factor Receptor (EGFR) antibody treatment.

Conclusions:

  • The developed workflow provides a simple, customizable method for exploring genetic alterations in cfDNA.
  • This approach facilitates noninvasive monitoring of cancer mutations and resistance mechanisms.
  • cfDNA analysis holds significant potential for personalized cancer therapy and management.
Keywords:
cfDNAcolorectal cancerliquid biopsynext-generation sequencing

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