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A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer

Mamoru Kato1, Hiromi Nakamura2, Momoko Nagai1

  • 1Department of Bioinformatics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan.

Genome Medicine
|June 9, 2018
PubMed

Insights

A new computational tool, cisCall, accurately detects DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples. This breakthrough facilitates clinical sequencing and molecularly targeted drug prescription in cancer diagnostics.

Area of Science:

  • Genomic Medicine
  • Computational Biology
  • Cancer Diagnostics

Background:

  • Advanced cancer genomics utilizes next-generation sequencing for identifying DNA alterations and guiding targeted therapies.
  • Clinical sequencing faces challenges with formalin-fixed paraffin-embedded (FFPE) samples, lacking accurate computational tools for DNA alteration detection.
  • Accurate detection of genetic mutations in FFPE tissues is crucial for personalized cancer treatment.

Purpose of the Study:

  • To develop a computational tool for precise detection of various DNA alterations in FFPE samples.
  • To address the limitations of existing tools in analyzing FFPE-derived genomic data.
  • To enhance the utility of FFPE samples in clinical cancer genomics.

Main Methods:

  • Development of a novel computational tool, cisCall, specifically designed for FFPE sample analysis.
  • Implementation of multilayer noise filters to improve accuracy and sensitivity in DNA alteration detection.
  • Validation using orthogonal technologies on tumor-unmatched normal samples to assess performance.

Main Results:

  • cisCall accurately detects single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples.
  • The tool's multilayer noise filters effectively reduce inherent noise while maintaining high sensitivity.
  • Performance evaluation confirmed the tool's reliability for clinical applications.

Conclusions:

  • cisCall is a valuable computational tool for accurate DNA alteration detection in FFPE samples.
  • The tool is expected to significantly facilitate routine clinical sequencing and molecularly targeted drug prescription.
  • cisCall is available to the research and clinical community at https://www.ciscall.org.

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