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Related Concept Videos

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Related Experiment Video

Updated: Aug 12, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal

Marcello Del Corvo1, Saveria Mazzara1, Stefano A Pileri1

  • 1Division of Haematopathology, IEO, European Institute of Oncology IRCCS, Milan 20141, Italy.

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|January 26, 2023
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Summary

We developed TOSCA, an automated tumor-only somatic variant calling workflow for accurate mutation identification without paired normal tissue. This tool provides reliable germline and somatic variant estimates comparable to paired analyses.

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Area of Science:

  • Genomics
  • Cancer Research
  • Bioinformatics

Background:

  • Accurate somatic variant classification typically requires paired normal tissue, which is not always available.
  • Tumor-only variant calling presents challenges in distinguishing somatic mutations from germline variants, limiting clinical research applications.
  • Existing in silico filtering methods lack sufficient accuracy and open-source solutions for tumor-only analysis.

Purpose of the Study:

  • To develop an automated, open-source workflow for accurate tumor-only somatic variant calling.
  • To address the limitations of current methods in the absence of paired normal tissue.
  • To provide a reliable tool for analyzing whole-exome and targeted panel sequencing data.

Main Methods:

  • Developed TOSCA, a Snakemake-based, end-to-end workflow for tumor-only somatic variant calling.
  • The workflow includes quality checks, alignment, variant calling, functional annotation, database filtering, and purity/ploidy estimation.
  • Applied TOSCA to tumor-only sequencing data.

Main Results:

  • TOSCA successfully performs automated, end-to-end analysis from raw reads to variant classification.
  • The workflow provides somatic and germline variant estimates consistent with paired tumor-normal analyses.
  • Demonstrated the utility of TOSCA for accurate variant calling in tumor-only samples.

Conclusions:

  • TOSCA is the first automated tumor-only somatic calling workflow, enhancing variant classification accuracy.
  • The freely available workflow overcomes limitations of paired-normal analysis and existing tumor-only methods.
  • TOSCA facilitates broader application of somatic variant calling in clinical research.