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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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Detection of Structural Variants in Circulating Cell-Free DNA from Sarcoma Patients Using Next Generation Sequencing.

Lauren Mc Connell1, Jana Gazdova1, Katja Beck2,3

  • 1Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast BT9 7AE, UK.

Cancers
|December 8, 2020
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) detects structural variants in circulating tumor DNA (ctDNA) from sarcoma patients. This blood test shows promise for sarcoma diagnosis and monitoring, complementing tissue analysis.

Keywords:
cell-free DNAnext generation sequencingsarcomatranslocations

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Area of Science:

  • Oncology
  • Genomics
  • Molecular Diagnostics

Background:

  • Circulating tumor DNA (ctDNA) analysis via next-generation sequencing (NGS) is increasingly used for cancer treatment stratification and monitoring.
  • Detecting structural variants (SVs) in ctDNA is challenging, particularly for sarcomas where SVs are common.

Purpose of the Study:

  • To evaluate the efficacy of a sarcoma-specific targeted NGS panel for identifying translocations and copy number variants in ctDNA.
  • To assess the concordance of SV detection between tumor tissue and cell-free DNA (cfDNA) in soft tissue sarcoma patients.

Main Methods:

  • A targeted NGS panel was developed and applied to 12 soft tissue sarcoma tissue specimens and matched plasma cfDNA samples.
  • Analysis focused on identifying translocations and copy number variants (CNVs) in both tissue and cfDNA.
  • Variant allele frequencies (VAFs) and sequencing depth were optimized for cfDNA analysis.

Main Results:

  • Structural variants were identified in 91.6% of tissue samples and 50% of plasma cfDNA samples.
  • SVs were detectable in cfDNA at VAFs >0.2% with an average sequencing depth of 1026×.
  • The study included a diverse cohort of sarcoma subtypes, such as alveolar rhabdomyosarcoma, Ewing's Sarcoma, and synovial sarcoma.

Conclusions:

  • NGS-based ctDNA analysis demonstrates clinical potential for aiding sarcoma diagnosis and monitoring.
  • Further studies with larger cohorts are warranted to validate these findings.
  • ctDNA analysis offers a minimally invasive approach for detecting genomic alterations in sarcomas.