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Updated: Sep 14, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Low-amplitude copy number gains shape cancer through known and novel oncogenes with associated therapeutic

Thomas F Eleveld1, Bauke Ylstra2, Leendert H J Looijenga1,3

  • 1Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.

Nucleic Acids Research
|July 22, 2025
PubMed

Insights

Large chromosomal copy number gains in cancer are driven by oncogenes. Analyzing these gains reveals new cancer-driving genes and links them to drug sensitivity, advancing precision oncology.

Area of Science:

  • Genomics
  • Cancer Biology
  • Precision Oncology

Background:

  • Large chromosomal copy number gains are common in cancer but the specific genes driving their advantage are not well understood.
  • This limits their clinical utility for diagnosis and treatment strategies.

Purpose of the Study:

  • To identify genes mediating the selective advantage of copy number gains in cancer.
  • To explore the relationship between copy number gains, oncogenes, and drug sensitivity/resistance.
  • To assess the potential of copy number gains as clinical biomarkers.

Main Methods:

  • Analysis of pan-cancer datasets for copy number patterns.
  • Utilized CRISPR screening data to identify mediating genes.
  • Correlated copy number gains with drug sensitivity and resistance data.

Main Results:

  • Copy number gains are largely driven by known oncogenes.
  • Identified 101 genes mediating copy number gain effects, including novel cancer-associated genes.
  • Found associations between specific copy number gains and drug sensitivity, particularly for oncogene inhibitors.

Conclusions:

  • Large copy number gains confer selective advantage through both known and novel oncogenes.
  • Systematic analysis of copy number gains can identify potential therapeutic targets and biomarkers.
  • This approach holds promise for advancing precision oncology.

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