Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing

NPJ Syst Biol Appl. 2025 Jun 7;11(1):62. doi: 10.1038/s41540-025-00536-8.

Abstract

Microbial infections contribute to ~20% of malignancy. Plasma-derived cell-free DNA presents a promising avenue for non-invasive cancer diagnostics, capturing microbial signatures. We analyzed 261 plasma from 50 patients with lung adenocarcinoma by targeted and whole exome sequencing at 10,000 × and 340 × depth, respectively. Comparative analyses of Kraken 2 and IPD2 reveal substantial discrepancies, highlighting challenges in microbial DNA quantification and the need for stringent bioinformatics approaches to ensure accurate cancer microbiome profiling.

MeSH terms

  • Adenocarcinoma of Lung / microbiology
  • Aged
  • Computational Biology / methods
  • Exome Sequencing* / methods
  • Female
  • Humans
  • Lung Neoplasms* / blood
  • Lung Neoplasms* / genetics
  • Lung Neoplasms* / microbiology
  • Male
  • Microbiota* / genetics
  • Middle Aged