Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing
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.
Authors
- Aniket Chowdhury (ORCID: https://orcid.org/0000-0003-3636-0086)
- Supriya Hait (ORCID: https://orcid.org/0000-0002-3786-9960)
- Vichitra Behel (ORCID: https://orcid.org/0000-0001-6522-6033)
- Hitesh Goswami
- Sanket Desai (ORCID: https://orcid.org/0000-0002-7929-8684)
- Atul Bharde
- Jayant Khandare (ORCID: https://orcid.org/0000-0002-7301-3107)
- Vidya Veldore (ORCID: https://orcid.org/0000-0001-5989-4836)
- Anuradha Choughule (ORCID: https://orcid.org/0000-0002-9889-2136)
- Neetu Tyagi
- Pratik Chandrani (ORCID: https://orcid.org/0000-0003-2572-0189)
- Rohit Mishra (ORCID: https://orcid.org/0000-0002-1786-8872)
- Amit Dutt (ORCID: https://orcid.org/0000-0002-1119-4774)
- Bhargavi Bawaskar
- Rajiv Kumar (ORCID: https://orcid.org/0000-0003-0363-3287)
- Minit Shah (ORCID: https://orcid.org/0000-0002-0979-9555)
- Gowhar Shafi (ORCID: https://orcid.org/0000-0002-5606-800X)
- Nandini Menon (ORCID: https://orcid.org/0000-0001-6639-7563)
- Vanita Noronha
- Kumar Prabhash
- Vijay Patil
- Ganesh Dahimbekar
Institutions
- University of Delhi (IN)
- Homi Bhabha National Institute (IN)
- Tata Memorial Hospital (IN)
- Institute of Bioinformatics and Applied Biotechnology (IN)
- Advanced Centre for Treatment, Research and Education in Cancer (IN)
Publication Details
- Journal
- npj Systems Biology and Applications
- Published
- 2025-06-07
- DOI
- https://doi.org/10.1038/s41540-025-00536-8
- Primary Topic
- Gut microbiota and health
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Indian Council of Medical Research
- Advanced Centre for Treatment, Research and Education in Cancer