RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach

Gregory D. Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D. Swafford and Rob Knight ()
Additional contact information
Gregory D. Poore: University of California San Diego
Evguenia Kopylova: University of California San Diego
Qiyun Zhu: University of California San Diego
Carolina Carpenter: University of California San Diego
Serena Fraraccio: University of California San Diego
Stephen Wandro: University of California San Diego
Tomasz Kosciolek: University of California San Diego
Stefan Janssen: University of California San Diego
Jessica Metcalf: Colorado State University
Se Jin Song: University of California San Diego
Jad Kanbar: University of California San Diego
Sandrine Miller-Montgomery: University of California San Diego
Robert Heaton: University of California San Diego
Rana Mckay: University of California San Diego Health
Sandip Pravin Patel: University of California San Diego
Austin D. Swafford: University of California San Diego
Rob Knight: University of California San Diego

Nature, 2020, vol. 579, issue 7800, 567-574

Abstract: Abstract Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1–10, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas11 (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia–IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma; 100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration.

Date: 2020
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DOI: 10.1038/s41586-020-2095-1

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