Revisiting the cancer microbiome using PRISM DOI Creative Commons
Bassel Ghaddar, Martin J. Blaser, Subhajyoti De

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Recent controversy around the cancer microbiome highlights need for improved microbial analysis methods human genomics data. We developed PRISM, a computational approach precise microorganism identification and decontamination from low-biomass sequencing PRISM removes spurious signals achieves excellent performance when benchmarked on curated dataset of 62,006 known true- false-positive taxa. then use to detect microbes in 8 types CPTAC TCGA datasets. identify rich microbiomes gastrointestinal tract tumors bacteria subset pancreatic that are associated with altered glycoproteomes, more extensive smoking histories, higher tumor recurrence risk. find relatively sparse other TCGA, which we demonstrate may reflect differing parameters. Overall, does not replace gold-standard controls, but it enables higher-confidence analyses reveals tumor-associated microorganisms potential molecular clinical significance.

Language: Английский

Revisiting the cancer microbiome using PRISM DOI Creative Commons
Bassel Ghaddar, Martin J. Blaser, Subhajyoti De

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Recent controversy around the cancer microbiome highlights need for improved microbial analysis methods human genomics data. We developed PRISM, a computational approach precise microorganism identification and decontamination from low-biomass sequencing PRISM removes spurious signals achieves excellent performance when benchmarked on curated dataset of 62,006 known true- false-positive taxa. then use to detect microbes in 8 types CPTAC TCGA datasets. identify rich microbiomes gastrointestinal tract tumors bacteria subset pancreatic that are associated with altered glycoproteomes, more extensive smoking histories, higher tumor recurrence risk. find relatively sparse other TCGA, which we demonstrate may reflect differing parameters. Overall, does not replace gold-standard controls, but it enables higher-confidence analyses reveals tumor-associated microorganisms potential molecular clinical significance.

Language: Английский

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