Data from: The cancer microbiome atlas (TCMA): A pan-cancer comparative analysis to distinguish organ-associated microbiota from equiprevalent contaminants

• Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated with original TCGA samples. "Mixed-evidence"species can be further distinguished by gene copy and nucleotide variants. We thus present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to discovery of prognostic species and blood signatures of mucosal barrier injuries, and enabled systematic matched microbe-host multi-omics analyses, which will help guide future studies of the microbiome's role in human health and disease. ... [Read More]

Total Size

77 files (2.14 GB)

Data Citation

• Dohlman, A., Arguijo Mendoza, D., Ding, S., Gao, M., Dressman, H., Iliyan, D., Lipkin, S., & Shen, X. (2022). Data from: The cancer microbiome atlas (TCMA): A pan-cancer comparative analysis to distinguish organ-associated microbiota from equiprevalent contaminants. Duke Research Data Repository. V2 https://doi.org/10.7924/r4bk1j35s

Creator

• Gao, Michael
• Arguijo-Mendoza, Diana
• Dressman, Holly
• Lipkin, Steven M.
• Iliev, Iliyan D.
• Dohlman, Anders B.
• Ding, Shengli
• Shen, Xiling

DOI

• 10.7924/r4bk1j35s

Subject

• Host-microbe interactions
• Human microbiome
• Colorectal cancer
• Contamination
• The Cancer Genome Atlas
• Pan-cancer
• Multi-omics

Publication Date

• August 4, 2022

ARK

• ark:/87924/r4bk1j35s

Replaces

• 10.7924/r4rn36833

Affiliation

• Duke Center for Genomic and Computational Biology
• Biomedical Engineering
• Duke Microbiome Center

Publisher

• Duke Research Data Repository

Type

• Dataset

Format

• RDS
• TXT

Related Materials

• Dohlman, A. B., Arguijo Mendoza, D., Ding, S., Gao, M., Dressman, H., Iliev, I. D., Lipkin, S. M., & Shen, X. (2021). The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host & Microbe.  https://doi.org/10.1016/j.chom.2020.12.001

Provenance

• This dataset has been updated with an improved decontamination algorithm.

Funding Agency

• DARPA
• NIH

Grant Number

• R35GM122465
• W911NF1920111
• DK119795

Contact

• Xiling Shen; xiling.shen@duke.edu

License

• Creative Commons CC0 1.0 Universal

Title

• Data from: The cancer microbiome atlas (TCMA): A pan-cancer comparative analysis to distinguish organ-associated microbiota from equiprevalent contaminants

License

• http://creativecommons.org/publicdomain/zero/1.0/

Repository

• Duke Research Data Repository

Versions

Version	DOI	Comment	Publication Date
2	10.7924/r4bk1j35s	This dataset has been updated with an improved decontamination algorithm.	2022-08-04
1	10.7924/r4rn36833		2020-09-29