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

49 files (164 MB)

Data Citation

• Dohlman, A., Arguijo Mendoza, D., Ding, S., Gao, M., Dressman, H., Iliev, I., Lipkin, S., & Shen, X. (2020). Data from: The cancer microbiome atlas (TCMA): A pan-cancer comparative analysis to distinguish organ-associated microbiota from contaminants. Duke Research Data Repository. https://doi.org/10.7924/r4rn36833

Creator

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

DOI

• 10.7924/r4rn36833

Subject

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

Publication Date

• September 29, 2020

ARK

• ark:/87924/r4rn36833

Is Replaced By

• 10.7924/r4bk1j35s

Affiliation

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

Publisher

• Duke Research Data Repository

Type

• Dataset

Format

• TXT
• RDS

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
• Users can explore the TCMA database here:  https://tcma.pratt.duke.edu

Funding Agency

• NIH
• DARPA

Grant Number

• R35GM122465
• DK119795
• W911NF1920111

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 contaminants

License

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

Repository

• Duke Research Data Repository

• Files
• Readme

Thumbnail	Title	Date Uploaded	Visibility	Actions
	metadata.WXS.solid.case.txt	2020-09-29	Public	Download
	metadata.WXS.solid.file.txt	2020-09-29	Public	Download
	metadata.WXS.solid.sample.txt	2020-09-29	Public	Download
	physeq.WGS.blood.case.clr.rds	2020-09-29	Public	Download
	physeq.WGS.blood.case.relabund.rds	2020-09-29	Public	Download
	physeq.WGS.blood.file.reads.rds	2020-09-29	Public	Download
	physeq.WGS.blood.sample.clr.rds	2020-09-29	Public	Download
	physeq.WGS.blood.sample.relabund.rds	2020-09-29	Public	Download
	physeq.WGS.solid.case.clr.rds	2020-09-29	Public	Download
	physeq.WGS.solid.case.relabund.rds	2020-09-29	Public	Download

View as Markdown View as Text

Versions