- 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, ... [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
- DOI
- 10.7924/r4rn36833
- Subject
- Publication Date
- September 29, 2020
- ARK
- ark:/87924/r4rn36833
- Is Replaced By
- 10.7924/r4bk1j35s
- Affiliation
- Publisher
- Type
- Related Materials
- Funding Agency
- NIH
- DARPA
- Grant Number
- R35GM122465
- DK119795
- W911NF1920111
- Contact
- Xiling Shen; xiling.shen@duke.edu
- Title
- Data from: The cancer microbiome atlas (TCMA): A pan-cancer comparative analysis to distinguish organ-associated microbiota from contaminants
- Repository
Thumbnail | Title | Date Uploaded | Visibility | Actions |
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README.txt | 2020-09-29 | Download | ||
bacteria.WGS.blood.case.clr.txt | 2020-09-29 | Download | ||
bacteria.WGS.blood.case.relabund.txt | 2020-09-29 | Download | ||
bacteria.WGS.blood.file.reads.txt | 2020-09-29 | Download | ||
bacteria.WGS.blood.sample.clr.txt | 2020-09-29 | Download | ||
bacteria.WGS.blood.sample.relabund.txt | 2020-09-29 | Download | ||
bacteria.WGS.solid.case.clr.txt | 2020-09-29 | Download | ||
bacteria.WGS.solid.case.relabund.txt | 2020-09-29 | Download | ||
bacteria.WGS.solid.file.reads.txt | 2020-09-29 | Download | ||
bacteria.WGS.solid.sample.clr.txt | 2020-09-29 | Download |
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 |