ArticleMicrobiome2017
Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.
Article in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 87 citations in OpenAlex.
- Setting higher standards for reports of microbial species in human cancers.Nature cancer · 2026Review
- Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations.Nature communications · 2025Article
- Dissecting the role of gut microbiota heterogeneity in the onset of chronic lung diseases.AMB Express · 2025Article
- Altered Bacteria Abundance Is Associated With Outcomes in Head and Neck Squamous Cell Carcinoma.Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2025Article
- Article
- The Role of Gut Microbiome on Glioblastoma Oncogenesis and Malignant Evolution.International journal of molecular sciences · 2025Review
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Anthocyanins from pomegranate peel (Heliyon · 2024Article
- The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour.Heliyon · 2024Article
- Robustness of cancer microbiome signals over a broad range of methodological variation.Oncogene · 2024Article
- Nine-Gene Prognostic Signature Related to Gut Microflora for Predicting the Survival in Gastric Cancer Patients.The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology · 2024Article
- Article
- Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes.ISME communications · 2023Article
- Identifying a locus in super-enhancer and its resident NFE2L1/MAFG as transcriptional factors that drive PD-L1 expression and immune evasion.Oncogenesis · 2023Article
- Environmental insults and compensative responses: when microbiome meets cancer.Discover oncology · 2023Review
- Exploring breast tissue microbial composition and the association with breast cancer risk factors.Breast cancer research : BCR · 2023Article
- Intratumour microbiome of pancreatic cancer.World journal of gastrointestinal oncology · 2023Review
- Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data.Genome medicine · 2023Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundA variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome.
resultsThrough careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples.
conclusionsThis approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.