Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Squamous cell carcinoma carcinoma, squamous cell, malignant,epidermoid carcinoma,epidermoid cell cancer,malignant epidermoid cell neoplasm,malignant epidermoid cell tumor,malignant squamous cell neoplasm,malignant squamous cell tumor,squamous carcinoma,squamous cell cancer,squamous cell carcinoma,squamous cell carcinoma (morphologic abnormality),squamous cell carcinoma NOS (morphologic abnormality),squamous cell epithelioma,Squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pharynx cancer cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histologically confirmed incident HNSCC involving the pharynx
- Group 0 sample size Number of subjects in the control (unexposed) group
- 254
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, date, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol drinking, sex, smoking status
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Table 2, Supplementary Table 6, Text
Description: Differential microbial abundance between controls and pharynx cancer patients
Abundance in Group 1: decreased abundance in Pharynx cancer cases
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces oris | ||
| Betaproteobacteria | ||
| Corynebacterium | ||
| Kingella | ||
| Neisseriales | ||
| Veillonella denticariosi |
Revision editor(s): Claregrieve1, WikiWorks
