Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer/Experiment 2
From BugSigDB
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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Head and neck squamous cell carcinoma carcinoma of the head and neck,craniocervical region squamous cell carcinoma,head and neck squamous cell carcinoma,HNSCC,SCCHN,squamous cell carcinoma of head and neck,squamous cell carcinoma of the head and neck,squamous cell carcinoma, head and neck,squamous cell carcinomas of head and neck,Head and neck squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Head and neck squamous cell cancer (HNSCC) participants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Case participants with Head and neck squamous cell cancer (HNSCC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 458
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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, time, race, sex, Matched on: "cohort" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.cohort
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, ethnic group, race, sex, smoking status, Confounders controlled for: "number of cigarettes consumption per day" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.number of cigarettes consumption per day, Confounders controlled for: "grams of ethanol consumption per day" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.grams of ethanol consumption per day, Confounders controlled for: "alcohol consumption status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.alcohol consumption status, Confounders controlled for: "oral HPV-16 status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.oral HPV-16 status
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: eTable 4
Description: Associations between bacteria species and risk of overall and site-specific Head and Neck squamous cell cancer (HNSCC)
Abundance in Group 1: increased abundance in Head and neck squamous cell cancer (HNSCC) participants
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter curvus | ||
| Schleiferilactobacillus harbinensis | ||
| Streptobacillus moniliformis | ||
| Treponema medium | ||
| Capnocytophaga sp. oral taxon 338 |
Revision editor(s): Tosin
Signature 2
Source: eTable 4
Description: Associations between bacteria species and risk of overall and site-specific Head and Neck squamous cell cancer (HNSCC)
Abundance in Group 1: decreased abundance in Head and neck squamous cell cancer (HNSCC) participants
Revision editor(s): Tosin
