Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Victoria
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
- 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
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HNSCC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)
- 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
- 129
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, smoking behavior, sex
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Table 2
Description: Differential microbial abundance between controls and HNSCC patients
Abundance in Group 1: increased abundance in HNSCC
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Table 2
Description: Differential microbial abundance between controls and HNSCC patients
Abundance in Group 1: decreased abundance in HNSCC
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria | ||
| Capnocytophaga leadbetteri | ||
| Corynebacterium | ||
| Kingella | ||
| Hoylesella nanceiensis | ||
| Selenomonas sputigena |
Revision editor(s): Claregrieve1, WikiWorks
