Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
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
Experiment 2
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- Larynx 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 larynx
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol drinking, sex, smoking status
Signature 1
Source: Table 2, Supplementary Table 6, Text
Description: Differential microbial abundance between controls and larynx cancer patients
Abundance in Group 1: decreased abundance in Larynx cancer cases
NCBI | Quality Control | Links |
---|---|---|
Abiotrophia | ||
Betaproteobacteria | ||
Capnocytophaga | ||
Corynebacterium | ||
Kingella | ||
Kingella denitrificans | ||
Neisseria | ||
Neisseriales | ||
Streptococcus sanguinis |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Signature 1
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
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oral cavity 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 oral cavity
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2, Supplementary Table 6, Text
Description: Differential microbial abundance between controls and oral cavity cancer patients
Abundance in Group 1: increased abundance in Oral cavity cancer cases
NCBI | Quality Control | Links |
---|---|---|
Actinomyces |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table 2, Supplementary Table 6, Text
Description: Differential microbial abundance between controls and oral cavity cancer patients
Abundance in Group 1: decreased abundance in Oral cavity cancer cases
NCBI | Quality Control | Links |
---|---|---|
Neisseria sicca | ||
Parvimonas micra |
Revision editor(s): Claregrieve1, WikiWorks