The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers/Experiment 2
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Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Subjects
- Location of subjects
- Australia
- 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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Head and neck carcinoma carcinoma of craniocervical region,carcinoma of head and neck,carcinoma of neck,carcinoma of the head and neck,carcinoma of the neck,craniocervical region carcinoma,head and neck cancer,head and neck carcinoma,neck carcinoma,Head and neck carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- OCC & OPC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6-V8
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 1B, Supp. Table 2, Text
Description: The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers
Abundance in Group 1: decreased abundance in OCC & OPC
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia | ||
| Haemophilus | ||
| Corynebacterium | ||
| Paludibacter | ||
| Porphyromonas | ||
| Capnocytophaga |
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