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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
Needs review
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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