The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M, Punyadeera C
Journal
Frontiers in cellular and infection microbiology
Year
2018
Keywords:
biomarker, oral cancer, oral microbiome, oral rinse, saliva
The oral microbiome can play a role in the instigation and progression of oral diseases that can manifest into other systemic conditions. These associations encourage the exploration of oral dysbiosis leading to the pathogenesis of cancers. In this study, oral rinse was used to characterize the oral microbiome fluctuation associated with oral cavity cancer (OCC) and oropharyngeal cancers (OPC). The study cohort consists of normal healthy controls (n = 10, between 20 and 30 years of age; n = 10, above 50 years of age), high-risk individuals (n = 11, above 50 years of age with bad oral hygiene and/or oral diseases) and OCC and OPC patients (n = 31, HPV-positive; n = 21, HPV-negative). Oral rinse samples were analyzed using 16S rRNA gene amplicon sequencing on the MiSeq platform. Kruskal-Wallis rank test was used to identify genera associated with OCC and OPC. A logistic regression analysis was carried out to determine the performance of these genera as a biomarker panel to predict OCC and OPC. In addition, a two-fold cross-validation with a bootstrap procedure was carried out in R to investigate how well the panel would perform in an emulated clinical scenario. Our data indicate that the oral microbiome is able to predict the presence of OCC and OPC with sensitivity and specificity of 100 and 90%, respectively. With further validation, the panel could potentially be implemented into clinical diagnostic and prognostic workflows for OCC and OPC.
Experiment 1
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
- High-risk individuals
- 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
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
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 1
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 |
|---|---|---|
| Paludibacter | ||
| Corynebacterium | ||
| Porphyromonas | ||
| Actinomyces | ||
| Actinobacillus | ||
| Capnocytophaga | ||
| Fusobacterium | ||
| Aggregatibacter | ||
| Lautropia |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Healthy Controls
- 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
Statistical Analysis
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 |
Revision editor(s): WikiWorks
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