The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers/Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-17

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

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 ControlLinks
Paludibacter
Corynebacterium
Porphyromonas
Actinomyces
Actinobacillus
Capnocytophaga
Fusobacterium
Aggregatibacter
Lautropia

Revision editor(s): WikiWorks