Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy
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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
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Epithelium of nasopharynx Epithelial tissue of nasal part of pharynx,Epithelial tissue of nasopharynx,Epithelial tissue of rhinopharynx,Epithelium of nasal part of pharynx,Epithelium of rhinopharynx,Nasal part of pharynx epithelial tissue,Nasal part of pharynx epithelium,Nasopharyngeal epithelium,Nasopharynx epithelial tissue,Nasopharynx epithelium,Rhinopharynx epithelial tissue,Rhinopharynx epithelium,Epithelium of nasopharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- nasopharyngeal neoplasm nasopharyngeal neoplasm,nasopharyngeal neoplasms,nasopharyngeal tumor,nasopharynx neoplasm,nasopharynx neoplasm (disease),nasopharynx tumor,neoplasm of nasopharynx,neoplasm of the nasopharynx,tumor of nasopharynx,tumor of the nasopharynx
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls at Baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nasopharyngeal carcinoma patients at baseline
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have not received treatment yet
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Metastats
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Table 3
Description: Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.
Abundance in Group 1: increased abundance in Nasopharyngeal carcinoma patients at baseline
NCBI | Quality Control | Links |
---|---|---|
Neisseria | ||
Leptotrichia | ||
Pseudomonas | ||
Pseudomonadota |
Revision editor(s): Andre
Signature 2
Source: Table 3
Description: Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.
Abundance in Group 1: decreased abundance in Nasopharyngeal carcinoma patients at baseline
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Bacillota |
Revision editor(s): Andre
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Nasopharyngeal carcinoma patients at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nasopharyngeal carcinoma patients after treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have received treatment after 7 or 12 months
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3
Description: Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.
Abundance in Group 1: increased abundance in Nasopharyngeal carcinoma patients after treatment
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Veillonella |
Revision editor(s): Andre
Signature 2
Source: Figure 3
Description: Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.
Abundance in Group 1: decreased abundance in Nasopharyngeal carcinoma patients after treatment
NCBI | Quality Control | Links |
---|---|---|
Prevotella | ||
Neisseria |
Revision editor(s): Andre