Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study
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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
- United States of America
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- pancreatic carcinoma cancer of pancreas,cancer of the pancreas,carcinoma of exocrine pancreas,carcinoma of pancreas,carcinoma of the pancreas,exocrine cancer,exocrine pancreas carcinoma,exocrine pancreatic carcinoma,pancreas cancer,pancreas carcinoma,pancreatic cancer,pancreatic cancer (not islets),pancreatic carcinoma,pancreatic carcinoma, familial
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pancreatic cancer cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects from the two cohorts with incident primary pancreatic adenocarcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 371
- Group 1 sample size Number of subjects in the case (exposed) group
- 361
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Logistic Regression
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, race, date
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body mass index, race, diabetes mellitus, smoking status, alcohol drinking
Signature 1
Source: Table 3
Description: Differential microbial abundance between controls and pancreatic cancer cases
Abundance in Group 1: increased abundance in pancreatic cancer cases
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella | ||
Bacteroidota |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table 3
Description: Differential microbial abundance between controls and pancreatic cancer cases
Abundance in Group 1: decreased abundance in pancreatic cancer cases
NCBI | Quality Control | Links |
---|---|---|
Fusobacteriota | ||
Fusobacteriales | ||
Fusobacteriia | ||
Leptotrichia | ||
Leptotrichiaceae |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects from the CPSII cohorts with incident primary pancreatic adenocarcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 170
- Group 1 sample size Number of subjects in the case (exposed) group
- 170
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, race, body mass index, smoking status, alcohol drinking, diabetes mellitus
Signature 1
Source: Supplementary Table 3a
Description: Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort
Abundance in Group 1: decreased abundance in pancreatic cancer cases
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella | ||
Fusobacteriota | ||
Fusobacteriales | ||
Fusobacteriia | ||
Leptotrichia | ||
Leptotrichiaceae |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects from the PLCO cohorts with incident primary pancreatic adenocarcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 201
- Group 1 sample size Number of subjects in the case (exposed) group
- 191
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 3b
Description: Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort
Abundance in Group 1: decreased abundance in pancreatic cancer cases
NCBI | Quality Control | Links |
---|---|---|
Leptotrichia | ||
Leptotrichiaceae |
Revision editor(s): Claregrieve1, WikiWorks