Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer
-
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. 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
- Colorectum Colorectum,colorectum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Average-Onset Colorectal Cancer(aoCRC)(tumor tissue)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Young-Onset Colorectal Cancer(yoCRC)(tumor tissue)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor tissue of patients diagnosed with colorectal cancer before the age of 50 years
- Group 0 sample size Number of subjects in the control (unexposed) group
- 140
- Group 1 sample size Number of subjects in the case (exposed) group
- 136
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Random Forest Analysis
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- race, sex, smoking status, Confounders controlled for: "aspirin use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.aspirin use, Confounders controlled for: "tumor location" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tumor location, Confounders controlled for: "tumor stage" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tumor stage, Confounders controlled for: "neoadjuvant treatment" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.neoadjuvant treatment
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table 2
Description: Relative abundance (%) between yoCRC and aoCRC tumor tissue
Abundance in Group 1: increased abundance in Young-Onset Colorectal Cancer(yoCRC)(tumor tissue)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroides |
Revision editor(s): Adenike Awotunde
Signature 2
Source: Table 2
Description: Relative abundance (%) between yoCRC and aoCRC tumor tissue.
Abundance in Group 1: decreased abundance in Young-Onset Colorectal Cancer(yoCRC)(tumor tissue)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Enterococcus | ||
| Escherichia/Shigella sp. | ||
| Fusobacterium | ||
| Lactobacillus | ||
| Listeria | ||
| Parabacteroides | ||
| Pseudomonas | ||
| Salmonella | ||
| Staphylococcus | ||
| Alistipes |
Revision editor(s): Adenike Awotunde
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Average-Onset Colorectal Cancer(aoCRC)(Adjacent non-malignant tissue)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Young-Onset Colorectal Cancer(yoCRC) (Adjacent non-malignant tissue)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adjacent non malignant(normal) tissue of patients diagnosed with colorectal cancer before the age of 50 years.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table 2
Description: Relative abundance (%) between yoCRC and aoCRC adjacent non-malignant tissue.
Abundance in Group 1: increased abundance in Young-Onset Colorectal Cancer(yoCRC) (Adjacent non-malignant tissue)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Adenike Awotunde
Signature 2
Source: Table 2
Description: Relative abundance (%) between yoCRC and aoCRC adjacent non-malignant tissue.
Abundance in Group 1: decreased abundance in Young-Onset Colorectal Cancer(yoCRC) (Adjacent non-malignant tissue)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Alistipes | ||
| Bacillus | ||
| Enterococcus | ||
| Escherichia/Shigella sp. | ||
| Fusobacterium | ||
| Lactobacillus | ||
| Listeria | ||
| Parabacteroides | ||
| Pseudomonas | ||
| Salmonella | ||
| Staphylococcus |
Revision editor(s): Adenike Awotunde
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Small-sized colorectal cancer tumors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Large-sized colorectal cancer tumors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor samples from patients whose colorectal tumors are classified as large in size
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Linear Regression
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4A
Description: Correlation analysis of yoCRC and aoCRC tumors depicting the linear association between specific microbial genera and tumor size
Abundance in Group 1: increased abundance in Large-sized colorectal cancer tumors
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium |
Revision editor(s): Adenike Awotunde
Signature 2
Source: Figure 4A
Description: Correlation analysis of yoCRC and aoCRC tumors depicting the linear association between specific microbial genera and tumor size
Abundance in Group 1: decreased abundance in Large-sized colorectal cancer tumors
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Adenike Awotunde
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Short overall survival in yoCRC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Long overall survival in yoCRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Young-onset colorectal cancer patients with longer overall survival.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4B
Description: Correlation analysis of yoCRC tumors depicting the linear association between specific microbial genera and overall survival
Abundance in Group 1: increased abundance in Long overall survival in yoCRC
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Adenike Awotunde
Signature 2
Source: Figure 4B
Description: Correlation analysis of yoCRC tumors depicting the linear association between specific microbial genera and overall survival.
Abundance in Group 1: decreased abundance in Long overall survival in yoCRC
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium |
Revision editor(s): Adenike Awotunde
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colon tumors in yoCRC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rectal tumors in yoCRC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rectal tumors in patients with Young-onset colorectal cancer.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Supplemental Table S1
Description: Microbial taxa associated with tumor location in yoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.
Abundance in Group 1: increased abundance in Rectal tumors in yoCRC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium |
Revision editor(s): Adenike Awotunde
Signature 2
Source: Supplemental Table S1
Description: Microbial taxa associated with tumor location in yoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.
Abundance in Group 1: decreased abundance in Rectal tumors in yoCRC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Adenike Awotunde
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colon tumors in aoCRC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rectal tumors in aoCRC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rectal tumors in patients with Average-onset colorectal cancer
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Supplemental Table S1
Description: Microbial taxa associated with tumor location in aoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.
Abundance in Group 1: increased abundance in Rectal tumors in aoCRC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium |
Revision editor(s): Adenike Awotunde
Signature 2
Source: Supplemental Table S1
Description: Microbial taxa associated with tumor location in aoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.
Abundance in Group 1: decreased abundance in Rectal tumors in aoCRC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Adenike Awotunde
