Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer
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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
- South Korea
- 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
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to platinum-based neoadjuvant chemotherapy Response to platinum-based neoadjuvant chemotherapy,response to platinum-based neoadjuvant chemotherapy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) responders
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-nCRT (Post-neoadjuvant chemoradiotherapy) responders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who responded post-neoadjuvant chemoradiotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3A
Description: Cladogram of differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) in responders
Abundance in Group 1: increased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy) responders
NCBI | Quality Control | Links |
---|---|---|
Betaproteobacteria |
Revision editor(s): Tosin
Signature 2
Source: Figure 3A
Description: Cladogram of differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) in responders
Abundance in Group 1: decreased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy) responders
NCBI | Quality Control | Links |
---|---|---|
Bacteroidia | ||
Bacteroidota |
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) non- responders
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-nCRT (Post-neoadjuvant chemoradiotherapy) non- responders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who did not respond, post-neoadjuvant chemoradiotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3A
Description: Cladogram of differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) in non-responders
Abundance in Group 1: increased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy) non- responders
NCBI | Quality Control | Links |
---|---|---|
Alphaproteobacteria | ||
Betaproteobacteria | ||
Gammaproteobacteria | ||
Pseudomonadota |
Revision editor(s): Tosin
Signature 2
Source: Figure 3A
Description: Cladogram of differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) in non-responders
Abundance in Group 1: decreased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy) non- responders
NCBI | Quality Control | Links |
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Bacillota | ||
Bacteroidia | ||
Bacteroidota | ||
Clostridia | ||
Deinococci | ||
Deinococcus_ThermusDeinococcus_Thermus |
Revision editor(s): Tosin
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-nCRT (Pre-neoadjuvant chemoradiotherapy)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-nCRT (Post-neoadjuvant chemoradiotherapy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients during post-neoadjuvant chemoradiotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3A
Description: Differentially abundant taxa before and after nCRT: red nodes indicate increased abundance post-nCRT; green nodes show decreased abundance
Abundance in Group 1: increased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy)
Revision editor(s): Tosin
Signature 2
Source: Figure 3A
Description: Differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) : red nodes indicate increased abundance post-nCRT (Neo-adjuvant chemoradiotherapy) : green nodes show decreased abundance
Abundance in Group 1: decreased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy)
NCBI | Quality Control | Links |
---|---|---|
Aeromonadaceae | ||
Aeromonadales | ||
Aeromonas | ||
Alloprevotella | ||
Bacteroidaceae | ||
Bacteroidales | ||
Bacteroides | ||
Eubacteriales | ||
Lachnospiraceae | ||
Prevotella | ||
Prevotellaceae |
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Non-responders
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Responders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer within Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) samples
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Signature 1
Source: Figure 3B and 3C
Description: Heatmap and relative abundance of pre-nCRT (pre-neoadjuvant chemoradiotherapy) microbiome composition at family and genera level. R, responder; NR, non-responder.
Abundance in Group 1: increased abundance in Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Responders
NCBI | Quality Control | Links |
---|---|---|
Lachnospiraceae | ||
Oscillospiraceae | ||
Ruminococcus | ||
Roseburia | ||
Lachnospira | ||
Faecalibacterium |
Revision editor(s): Tosin
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Post-nCRT (Post-neoadjuvant chemoradiotherapy) Non-responders
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-nCRT (Post-neoadjuvant chemoradiotherapy) Responders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients during Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer within Post-nCRT (Post-neoadjuvant chemoradiotherapy) samples
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3D and 3E
Description: Heatmap and relative abundance of post-nCRT (post-neoadjuvant chemoradiotherapy) microbiome composition at family and genera level. R, responder; NR, non-responder.
Abundance in Group 1: decreased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy) Responders
NCBI | Quality Control | Links |
---|---|---|
Corynebacteriaceae | ||
Corynebacterium | ||
Enterobacter | ||
Enterobacteriaceae | ||
Mycobacteriaceae | ||
Mycobacterium | ||
Pseudomonadaceae | ||
Pseudomonas |
Revision editor(s): Tosin