The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-4-9
Subjects
- Location of subjects
- China
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Digestive System Carcinoma carcinoma of digestive system,carcinoma of the gastrointestinal system,digestive system carcinoma,gastrointestinal carcinoma,gastrointestinal carcinoma (disease),gastrointestinal system carcinoma,Digestive System Carcinoma,digestive System Carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders to anti–PD-1/PD-L1 immunotherapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders to anti–PD-1/PD-L1 immunotherapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with stage 3 or stage 4 gastrointestinal cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Zero-Inflated Negative Binomial 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
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-4-9
Source: Fig. 3A, Supp. Table S6
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer
Abundance in Group 1: increased abundance in Responders to anti–PD-1/PD-L1 immunotherapy
Revision editor(s): Hamza, Scholastica
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-4-9
Source: Fig. 3A, Supp. Table S6
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer
Abundance in Group 1: decreased abundance in Responders to anti–PD-1/PD-L1 immunotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Catenibacterium | ||
| Hungatella | ||
| Ruminococcus_2Ruminococcus_2 | ||
| Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group | ||
| uncultured Oscillospiraceae bacterium |
Revision editor(s): Hamza, Scholastica
