The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-4-10
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
- Gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer,Gastric cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders (gastric cancer)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders (gastric cancer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with gastric 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
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- 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. 3D, Supp. Table S9
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients
Abundance in Group 1: increased abundance in Responders (gastric cancer)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella_9Prevotella_9 | ||
| Bifidobacterium | ||
| Prevotella_2Prevotella_2 | ||
| Lachnospira | ||
| Bacteroides | ||
| Ruminococcaceae bacterium UCG-005 | ||
| Agathobacter |
Revision editor(s): Scholastica
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-4-9
Source: Fig. 3D, Supp. Table S9
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients
Abundance in Group 1: decreased abundance in Responders (gastric cancer)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Bacteroides | ||
| Bifidobacterium | ||
| Butyricimonas | ||
| Megamonas | ||
| uncultured Lachnospiraceae bacterium |
Revision editor(s): Scholastica
