An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23
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
- Hepatocellular carcinoma adult hepatoma,adult primary hepatocellular carcinoma,cancer, hepatocellular,carcinoma of liver,carcinoma of liver cells,carcinoma of the liver cells,carcinoma, hepatocellular, malignant,HCC,hepatoblastoma,hepatoblastoma caused by somatic mutation,hepatocellular adenocarcinoma,hepatocellular cancer,hepatocellular carcinoma,hepatoma,liver and intrahepatic bile duct carcinoma,liver cancer,liver carcinoma,liver cell cancer (hepatocellular carcinoma),liver cell carcinoma,primary carcinoma of liver cells,primary carcinoma of the liver cells,Hepatocellular carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders to Immune checkpoint inhibitors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders to Immune checkpoint inhibitors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who responded to ICI therapy, defined as complete or partial response per Response Evaluation Criteria in Solid Tumors (RECIST) v.1.1.
- 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
- 10
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).
- relative abundances
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23
Source: Figure 3a
Description: Differential microbial abundance in baseline gut microbiome between responders and nonresponders
Abundance in Group 1: increased abundance in Responders to Immune checkpoint inhibitors
| NCBI | Quality Control | Links |
|---|---|---|
| Succinivibrio | ||
| Tyzzerella |
Revision editor(s): Mary Bearkland, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23
Source: Figure 3a
Description: Differential microbial abundance in baseline gut microbiome between responders and nonresponders
Abundance in Group 1: decreased abundance in Responders to Immune checkpoint inhibitors
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Akkermansiaceae | ||
| Peptostreptococcaceae | ||
| Verrucomicrobiae | ||
| Verrucomicrobiales | ||
| Verrucomicrobiota |
Revision editor(s): Mary Bearkland, Claregrieve1
