An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma
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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
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- “Objective response” was 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
- Statistical test
- LEfSe
- 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
Source: Figure 3a
Description: Figure 3 Compositional differences in baseline gut microbiome. The differentially abundant taxa in the baseline gut microbiome were analyzed with linear discriminate analysis coupled with effect size measurements (LEfSe) projected with a histogram. The length indicates the effect size associated with a taxon. LDA > 3 in the baseline 16S rRNA sequencing cohort were considered statistically different.
Abundance in Group 1: increased abundance in Responders to Immune checkpoint inhibitors
| NCBI | Links |
|---|---|
| Succinivibrio ⚠ | |
| Tyzzerella |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 3a
Description: Figure 3 Compositional differences in baseline gut microbiome. The differentially abundant taxa in the baseline gut microbiome were analyzed with linear discriminate analysis coupled with effect size measurements (LEfSe) projected with a histogram. The length indicates the effect size associated with a taxon. LDA > 3 in the baseline 16S rRNA sequencing cohort and LDA >2 in the baseline shotgun whole-genome sequencing subset were considered statistically different. (A) R (responders; green) vs NR (nonresponders; red);
Abundance in Group 1: decreased abundance in Responders to Immune checkpoint inhibitors
| NCBI | Links |
|---|---|
| Peptostreptococcaceae | |
| Verrucomicrobiota | |
| Verrucomicrobiae | |
| Akkermansia | |
| Akkermansiaceae | |
| Verrucomicrobiales |
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Disease control with Immune checkpoint inhibitors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Disease control with Immune checkpoint inhibitors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- “disease control” was defined as objective response or stable disease lasting =16 weeks.” Objective response was 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
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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
Source: Figure 3a
Description: Figure 3 Compositional differences in baseline gut microbiome. The differentially abundant taxa in the baseline gut microbiome were analyzed with linear discriminate analysis coupled with effect size measurements (LEfSe) projected with a histogram. The length indicates the effect size associated with a taxon. LDA > 3 in the baseline 16S rRNA sequencing cohort were considered statistically different.
Abundance in Group 1: increased abundance in Disease control with Immune checkpoint inhibitors
Revision editor(s): Mary Bearkland, Aiyshaaaa
Signature 2
Source: Figure 3a
Description: Figure 3 Compositional differences in baseline gut microbiome. The differentially abundant taxa in the baseline gut microbiome were analyzed with linear discriminate analysis coupled with effect size measurements (LEfSe) projected with a histogram. The length indicates the effect size associated with a taxon. LDA > 3 in the baseline 16S rRNA sequencing cohort were considered statistically different.
Abundance in Group 1: decreased abundance in Disease control with Immune checkpoint inhibitors
| NCBI | Links |
|---|---|
| Faecalibacterium |
Revision editor(s): Mary Bearkland
Experiment 3
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- “Objective response” was 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
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3a
Description: Figure 3 Compositional differences in baseline gut microbiome. The differentially abundant taxa in the baseline gut microbiome were analyzed with linear discriminate analysis coupled with effect size measurements (LEfSe) projected with a histogram. The length indicates the effect size associated with a taxon. LDA >2 in the baseline shotgun whole-genome sequencing subset were considered statistically different.
Abundance in Group 1: decreased abundance in Responders to Immune checkpoint inhibitors
| NCBI | Links |
|---|---|
| Alloprevotella | |
| Alloprevotella sp. |
Revision editor(s): Mary Bearkland
