Gut microbiome and ICI therapy in rare cancers, Australia
107 stool samples from adult and elderly rare-cancer patients (biliary tract, adrenocortical, rare gynaecological, neuroendocrine) in Australia, studying gut microbiome association with combination immune checkpoint inhibitor drug therapy; intervention trial design. machine-written summary
107 samples · 107 runs · AU · Adult · 2024 · 6.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 211 sample values (sex, subject id) |
| ✓ Abstract / description | 109 sample values (country, health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10957475, PMC11937697, PMC13114121, PMC13173278, PMC13334858 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 530 sample values (age, antibiotic exposure, bmi, country, health condition) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population other_cancer · Combination ipilimumab and nivolumab immune checkpoint blockade in rare cancers
“patients with diverse rare cancers treated with combination ICB” — abstract:38429524 (study level; per-sample arms are in the intervention column below)
sex: sequence archive and curatedMetagenomicData disagree for 2 samples (e.g. male vs female) — withheld.
The sources disagree on 2 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (2)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA12111351 | sex | male (sequence archive) | female (curatedMetagenomicData) | withheld: neither value published |
| SAMEA12111371 | sex | female (sequence archive) | male (curatedMetagenomicData) | withheld: neither value published |
Genera, mean relative abundance over 94 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 107 | 100% | ||||
| country | 107 | 100% | 106 | 1 | ||
| health_condition | 107 | 100% | 106 | 1 | ||
| subject_id | 107 | 100% | 107 | |||
| health_condition_detail | 107 | 100% | 107 | |||
| age_at_collection_days | 106 | 99% | 106 | |||
| antibiotic_exposure | 106 | 99% | 106 | |||
| bmi | 106 | 99% | 106 | |||
| sex | 104 | 97% | 104 |
- A gut microbial signature for combination immune checkpoint blockade across cancer types. 2024 PMID 38429524 PMC10957475 unsure
- Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types. 2025 PMID 40151642 PMC11937697 unsure
- A Microbial Lipid-ATP Synthase Axis Fuels NK Cell Antitumor Activity. 2026 PMID 41972457 PMC13334858 unsure
- Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types. 2026 PMID 42026803 PMC13114121 unsure
- Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types. 2026 PMID 42146906 PMC13173278 unsure
Archive description
Combination immune checkpoint inhibitor (ICI) therapy with anti-CTLA-4 and anti-PD-1 blockade has demonstrated significant clinical activity across tumour types. Rare cancer patients have limited treatment options due to the scarcity of studies of novel treatment options, so they are often offered chemotherapies untested in their disease. ONJ2016-001/CA209-538 is a prospective, multicentre clinical trial of combination ICI (ipilimumab and nivolumab) in patients with advanced rare cancers, including biliary tract, adrenocortical, rare gynaecological and neuroendocrine cancers (https://clinicaltrials.gov/ct2/show/NCT02923934). The prespecified primary outcome measure is clinical benefit rate (complete response + partial response + stable disease >3 months) by RECIST 1.1. The prespecified secondary outcome measure is to identify common predictive biomarkers or signature in responding patient irrespective of rare tumour type. We hypothesise that the gut microbiome may be associated with cancer subtype, and may be predictive of clinical benefit to ICI in these patients with rare cancers. This study involves generation and analysis of stool DNA sequencing data, to pair with other biological and clinical data set, in order to potentially identify combinatorial biomarkers that associate with clinical benefit or other clinical efficacy / toxicity metric. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host study.description · “patients with advanced rare cancers”
- body site study.description · “generation and analysis of stool DNA sequencing”
- life stage study.description · “combination ICI (ipilimumab and nivolumab) in patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA12111276 | age_at_collection_days | 13514.25 | R2 | 0.75 | external.cmd source | age: 37; age_unit: (empty); age_group: Adult |
| SAMEA12111276 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA12111276 | bmi | 21.34 | R2 | 0.75 | external.cmd source | bmi: 21.34 |
| SAMEA12111276 | country | AU | R2 | 0.75 | external.cmd source | country: Australia |
| SAMEA12111383 | country | AU | R4 | 0.50 | study.title | Role_of_microbiome_in_rare_cancers_in_Australia |
| SAMEA12111276 | health_condition | other_cancer | R2 | 0.75 | external.cmd source | target_condition: Malignant Neoplasm |
| SAMEA12111383 | health_condition | other_cancer | R4 | 0.50 | study.description | advanced rare cancers, including biliary tract, adrenocortical |
| SAMEA12111276 | health_condition_detail | advanced rare cancers (biliary tract, adrenocortical, rare gynaecological, neuroendocrine) | R4 | 0.50 | study.description | advanced rare cancers, including biliary tract, adrenocortical, rare gynaecological and neuroendocrine cancers |
| SAMEA12111276 | sex | female | R1 | 0.90 | sample.attr.arrayexpress_sex | female |
| SAMEA12111276 | subject_id | Mib_aus11766159 | R1 | 0.85 | sample.attr.subject_id | Mib_aus11766159 |
Sequencing
107 runs over 107 samples · mean 6.29 Gbp per run (median 6.15 Gbp, total 672.59 Gbp; 107 runs with a base count) · layout PAIRED 107 · platform ILLUMINA 107 · models Illumina NovaSeq 6000 (107) · 88% of runs with a Sandpiper profile · first public 2024-01-03
Authors (62)
Gunjur A first · Shao Y · Rozday T · Klein O · Mu A · Haak BW · Markman B · Kee D · Carlino MS · Underhill C · Frentzas S · Michael M · Gao B · Palmer J · Cebon J · Behren A · Adams DJ · Lawley TD last · Cai X first · Cho JY · Chen L · Liu Y · Ji F · Salgado K · Ge S · Yang D · Yu H · Shao J · Futreal PA · Sepesi B · Gibbons D · Chen Y · Wang G · Cheng C · Wu M · Zhang J · Hsiao A · Xia T last · Yu K first · Sun X · Ma W · Yang J · Zhang L · Ren T · Wang Q · Wang J · Li X · Peng X · Yang L · Lv J · Yao Z · Zhang ZS · Zhang F first · Hu K · Sun C · Chen R · Ni G · Liu X · Wei L · Su R last · Orletskaia VA first · Olekhnovich EI last
Downloads
PRJEB49516.csv.gz (4.6 KB) · parquet (76.1 KB) — all 107 samples, every field with route and confidence · PRJEB49516_determinations.csv.gz (10.7 KB) — 850 evidence rows