Gut metagenomics in nivolumab-treated cancer, Netherlands
159 stool samples from the Netherlands (DRUP-MSI cohort), from patients with other cancers (91) or colorectal cancer (68), collected pre-treatment, at 8 weeks on-treatment, or at progression during nivolumab drug therapy. machine-written summary
159 samples · 159 runs · NL · Adult · 2025 · 6.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,574 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, intervention, intervention detail, medication) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
70 people have samples in more than one arm.
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population other_cancer · Nivolumab immune checkpoint blockade therapy
“DRUP-MSI cohort treated with nivolumab” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
70 of 83 people sampled more than once (146 samples; median 2, up to 3 per person) · follow-up median 59 d (max 9 mo) · median interval between samples 58 d (time from collection dates). Schedule stated by the source: “Samples collected pre-treatment, at 8 weeks on-treatment, or upon progression (timepoint_description: Pre-treatment | On-treatment (8 weeks) | Upon progression).” (time origin: treatment start).
Each row is one person (36 shown of 70); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 158 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 | 159 | 100% | ||||
| country | 159 | 100% | 159 | |||
| health_condition | 159 | 100% | 159 | |||
| subject_id | 159 | 100% | 159 | |||
| health_condition_detail | 159 | 100% | 159 | |||
| intervention | 159 | 100% | 159 | |||
| intervention_detail | 159 | 100% | 159 | |||
| timepoint_label | 159 | 100% | 159 | |||
| collection_date | 143 | 90% | 143 | |||
| antibiotic_exposure | 139 | 87% | 139 | |||
| sex | 98 | 62% | 98 | |||
| medication | 81 | 51% | 81 |
- Microbial Metabolic Pathways Guide Response to Immune Checkpoint Blockade Therapy. 2026 PMID 40996449 own_data
Archive description
Stool metagenomics data from DRUP-MSI cohort treated with nivolumab. Samples were collected pre-treatment, 8 weeks on-treatment, or upon progression
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.description · “Stool metagenomics data from”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA118750491 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:atb_use | atb_use: No |
| SAMEA118750491 | collection_date | 2020-05-28 | R1 | 0.90 | biosample.attribute:collection_date | 2020-05-28 |
| SAMEA118750491 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA118750491 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | Carcinoma |
| SAMEA118750491 | health_condition_detail | Other-GI | R1 | 0.90 | sample.attr.tumor_groups | Other-GI |
| SAMEA118750491 | intervention | no_intervention | R1 | 0.90 | biosample.attribute:timepoint_description | timepoint_description: Pre-treatment |
| SAMEA118750491 | intervention_detail | pre-treatment baseline before nivolumab | R1 | 0.90 | biosample.attribute:timepoint_description | timepoint_description: Pre-treatment |
| SAMEA118750491 | medication | ppi | R1 | 0.90 | biosample.attribute:ppi_use | Yes |
| SAMEA118750491 | sex | male | R1 | 0.90 | sample.attr.sex | MALE |
| SAMEA118750491 | subject_id | HMF004509 | R1 | 0.85 | sample.attr.hmfpatientid | HMF004509 |
| SAMEA118750491 | timepoint_label | Pre-treatment | R1 | 0.85 | sample.attr.timepoint_description | Pre-treatment |
Sequencing
159 runs over 159 samples · mean 7.15 Gbp per run (median 6.58 Gbp, total 1,137.00 Gbp; 159 runs with a base count) · layout PAIRED 159 · platform ILLUMINA 159 · models Illumina NovaSeq 6000 (159) · 99% of runs with a Sandpiper profile · first public 2025-08-21
Authors (0)
No author record.
Downloads
PRJEB91542.csv.gz (6.6 KB) · parquet (78.8 KB) — all 159 samples, every field with route and confidence · PRJEB91542_determinations.csv.gz (11.9 KB) — 1,574 evidence rows