Gut microbiota during anti-PD-1 therapy in melanoma, Italy
65 stool samples from advanced melanoma patients in Italy (Milan and Naples), collected longitudinally during anti-PD-1 immune checkpoint inhibitor therapy to study gut microbiota changes. machine-written summary
65 samples · 65 runs · IT · Adult · 2024 · 8.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 390 sample values (collection date, country, health condition, health condition detail, intervention, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11629153 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
longitudinal — not resolved
11 of 14 people sampled more than once (62 samples; median 6, up to 9 per person).
Genera, mean relative abundance over 63 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 | 65 | 100% | ||||
| country | 65 | 100% | 65 | |||
| health_condition | 65 | 100% | 65 | |||
| subject_id | 65 | 100% | 65 | |||
| collection_date | 65 | 100% | 65 | |||
| health_condition_detail | 65 | 100% | 65 | |||
| intervention | 65 | 100% | 65 |
- Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients. 2024 PMID 39481388 PMC11629153 unsure
Archive description
The microbiome immune oncology (MIO) studies are two separate observational cohort studies recruiting subjects in parallel in the Milan. (MIO-IEO) and Naples (MIO-FGP) since 2018. These cohorts of advanced melanoma patients were used to study changes in the gut microbiome of patients during treatment with monoclonal antibodies targeting the immune checkpoint protein PD-1. We used 16S rRNA and shotgun metagenomic sequencing of stool samples collected over 13 months from the starting of the therapy and compared them with 9 publicly available external cohorts.
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.title · “study of the gut microbiota during anti-pd1”
- body site study.description · “changes in the gut microbiome of patients”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA116143071 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA116143071 | country | IT | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Italy |
| SAMEA116143071 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:description | fecal sample from melanoma patient undergoing anti-PD1 |
| SAMEA116143071 | health_condition_detail | fecal sample from melanoma patient undergoing anti-PD1 | R1 | 0.85 | biosample.attribute:description | fecal sample from melanoma patient undergoing anti-PD1 |
| SAMEA116143071 | intervention | drug_therapy | R1 | 0.85 | biosample.attribute:description | fecal sample from melanoma patient undergoing anti-PD1 |
| SAMEA116143071 | subject_id | IEO-001 | R1 | 0.70 | sample.name_rule:alias | IEO-001-WGS_1144 |
Sequencing
65 runs over 65 samples · mean 8.63 Gbp per run (median 8.20 Gbp, total 560.68 Gbp; 65 runs with a base count) · layout PAIRED 65 · platform ILLUMINA 65 · models Illumina NovaSeq 6000 (65) · 97% of runs with a Sandpiper profile · first public 2024-10-23
Authors (32)
Macandog ADG first · Catozzi C · Capone M · Nabinejad A · Nanaware PP · Liu S · Vinjamuri S · Stunnenberg JA · Galiè S · Jodice MG · Montani F · Armanini F · Cassano E · Madonna G · Mallardo D · Mazzi B · Pece S · Tagliamonte M · Vanella V · Barberis M · Ferrucci PF · Blank CU · Bouvier M · Andrews MC · Xu X · Santambrogio L · Segata N · Buonaguro L · Cocorocchio E · Ascierto PA · Manzo T · Nezi L last
Downloads
PRJEB61942.csv.gz (2.5 KB) · parquet (72.3 KB) — all 65 samples, every field with route and confidence · PRJEB61942_determinations.csv.gz (3.2 KB) — 390 evidence rows