Gut microbiome, CRC on fluoropyrimidine therapy, USA
54 longitudinal stool samples from adult colorectal cancer patients in the USA, studying gut microbiome changes during oral fluoropyrimidine-based chemotherapy regimens (including combinations with radioembolization or immunotherapy). machine-written summary
54 samples · 54 runs · US · Adult · 2021 · 5.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 452 sample values (collection date, country, intervention, intervention detail, latitude, location region, longitude, medication) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9530025 |
| ○ 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 |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population colorectal_cancer · Oral fluoropyrimidine (capecitabine/TAS-102) +/- pembrolizumab/bevacizumab chemotherapy
“treated with oral fluoropyrimidine CAP” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
11 of 11 people sampled more than once (54 samples; median 5, up to 6 per person) · follow-up median 42 d (max 42 d) · median interval between samples 10 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Baseline and on-treatment stool samples at labels Baseline, C1D1, C1D3, C1D7, C2D1, C3D1” (time origin: treatment_start).
Each row is one person (1 shown of 11); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 49 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 | 54 | 100% | ||||
| country | 54 | 100% | 54 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 54 | 100% | 54 | |||
| collection_date | 54 | 100% | 54 | |||
| detailed_location | 54 | 100% | ||||
| latitude | 54 | 100% | 54 | |||
| location_region | 54 | 100% | 54 | |||
| longitude | 54 | 100% | 54 | |||
| medication | 54 | 100% | 54 | |||
| timepoint_label | 54 | 100% | 54 | |||
| intervention | 10 | 19% | 10 | |||
| intervention_detail | 10 | 19% | 10 |
- Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. 2022 PMID 36138165 PMC9530025 own_data
Archive description
This is a pilot feasibility study designed to investigate the alterations in the gut microbiome that occur during the course of treatment for colorectal cancer (CRC). Three patient cohorts will be followed. Cohort A: patients treated with oral fluoropyrimidine CAP as part of standard of care (SOC) chemotherapy. Cohort B: patients treated with TAS-102 including those receiving it in combination with Y-90 radioembolization as part of a clinical trial. Cohort C: patients receiving CAP plus immunotherapy (pembrolizumab) and bevacizumab as part of a clinical trial. Investigators will replace participants as needed to ensure a minimum of 10 evaluable participants per cohort (or minimum total of 30 evaluable patients). Evaluable participants are defined as patients with two analyzable stool samples including a baseline sample and at least one on-treatment sample to be used in endpoint analysis. More details can be found at ClinicalTrials.gov NCT04054908.
How this project entered the registry
Classified as human gut / stool / oral cavity 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 · “GO: Gut Microbiome and Oral”
- body site study.description · “alterations in the gut microbiome that occur”
- body site study.title · “Gut Microbiome and Oral Fluoropyrimidine Study in”
- body site study.description · “patients treated with oral fluoropyrimidine CAP as”
- 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 |
|---|---|---|---|---|---|---|
| SAMN18642088 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN18642088 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN18642088 | intervention | no_intervention | R1 | 0.90 | biosample.attribute:treatment_cycle | treatment_cycle: Baseline |
| SAMN18642088 | intervention_detail | pre-treatment baseline | R1 | 0.90 | biosample.attribute:treatment_cycle | treatment_cycle: Baseline |
| SAMN18642088 | latitude | 36.7783 | R1 | 0.90 | biosample.attribute:lat_lon | 36.7783 N 119.4179 W |
| SAMN18642088 | location_region | California | R1 | 0.60 | biosample.attribute:lat_lon | 36.7783 N 119.4179 W |
| SAMN18642088 | longitude | -119.4179 | R1 | 0.90 | biosample.attribute:lat_lon | 36.7783 N 119.4179 W |
| SAMN18642088 | medication | chemotherapy | R1 | 0.85 | biosample.attribute:chem_administration | CAP |
| SAMN18642088 | subject_id | 11 | R1 | 0.85 | sample.attr.host_subject_id | 11 |
| SAMN18642088 | timepoint_label | Baseline | R1 | 0.85 | biosample.attribute:treatment_cycle | Baseline |
Sequencing
54 runs over 54 samples · mean 5.36 Gbp per run (median 5.19 Gbp, total 289.64 Gbp; 54 runs with a base count) · layout PAIRED 54 · platform ILLUMINA 54 · models Illumina NovaSeq 6000 (54) · 91% of runs with a Sandpiper profile · first public 2021-04-07
Authors (18)
Spanogiannopoulos P first · Kyaw TS · Guthrie BGH · Bradley PH · Lee JV · Melamed J · Malig YNA · Lam KN · Gempis D · Sandy M · Kidder W · Van Blarigan EL · Atreya CE · Venook A · Gerona RR · Goga A · Pollard KS · Turnbaugh PJ last
Downloads
PRJNA720145.csv.gz (2.3 KB) · parquet (72.2 KB) — all 54 samples, every field with route and confidence · PRJNA720145_determinations.csv.gz (3.5 KB) — 452 evidence rows