Gut microbiome and mCRC therapy response in Taiwan
54 stool samples from Taiwanese patients with metastatic colorectal cancer, collected before chemotherapy plus targeted therapy (anti-EGFR or anti-VEGF); a case-control design compared patients with progressive disease versus partial response. machine-written summary
54 samples · 54 runs · TW · Adult · 2022 · 10.32 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 324 sample values (collection date, country, health condition, health condition detail, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9539537 |
| – 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 |
Genera, mean relative abundance over 51 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 | 54 | 100% | 54 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 54 | 100% | 54 | |||
| health_condition_detail | 54 | 100% | 54 | |||
| latitude | 54 | 100% | 54 | |||
| longitude | 54 | 100% | 54 |
- Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer. 2022 PMID 36212420 PMC9539537 own_data
Archive description
This study investigates the role of the gut microbiome in the treatment of metastatic colorectal cancer (mCRC) patients. Stools from patients before chemotherapy and targeted therapy were collected and performed whole genome sequencing. Patients with progressive disease or partial response to the therapy were included in this study.
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 · “from patients with colorectal cancer. Patients were”
- body site study.description · “role of the gut microbiome in the”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA110645760 | collection_date | 2019-07-06 | R1 | 0.90 | biosample.attribute:collection_date | 2019-07-06 |
| SAMEA110645760 | country | TW | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Taiwan |
| SAMEA110645760 | health_condition | colorectal_cancer | R1 | 0.90 | biosample_attr | colorectal carcinoma |
| SAMEA110645760 | health_condition_detail | colorectal carcinoma | R1 | 0.90 | sample.attr.host_disease_status | colorectal carcinoma |
| SAMEA110645760 | latitude | 23.6978 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 23.6978 120.9605 |
| SAMEA110645760 | longitude | 120.9605 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 23.6978 120.9605 |
Sequencing
54 runs over 54 samples · mean 10.53 Gbp per run (median 10.32 Gbp, total 568.86 Gbp; 54 runs with a base count) · layout PAIRED 54 · platform ILLUMINA 54 · models HiSeq X Ten (54) · 94% of runs with a Sandpiper profile · first public 2022-09-08
Authors (10)
Chen YC first · Chuang CH · Miao ZF · Yip KL · Liu CJ · Li LH · Wu DC · Cheng TL · Lin CY · Wang JY last
Downloads
PRJEB55366.csv.gz (2.4 KB) · parquet (71.6 KB) — all 54 samples, every field with route and confidence · PRJEB55366_determinations.csv.gz (2.4 KB) — 324 evidence rows