Gut metagenomes in CRC liver metastasis patients on ABFOLFOX
59 stool metagenomic samples from patients with unresectable colorectal cancer liver metastases treated with neoadjuvant atezolizumab and ABFOLFOX, from a prospectively registered intervention cohort. machine-written summary
59 samples · 59 runs · KR · Age unknown · 2026 · 4.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 472 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 177 sample values (health condition, health condition detail, location site) · PMC13439765 |
| ○ 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 single_arm_before_after · population colorectal_cancer · Neoadjuvant atezolizumab + bevacizumab + FOLFOX (ABFOLFOX)
“neoadjuvant atezolizumab and ABFOLFOX” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
20 of 20 people sampled more than once (59 samples; median 3, up to 3 per person) · follow-up median 7 mo (max 8 mo) · median interval between samples 16 d (time from collection dates). Schedule stated by the source: “Stool/fecal samples collected at three timepoints: T0 (baseline), T1 (after atezolizumab), T2 (after atezolizumab plus bevacizumab)” (time origin: enrolment).
Each row is one person (20 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 59 | 100% | 59 | |||
| health_condition | 59 | 100% | 59 | |||
| subject_id | 59 | 100% | 59 | |||
| collection_date | 59 | 100% | 59 | |||
| detailed_location | 59 | 100% | ||||
| health_condition_detail | 59 | 100% | 59 | |||
| latitude | 59 | 100% | 59 | |||
| location_locality | 59 | 100% | 59 | |||
| location_region | 59 | 100% | 59 | |||
| location_site | 59 | 100% | 59 | |||
| longitude | 59 | 100% | 59 | |||
| timepoint_label | 59 | 100% | 59 |
- Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis. 2026 PMID 42218533 PMC13439765 own_data
Archive description
This project generated shotgun metagenomic sequencing data from clinical microbiome samples obtained from patients with unresectable colorectal cancer liver metastases treated with neoadjuvant atezolizumab and ABFOLFOX. Human genome contamination was removed by alignment to the PacBio (T2T-CHM13) human reference genome reference genome prior to downstream analysis and public data submission.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host study.description · “clinical microbiome samples obtained from patients”
- body site study.title · “colorectal cancer liver metastases”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN60282418 | collection_date | 2019-08-20 | R1 | 0.90 | biosample.attribute:collection_date | 2019-08-20 |
| SAMN60282418 | country | KR | R1 | 0.90 | sample.attr.geo_loc_name | South Korea: Seoul |
| SAMN60282418 | health_condition | colorectal_cancer | R3 | 0.70 | paper.fulltext.abstract | patients with unresectable colorectal liver metastases |
| SAMN60282418 | health_condition_detail | unresectable colorectal liver metastases (CRLM) | R3 | 0.70 | paper.fulltext.abstract | patients with unresectable colorectal liver metastases |
| SAMN60282418 | latitude | 37.5665 | R1 | 0.90 | biosample.attribute:lat_lon | 37.5665 N 126.9780 E |
| SAMN60282418 | location_locality | Seoul | R1 | 0.85 | biosample.attribute:geo_loc_name | South Korea: Seoul |
| SAMN60282418 | location_region | Seoul | R1 | 0.60 | biosample.attribute:lat_lon | 37.5665 N 126.9780 E |
| SAMN60282418 | location_site | Asan Medical Center | R3 | 0.70 | paper.fulltext.methods | single-center, tertiary academic hospital (Asan Medical Center, Republic of Korea) |
| SAMN60282418 | longitude | 126.9780 | R1 | 0.90 | biosample.attribute:lat_lon | 37.5665 N 126.9780 E |
| SAMN60282418 | subject_id | AMC005 | R1 | 0.70 | sample.name_rule:isolation_source | AMC005_t1_feces |
| SAMN60282418 | timepoint_label | t1 | R1 | 0.70 | sample.name_rule:isolation_source | AMC005_t1_feces |
Sequencing
59 runs over 59 samples · mean 4.33 Gbp per run (median 4.63 Gbp, total 255.65 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models Illumina NovaSeq 6000 (59) · 0% of runs with a Sandpiper profile · first public 2026-05-21
Authors (12)
Kim W first · Kim JE · Hong YS · Hwang DW · Kim J · Lee JS · Shin JH · Kim TW · Nagarkar D · Byrd A · Sung CO · Kim SY last
Downloads
PRJNA1468465.csv.gz (2.8 KB) · parquet (73.2 KB) — all 59 samples, every field with route and confidence · PRJNA1468465_determinations.csv.gz (5.6 KB) — 649 evidence rows