Gut microbiome in HCC patients on anti-PD-1 therapy, China
50 fecal microbiome samples from adult liver cancer patients in China receiving anti-PD-1 immunotherapy, compared between responders and non-responders, as part of an intervention study. machine-written summary
50 samples · 50 runs · CN · Adult · 2019 · 10.54 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 450 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11446285 |
| ○ 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
8 of 8 people sampled more than once (50 samples; median 5, up to 13 per person) · follow-up median 10 d (max 39 d) · median interval between samples 3 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Serial fecal sampling per patient during anti-PD-1 immunotherapy starting at baseline (day 0); published timepoint labels 0,1,3,6,9,12,18,21,27,30” (time origin: intervention start).
Each row is one person (8 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 | 50 | 100% | ||||
| country | 50 | 100% | 50 | |||
| health_condition | 50 | 100% | 50 | |||
| subject_id | 50 | 100% | 50 | |||
| collection_date | 50 | 100% | 50 | |||
| detailed_location | 50 | 100% | ||||
| health_condition_detail | 50 | 100% | 50 | |||
| latitude | 50 | 100% | 50 | |||
| location_region | 50 | 100% | 50 | |||
| longitude | 50 | 100% | 50 | |||
| timepoint_label | 50 | 100% | 50 |
- Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma. 2019 PMID 31337439 PMC6651993 own_data
- Activation of NOD1 on tumor-associated macrophages augments CD8<sup>+</sup> T cell-mediated antitumor immunity in hepatocellular carcinoma. 2024 PMID 39356756 PMC11446285 own_data
- Modulating <i>Bacteroides</i> to boost anti-PD-1 immunotherapy in HCC. 2026 PMID 41702649 PMC12918670 own_data
- A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors. 2021 PMID 33593881 PMC9053858 unsure
Archive description
The data is about the fecal microbiome of patients with liver cancer and receiving immunotherapy. The correspondence between the sample labels in the NCBI BioProject and the sample labels in the manuscript is 10002 for R1, 10006 for R2, 10009 for R3, 10003 for NR1, 10007 for NR2, 10008 for NR3, 10010 for NR4 and 10011 for NR5.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “fecal microbiome of patients with liver cancer”
- life stage study.description · “patients with liver cancer and receiving immunotherapy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10412282 | collection_date | 2017-05 | R1 | 0.90 | biosample.attribute:collection_date | 2017-05 |
| SAMN10412282 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN10412282 | health_condition | other_cancer | R1 | 0.70 | sample.name_rule:alias | 10002-0 |
| SAMN10412282 | health_condition_detail | HCC patient R1, anti-PD-1 responder | R1 | 0.70 | sample.name_rule:alias | 10002-0 |
| SAMN10412282 | latitude | 30.2800 | R1 | 0.90 | biosample.attribute:lat_lon | 30.28 N 120.15 E |
| SAMN10412282 | location_region | Zhejiang Sheng | R1 | 0.60 | biosample.attribute:lat_lon | 30.28 N 120.15 E |
| SAMN10412282 | longitude | 120.1500 | R1 | 0.90 | biosample.attribute:lat_lon | 30.28 N 120.15 E |
| SAMN10412282 | subject_id | 10002 | R1 | 0.70 | sample.name_rule:alias | 10002-0 |
| SAMN10412282 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | 10002-0 |
Sequencing
50 runs over 50 samples · mean 10.79 Gbp per run (median 10.54 Gbp, total 539.53 Gbp; 50 runs with a base count) · layout PAIRED 50 · platform BGISEQ 50 · models BGISEQ-500 (50) · 0% of runs with a Sandpiper profile · first public 2019-10-26
Authors (50)
Zheng Y first · Wang T · Tu X · Huang Y · Zhang H · Tan D · Jiang W · Cai S · Zhao P · Song R · Li P · Qin N · Fang W last · Shaikh FY first · White JR · Gills JJ · Hakozaki T · Richard C · Routy B · Okuma Y · Usyk M · Pandey A · Weber JS · Ahn J · Lipson EJ · Naidoo J · Pardoll DM · Sears CL last · Zhang F first · Jiang Q · Cai J · Meng F · Tang W · Liu Z · Lin X · Liu W · Zhou Y · Shen X · Xue R · Dong L · Zhang S last · Qi X first · Yang M · Liu X · Ma L · Kaifi JT · Ericsson AC · Kimchi ET · Staveley-O'Carroll KF · Li G last
Downloads
PRJNA505228.csv.gz (2.2 KB) · parquet (72.2 KB) — all 50 samples, every field with route and confidence · PRJNA505228_determinations.csv.gz (3.8 KB) — 450 evidence rows