Colon cancer tumor and normal tissue microbiome, Netherlands
534 samples (16S rDNA and WGS non-human reads) from fresh-frozen tumor and matched normal colon tissue of colon adenocarcinoma patients at a Netherlands hospital, case-control design, as part of a multi-omics colon cancer cohort study. machine-written summary
534 samples · 701 runs · NL · Age unknown · 2023 · 0.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,670 sample values (country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2,136 sample values (collection date, health condition, health condition detail, location site) · PMC10202816, PMC10875018, PMC12496564, PMC12789584 |
| ○ 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
246 of 288 people sampled more than once (492 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 133 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 | 0 | 0% | ||||
| country | 534 | 100% | 534 | |||
| health_condition | 534 | 100% | 534 | |||
| subject_id | 534 | 100% | 534 | |||
| collection_date | 534 | 100% | 534 | |||
| detailed_location | 534 | 100% | ||||
| health_condition_detail | 534 | 100% | 534 | |||
| latitude | 534 | 100% | 534 | |||
| location_region | 534 | 100% | 534 | |||
| location_site | 534 | 100% | 534 | |||
| longitude | 534 | 100% | 534 |
- An integrated tumor, immune and microbiome atlas of colon cancer. 2023 PMID 37202560 PMC10202816 own_data
- Location matters: spatial dynamics of tumor-infiltrating T cell subsets is prognostic in colon cancer. 2024 PMID 38375478 PMC10875018 own_data
- Tissue-resident microbiota impacts colorectal cancer progression and prognosis. 2025 PMID 41354681 PMC12789584 own_data
- UEG Week 2025 Moderated Posters 2025 PMC12496564 unsure
Archive description
Fresh frozen tumor samples and matched normal colon specimens from chemotherapy naive, consecutive patients with a histological diagnosis of colon adenocarcinoma at Leiden University Medical Center (LUMC) were subjected to multi-omics profiling at Sidra Integrated Genomics Services, part of Sidra Medicine, Doha, Qatar. This resulted in a high-quality dataset of samples collected between 2001 and 2015. Multi-step QC was performed, including assessment of the quality of the nucleic acid extraction, sequencing, and genetic concordance between DNA/RNA sequences from the same patient. After QC, this resulted in RNA sequencing on 348 tumor samples, whole exome sequencing (WES) on 281 tumor-normal sample pairs (n=562 samples), TCR sequencing of the TCR Beta locus (TRB) for 114 tumor and 10 matched normal samples, and 16S rDNA sequencing on 246 tumor-normal sample pairs (n=492 samples) and 42 tumor only samples, and 167 WGS non human-aligned reads of the tumor samples. Extensive clinicopathological and survival data of the cohort are available. The median follow-up time for this cohort is 4.6 years, and the distribution of gender and pathological stage are within expected ranges for this patient population with a mean age of 68. We refer to this resource as the Sidra-LUMC (SILU) colon adenocarcinoma (COAD) Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM).
How this project entered the registry
Classified as human gut / stool mixed assays of age unknown by sonnet_x2 with confidence 0.60. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “Fresh frozen tumor samples and matched normal colon specimens”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33610904 | collection_date | 2001/2015 | R3 | 0.70 | paper.fulltext.methods | colon cancer diagnosed at Leiden University Medical Center |
| SAMN33610904 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN33610904 | health_condition | colorectal_cancer | R3 | 0.70 | paper.fulltext.abstract | patients affected by primary colon cancer |
| SAMN33610904 | health_condition_detail | primary colon cancer | R3 | 0.70 | paper.fulltext.abstract | patients affected by primary colon cancer |
| SAMN33610904 | latitude | 52.1658 | R1 | 0.90 | biosample.attribute:lat_lon | 52.165833 N 4.4775 E |
| SAMN33610904 | location_region | South Holland | R1 | 0.60 | biosample.attribute:lat_lon | 52.165833 N 4.4775 E |
| SAMN33610904 | location_site | Leiden University Medical Center | R3 | 0.70 | paper.fulltext.methods | diagnosed at Leiden University Medical Center, the Netherlands |
| SAMN33610904 | longitude | 4.4775 | R1 | 0.90 | biosample.attribute:lat_lon | 52.165833 N 4.4775 E |
| SAMN33610904 | subject_id | P0002 | R1 | 0.85 | sample.attr.patient | P0002 |
Sequencing
701 runs over 534 samples · mean 0.60 Gbp per run (median 0.12 Gbp, total 418.84 Gbp; 701 runs with a base count) · layout PAIRED 701 · platform ILLUMINA 701 · models Illumina MiSeq (534), Illumina NovaSeq 6000 (114), HiSeq X Ten (53) · 21% of runs with a Sandpiper profile · first public 2023-06-05 – 2023-08-18
Authors (70)
Roelands J first · Kuppen PJK · Ahmed EI · Mall R · Masoodi T · Singh P · Monaco G · Raynaud C · de Miranda NFCC · Ferraro L · Carneiro-Lobo TC · Syed N · Rawat A · Awad A · Decock J · Mifsud W · Miller LD · Sherif S · Mohamed MG · Rinchai D · Van den Eynde M · Sayaman RW · Ziv E · Bertucci F · Petkar MA · Lorenz S · Mathew LS · Wang K · Murugesan S · Chaussabel D · Vahrmeijer AL · Wang E · Ceccarelli A · Fakhro KA · Zoppoli G · Ballestrero A · Tollenaar RAEM · Marincola FM · Galon J · Khodor SA · Ceccarelli M · Hendrickx W · Bedognetti D last · Zhu H first · Stouten I · Hoorntje R · van Vlierberghe RLP · Ijsselsteijn ME · Lei X · Hendrickx WRL · Shi Z first · Ren H · Lin C · Li F · Wu M · Yang F · Luo T · Nunes L · Isaksson A · Hammarström K · Zhu T · Zhu S · Zhong Y · Ljuslinder I · Uhlén M · Palmqvist R · Glimelius B · Wu K · Sjöblom T · Zhong H last
Downloads
PRJNA941834.csv.gz (13.6 KB) · parquet (90.0 KB) — all 534 samples, every field with route and confidence · PRJNA941834_determinations.csv.gz (26.0 KB) — 4,806 evidence rows