External validation cohort for CRC microbial SNV model
20 gut metagenome samples, case-control design, used as an external validation cohort for a colorectal cancer prediction model based on microbial single nucleotide variant markers; country and health condition details not reported. machine-written summary
20 samples · 40 runs · Age unknown · 2020 · 12.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 20 sample values (health condition) |
| ✓ Abstract / description | 20 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10734426, PMC10989788, PMC7808391, PMC8693921 |
| ○ 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 |
Genera, mean relative abundance over 19 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 | 0 | 0% | ||||
| health_condition | 20 | 100% | 20 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 20 | 100% | 20 |
- Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. 2021 PMID 33430705 PMC7808391 unsure
- Expanding the Colorectal Cancer Biomarkers Based on the Human Gut Phageome. 2021 PMID 34935421 PMC8693921 unsure
- Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426 unsure
- Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota. 2022 PMID 38868717 PMC10989788 unsure
Archive description
In this study, we established a novel colorectal cancer prediction model based on unique microbial single nucleotide variants markers
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16175923 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:alias | EVC_HN_C1 |
| SAMN16175923 | health_condition_detail | mixed_case_control: CRC patients vs healthy controls | R4 | 0.50 | study.description | colorectal cancer prediction model |
Sequencing
40 runs over 20 samples · mean 6.16 Gbp per run (median 6.19 Gbp, total 246.41 Gbp; 40 runs with a base count) · layout SINGLE 37, PAIRED 3 · platform ILLUMINA 40 · models Illumina HiSeq 2500 (40) · 85% of runs with a Sandpiper profile · first public 2020-09-17 – 2020-10-10
Authors (31)
Ma C first · Chen K · Wang Y · Cen C · Zhai Q · Zhang J last · Shen S first · Huo D · Jiang S · Zhang Y · Teng F · Huang S · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Chen D · Liu H
Downloads
PRJNA663646.csv.gz (1.4 KB) · parquet (69.2 KB) — all 20 samples, every field with route and confidence · PRJNA663646_determinations.csv.gz (742 B) — 40 evidence rows