Japanese Lynch Syndrome Gut Microbiome, Cross-Sectional
71 fecal samples from adult Japanese patients who underwent colonoscopy at a national cancer research center, including subjects diagnosed with Lynch Syndrome; cross-sectional design. machine-written summary
71 samples · 71 runs · JP · Adult · 2024 · 6.58 Gbp / sample · cohort <i>Fusobacterium</i> species are disti
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 213 sample values (country, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 218 sample values (health condition, health condition detail, location locality, location site) · PMC11237946 |
| ✓ Supplementary tables | 343 sample values (age, bmi, health condition, health condition detail, sex, subject id) |
| – 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 64 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 | 71 | 100% | ||||
| country | 71 | 100% | 71 | |||
| health_condition | 71 | 100% | 33 | 38 | ||
| subject_id | 70 | 99% | 70 | |||
| detailed_location | 71 | 100% | ||||
| health_condition_detail | 71 | 100% | 33 | 38 | ||
| latitude | 71 | 100% | 71 | |||
| location_locality | 71 | 100% | 71 | |||
| location_site | 71 | 100% | 71 | |||
| longitude | 71 | 100% | 71 | |||
| age_at_collection_days | 70 | 99% | 70 | |||
| sex | 70 | 99% | 70 | |||
| bmi | 67 | 94% | 67 |
- Fusobacterium species are distinctly associated with patients with Lynch syndrome colorectal cancer. 2024 PMID 38993678 PMC11237946 own_data
Archive description
Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains subjects diagnosed with Lynch Syndrome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “fecal samples of Japanese patients”
- life stage study.description · “patients who underwent colonoscopy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00658659 | age_at_collection_days | 10227.0 | R2 | 0.85 | paper.supp.mmc2.xlsx[Clinical Data (Matched)!age] | 10082 | 28 |
| SAMD00658659 | bmi | 17.58 | R2 | 0.85 | paper.supp.mmc2.xlsx[Clinical Data (LS)!BMI] | 10082 | 17.578125 |
| SAMD00658659 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00658661 | health_condition | colorectal_cancer | R2 | 0.85 | paper.supp.mmc2.xlsx[Clinical Data (LS)!grp] | 10478 | LS CRC |
| SAMD00658659 | health_condition | other_disease | R3 | 0.70 | paper.body.text | The inclusion criterion was a positive diagnosis of a pathogenic mutation in germline MMR genes |
| SAMD00658661 | health_condition_detail | LS CRC | R2 | 0.85 | paper.supp.mmc2.xlsx[Clinical Data (LS)!grp] | 10478 | LS CRC |
| SAMD00658659 | health_condition_detail | Lynch Syndrome (pathogenic germline mutation in MMR genes MLH1, MSH2, MSH6, PMS2, or EPCAM+MSH2) | R3 | 0.70 | paper.body.text | The inclusion criterion was a positive diagnosis of a pathogenic mutation in germline MMR genes |
| SAMD00658659 | latitude | 35.6600 | R1 | 0.90 | biosample.attribute:lat_lon | 35.66 N 139.76 E |
| SAMD00658659 | location_locality | Tokyo | R3 | 0.70 | paper.body.text | Patients undergoing colonoscopy at the National Cancer Center Hospital, Tokyo, Japan, were enrolled in the study |
| SAMD00658659 | location_site | National Cancer Center Hospital | R3 | 0.70 | paper.body.text | Patients undergoing colonoscopy at the National Cancer Center Hospital, Tokyo, Japan, were enrolled in the study |
| SAMD00658659 | longitude | 139.7600 | R1 | 0.90 | biosample.attribute:lat_lon | 35.66 N 139.76 E |
| SAMD00658659 | sex | female | R2 | 0.85 | paper.supp.mmc2.xlsx[Clinical Data (Matched)!gender] | 10082 | female |
| SAMD00658659 | subject_id | 10082 | R2 | 0.85 | paper.supp.mmc2.xlsx[Clinical Data (LS)!patient_id] | 10082 | 10082 |
Sequencing
71 runs over 71 samples · mean 6.74 Gbp per run (median 6.58 Gbp, total 478.57 Gbp; 71 runs with a base count) · layout PAIRED 71 · platform ILLUMINA 71 · models Illumina HiSeq 2500 (71) · 90% of runs with a Sandpiper profile · first public 2024-06-30
Authors (0)
No author record.
Downloads
PRJDB17048.csv.gz (3.8 KB) · parquet (75.4 KB) — all 71 samples, every field with route and confidence · PRJDB17048_determinations.csv.gz (8.3 KB) — 774 evidence rows