Gut microbiome in Lynch syndrome, longitudinal study
131 stool and mucosal biopsy samples from Lynch syndrome patients, studied longitudinally to assess gut microbiome changes preceding colorectal neoplasia, using 16S rRNA, metagenomic, and metatranscriptomic sequencing. machine-written summary
131 samples · 131 runs · US · Age unknown · 2024 · 1.51 Gbp / sample · cohort Structure of the Mucosal and Stool Microbiome in L
One study deposited as 2 BioProjects (218 catalog samples together): PRJNA526861 · PRJNA699934 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 524 sample values (health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 131 sample values (country) · PMC7453618 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
38 of 39 people sampled more than once (130 samples; median 4, up to 4 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 131 | 100% | 131 | |||
| health_condition | 131 | 100% | 131 | |||
| subject_id | 131 | 100% | 131 | |||
| health_condition_detail | 131 | 100% | 131 | |||
| sex | 131 | 100% | 131 |
- Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. 2020 PMID 32240601 PMC7453618 own_data
Archive description
The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched in both stool and mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded... (for more see dbGaP study page.)
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.scientific_name · “Homo sapiens”
- body site study.description · “metagenomic and metatranscriptomic sequencing of feces”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29882506 | country | US | R3 | 0.70 | paper.body.fulltext | Massachusetts General Hospital (MGH) or the Clinical Genetics and/or Gastroenterology Services at Memorial Sloan Kettering Cancer Center (MSKCC) |
| SAMN29882506 | health_condition | colorectal_cancer | R1 | 0.90 | biosample_attr | Colorectal Neoplasms |
| SAMN29882506 | health_condition_detail | Colorectal Neoplasms | R1 | 0.90 | sample.attr.study_disease | Colorectal Neoplasms |
| SAMN29882506 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN29882506 | subject_id | 4260657 | R1 | 0.85 | sample.attr.gap_subject_id | 4260657 |
Sequencing
131 runs over 131 samples · mean 1.47 Gbp per run (median 1.51 Gbp, total 192.35 Gbp; 131 runs with a base count) · layout SINGLE 131 · platform ILLUMINA 131 · models Illumina MiSeq (131) · 0% of runs with a Sandpiper profile · first public 2024-06-14
Authors (0)
No author record.
Downloads
PRJNA699934.csv.gz (4.1 KB) · parquet (74.2 KB) — all 131 samples, every field with route and confidence · PRJNA699934_determinations.csv.gz (4.0 KB) — 655 evidence rows