Gut microbiome in African Americans with colon polyps
12 fecal samples from African American adults, comparing microbiota composition between colorectal adenoma patients and healthy controls in a case-control design. machine-written summary
12 samples · 12 runs · US · Adult · 2013 · 32.4 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 24 sample values (collection date, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC3869648 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 36 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| health_condition_detail | 12 | 100% | 12 |
- Microbiome analysis of stool samples from African Americans with colon polyps. 2013 PMID 24376500 PMC3869648 own_data
Archive description
Colonic polyps are common tumors occurring in ~50% of Western populations with ~10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation. The goal of this study was to analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions. This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Microbiome analysis of stool samples from African”
- body site study.description · “Colonic polyps are common”
- body site study.description · “polyps are common tumors occurring in ~50%”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02373755 | collection_date | 2010 | R1 | 0.90 | biosample.attribute:collection_date | 2010 |
| SAMN02373755 | country | US | R2 | 0.75 | external.gmrepo source | country: United States |
| SAMN02373755 | health_condition | colorectal_adenoma | R2 | 0.75 | external.gmrepo source | phenotype: Colonic Polyps |
| SAMN02373755 | health_condition_detail | Colonic Polyps | R2 | 0.75 | external.gmrepo source | phenotype: Colonic Polyps |
| SAMN02373755 | subject_id | AFR001 | R1 | 0.75 | sample.name_rule:alias | alias: GRB1J5U01.AFR001 |
Sequencing
12 runs over 12 samples · mean 31.5 Mbp per run (median 32.4 Mbp, total 0.38 Gbp; 12 runs with a base count) · layout SINGLE 12 · platform LS454 12 · models 454 GS FLX Titanium (12) · 0% of runs with a Sandpiper profile · first public 2013-11-13
Authors (0)
No author record.
Downloads
PRJNA222611.csv.gz (1.1 KB) · parquet (69.5 KB) — all 12 samples, every field with route and confidence · PRJNA222611_determinations.csv.gz (1.2 KB) — 60 evidence rows