Oral and fecal microbiome in allo-HCT patients with cGVHD
332 longitudinal oral and fecal samples from allogeneic hematopoietic cell transplant recipients, comparing patients with oral chronic GVHD (cases) to patients without cGVHD (controls) in a case-control design. machine-written summary
332 samples · 332 runs · Age unknown · 2024 · 3.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 996 sample values (health condition, health condition detail, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11398982 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “baseline, oral cGVHD onset, first post-cGVHD onset visit, and 1-year post-HCT” (time origin: transplant); stated follow-up 12 mo.
Genera, mean relative abundance over 272 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 | 332 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 332 | 100% | 332 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 332 | 100% | 332 | |||
| timepoint_label | 332 | 100% | 332 |
- Oral and Gut Microbiome Alterations in Oral Chronic GVHD Disease: Results from Close Assessment and Testing for Chronic GVHD (CATCH Study). 2024 PMID 39017661 PMC11398982 own_data
Archive description
Shotgun metagenomic sequencing of longitudinal oral and fecal microbiome in allogeneic hematopoietic cell transplant recipients the CATCH study
How this project entered the registry
Classified as human oral cavity / gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “longitudinal oral and fecal microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40476594 | health_condition | transplant_or_immunocompromised | R1 | 0.70 | sample.name_rule:unique_sample_id | CATCH0000016_t0_case_oral_1 |
| SAMN40476596 | health_condition | transplant_or_immunocompromised | R1 | 0.70 | sample.name_rule:experiment_title | t0_ctrl_oral_1 |
| SAMN40476594 | health_condition_detail | case | R1 | 0.70 | sample.name_rule:unique_sample_id | CATCH0000016_t0_case_oral_1 |
| SAMN40476596 | health_condition_detail | allogeneic HCT recipient (abstract) | R1 | 0.70 | sample.name_rule:experiment_title | t0_ctrl_oral_1 |
| SAMN40476594 | timepoint_label | t0 | R1 | 0.70 | sample.name_rule:experiment_title | t0_case_oral_1 |
Sequencing
332 runs over 332 samples · mean 3.14 Gbp per run (median 3.38 Gbp, total 1,043.38 Gbp; 332 runs with a base count) · layout PAIRED 332 · platform ILLUMINA 332 · models Illumina NovaSeq 6000 (332) · 85% of runs with a Sandpiper profile · first public 2024-07-29
Authors (8)
Rashidi A first · Pidala J · Hamilton BK · Pavletic SZ · Kim K · Zevin A · Mays JW · Lee SJ last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, subject_id. Share metadata
Downloads
PRJNA1088546.csv.gz (8.0 KB) · parquet (80.9 KB) — all 332 samples, every field with route and confidence · PRJNA1088546_determinations.csv.gz (8.2 KB) — 996 evidence rows