Fecal microbiome & GVHD severity in allo-HCT, New York
Cross-sectional study of 173 fecal samples from adult allogeneic hematopoietic cell transplant (allo-HCT) patients in New York, USA, examining microbiome dysbiosis in relation to graft-versus-host disease (GVHD) onset and severity. machine-written summary
173 samples · 280 runs · US · Adult · 2022 · 4.62 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,223 sample values (country, health condition, health condition detail, latitude, location region, longitude, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – 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
30 of 126 people sampled more than once (76 samples; median 2, up to 5 per person). Schedule stated by the source: “Multiple timepoints per subject; 9 distinct timepoints recorded (labels: 2, 3, 6, 7, 8, 10, 14, 15). 30 subjects sampled more than once.”.
Genera, mean relative abundance over 155 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 | 173 | 100% | ||||
| country | 173 | 100% | 173 | |||
| health_condition | 173 | 100% | 173 | |||
| subject_id | 172 | 99% | 172 | |||
| detailed_location | 173 | 100% | ||||
| health_condition_detail | 173 | 100% | 173 | |||
| latitude | 173 | 100% | 173 | |||
| location_region | 173 | 100% | 173 | |||
| longitude | 173 | 100% | 173 | |||
| timepoint_label | 13 | 8% | 13 |
Archive description
Patterns of microbial dysbiosis can be detected in fecal samples of GI-aGVHD patients peri-aGVHD onset. Markers of microbial health pre-GVHD onset are associated with longer survival and lower risk of GVHD-related mortality after allo-HCT.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “allo-HCT”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07491337 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07491337 | health_condition | transplant_or_immunocompromised | R1 | 0.85 | ena.experiment_title | Stool sample of allo-HCT patient |
| SAMN07491337 | health_condition_detail | allo-HCT patient | R1 | 0.85 | ena.experiment_title | Stool sample of allo-HCT patient |
| SAMN07491337 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491337 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07491337 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491337 | subject_id | 1066 | R1 | 0.85 | sample.attr.patient_id | 1066 |
| SAMN13270923 | subject_id | 1015 | R1 | 0.70 | biosample.name_rule:sample_id_unique | 1015G |
| SAMN12007735 | timepoint_label | 10 | R1 | 0.85 | sample.attr.bmtday | 10 |
Sequencing
280 runs over 280 samples · mean 5.09 Gbp per run (median 4.62 Gbp, total 1,426.18 Gbp; 280 runs with a base count) · layout PAIRED 280 · platform ILLUMINA 280 · models Illumina HiSeq 4000 (280) · 89% of runs with a Sandpiper profile · first public 2022-06-20 – 2022-06-21
Authors (0)
No author record.
Downloads
PRJNA810891.csv.gz (5.7 KB) · parquet (77.5 KB) — all 173 samples, every field with route and confidence · PRJNA810891_determinations.csv.gz (10.3 KB) — 1,223 evidence rows