Gut microbiome and steroid response in LGI aGVHD, USA
42 fecal metagenome samples from allogeneic HCT recipients in the USA, examining whether pre-onset gut microbiota changes predict response to frontline high-dose steroids for lower GI acute graft-versus-host disease; case-control design. machine-written summary
42 samples · 42 runs · US · Age unknown · 2020 · 1.78 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 252 sample values (collection date, country, latitude, location region, longitude, subject id) |
| – 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
7 of 9 people sampled more than once (40 samples; median 4, up to 14 per person). Schedule stated by the source: “Fecal samples collected serially before LGI aGVHD onset to evaluate gut microbiota changes predictive of steroid response; 9 subjects with multiple samples each (median 3 per subject)”.
Genera, mean relative abundance over 37 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 | 0 | 0% | ||||
| country | 42 | 100% | 42 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 42 | 100% | 42 | |||
| collection_date | 42 | 100% | 42 | |||
| detailed_location | 42 | 100% | ||||
| latitude | 42 | 100% | 42 | |||
| location_region | 42 | 100% | 42 | |||
| longitude | 42 | 100% | 42 |
- Shotgun sequencing of the faecal microbiome to predict response to steroids in patients with lower gastrointestinal acute graft-versus-host disease: An exploratory analysis. 2021 PMID 33222185 own_data
Archive description
Acute graft-versus-host disease (aGVHD) is a major cause of morbidity and mortality in allogeneic hematopoietic cell transplantation (HCT) recipients. High-dose steroids are the conventional frontline treatment for aGVHD. Because steroid- refractory aGVHD, esp. lower gastrointestinal (LGI) aGVHD, has a dismal prognosis, early identification of patients unlikely to respond to frontline treatment is of critical importance and highlights a target population for novel therapeutics. Specifically, biomarkers of treatment refractoriness, if found before the onset of aGVHD, would potentially guide monitoring and preparation for high-risk disease in the following days to weeks. We report an exploratory analysis using shotgun metagenomic sequencing to evaluate whether gut microbiota changes before LGI aGVHD onset are predictive of response to frontline high-dose steroids.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “fecal microbiome to predict response”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7487968 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA7487968 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA7487968 | latitude | 44.9710 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.970967 -93.231029 |
| SAMEA7487968 | location_region | Minnesota | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.970967 -93.231029 |
| SAMEA7487968 | longitude | -93.2310 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.970967 -93.231029 |
| SAMEA7487968 | subject_id | 016 | R1 | 0.70 | sample.name_rule:alias | alias: p016.s005 |
Sequencing
42 runs over 42 samples · mean 3.84 Gbp per run (median 1.78 Gbp, total 161.08 Gbp; 42 runs with a base count) · layout PAIRED 42 · platform ILLUMINA 42 · models Illumina HiSeq 2500 (33), Illumina NovaSeq 6000 (9) · 88% of runs with a Sandpiper profile · first public 2020-11-09
Authors (0)
No author record.
Downloads
PRJEB40960.csv.gz (1.8 KB) · parquet (70.7 KB) — all 42 samples, every field with route and confidence · PRJEB40960_determinations.csv.gz (2.2 KB) — 252 evidence rows