Pediatric allo-HCT gut decontamination trial, Massachusetts
155 stool metagenome samples from pediatric and adult allogeneic HCT patients in Massachusetts, from a randomized trial of oral vancomycin-polymyxin B gut decontamination versus no decontamination, assessing microbiome composition, aGVHD, and bloodstream infections. machine-written summary
155 samples · 155 runs · US · Child · 2022 · 4.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,494 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ✓ Abstract / description | 9 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC9057614 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population transplant_or_immunocompromised · Oral vancomycin-polymyxin B gut decontamination vs no-GD in allo-HCT patients
“randomized 20 patients undergoing allogeneic HCT to receive (GD)” — abstract:35239511 (study level; per-sample arms are in the intervention column below)
longitudinalsiblings — not resolved
22 of 23 people sampled more than once (144 samples; median 6, up to 11 per person) · follow-up median 2 mo (max 11 mo) · median interval between samples 7 d (time from timepoint labels). Schedule stated by the source: “Weekly (±3 days) prior to neutrophil engraftment; monthly (±2 weeks) after engraftment until 6 months; 6 months and 1 year (±1 month); within 48 hours of aGVHD diagnosis or positive blood culture”; stated follow-up 12 mo.
Each row is one person (22 shown); dots are samples at days since that person's first sample.
HCT patients plus 2 healthy sibling donors as comparison group (small subset of cohort).
Genera, mean relative abundance over 126 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 | 146 | 94% | ||||
| country | 155 | 100% | 155 | |||
| health_condition | 155 | 100% | 149 | 6 | ||
| subject_id | 155 | 100% | 155 | |||
| collection_date | 155 | 100% | 155 | |||
| detailed_location | 155 | 100% | ||||
| health_condition_detail | 155 | 100% | 152 | 3 | ||
| latitude | 155 | 100% | 155 | |||
| location_region | 155 | 100% | 155 | |||
| longitude | 155 | 100% | 155 | |||
| timepoint_label | 155 | 100% | 155 | |||
| age_at_collection_days | 108 | 70% | 108 |
- Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation. 2022 PMID 35239511 PMC9057614 own_data
- Randomized controlled trial of gut decontamination in pediatric patients undergoing allogeneic hematopoietic cell transplantation 2021 own_data
Archive description
A Randomized Phase 2 Study to examine the impact of gut decontamination (GD) with oral vancomycin-polymyxin B on the intestinal microbiome composition in pediatric patients undergoing allogeneic hematopoietic cell transplant (allo-HCT). Exploratory aims look at clinical outcomes including acute graft-versus-host disease (aGVHD) and the risk of bloodstream infections (BSI).
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child and adult and adolescent by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome(145)”
- body site run.scientific_name · “human blood metagenome(10)”
- life stage study.title · “Pediatrics Gut Decontamination”
- life stage study.description · “pediatric patients undergoing allogeneic hematopoietic cell transplant”
- life stage sample.attr.age_at_transplant_yrs · “24.6 (n=32/155)”
- life stage sample.attr.age_at_transplant_yrs · “17.5 (n=30/155)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN24247898 | age_at_collection_days | 7388.0 | R1 | 0.85 | sample.attr.age_at_transplant_yrs | 20.2 |
| SAMN24247886 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN24247886 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Massachusetts |
| SAMN24247886 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | AML |
| SAMN24247962 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | paper.abstract | patients undergoing allogeneic HCT |
| SAMN24247886 | health_condition_detail | AML | R1 | 0.90 | sample.attr.disease | AML |
| SAMN24248028 | health_condition_detail | allogeneic hematopoietic cell transplant (allo-HCT) | R4 | 0.50 | study.description | allogeneic hematopoietic cell transplant (allo-HCT) |
| SAMN24247886 | latitude | 42.3375 | R1 | 0.90 | biosample.attribute:lat_lon | 42.337483 N 71.105512 W |
| SAMN24247886 | location_region | Massachusetts | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Massachusetts |
| SAMN24247886 | longitude | -71.1055 | R1 | 0.90 | biosample.attribute:lat_lon | 42.337483 N 71.105512 W |
| SAMN24247886 | subject_id | C01 | R1 | 0.85 | sample.attr.patient_code | C01 |
| SAMN24247886 | timepoint_label | day -7 | R1 | 0.85 | biosample.attribute:day_rel_hct | -7 |
Sequencing
155 runs over 155 samples · mean 4.60 Gbp per run (median 4.58 Gbp, total 713.64 Gbp; 155 runs with a base count) · layout PAIRED 155 · platform ILLUMINA 155 · models Illumina HiSeq 4000 (155) · 88% of runs with a Sandpiper profile · first public 2022-04-09
Authors (21)
Severyn CJ first · Siranosian BA · Kong ST · Moreno A · Li MM · Chen N · Duncan CN · Margossian SP · Lehmann LE · Sun S · Andermann TM · Birbrayer O · Silverstein S · Reynolds CG · Kim S · Banaei N · Ritz J · Fodor AA · London WB · Bhatt AS · Whangbo JS last
Downloads
PRJNA787952.csv.gz (5.5 KB) · parquet (77.7 KB) — all 155 samples, every field with route and confidence · PRJNA787952_determinations.csv.gz (10.9 KB) — 1,503 evidence rows