Gut microbiome and drug exposures in allo-HCT patients, USA
558 fecal samples from allogeneic hematopoietic cell transplant (allo-HCT) patients in New York, USA, studied to assess associations between drug exposures, intestinal microbiome dynamics, and clinical outcomes using the PARADIGM computational method. machine-written summary
558 samples · 932 runs · US · Age unknown · 2022 · 6.17 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,893 sample values (country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 1,116 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10390075 |
| – 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
122 of 351 people sampled more than once (329 samples; median 2, up to 16 per person). Schedule stated by the source: “Serial fecal samples collected at multiple days relative to transplant (DayRelativeToNearestHCT/bmtday, e.g. -7 to 160)”.
Genera, mean relative abundance over 516 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 | 558 | 100% | 558 | |||
| health_condition | 558 | 100% | 558 | |||
| subject_id | 558 | 100% | 558 | |||
| detailed_location | 558 | 100% | ||||
| health_condition_detail | 558 | 100% | 558 | |||
| latitude | 558 | 100% | 558 | |||
| location_region | 558 | 100% | 558 | |||
| longitude | 558 | 100% | 558 | |||
| timepoint_label | 103 | 18% | 103 |
- High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients. 2023 PMID 37295406 PMC10390075 own_data
Archive description
This study investigated the associations between drug exposures, the intestinal microbiome and clinical outcomes in allo-HCT patients by developing a novel computational method called PARADIGM (PARameters Associated with DynamIcs of Gut Microbiome).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “allo-HCT patients”
- body site study.title · “the intestinal microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07491315 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07491315 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | paper.abstract | patients undergoing allogeneic hematopoietic cell transplantation |
| SAMN07491315 | health_condition_detail | patients undergoing allogeneic hematopoietic cell transplantation | R4 | 0.50 | paper.abstract | patients undergoing allogeneic hematopoietic cell transplantation |
| SAMN07491315 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491315 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07491315 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491315 | subject_id | 1064 | R1 | 0.85 | sample.attr.patient_id | 1064 |
| SAMN13270437 | subject_id | 1588 | R1 | 0.70 | sample.name_rule:alias | 1588E |
| SAMN12007085 | timepoint_label | -7 | R1 | 0.85 | sample.attr.bmtday | -7 |
Sequencing
932 runs over 932 samples · mean 6.57 Gbp per run (median 6.17 Gbp, total 6,119.06 Gbp; 932 runs with a base count) · layout PAIRED 932 · platform ILLUMINA 932 · models Illumina NovaSeq 6000 (517), Illumina HiSeq 4000 (406), Illumina HiSeq 2500 (9) · 91% of runs with a Sandpiper profile · first public 2022-10-15 – 2022-11-02
Authors (0)
No author record.
Downloads
PRJNA885489.csv.gz (15.4 KB) · parquet (92.4 KB) — all 558 samples, every field with route and confidence · PRJNA885489_determinations.csv.gz (31.0 KB) — 4,009 evidence rows