Pediatric leukemia/lymphoma patient stool microbiome, Canada
Longitudinal cohort of 67 stool samples from pediatric leukemia and lymphoma patients in Canada undergoing treatment, examining how age, antibiotic use, and antifungal use affected the microbiome. machine-written summary
67 samples · 67 runs · CA · Infant / toddler · 2022 · 0.74 Gbp / sample · cohort Antibiotic and antifungal use in pediatric leukemi
One study deposited as 2 BioProjects (114 catalog samples together): PRJEB46214 · PRJEB53954 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 134 sample values (country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 216 sample values (health condition, health condition detail, location region, location site) · PMC9363618, PMC9998685 |
| ✓ Supplementary tables | 52 sample values (health condition, health condition detail) |
| – 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
14 of 32 people sampled more than once (49 samples; median 2, up to 11 per person). Schedule stated by the source: “Convenience sampling pre-chemotherapy and during treatment; no fixed schedule, timing/number of samples varied per patient (median ~2/patient)” (time origin: intervention start).
Genera, mean relative abundance over 60 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 | 67 | 100% | 67 | |||
| health_condition | 67 | 100% | 26 | 41 | ||
| subject_id | 67 | 100% | 67 | |||
| detailed_location | 67 | 100% | ||||
| health_condition_detail | 67 | 100% | 26 | 41 | ||
| location_region | 67 | 100% | 67 | |||
| location_site | 67 | 100% | 67 |
- Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense. 2022 PMID 35967843 PMC9363618 own_data
- The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients. 2023 PMID 36909730 PMC9998685 own_data
Archive description
This study examined pediatric patients undergoing treatment for leukemia and lymphoma. It examined how age, antibiotic use and antifungal use impacted the microbiome during treatment.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “and Lymphoma patient stool microbiome”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage study.title · “Pediatric Leukemia and Lymphoma”
- life stage study.description · “This study examined pediatric patients undergoing treatment”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110266503 | country | CA | R1 | 0.90 | biosample_attr | Canada |
| SAMEA110266515 | health_condition | other_cancer | R2 | 0.85 | paper.supp.DataSheet_1.docx[table2!Cancer type] | ERR9922144: hodgkin’s lymphoma |
| SAMEA110266503 | health_condition | other_cancer | R3 | 0.70 | paper.body.methods_results | pediatric patients with either leukemia (33) or lymphoma (6) from the Atlantic Maritime provinces of Canada |
| SAMEA110266515 | health_condition_detail | hodgkin’s lymphoma | R2 | 0.85 | paper.supp.DataSheet_1.docx[table2!Cancer type] | ERR9922144: hodgkin’s lymphoma |
| SAMEA110266503 | health_condition_detail | leukemia (33) or lymphoma (6) | R3 | 0.70 | paper.body.methods_results | pediatric patients with either leukemia (33) or lymphoma (6) from the Atlantic Maritime provinces of Canada |
| SAMEA110266503 | location_region | Nova Scotia | R3 | 0.70 | paper.body.methods_results | undergoing care at the IWK Health Centre in Nova Scotia, Canada |
| SAMEA110266503 | location_site | IWK Health Centre | R3 | 0.70 | paper.body.methods_results | undergoing care at the IWK Health Centre in Nova Scotia, Canada |
| SAMEA110266503 | subject_id | MALL-007 | R1 | 0.70 | sample.name_rule:ena_sample_alias | S2-MALL-007-WGS |
Sequencing
67 runs over 67 samples · mean 0.90 Gbp per run (median 0.74 Gbp, total 60.31 Gbp; 67 runs with a base count) · layout SINGLE 67 · platform ILLUMINA 67 · models NextSeq 550 (67) · 90% of runs with a Sandpiper profile · first public 2022-07-14
Authors (0)
No author record.
Downloads
PRJEB53954.csv.gz (2.8 KB) · parquet (73.1 KB) — all 67 samples, every field with route and confidence · PRJEB53954_determinations.csv.gz (3.4 KB) — 402 evidence rows