Gut microbiome, asparaginase activity, pediatric ALL, Canada
14 stool samples from children with acute lymphoblastic leukemia in Canada, studied longitudinally during pegaspargase drug therapy to compare gut microbial communities between doses with decreased versus increased serum asparaginase activity. machine-written summary
14 samples · 14 runs · CA · Child · 2020 · 0.38 Gbp / sample · cohort Antibiotic and antifungal use in pediatric leukemi
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 70 sample values (collection date, country, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10269646 |
| ○ 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
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population other_cancer · Pegaspargase (pegylated asparaginase) chemotherapy in pediatric ALL
“during pegaspargase treatment” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
3 of 11 people sampled more than once (6 samples; median 2, up to 2 per person). Schedule stated by the source: “Samples taken at consecutive pegaspargase doses during treatment; no explicit day offsets given.” (time origin: treatment start).
Genera, mean relative abundance over 11 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 | 14 | 100% | ||||
| country | 14 | 100% | 14 | |||
| health_condition | 14 | 100% | 14 | |||
| subject_id | 14 | 100% | 14 | |||
| collection_date | 14 | 100% | 14 | |||
| health_condition_detail | 14 | 100% | 14 |
- 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 unsure
- The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients. 2023 PMID 36909730 PMC9998685 unsure
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. 2023 PMID 37191543 PMC10269646 unsure
Archive description
Asparaginase is an effective treatment of pediatric acute lymphoblastic leukemia (ALL). Changes in asparaginase activity may lead to suboptimal treatment and poorer outcomes. The gut microbiome produces metabolites that could impact asparaginase therapy, however remains uninvestigated. We examined gut-microbial community and microbial-asparaginase and asparagine synthetase genes using 16SrRNA and metagenomic sequence data from stool samples of pediatric ALL patients. Comparing ASNase activity between consecutive asparaginase-doses we found microbial communities differed between decreased- and increased-activity samples.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child by deterministic_rule with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host study.title · “and genes in child ren with acute”
- body site study.title · “Examining the gut microbial community and”
- body site study.description · “poorer outcomes. The gut microbiome produces metabolites”
- body site study.title · “of change in serum asparaginase activity during”
- life stage study.title · “and genes in children with acute lymphoblastic”
- life stage study.description · “effective treatment of pediatric acute lymphoblastic leukemia”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7608576 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA7608576 | country | CA | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Canada |
| SAMEA7608576 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | acute lymphoblastic leukemia |
| SAMEA7608576 | health_condition_detail | acute lymphoblastic leukemia | R1 | 0.90 | sample.attr.host_disease_status | acute lymphoblastic leukemia |
| SAMEA7608576 | subject_id | 1 | R1 | 0.70 | biosample.name_rule:alias | SD1_P1-mgs |
Sequencing
14 runs over 14 samples · mean 0.55 Gbp per run (median 0.38 Gbp, total 7.76 Gbp; 14 runs with a base count) · layout SINGLE 14 · platform ILLUMINA 14 · models NextSeq 550 (14) · 79% of runs with a Sandpiper profile · first public 2020-12-01
Authors (22)
Dunn KA first · MacDonald T · Rodrigues GJ · Forbrigger Z · Bielawski JP · Langille MGI · Van Limbergen J · Kulkarni K last · MacDonald J · Van Limbergen JE · Rizzo SM first · Alessandri G · Lugli GA · Fontana F · Tarracchini C · Mancabelli L · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Ventura M · Turroni F last
Downloads
PRJEB41463.csv.gz (1.2 KB) · parquet (69.6 KB) — all 14 samples, every field with route and confidence · PRJEB41463_determinations.csv.gz (1.1 KB) — 70 evidence rows