Gut Microbiome in ALL Survivors vs Siblings, USA
Case-control study of 57 stool samples from pediatric/adolescent/adult acute lymphoblastic leukemia survivors (in remission) and their siblings in the USA, using shotgun metagenomic sequencing. machine-written summary
57 samples · 57 runs · US · Adult · 2025 · 6.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 627 sample values (age, collection date, country, family id, family role, health condition, health condition detail, latitude) |
| ○ Abstract / description | read; no usable statement |
| – 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 resolvedhouseholdssiblings
19 of 19 people sampled more than once (57 samples; median 3, up to 3 per person). Schedule stated by the source: “Multiple stool samples (Sample1, Sample2, Sample3) collected per participant; exact collection intervals not stated”.
9 ALL survivors with sampled biological siblings (9 families; one family with 2 siblings); each survivor had a sibling living in the same home · 9 families with 19 sampled people.
sibling · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 9 families. 19 people in the project overall.
Families (9)
Genera, mean relative abundance over 55 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 | 57 | 100% | ||||
| country | 57 | 100% | 57 | |||
| health_condition | 57 | 100% | 57 | |||
| subject_id | 57 | 100% | 57 | |||
| age_at_collection_days | 57 | 100% | 57 | |||
| collection_date | 57 | 100% | 57 | |||
| detailed_location | 57 | 100% | ||||
| family_id | 57 | 100% | 57 | |||
| family_role | 57 | 100% | 57 | |||
| health_condition_detail | 57 | 100% | 57 | |||
| latitude | 57 | 100% | 57 | |||
| location_region | 57 | 100% | 57 | |||
| longitude | 57 | 100% | 57 |
- Shotgun Metagenomics Identify Unique Changes of the Intestinal Microbiome in Pediatric Survivors of Acute Lymphoblastic Leukemia. 2026 PMID 42520232 own_data
- Gut Microbiome Shotgun Metagenomic Sequencing in Survivors of Acute Lymphoblastic Leukemia Compared to Siblings 2025 own_data
Archive description
Metagenomic shot gun sequencing was completed on stool samples of 9 survivors of pediatric and adolescent acute lymphoblastic leukemia (ALL) compared to their siblings. Survivors of ALL were between the ages of 3 and 30, had a history of pre-B cell ALL currently in remission, and were at least 6 months from the completion of therapy. Each survivor had at least one biological sibling who lived in the same home full-time.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and child and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut Microbiome Shotgun Metagenomic”
- body site study.description · “was completed on stool samples of 9”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “9 survivors of pediatric and adolescent acute”
- life stage study.description · “of pediatric and adolescent acute lymphoblastic leukemia”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47339699 | age_at_collection_days | 2554.0 | R1 | 0.85 | sample.attr.host_age | 7 |
| SAMN47339699 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN47339699 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN47339699 | family_id | Family.A | R1 | 0.70 | sample.name_rule:sample_title | Family.A.SurvivorSample1 |
| SAMN47339699 | family_role | sibling | R1 | 0.70 | sample.name_rule:sample_title | Family.A.SurvivorSample1 |
| SAMN47339699 | health_condition | other_cancer | R1 | 0.70 | biosample_attr | ALL.Survivor |
| SAMN47339702 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:host_disease | Unaffected.Sibling |
| SAMN47339699 | health_condition_detail | ALL.Survivor | R1 | 0.90 | sample.attr.host_disease | ALL.Survivor |
| SAMN47339699 | latitude | 41.8246 | R1 | 0.90 | biosample.attribute:lat_lon | 41.8246 N 71.4142 W |
| SAMN47339699 | location_region | Rhode Island | R1 | 0.60 | biosample.attribute:lat_lon | 41.8246 N 71.4142 W |
| SAMN47339699 | longitude | -71.4142 | R1 | 0.90 | biosample.attribute:lat_lon | 41.8246 N 71.4142 W |
| SAMN47339699 | subject_id | Family.A.Survivor | R1 | 0.70 | sample.name_rule:sample_title | Family.A.Survivor |
Sequencing
57 runs over 57 samples · mean 6.01 Gbp per run (median 6.04 Gbp, total 342.58 Gbp; 57 runs with a base count) · layout PAIRED 57 · platform ILLUMINA 57 · models Illumina HiSeq X (57) · 96% of runs with a Sandpiper profile · first public 2025-03-15
Authors (0)
No author record.
Downloads
PRJNA1235679.csv.gz (2.4 KB) · parquet (72.8 KB) — all 57 samples, every field with route and confidence · PRJNA1235679_determinations.csv.gz (5.6 KB) — 627 evidence rows