Long. virome study in Finnish/Estonian children with T1D
Cohort-longitudinal study of 220 gut virome samples from children in Finland (Jorvi) and Estonia (Tartu), comparing 163 healthy-control samples with 57 type 1 diabetes samples to examine virome changes preceding autoimmunity. machine-written summary
220 samples · 220 runs · FI, EE · Infant / toddler · 2017 · 0.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 609 sample values (age, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10904392, PMC13434738 |
| ✓ Supplementary tables | 440 sample values (diet, timepoint) |
| ✓ External resources | 660 sample values (health condition, health condition detail, sex) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
22 of 22 people sampled more than once (220 samples; median 10, up to 16 per person) · follow-up median 14 mo (max 19 mo) · median interval between samples 33 d (time from age at collection).
Each row is one person (18 shown of 22); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 169 | 77% | ||||
| country | 220 | 100% | 220 | |||
| health_condition | 220 | 100% | 220 | |||
| subject_id | 220 | 100% | 220 | |||
| diet | 220 | 100% | 220 | |||
| health_condition_detail | 220 | 100% | 220 | |||
| sex | 220 | 100% | 220 | |||
| timepoint_label | 220 | 100% | 220 | |||
| age_at_collection_days | 169 | 77% | 169 |
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392 curated
- A meta-analysis of infant gut viromes reveals global patterns in bacteriophage community assembly and functional capacity over the first three years of life. PMID 42315844 PMC13434738 curated
Archive description
The goal of this study is to determine if the enteric virome is altered in children who develop diabetes.
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 · “Intestinal Virome Changes Precede”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage study.title · “I Diabetes Susceptible Children”
- life stage study.description · “is altered in children who develop diabetes.”
- 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 |
|---|---|---|---|---|---|---|
| SAMN07163334 | age_at_collection_days | 120.0 | R1 | 0.85 | biosample.attribute:Age_at_Collection | 120 |
| SAMN07163334 | country | FI | R1 | 0.90 | biosample_attr | Finland: Jorvi |
| SAMN07163334 | diet | other_diet | R2 | 0.85 | paper.supp.41467_2024_45793_MOESM4_ESM.xlsx[Sheet1!Feed] | combined |
| SAMN07163334 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07163334 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07163334 | sex | female | R2 | 0.75 | external.gmrepo source | sex: Female |
| SAMN07163334 | subject_id | 1.1 | R1 | 0.70 | sample.name_rule:sample_id | 1.1_120 |
| SAMN07163334 | timepoint_label | 6 | R2 | 0.85 | paper.supp.fig2b_vlp.xlsx[Sheet1!period] | 6 |
Sequencing
220 runs over 220 samples · mean 0.48 Gbp per run (median 0.47 Gbp, total 106.39 Gbp; 220 runs with a base count) · layout PAIRED 220 · platform ILLUMINA 220 · models Illumina MiSeq (220) · 0% of runs with a Sandpiper profile · first public 2017-06-23 – 2018-06-02
Authors (14)
Zeng S first · Almeida A · Li S · Ying J · Wang H · Qu Y · Paul Ross R · Stanton C · Zhou Z · Niu X · Mu D · Wang S last · Shamash M first · Maurice CF last
Downloads
PRJNA387903.csv.gz (7.3 KB) · parquet (80.1 KB) — all 220 samples, every field with route and confidence · PRJNA387903_determinations.csv.gz (13.7 KB) — 1,709 evidence rows