Gut microbiome, CHAPLE children on eculizumab, Turkey
21 fecal samples from children, adolescents, and infants with CHAPLE disease in Turkey, collected over 14 months during a case series testing eculizumab (complement C5 inhibitor) drug therapy. machine-written summary
21 samples · 21 runs · TR · Infant / toddler · 2020 · 3.40 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (age, collection date, country, health condition, health condition detail, intervention, medication, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10175488 |
| ○ 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 resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population autoimmune_inflammatory · Eculizumab (C5 inhibitor) therapy in CHAPLE disease, 14 months
“tested the complement C5 inhibitor eculizumab” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
6 of 6 people sampled more than once (21 samples; median 4, up to 4 per person) · follow-up median 13 mo (max 16 mo) · median interval between samples 5 mo (time from collection dates). Schedule stated by the source: “Baseline, 1 month, 6 month, and 12 month fecal samples collected from each patient during eculizumab treatment.”.
Each row is one person (6 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 19 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 | 21 | 100% | ||||
| country | 21 | 100% | 21 | |||
| health_condition | 21 | 100% | 21 | |||
| subject_id | 21 | 100% | 21 | |||
| age_at_collection_days | 21 | 100% | 21 | |||
| collection_date | 21 | 100% | 21 | |||
| health_condition_detail | 21 | 100% | 21 | |||
| intervention | 21 | 100% | 21 | |||
| medication | 21 | 100% | 21 | |||
| sex | 21 | 100% | 21 | |||
| timepoint_label | 21 | 100% | 21 |
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
Archive description
Complement hyperactivation, angiopathic thrombosis, and protein-losing enteropathy (CHAPLE disease) is a lethal disease caused by genetic loss of the complement regulator CD55. We tested the complement C5 inhibitor eculizumab in a case series of 6 children. Over 14 months, fecal samples were collected for metagenomic sequencing of the gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “Over 14 months, fecal samples were collected”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “series of 6 children . Over 14”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14775291 | age_at_collection_days | 4018 | R1 | 0.80 | sample.attr.host_age | 11 |
| SAMN14775291 | collection_date | 2018-02-01 | R1 | 0.85 | biosample.attribute:collection_date | 2018-02-01 |
| SAMN14775291 | country | TR | R1 | 0.90 | biosample_attr | Turkey |
| SAMN14775291 | health_condition | autoimmune_inflammatory | R1 | 0.85 | biosample.attribute:gastrointest_disord | CHAPLE Disease |
| SAMN14775291 | health_condition_detail | CHAPLE Disease | R1 | 0.90 | biosample.attribute:gastrointest_disord | gastrointest_disord: CHAPLE Disease |
| SAMN14775291 | intervention | drug_therapy | R1 | 0.85 | biosample.attribute:chem_administration | eculizumab [NCIT:C48386] |
| SAMN14775291 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:chem_administration | eculizumab [NCIT:C48386] |
| SAMN14775291 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN14775291 | subject_id | P7 | R1 | 0.85 | biosample_attr | P7 |
| SAMN14775291 | timepoint_label | baseline | R1 | 0.80 | biosample_attr | baseline |
Sequencing
21 runs over 21 samples · mean 3.14 Gbp per run (median 3.40 Gbp, total 65.94 Gbp; 21 runs with a base count) · layout PAIRED 21 · platform ILLUMINA 21 · models NextSeq 500 (21) · 90% of runs with a Sandpiper profile · first public 2020-05-01
Authors (54)
Ozen A first · Kasap N · Vujkovic-Cvijin I · Apps R · Cheung F · Karakoc-Aydiner E · Akkelle B · Sari S · Tutar E · Ozcay F · Uygun DK · Islek A · Akgun G · Selcuk M · Sezer OB · Zhang Y · Kutluk G · Topal E · Sayar E · Celikel C · Houwen RHJ · Bingol A · Ogulur I · Eltan SB · Snow AL · Lake C · Fantoni G · Alba C · Sellers B · Chauvin SD · Dalgard CL · Harari O · Ni YG · Wang MD · Devalaraja-Narashimha K · Subramanian P · Ergelen R · Artan R · Guner SN · Dalgic B · Tsang J · Belkaid Y · Ertem D · Baris S · Lenardo MJ last · Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA629392.csv.gz (1.7 KB) · parquet (71.6 KB) — all 21 samples, every field with route and confidence · PRJNA629392_determinations.csv.gz (2.2 KB) — 210 evidence rows