Gut microbiome in X-linked SCID patients post gene therapy
116 samples (USA and France) from a longitudinal cohort/case series study assessing gut microbial community changes in SCID patients following gene therapy and immune reconstitution. machine-written summary
116 samples · 122 runs · US, FR · Infant / toddler · 2018 · 0.99 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 780 sample values (collection date, country, health condition, health condition detail, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6161392 |
| ○ 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
design single_arm_before_after · Gene therapy and immune reconstitution in SCID patients, pre/post sampling
longitudinal
9 of 12 people sampled more than once (74 samples; median 5, up to 21 per person) · follow-up median 7 mo (max 9 mo) · median interval between samples 2 mo (time from collection dates). Schedule stated by the source: “archive time labels: 1, 2, 4, 3, 5, 7, 6, 8” (time origin: intervention_start).
Each row is one person (2 shown of 9); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 62 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 | 116 | 100% | 116 | |||
| health_condition | 116 | 100% | 116 | |||
| subject_id | 116 | 100% | 116 | |||
| health_condition_detail | 116 | 100% | 116 | |||
| intervention | 116 | 100% | 116 | |||
| collection_date | 100 | 86% | 100 | |||
| timepoint_label | 100 | 86% | 100 |
- T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency. 2018 PMID 30261899 PMC6161392 own_data
Archive description
Assessing changes in the microbial community of SCID patients after gene therapy and immune reconstitution.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by opus_adjudicated with confidence 0.40. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “SCID patients after gene therapy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09467083 | collection_date | 2012-01-01 | R1 | 0.85 | biosample.attribute:collection_date | 2012-01-01 |
| SAMN09467083 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN09467083 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:study_group | Healthy |
| SAMN09467083 | health_condition_detail | Healthy | R1 | 0.85 | biosample.attribute:study_group | Healthy |
| SAMN09467083 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:study_group | Healthy |
| SAMN09467083 | subject_id | HC01 | R1 | 0.85 | biosample_attr | HC01 |
| SAMN09467083 | timepoint_label | 1 | R1 | 0.80 | biosample_attr | 1 |
Sequencing
122 runs over 116 samples · mean 1.15 Gbp per run (median 0.99 Gbp, total 139.84 Gbp; 122 runs with a base count) · layout PAIRED 122 · platform ILLUMINA 122 · models Illumina HiSeq 2500 (122) · 64% of runs with a Sandpiper profile · first public 2018-06-26
Authors (0)
No author record.
Downloads
PRJNA477357.csv.gz (4.2 KB) · parquet (75.3 KB) — all 116 samples, every field with route and confidence · PRJNA477357_determinations.csv.gz (4.9 KB) — 780 evidence rows