Microbiome of RAG-deficient patients, USA (case-control)
95 samples from the skin, nares and gastrointestinal tract of RAG-deficient patients in the USA, studying microbiomes associated with this immunodeficiency; case-control design. machine-written summary
95 samples · 122 runs · US · Age unknown · 2023 · 4.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 570 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10591041, PMC12114289 |
| ✓ Supplementary tables | 174 sample values (health condition, health condition detail) |
| – 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 resolved
3 of 7 people sampled more than once (13 samples; median 4, up to 6 per person).
Genera, mean relative abundance over 16 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 | 95 | 100% | 95 | |||
| health_condition | 87 | 92% | 87 | |||
| subject_id | 95 | 100% | 95 | |||
| collection_date | 95 | 100% | 95 | |||
| detailed_location | 95 | 100% | ||||
| latitude | 95 | 100% | 95 | |||
| location_region | 95 | 100% | 95 | |||
| longitude | 95 | 100% | 95 | |||
| health_condition_detail | 87 | 92% | 87 |
- First Animal Source Metagenome Assembly of <i>Lawsonella clevelandensis</i> from Canine External Otitis. 2025 PMID 40430785 PMC12114289 own_data
- Expanded microbiome niches of RAG-deficient patients. 2023 PMID 37757827 PMC10591041 unsure
Archive description
Recombination-activating gene 1 (RAG1) and RAG2 proteins initiate the process of V(D)J recombination in developing lymphocytes. Hypomorphic RAG mutations result in a combination of immunodeficiency and immune dysregulation and result is a broad spectrum of clinical phenotypes including an increased propensity for viral, bacterial and fungal infections. In this study, we sought to investigate the human skin, nares, and gastrointestinal tract microbiomes associated with eight RAG-deficient patients.
How this project entered the registry
Classified as human skin / gut / stool / nasal / nasopharyngeal / multiple sites shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.description · “human skin, nares, and gastrointestinal tract microbiomes”
- body site run.scientific_name · “skin metagenome”
- body site run.scientific_name · “gut metagenome”
- body site study.description · “human skin, nares, and gastrointestinal tract microbiomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30890116 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN30890116 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN30890116 | health_condition | transplant_or_immunocompromised | R2 | 0.75 | paper.supp.mmc2.xlsx[Supp Table 2 - patient data!RAG subtype] | RAG subtype: LS |
| SAMN30890116 | health_condition_detail | LS | R2 | 0.75 | paper.supp.mmc2.xlsx[Supp Table 2 - patient data!RAG subtype] | RAG subtype: LS |
| SAMN30890116 | latitude | 38.9998 | R1 | 0.90 | biosample.attribute:lat_lon | 38.999838 N 77.106017 W |
| SAMN30890116 | location_region | Maryland | R1 | 0.60 | biosample.attribute:lat_lon | 38.999838 N 77.106017 W |
| SAMN30890116 | longitude | -77.1060 | R1 | 0.90 | biosample.attribute:lat_lon | 38.999838 N 77.106017 W |
| SAMN30890116 | subject_id | RAG_pt01 | R1 | 0.85 | sample.attr.host_subject_id | RAG_pt01 |
Sequencing
122 runs over 95 samples · mean 5.12 Gbp per run (median 5.10 Gbp, total 624.94 Gbp; 122 runs with a base count) · layout PAIRED 122 · platform ILLUMINA 122 · models Illumina NovaSeq 6000 (122) · 84% of runs with a Sandpiper profile · first public 2023-06-30
Authors (26)
Blaustein RA first · Shen Z · Kashaf SS · Lee-Lin S · Conlan S · NISC Comparative Sequencing Program · Bosticardo M · Delmonte OM · Holmes CJ · Taylor ME · Banania G · Nagao K · Dimitrova D · Kanakry JA · Su H · Holland SM · Bergerson JRE · Freeman AF · Notarangelo LD · Kong HH · Segre JA last · Tóth AG first · Solymosi N · Tenk M · Káldy Z · Németh T last
Downloads
PRJNA872116.csv.gz (3.2 KB) · parquet (73.6 KB) — all 95 samples, every field with route and confidence · PRJNA872116_determinations.csv.gz (4.9 KB) — 744 evidence rows