Human tissue studies are small and raw human sequence data are often not open
Evidence level: proposed bottleneck; synthesis of abstract-level sources; pending approval
Many mechanistic human studies use a handful of explants, and several public GEO series state that raw human sequence files were withheld or put under controlled access.
As of . Primary source: GEO GSE290834 (raw human files not submitted).
Summary
Imaging mass cytometry compared 4 BOS, 4 RAS and 4 control lungs; micro-CT used 18 Leuven explants; a single-cell ALAD pilot included 20 participants. Among public series recorded on this site, the records for GSE289881 and GSE290834 state that raw human files were not submitted to GEO because of concerns about identifiable sequence data, and GSE274199 states that raw human files are under controlled access in dbGaP. Small samples and restricted access were observed in the sources opened; this record does not claim how common the pattern is across the field. Explant studies also capture end-stage disease only.
Details
- barrier type
- data and samples
Sources and links
Related
Links from this record
- evidence: GEO GSE290834: single-cell RNA-seq of explanted human lungs with CLAD-BOS and cGVHD-BOS
- evidence: GEO GSE289881: single-cell RNA-seq of fibroblast activation protein in human CLAD
- evidence: GEO GSE274199: single-cell analysis of acute cellular rejection and fibrogenic shift in lung allografts
- evidence: Detailed cellular and spatial characterization of chronic lung allograft dysfunction using imaging mass cytometry
- evidence: Ventilatory capacity in CLAD is driven by dysfunctional airway structure
- evidence: Persistent and progressive acute lung allograft dysfunction is linked to cell compositional and transcriptional changes in small airways
- affects: Molecular endotypes of CLAD (proposed framework)
Known gaps in this record
- overall proportion of human CLAD datasets with open raw data (no systematic survey done)
- reasons for access restrictions beyond the statements in the series records
Information resource only. Not medical advice. Not a substitute for the care of the patient's transplant team.