{ "registry_schema": "nmd-vcell-cell-context-registry/1.0", "interface_build": "EA-20260817-57", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "score_policy": "No scalar context-readiness score is computed.", "counts": { "context_records": 10, "diseases": 4, "observed_or_measured_contexts": 9, "required_outcome_missing_contexts": 1, "required_truth_missing_contexts": 1, "direct_dmd_candidate_perturbation_outcomes": 0 }, "records": [ { "context_id": "CTX-DMD-MYOGENIC-CORRECTION", "disease": "DMD", "context": "Myogenic induction / DMD-locus correction", "evidence_state": "MEASURED_CORRECTION_REFERENCE", "coverage_group": "observed", "source_dataset": "GSE272233", "unit_structure": "Biological repeat / sample; 3 repeats per group", "observed_result": "21 samples; 24 background-specific dual-supported reversal pathways; 0 strict reversals shared across all 3 backgrounds.", "permitted_use": "DMD induction and locus-correction reference", "claim_ceiling": "No candidate-gene response prediction", "href": "/resource/measured-dmd-evidence/", "statistical_unit": "Biological repeat / sample; 3 repeats per group" }, { "context_id": "CTX-DMD-PATIENT-MUSCLE", "disease": "DMD", "context": "Patient skeletal muscle", "evidence_state": "MEASURED_DISEASE_REFERENCE", "coverage_group": "observed", "source_dataset": "PRJNA772047", "unit_structure": "Independent patient sample / pathway-level pseudobulk analysis", "observed_result": "291 sample-level DMD disease pathways supported by CAMERA in the external patient-muscle reference.", "permitted_use": "External disease-pathway replication", "claim_ceiling": "No candidate-gene perturbation efficacy", "href": "/resource/measured-dmd-evidence/", "statistical_unit": "Independent patient sample / pathway-level pseudobulk analysis" }, { "context_id": "CTX-DMD-CANDIDATE-PERTURBATION", "disease": "DMD", "context": "Candidate perturbation in DMD muscle", "evidence_state": "MISSING_REQUIRED_OUTCOME", "coverage_group": "missing", "source_dataset": null, "unit_structure": "Required matched DMD/control biological repeats", "observed_result": "0/21 candidates have an independent perturbation outcome in a DMD muscle model.", "permitted_use": "Study design and predictability gating only", "claim_ceiling": "Prediction locked; absence is not a negative effect", "href": "/resource/prediction_readiness", "statistical_unit": "Required matched DMD/control biological repeats" }, { "context_id": "CTX-FSHD-PATIENT-MYOTUBE", "disease": "FSHD", "context": "Patient myotube nuclei", "evidence_state": "MEASURED_DESCRIPTIVE", "coverage_group": "observed", "source_dataset": "GSE143452", "unit_structure": "8 samples from 1 FSHD2 and 1 control donor", "observed_result": "32,273 nuclei; all 17 requested DUX4-axis genes detected; donor-general prevalence is not estimable.", "permitted_use": "Descriptive state stratification", "claim_ceiling": "No donor-general or patient treatment estimate", "href": "/resource/disease/fshd/", "statistical_unit": "8 samples from 1 FSHD2 and 1 control donor" }, { "context_id": "CTX-FSHD-IDUX4", "disease": "FSHD", "context": "Inducible DUX4 myoblast time course", "evidence_state": "INDUCED_CELL_LINE_RESPONSE", "coverage_group": "observed", "source_dataset": "GSE205421", "unit_structure": "4 culture wells per condition across 6 conditions", "observed_result": "24 samples; 6,986 genes significant at 14 h using q < 0.05 and |log2FC| ≥ 1.", "permitted_use": "DUX4-response timing and experiment design", "claim_ceiling": "Cell-line response, not patient therapeutic efficacy", "href": "/resource/disease/fshd/", "statistical_unit": "4 culture wells per condition across 6 conditions" }, { "context_id": "CTX-DM1-ISOGENIC-MYOBLAST", "disease": "DM1", "context": "Isogenic repeat-corrected myoblast", "evidence_state": "MEASURED_CORRECTION_REFERENCE", "coverage_group": "observed", "source_dataset": "GSE127296", "unit_structure": "Independently derived clone; clone identity retained", "observed_result": "8 clones; 163 differential splicing events at FDR < 0.05; clone effects remain a stated boundary.", "permitted_use": "Expression and splicing correction reference", "claim_ceiling": "Clones are not independent patients", "href": "/resource/disease/dm1/", "statistical_unit": "Independently derived clone; clone identity retained" }, { "context_id": "CTX-DM1-PATIENT-MUSCLE", "disease": "DM1", "context": "Patient skeletal muscle", "evidence_state": "MEASURED_DISEASE_REFERENCE", "coverage_group": "observed", "source_dataset": "GSE201255", "unit_structure": "Independent biopsy; repeat biopsies excluded", "observed_result": "36 genes overlap the isogenic and patient splicing signals; global expression alignment is negligible (Spearman ρ = -0.039).", "permitted_use": "Patient expression/splicing comparison", "claim_ceiling": "No prognosis or treatment ranking", "href": "/resource/disease/dm1/", "statistical_unit": "Independent biopsy; repeat biopsies excluded" }, { "context_id": "CTX-SMA-SPINAL-ORGANOID", "disease": "SMA", "context": "Spinal organoid / ASO response", "evidence_state": "MEASURED_INTERVENTION_REFERENCE", "coverage_group": "observed", "source_dataset": "GSE290979 / GSE290980", "unit_structure": "Donor-derived line after technical aggregation", "observed_result": "31 samples from 3 control, 2 SMA and 2 ASO-treated SMA lines; no global gene-expression reversal.", "permitted_use": "Human neural intervention-response design", "claim_ceiling": "No patient motor-outcome prediction", "href": "/resource/disease/sma/", "statistical_unit": "Donor-derived line after technical aggregation" }, { "context_id": "CTX-SMA-TREATED-MUSCLE", "disease": "SMA", "context": "Treated patient skeletal muscle", "evidence_state": "MEASURED_RESIDUAL_REFERENCE", "coverage_group": "observed", "source_dataset": "GSE252128", "unit_structure": "Independent biopsy", "observed_result": "8 treated SMA versus 7 control samples; 0 genes at q < 0.05 and |log2FC| ≥ 0.5; residual-module q-values exceed 0.30.", "permitted_use": "Residual muscle-module experiment design", "claim_ceiling": "Null threshold result is not proof of full correction", "href": "/resource/disease/sma/", "statistical_unit": "Independent biopsy" }, { "context_id": "CTX-SMA-NEURONAL", "disease": "SMA", "context": "Motor and cortical neurons", "evidence_state": "MEASURED_DISEASE_REFERENCE", "coverage_group": "observed", "source_dataset": "GSE302774", "unit_structure": "Independent culture replicate; n = 3 per condition and context", "observed_result": "KIF5A decreased concordantly in both neuronal contexts (log2FC approximately -1.31 in each).", "permitted_use": "Cross-neuronal disease-context comparison", "claim_ceiling": "No calibrated intervention or patient response", "href": "/resource/disease/sma/", "statistical_unit": "Independent culture replicate; n = 3 per condition and context" } ], "claim_boundary": "Context records summarize released measurements and explicit missing target-context outcome. They do not create a calibrated perturbation response, therapeutic ranking, patient trajectory or clinical recommendation." }