{ "object_id": "SC:v1.0.0-database-resource:NAGLU:1.5-DRAFT", "card_schema": "nmd-vcell-study-card/1.5", "card_version": "1.5", "resource_release": "v1.0.0-database-resource", "evidence_freeze": "2026-07-25", "interface_build": "EA-20260729-18", "gene": "NAGLU", "card_type": "risk_context_review", "current_action_code": "risk_review", "current_action": "Risk/context review", "lifecycle": { "state": "DRAFT", "revision": 1, "immutable": false, "registered_at": null, "supersedes": null, "immutable_after_registration": true }, "decision_blocking_gap": { "code": "GAP-08", "label": "Safety and dependency context blocks escalation" }, "highest_missing_evidence_layer": "L4_dmd_functional_validation", "secondary_gaps": [ "GAP-02 independent muscle-context perturbation", "GAP-03 DMD-relevant functional validation", "GAP-07 independent replication" ], "frozen_evidence_snapshot": { "snapshot_schema": "nmd-vcell-study-card-frozen-evidence-snapshot/1.0", "source_record": "gene/NAGLU", "highest_supported_level": "L2_observed_same_context_perturbation", "highest_assessed_level": "L3a_external_context_screen", "observed_hepg2_perturbation": { "assessment_status": "assessed", "support_status": "supported", "observed_cells": 88 }, "external_context_screen": { "assessment_status": "assessed", "support_status": "context_evidence_present", "hit": false, "effect_size": 0.061132, "fdr": 0.685034, "interpretation": "assessed_no_current_hit" }, "dmd_prior": { "integrated_prior_direction": "up", "source_direction_state": "conflicted", "source_agreement_proportion": 0.75, "agreeing_sources": 3, "assessed_sources": 4, "coverage_state": "4_of_4_sources", "uncertainty_state": "direction_conflict_retained" }, "context_metrics": { "skeletal_muscle_median_tpm": 8.66362, "depmap_median_gene_effect": -0.3062173666837822, "moderate_dependency_flag": true }, "visual_boundary": "Descriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated." }, "unresolved_question": "Does perturbing NAGLU have a context-dependent dependency or toxicity profile that blocks escalation?", "biological_context": "Matched disease-relevant and non-disease human myogenic contexts plus a tissue-breadth/dependency audit.", "perturbation_modality": "Dose/time perturbation series only after expression feasibility; include at least two reagents where feasible.", "comparator_and_controls": [ "Non-targeting and mock controls.", "Positive toxicity control.", "Matched healthy/DMD or isogenic context.", "Dose and time vehicle controls." ], "primary_endpoint": "Predeclared viability or essentiality endpoint across dose and time.", "secondary_endpoints": [ "Target engagement.", "Functional muscle phenotype.", "Off-target and tissue-breadth context." ], "primary_estimand": "Context-by-dose interaction for the primary safety endpoint.", "state_transition_design": { "scientific_object": "perturbation × cell state × disease context × time × phenotype", "mechanism_hypothesis": "Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence.", "cell_context_fields": { "disease_background": "Required before registration: healthy, DMD or isogenic corrected.", "myogenic_state": "Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube.", "donor_or_isogenic_pair": "Required before registration; preserve donor-specific estimates." }, "timepoint_plan": [ { "window": "6–12 h", "role": "early molecular or signalling response", "status": "planning_default_requires_assay_calibration" }, { "window": "24–48 h", "role": "regulatory program and cell-state transition", "status": "planning_default_requires_assay_calibration" }, { "window": "4–7 d", "role": "differentiation and functional phenotype", "status": "planning_default_requires_assay_calibration" } ], "endpoint_domains": { "target_engagement": [ "mRNA", "protein where validated", "perturbation efficiency" ], "functional": [ "fusion", "morphology", "membrane integrity", "calcium", "contraction" ], "safety": [ "viability", "proliferation", "differentiation blockade", "global stress" ], "replication": [ "reagent", "donor or isogenic pair", "future batch" ] }, "cell_cell_consequence": { "current_status": "not_assessed", "future_levels": [ "conditioned medium", "two-cell co-culture", "three-dimensional muscle model", "spatial perturbation model" ] }, "response_archetype": { "current_status": "not_assessed", "allowed_values": [ "robust_responder", "dmd_specific_responder", "donor_variable", "state_specific", "toxic_responder", "null_with_equivalence_margin", "discordant", "qc_failure", "inconclusive" ] } }, "perturbation_direction_rationale": { "selected_hypothesis": "unresolved_requires_registration", "allowed_hypotheses": [ "activation", "inhibition", "bidirectional_exploration", "direction_not_identifiable" ], "required_justification": "State whether the disease-associated direction is hypothesized as causal, compensatory or accompanying, and preserve the opposite-direction alternative. DMD direction and counteralignment never choose an intervention automatically." }, "minimally_important_effect": "Required before registration; derive from assay biology or a justified pilot and store the numeric value with units.", "negligible_effect_margin": "Required before interpreting a null result; store a symmetric or asymmetric numeric margin with units.", "suggested_sample_size_range": "3–6 independent biological replicates per context for a pilot dose/time grid; final n requires interaction-effect power analysis.", "randomisation_unit": "Independent culture well/biological replicate.", "blocking_factors": [ "Donor/isogenic pair.", "Plate.", "Dose/time batch.", "Reagent." ], "statistical_model": "Mixed-effects dose-response model with context interaction and blocked reagent estimates.", "multiple_testing_family": "Primary safety endpoint across frozen doses/times; functional endpoints are secondary.", "missing_data_rule": "Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.", "assay_qc_thresholds": [ "Numeric viability floor.", "Numeric target-engagement floor.", "Predeclared off-target exclusion criteria." ], "guide_concordance_rule": "Escalation requires directionally compatible safety estimates from two reagents.", "donor_replication_rule": "A favourable window must not be attributable to one donor/context.", "estimated_time_band": "6–12 weeks after model readiness; planning estimate only.", "estimated_cost_band": "Institution- and assay-dependent; obtain a local itemised quote before registration.", "preregistration_status": "draft_requires_direction_rationale_numeric_effect_margin_sample_size_and_qc_thresholds", "inferential_unit": "Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.", "evidence_import_requirements": [], "planning_fields_not_applicable": [], "stop_rules": [ "Stop or classify as infeasible if a required numeric QC threshold fails.", "Do not interpret a nonsignificant result as no material effect without a negligible-effect interval.", "Do not change canonical candidate status automatically; require governed review." ], "escalation_rule": "Escalate from L2 to L3b only after independent context-matched perturbation replication; L4 requires replicated DMD-relevant muscle evidence.", "evidence_transition": "Current evidence state → predeclared independent test → governed evidence-level review.", "data_release_plan": "Release the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card.", "boundary": "This Study Card is an evidence-gated design scaffold, not a protocol, power calculation, safety claim, prediction or therapeutic recommendation.", "stable_url": "study-card/NAGLU", "exports": { "json": "api/v1.1/study-cards/NAGLU.json", "yaml": "downloads/study-cards/NAGLU.yaml", "tsv": "downloads/study-cards/NAGLU.tsv" } }