NMD-VCell Neuromuscular Virtual Cell Research Platform Module: Design · Evidence → perturbation → experiment → outcome NMD = neuromuscular disorders
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Release 2026.08DMD context observedDMD candidate-conditioned prediction not yet eligible

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Evidence freeze: 3 August 2026 Resource: v1.2.0-measured-dmd-evidence Schema: 1.1 Open release status →

DNAAF3 Study Card

Truth-generation Study Card

SC:v1.2.0-measured-dmd-evidence:DNAAF3:1.5-DRAFTDRAFT

DNAAF3

expression verification Verify expression

Is DNAAF3 detectably expressed at RNA and protein level in the intended human myogenic state?

Registration completeness38%
Missing before registration
  • direction rationale
  • numeric minimally important effect
  • numeric negligible-effect margin
  • QC thresholds
  • final powered sample size

Decision summary

DNAAF3 is ready for a bounded next step, not a DMD response claim.

Is DNAAF3 detectably expressed at RNA and protein level in the intended human myogenic state?

What we know
observed same context perturbation
What remains uncertain
GAP-06 Expression feasibility is not verified in the intended model
Experiment entry state
Draft design; registration fields remain open
Next action
Verify expression
Lifecycle track
Generate new truth. A prediction is not required for this study.
First fields to close
  • direction rationale
  • numeric minimally important effect
  • numeric negligible-effect margin
  • QC thresholds
  • final powered sample size
Continue the designInspect the evidence

Study Freeze Gate

Complete the required design fields before creating a review-ready frozen dossier.

Readiness: 38% · 5 required fields remain open.

Complete required fields

Freezing creates an immutable, checksum-bound Study dossier. External registration remains a separate authority action.

Research object trace

GENE:v1.2.0-measured-dmd-evidence:DNAAF3 → comparison-not-available → PLN:v1.2.0-measured-dmd-evidence:DNAAF3:1.0-DRAFT → SC:v1.2.0-measured-dmd-evidence:DNAAF3:1.5-DRAFT → OUT:v1.2.0-measured-dmd-evidence:DNAAF3:PENDING

Traceability only; object links do not register a prediction or measured DMD outcome.

SuggestedSelectedFrozenMeasuredCurrent protocol values are suggestions until experimental authority selects and freezes them.

Study Card visual summary

Frozen evidence and registration route

This multi-panel view turns the frozen Study Card fields into a visual audit of what is known, what is missing and what must be registered next.

BoundaryDescriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated.
Registration readiness 38% 5 open fields
Current supported level L2 observed same context perturbation Observed evidence ceiling in this record
Highest assessed context L2 observed same context perturbation Assessment does not imply support
Target closure layer L4 DMD functional validation required
DMD source agreement 100% 1/1 sources · consistent up
Muscle expression 0.08 TPM below 1 TPM context flag
a

Frozen evidence route

  1. L1Resource recordHGNC-resolved typed research object
  2. L2Observed HepG2 perturbation115 observed cells
  3. L3aExternal context screennot assessed
  4. L3bIndependent perturbation replicationsame-perturbation replication absent
  5. L4DMD muscle functional validationDMD-relevant functional validation absent
  6. REGRegistered Study Card5 open fields before registration
b

Bioinformatics result snapshot

Legacy integrated DMD priorup
Source agreement100%
Skeletal-muscle TPM0.08
External screennot assessed
Dependency cautionnot flagged
DepMap effect0.06
c

Evidence-to-experiment route

Context

Intended human myoblast/myotube model; healthy, DMD or isogenic status must be declared before registration.

Perturb

No perturbation escalation. Verify RNA by qPCR/ddPCR and protein by an orthogonal assay where a validated reagent exists.

Endpoint

Predeclared RNA detectability and, where feasible, protein detectability in the intended cell state.

Infer

Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.

Model

Linear mixed model on log expression with state fixed effect and donor/batch random intercepts when supported.

d

Registration gap map

  • direction rationale
  • numeric minimally important effect
  • numeric negligible-effect margin
  • QC thresholds
  • final powered sample size

These bars are field-state indicators only. They do not create a target score, rank, cluster or prediction claim.

Field state · Suggested

Design options for experimental review

Biological context

Intended human myoblast/myotube model; healthy, DMD or isogenic status must be declared before registration.

Perturbation modality

No perturbation escalation. Verify RNA by qPCR/ddPCR and protein by an orthogonal assay where a validated reagent exists.

Primary endpoint

Predeclared RNA detectability and, where feasible, protein detectability in the intended cell state.

Primary estimand

Mean log-scale expression in the intended state and the proportion of independent biological replicates above the predeclared detection threshold.

Inferential unit

Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.

Planning sample size

3–6 independent biological replicates/donors per intended state as a planning range; final n requires variance-based power analysis.

Randomisation unit

Independent culture/donor allocation to assay batch.

Statistical model

Linear mixed model on log expression with state fixed effect and donor/batch random intercepts when supported.

Decision-blocking gap

GAP-06 Expression feasibility is not verified in the intended model

Highest missing evidence layer

L4 dmd functional validation

GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication

Perturbation-direction rationale

Current selection: unresolved requires registration

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.

Allowed registered hypotheses: activation; inhibition; bidirectional exploration; direction not identifiable.

Comparator and controls

  • No-template and no-reverse-transcriptase controls.
  • Positive-expression tissue/cell control.
  • Housekeeping genes and assay-specific protein control.

Secondary endpoints

  • Myoblast-to-myotube expression change.
  • Between-donor expression heterogeneity.
  • Assay limit of detection and quantification.

State-transition extension

Mechanism hypothesis and registered time axis

Scientific object: perturbation × cell state × disease context × time × phenotype

Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence.

6–12 hearly molecular or signalling response

planning default requires assay calibration

24–48 hregulatory program and cell-state transition

planning default requires assay calibration

4–7 ddifferentiation and functional phenotype

planning default requires assay calibration

Cell context fields

Required before registration: healthy, DMD or isogenic corrected. Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube. Required before registration; preserve donor-specific estimates.

Cell–cell consequence

Current status: not assessed. Future levels: conditioned medium; two-cell co-culture; three-dimensional muscle model; spatial perturbation model.

Blocking factors

  • Donor or isogenic pair.
  • Differentiation batch.
  • Assay plate.

Assay QC thresholds

  • Numeric RNA/protein detection thresholds must be filled before registration.
  • Replicate CV and amplification-efficiency limits must be assay validated.

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.

Multiplicity and missing data

Primary gene × assay endpoints declared on this card; adjust secondary panels separately.

Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.

Replication rules

Not applicable until a perturbation study is registered.

The expression gate must be met in at least two independent biological replicates and not be driven by one donor.

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.
Time and cost2–4 weeks after assay setup; planning estimate only. Institution- and assay-dependent; obtain a local itemised quote before registration.
Preregistration statusdraft requires direction rationale numeric effect margin sample size and qc thresholds
Lifecycle ruleThis draft is editable. Registration requires a timestamp and checksum; a registered revision is immutable and any correction must supersede it.
Escalation ruleEscalate from L2 to L3b only after independent context-matched perturbation replication; L4 requires replicated DMD-relevant muscle evidence.
Evidence transitionCurrent evidence state → predeclared independent test → governed evidence-level review.

Version history

Study Card 1.4 → 1.5

Field groupChangeScientific effect
Object identityCard schema and object version advanced to 1.5.Traceability only
State-transition designCell context, timepoint roles, mechanism hypothesis and cell–cell consequence fields added.Design scaffold expanded
Frozen evidenceNo supporting evidence, evidence level or outcome was added.Unchanged

This is a draft-to-draft schema revision, not a registered-study amendment and not an evidence upgrade.

Data-release planRelease 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.