Alzheimer cfDNA application pack (example)¶

Instance of the methylation application-pack pattern (disease application). A staged (Control -> MCI -> AD) cfDNA DNA-methylation study on the existing methylation SaMD control plane. It selects assay procedure cfdna_wgbs_plasma (linear WGBS, fragmentomics, gene FeatureCuts, no cell deconvolution), the samd_* profile ladder, and the cfDNA analyte profile. The pack is config + cohorts + partitions + a disease overlay — no new actions or aligners.

See the operator guide: Usage ch.21 Alzheimer cfDNA pack and the shared methylation workflow: end-to-end workflow.

Files¶

File	Role
`project_Healthy_vs_AD_Stages.json`	Study manifest: Control vs MCI vs AD stages, cfDNA analyte, `methylation` modality, progression labels, partitions (placeholder IDs)
`context_alzheimer_cfdna.json`	Disease overlay: `pipelineProcedure=cfdna_wgbs_plasma`, `mapper.disease_term=Alzheimer's disease`, `enricher.library_preset=neuro-core`, progression
`data/*.csv`	Cohort CSV stubs (replace placeholder IDs with real, patient-disjoint sample IDs)

Instantiate on /work¶

Studies live under /work/projects/<study>/. Scaffold with the CLI, then copy this manifest/overlay in:

methyl-study-init \
  --study-id alzheimer-cfdna \
  --name Healthy_vs_AD_Stages \
  --analyte cfdna \
  --modality methylation \
  --stages 2 \
  --intended-use "Research-use cfDNA methylation classifier for Alzheimer detection." \
  --output-root /work/projects
# then rename the two disease stages to MCI / AD (see this manifest), fill data/*.csv,
# and assign patient-disjoint validation_partitions.

Run the SaMD ladder¶

# Research (procedure points at no-deconv lifecycle)
methyl-workflow-run \
  --program workflow_engine/domain/fixtures/study_validation_lifecycle_no_deconv.program.json \
  --context-file docs/examples/samd/alzheimer-cfdna/context_alzheimer_cfdna.json

# Enrichment (requires non-empty locked_test) -> switch pipelineProfile to samd_holdout_enrichment
# Pivotal (requires non-empty pivotal_validation) -> switch pipelineProfile to samd_pivotal

Enrichment uses the neuro-core library preset from the enrichment preset registry (methyl-cfg sync-library-presets), not the oncology cancer-core default.