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Roadmap

Product direction and platform summary. For the detailed engineering + regulatory action plan see IMPROVEMENT-WORKPLAN.md; for the IVDR technical file see regulatory/.

Current Platform

  • FastAPI backend, React/Vite (TypeScript + Tailwind) frontend, orchestrated via Docker Compose.
  • Postgres for metadata, access control, review state, and the clinical audit/sign-out trail; ClickHouse for variant storage.
  • Family workspace spanning small variants, structural variants, CNVs, a cross-modality variant summary, repeat expansions (TRGT), Paraphase, and mtDNA analysis.
  • Visualization suite: coverage/APCAD charts, small-variant / SV / CNV / gene / segmental-duplication / DGV / blacklist tracks, ideograms, Circos, pedigrees, and the PGT haplotype/lineage tracks (IBD founder colouring + raw phased markers + ROI overview).
  • Clinical pipeline: semi-automatic ACMG/AMP classification (SNV + CNV + mtDNA), HPO/Monarch phenotype scoring, variant prioritization with a ranking cache, and family report drafting.
  • Monogenic NIPT (cfDNA-from-plasma): fetal-fraction estimation, the maternal/fetal VAF category model, and sample-integrity QC.
  • Clinical traceability: annotation/reference-version manifest, per-classification evidence snapshots, classification-drift detection, an append-only hash-chained audit trail with integrity anchors, and case sign-out with a frozen, versioned report snapshot.
  • Gene Explorer with MANE/RefSeq/canonical transcript badges; Global Small Variant Explorer for cross-project, variant-centric aggregation (keyset-paginated).
  • Operability: build/version identity scaffolding, scheduled ClickHouse integrity monitoring, durable audit/telemetry pipeline, external-call resilience (bounded timeouts + backoff), and TLS for Postgres/ClickHouse.

Regulatory Framing

CoGA is operated as an in-house IVD under IVDR Article 5(5) at CMGG (ISO 15189). The device boundary is annotated VCF → signed clinical report, and the technical file lives in regulatory/. Engineering work is weighed for its GSPR / ISO 14971 / IEC 62304 / ISO 27001 / GDPR consequences, not engineering merit alone — see the workplan for the per-finding mapping.

Near-Term Direction

  • Close the live workplan's Phase 1/3 items — finish the version-identity → sign-out binding, reference-DB/SOUP provenance capture, and the change-control evidence (release tags, CHANGELOG, signed release records).
  • Execute the performance evaluation (TF-10 → TF-11): the largest substantive regulatory gap; gated on clinical-lead comparators/thresholds/N.
  • Operational maturity: backups + tested restore, a /metrics substrate, the versioned migration ledger, and a stuck-import reaper.

Product Work

  • Extend the variant explorer toward additional aggregation views (gene-centric, transcript-centric, cohort allele frequencies).
  • Continue refining family review and sign-out workflows.
  • Improve project-level administration and import observability.
  • Ingest per-transcript MANE Select / MANE Plus Clinical tags during gene-reference sync so the Gene Explorer badges populate from source data.