FMRP-LEAN: A HIPAA-Compliant AI-Augmented LIMS Architecture for End-to-End Clinical Assay Workflow Optimization

Abstract

Clinical biomarker workflows in translational research settings often rely on spreadsheet-driven tracking, manual quality control (QC) reconciliation, and loosely integrated systems, resulting in limited state visibility, delayed reporting, and increased operational risk. These challenges are particularly pronounced in multi-day assays such as Luminex-based quantification of Fragile X Messenger Ribonucleoprotein (FMRP), where HIPAA-compliant data governance, deterministic workflow progression, and coordinated communication across laboratory and clinical teams are required. This paper presents FMRP-LEAN, a HIPAA-compliant, AI-augmented Laboratory Information Management System (LIMS) architecture that formalizes biospecimen lifecycle management through a finite-state workflow model with explicit transition guards and dwell-time observability. The system integrates a self-hosted Supabase/PostgreSQL stack deployed within hospital-controlled infrastructure, hybrid edge-internal isolation with encrypted tunneling and loopback-only services, and bi-directional REDCap synchronization. A unified MRN-UUIDv7 identifier framework with QR-based tracking ensures traceable clinical-research linkage under PHI residency constraints. FMRP-LEAN incorporates automated statistical QC pre-screening and a governance-constrained AI operations module that operates exclusively on aggregate projections, with deterministic fallback guarantees. Deployment demonstrates improved workflow observability, reduced QC latency, and enhanced cross-role transparency between laboratory technicians, research coordinators, and patient-facing teams. The architecture provides a reproducible model for secure, state-explicit, and AI-augmented clinical research workflows in regulated healthcare environments.