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ETL2019Data Platform Architect

Healthcare Analytics ETL Pipeline

Scalable ETL platform ingesting clinical, claims, and operational data into a governed lakehouse for population health analytics and value-based care reporting.

Overview

An accountable care organization needed a unified analytics foundation to measure quality metrics, track attributed patient populations, and report on shared savings under value-based contracts. Data resided in siloed EHR extracts, claims feeds, and manual spreadsheets with inconsistent patient identifiers and delayed refresh cycles. I architected a medallion lakehouse pipeline using Azure Data Factory for orchestration, Databricks for transformation, and Delta Lake for ACID-compliant storage with time travel for audit replay. The platform serves curated datasets to Power BI and external quality registries through row-level security aligned to care team assignments.

Business Problem

Quality metric reporting lagged 45 days behind clinical activity, preventing timely care gap closure interventions. Analysts spent 60% of their time reconciling conflicting patient counts across claims and clinical sources. Value-based contract calculations lacked auditable lineage, creating disputes with payer partners over attributed population denominators. HIPAA compliance reviews flagged uncontrolled PHI copies on analyst workstations fed by ad hoc extracts.

Solution

Azure Data Factory pipelines ingest HL7 extracts, X12 claims, and reference data on scheduled and trigger-based cadences, landing raw files in bronze Delta tables with ingestion metadata. Databricks notebooks apply standardized de-identification, patient matching, and clinical concept mapping (ICD, CPT, LOINC) in silver layers. dbt models build gold-layer quality measure calculations with unit tests and schema contracts enforced in CI. Access is brokered through Synapse serverless SQL with Azure AD groups and column-level masking for sensitive attributes.

Architecture

The pipeline follows medallion architecture: bronze for immutable raw ingestion, silver for cleansed and conformed entities, gold for business-level aggregates and measure definitions. Orchestration dependencies are DAG-modeled in Data Factory with checkpoint files enabling idempotent replays after failure. Spark jobs run on autoscaling Databricks clusters sized by workload class, with job clusters terminated after batch completion to control cost. Metadata and lineage are captured in Azure Purview, linking source systems to downstream reports for audit requests.

Tech Stack

Azure Data FactoryAzure Synapse AnalyticsAzure DatabricksDelta LakeSQL Server.NET CoredbtApache Spark

Challenges

  • Patient matching across claims and clinical records without a universal identifier required probabilistic linkage with manual override tables maintained by data stewards.
  • Late-arriving claims data caused measure recalculation cascades; we implemented incremental gold-layer updates with effective-date versioning.
  • Source schema changes from EHR upgrades broke ingestion mappings; contract tests on bronze layer row counts and schema hashes detected drift within one pipeline run.
  • De-identification rules for research use cases conflicted with operational analytics needs, requiring dual gold layers with separate access policies.

Results

  • Reduced quality metric reporting latency from 45 days to 5 days after clinical period close.
  • Decreased analyst data preparation time by 62%, redirecting capacity to care gap analysis.
  • Established auditable lineage for 100% of value-based contract measure inputs, resolving payer disputes within one reporting cycle.
  • Eliminated ad hoc PHI extracts by providing governed self-service access through Synapse and Power BI row-level security.

Screenshots

Key interfaces and system views from the engagement.

Healthcare Analytics ETL Pipeline screenshot 1
Healthcare Analytics ETL Pipeline screenshot 2

Lessons Learned

  • Medallion architecture discipline prevents silver-layer shortcuts that recreate the silos you are consolidating.
  • Data quality checks belong at ingestion, not after gold-layer publication—downstream fixes are exponentially more expensive.
  • Patient identity resolution is a domain problem requiring clinical stakeholder governance, not purely algorithmic matching.
  • Lineage metadata is a compliance deliverable, not a documentation nicety; build it into the pipeline from the first source connection.

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