Healthcare Data Engineering

Healthcare Data Engineering for Genomics, Clinical Labs & Life Sciences

Three numbers decide whether your data platform is working. Audit-evidence assembly: weeks or minutes? Analyst data-prep time: 40% or under 10%? AI on internal data: production or proof-of-concept? NonStop fixes the math.

Schedule a 45-Minute Architecture Review →
Platform HealthLive
98%
Audit Readiness
<10%
Data Prep Time
4min
MTTD
HIPAA Compliance
100%
ETL Pipeline Health
96%
AI/ML Readiness
88%
<10%
Analyst data-prep time (from 40-50%)
4min
Mean time to detect data incidents
50%
Cloud data infrastructure cost reduction
Continuous
Audit-ready evidence assembly
The Problem in 2026

The data crisis inside clinical labs and genomics companies

Most healthcare data infrastructure was built before WGS became routine, FHIR was a delivery requirement, or HHS OCR expanded enforcement.

Scientists spend 40%+ of their time wrangling data
High-value analysts blocked by manual data prep instead of doing science.
Pipelines fail silently
No one notices until dashboards go stale. Incidents take hours to days to surface.
Audit prep eats weeks of engineering time
4-8 week audit cycles drain bandwidth every quarter instead of being continuous.
Cloud spend grows faster than throughput
LIMS, EHR, sequencer, and research data live in disconnected, costly silos.
AI stuck in proof-of-concept forever
No production feature store. Internal data not AI-ready. Models never ship.
NonStop Targets

Five outcomes every engagement delivers

Data prep time - from 40-50% down to under 10% of analyst hours
Mean time to detect incidents - hours to days, down to minutes
Cloud data infrastructure cost - 30-50% reduction
Audit evidence assembly - 4-8 weeks down to continuous, audit-ready
AI/ML readiness - stuck in PoC moved to production feature store
Every contract names the target, the measurement methodology, and the timeline.
<10%
Analyst data-prep time (from 40-50%)
4min
Mean time to detect data incidents
50%
Cloud data infrastructure cost reduction
Continuous
Audit-ready evidence assembly
What We Build

Eight disciplines. Most engagements include four to six.

HIPAA-compliant by architecture. Scoped to named outcomes: TAT, cost-per-sample, audit cycle, AI-readiness.

01
Healthcare Data Lakes and Lakehouses
Snowflake, Databricks, AWS HealthOmics, Redshift. Bronze/Silver/Gold medallion architecture. Apache Iceberg or Delta as the storage layer. Unity Catalog governance.
IcebergDelta LakeDatabricks
02
Healthcare ETL and ELT Pipelines
Apache Airflow, dbt, Databricks Workflows, AWS Glue. FHIR R4 ingestion as first-class flow. HL7 v2 normalization. EHR extraction, claims ETL, clinical trial pipelines.
AirflowdbtFHIR R4
03
Bioinformatics and Genomic Pipelines
Nextflow DSL2, Snakemake, WDL. GATK HaplotypeCaller, DeepVariant, Mutect2. RNA-Seq, single-cell, VCF on Iceberg. NIST GIAB benchmarking before production.
NextflowGATKWGS/WES
04
Real-Time Health Data Streaming
Apache Kafka, Flink, AWS Kinesis, MSK. Sequencer events, lab instrument events, EHR events. TAT alerting. QC anomaly detection. Dashboards in seconds, not batch runs.
KafkaFlinkKinesis
05
Clinical Data Integration
HL7 v2 to FHIR R4/R5 translation. SMART on FHIR v2, FAST UDAP. Epic, Cerner, athenahealth, Meditech integrations. ONC Inferno-validated CI. US Core 6.1.0 conformance.
FHIR R4/R5EpicCerner
06
HIPAA-Compliant Data Engineering
HIPAA-aligned VPC, KMS encryption, ABAC for PHI, dynamic PHI masking, synthetic data for non-prod, immutable audit trails per 45 CFR 164.312(b). SOC 2, CAP/CLIA, GDPR.
HIPAASOC 2GDPR
07
Data Quality, Lineage and Observability
Great Expectations, Soda, automated quality gates at every stage. Monte Carlo, Lightup for freshness and schema drift. MTTD for data incidents from hours to minutes.
Monte CarloOpenMetadata
08
Data Engineering for AI and ML
Feature engineering for omic and clinical datasets. Training warehouses on Databricks or Snowflake. MLflow, Feast, Tecton. The infrastructure that moves AI from PoC to production.
MLflowFeastTecton
Sector-Specific Work

Built for the complexity of your specific sector

Every sector has distinct regulatory requirements, data formats, and infrastructure patterns. NonStop brings production experience across all five.

Genomics
Genomics and Bioinformatics Labs
  • WGS, WES, panel, and array pipelines
  • Variant data management on Iceberg-backed storage
  • Spark-native VCF processing via Glow
  • Pharmacogenomics and single-cell platforms
  • Federated genomics architectures
Clinical
Clinical Reference and Hospital Labs
  • CAP/CLIA-compliant pipelines under 42 CFR Part 493
  • Real-time LIMS-to-EHR via HL7 v2 and FHIR R4
  • TAT and QC observability dashboards
  • FHIR DiagnosticReport output
  • De-identified data pipelines for AI
Precision Medicine
Precision Medicine and Biotech
  • Multi-omic data warehouses
  • Biobank platforms and cohort management
  • Drug discovery pipelines
  • Phenotypic-genomic harmonization
  • Biomarker and target identification infrastructure
Pharma R&D
Pharma R&D and CROs
  • Real-world evidence pipelines
  • Clinical trial data management
  • 21 CFR Part 11 and GDPR-compliant engineering
  • Multi-sponsor data segregation
  • Federated architectures
Life Sciences SaaS
Life Sciences SaaS Companies
  • Multi-tenant HIPAA and SOC 2 isolation
  • FHIR-native APIs
  • Customer-controlled data residency
  • Enterprise-deal-ready data engineering
Why NonStop
Domain depth. Compliance by architecture. Outcome-targeted.
  • Engineers who shipped production genomics or life sciences platforms
  • Compliance in the IaC and data platform, not in a slide deck
  • Every contract names the output and measurement methodology
Technology

Production-grade, clinically-validated tech stack

Every technology choice is deliberate. Selected for HIPAA-aligned architecture, clinical-grade reliability, and petabyte-scale genomic data processing.

Cloud and Lakehouse
AWS HealthOmicsS3 TablesGlueRedshiftDatabricksSnowflakeMicrosoft FabricBigQueryAzure Synapse
Storage and Processing
Apache IcebergDelta LakeApache SparkPySparkApache FlinkApache KafkadbtAirflow
Bioinformatics
Nextflow DSL2SnakemakeWDLGATK4DeepVariantMutect2STARCell RangerVEPgnomADHail
Quality and Governance
Great ExpectationsSodaMonte CarloOpenMetadataUnity CatalogApache PolarisAtlan
Compliance and PHI
AWS KMSHashiCorp VaultPrivaceraImmutaTonic.aiMostly AICustom ABAC
MLOps and Standards
MLflowFeastTectonSageMakerFHIR R4/R5HL7 v2US Core 6.1GA4GH
How We Engage

Three engagement shapes. Pick the one that fits.

Most engagements start with a 45-minute Architecture Review. We map your current state across the eight disciplines, identify the highest-ROI investment, and scope a phased plan with named outcomes.

1
Architecture Review
Map your current state across the eight disciplines. Identify the highest-ROI investment. Scope a phased plan with named outcomes. 45 minutes. No pitch.
2
Single-Discipline Build
One discipline, end-to-end. Genomic data lake. Streaming layer. ETL modernization. Includes design, build, validation, observability, governance, and runbooks.
3
Multi-Discipline Platform
Four to six disciplines integrated as one platform. Architecture decision records. SLA dashboards. Audit-readiness wired in. Phased rollout with clear milestones.

"Stop maintaining the data infrastructure. Start running it as a platform. We will come back with a realistic scope, a phased timeline, and outcome targets you can take to your CFO."

NonStop Healthcare Data Engineering Team
What to bring to the Architecture Review
Your current data stack, your sequencing or claims volume, your top three compliance requirements, and the named outcome you would measure success against.
Why NonStop

Why labs choose us over generic data consultancies

Three reasons every Tier-1 ICP asks about. Here are the answers.

01

Domain depth, not just data engineering

Knowing Spark is not knowing how multi-allelic variants split. Or why GRCh38 reference handling breaks naive normalization. Or what FHIR Genomics Reporting actually requires. Every NonStop healthcare data team includes engineers who have shipped production for clinical genomics or life sciences customers.

02

Compliance built into the architecture

HIPAA, CAP/CLIA, SOC 2, GDPR, and 21 CFR Part 11 controls live in the IaC and the data platform — not in a slide deck. SOC 2 readiness comes from how the platform is built, not how it is documented. We engineer compliance in, not bolt it on after.

03

Outcome-targeted engagements

Hours and resources are inputs. TAT, cost-per-sample, query latency, audit cycle time, and AI-readiness are outputs. Every contract names the output and the measurement methodology. You take those targets to your CFO before we start.

Frequently Asked Questions

Do you build full data platforms, or specific layers?

Both. Most engagements scope to four to six disciplines. Some are full-platform builds for Series A/B precision medicine companies. Some are single-discipline rebuilds for established labs.A production-ready clinical bioinformatics pipeline must be reproducible across runs, scalable for clinical sample volumes, auditable for regulatory compliance, and integrated with clinical systems such as LIMS and reporting platforms.

Can you migrate us off on-prem HPC and a legacy LIMS?

Yes. Migrations to AWS HealthOmics, Databricks, or Snowflake with Iceberg are one of our most common engagements. Typical timeline: 4–9 months end-to-end with a 60–90-day parallel-run period.

Do you handle US, UK, and EU compliance together?

Yes. We engineer platforms that satisfy HIPAA, CAP/CLIA, SOC 2 Type II, GDPR, and 21 CFR Part 11 simultaneously. Data residency, encryption, and access controls are handled at the architectural level, not as per-region overlays.

When should a clinical lab outsource How do you handle PHI in non-production environments?bioinformatics pipeline development?

Through dynamic PHI masking and synthetic data generation. Developers and data scientists work with synthetic or masked datasets that preserve statistical properties while not exposing real PHI.

Can you scale to petabyte-scale genomic data?

Yes. Several NonStop engagements run on cloud lakehouse architectures with sustained processing of population-scale cohorts. Scale is a function of architectural choices made early - Iceberg partitioning, Spark execution tuning, storage tiering, spot-instance optimization.

Get In Touch

Stop maintaining the data infrastructure. Start running it as a platform

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We will come back with a realistic scope, a phased timeline, and outcome targets you can take to your CFO.