On-Premises NGS Deployment for Data-Privacy-Constrained Hospital Networks

A hospital network running clinical genomics programs needed the analytical capabilities of a cloud-native NGS platform — but strict data-residency requirements meant patient sequencing data could not leave the hospital perimeter. Sequoia re-architected the platform for on-premises deployment, preserving full cloud feature parity with zero external network dependencies.

The Challenge

The existing NGS platform was built cloud-native: object storage for reference data, managed databases for sample tracking, cloud-based container orchestration for pipeline execution, and managed APIs for data access. Every core function depended on external cloud services that the hospital's data governance policies prohibited.

The clinical genomics team couldn't simply use a different tool — the platform had been designed around their workflows and validated for their regulatory requirements. What they needed was the same platform, running entirely inside the hospital network boundary.

“We couldn't send a single byte of patient genomic data outside our network — and we needed the same analysis capabilities our colleagues at cloud-connected sites were using. We needed parity, not compromise.”

— Clinical Genomics Director

Our Approach

Sequoia systematically audited every cloud service dependency and mapped each to an on-premises equivalent — preserving all platform behaviors without any external network calls:

• Cloud-to-on-prem architecture decomposition — Every managed cloud service — object storage, databases, container orchestration, API gateways — replaced with a self-hosted equivalent deployable on the hospital's existing compute infrastructure.
• Local container orchestration — Cloud-managed Kubernetes replaced with a self-hosted cluster. Auto-scaling and resource management behaviors preserved through cluster autoscaler configurations tuned for on-premises resource pools.
• Air-gapped pipeline execution — All container images, reference datasets, and tool binaries served from an internal registry and local storage. The deployment package ships as an offline bundle — no outbound internet access required at runtime.
• Data privacy and audit controls — Role-based access controls, audit logging, and encryption at rest and in transit enforced by the on-premises infrastructure — meeting HIPAA technical safeguards and local data governance requirements.

The Outcome

The platform deployed inside the hospital network with no outbound internet access required — pipeline management, auto-scaling, real-time QC, and sample tracking all operational on-premises. The clinical genomics team gained access to the same capabilities as cloud-connected peers without any data residency compromise.

The deployment model is now being adopted at additional data-privacy-constrained sites within the network — the offline bundle and standardized deployment process make each new site a days-long rollout rather than a custom re-architecture effort.

Published by the Sequoia Team