A guide to building and securing the genomic infrastructure that powers modern clinical labs and genome centers — from data warehousing and cybersecurity to deployment architecture and regulatory compliance.
Hospitals and testing laboratories are undergoing a digital transformation that places personal identity and medical records at the center of daily operations. In the field of genomics, diagnostic processes depend on cross-referencing patient-specific data with specialized databases — expanding the attack surface that laboratories must defend.
The architecture chosen to store and analyze this data is critical to providing the best protection against a data breach. Liability and institutional risk are highly regulated in the healthcare space, and the consequences of a breach extend far beyond financial penalties — genomic data, unlike a credit card number, cannot be reissued once exposed.
Modern precision medicine workflows require open IT infrastructure, internet-connected annotation resources, and cloud-based analytics. This shift has dramatically expanded the attack surface that laboratories must defend.
Healthcare data is uniquely sensitive because it is irreversible. Unlike a compromised credit card number which can be cancelled and reissued, genomic data, medical histories, and biometric identifiers cannot be changed once exposed.
Malicious software encrypts mission-critical data and demands payment. Offline and air-gapped systems are immune to network-delivered encryption attacks.
Social engineering campaigns target lab personnel to disclose credentials or personally identifiable information.
Attackers flood networks to exhaust resources or compromise DNS to redirect legitimate traffic to malicious locations.
Two major regulatory frameworks govern the protection of patient data in genomic testing. Both motivate investment in software architectures that are secure by design.
The primary US regulation establishing standards for the protection of electronic protected health information (ePHI). Laboratories must implement administrative, physical, and technical safeguards to ensure confidentiality, integrity, and availability.
The EU regulation strengthening individual privacy rights. Applies to any organization handling data of EU residents and imposes strict requirements on data processing, storage, and cross-border transfer of health data.
As genomic testing expands internationally, laboratories face increasing requirements to keep data within specific jurisdictional boundaries. The deployment model chosen determines the security posture and sovereignty guarantees available.
Deploy behind your institutional firewall. Full control over data storage and compute resources. All patient data, annotations, and analysis results remain within the physical boundaries of the institution.
Bring Your Own Cloud — scale compute and storage using your own AWS or Azure instance. Maintain full administrative control over your genomic environment in your chosen region.
Fully offline deployment with no internet connection. All software, annotations, and licensing operate on an isolated internal network. Updates are transferred manually via physical media.
A genomic data warehouse serves as a centralized, genetically-aware repository that captures every sample, variant call, annotation, and clinical report produced by a lab's sequencing pipeline — turning raw sequencing output into an evolving institutional knowledge base.
Query internal allele frequencies and prior observations — "Have we seen this variant before?" and "At what frequency does it occur in our own patient population?"
Monitor external sources and alert clinicians when classifications change for variants previously observed in their patient cohort — a safety-critical function.
Enable cohort studies comparing affected and unaffected participants at the genomic level, supporting population-frequency analyses across stored samples.
Exchange data with LIMS, EHR, and billing systems through standardized APIs. Automate downstream workflows and report delivery.
A central warehouse coexists with departmental data marts. Enforces common standards and supports enterprise-wide queries while giving individual labs autonomy.
All data resides in one monolithic warehouse. Simplifies global access but reduces departmental flexibility. Best suited when most use cases require organization-wide data access.
Each lab maintains its own independent instance, with data exchanged through bidirectional import/export. Works well for loosely-coupled collaborations across research labs.
Lab directors face the challenge of growing sample volumes while maintaining strict clinical consistency and regulatory compliance. Enterprise infrastructure turns individual analysts into a synchronized clinical engine.
Build a reusable knowledgebase of variant assessments. Once classified, a variant is instantly available across the organization for future samples.
Manage analysts, reviewers, and directors with fine-grained permissions and SAML/LDAP/Active Directory SSO integration.
Process hundreds of exomes or genomes in parallel using standardized filter chains and validated pipeline controls with full audit trails.
Automatically track variant frequencies across your internal cohort to identify common artifacts or rare occurrences within your patient population.
Explore the Golden Helix platform and deployment options that put these infrastructure principles into practice.
Enterprise variant data management, centralized assessment catalogs, and reclassification monitoring.
Cloud, on-premises, and air-gapped deployment options for your security requirements.
ISO 13485 certified QMS, CE marking (IVDR), and CAP/CLIA support for clinical laboratories.
Expert-led technical articles and webcasts on scaling clinical lab infrastructure, data management, and security.
Join the world's leading genome centers and clinical labs using Golden Helix to automate high-throughput pipelines and maintain global clinical standards.