Lab & Clinical Workflow Platforms

LIMS Development for Genomics and Clinical Genomics Workflow Automation for Genomic Testing Operations

From test order to clinical report delivery — we engineer the genetic testing workflow software and lab informatics platforms that make every step traceable, automated, and clinically defensible.

Lab Order #LO-20240506-0041Patient: J. Smith · Test: WES Hereditary Cancer Panel · Ordered: 09:02 UTCTestOrderAccessionSample InQCPipelineReportDeliverySample Tracking✓ Accessioned 09:18✓ QC Pass · Routing: Seq-Bay-3TAT MonitorSLA Target: 5 daysCurrent: Day 2 · On TrackClinical Report — Auto-GeneratedBRCA1 c.5266dupC · Pathogenic · ACMG Class 5 · FHIR R4 DiagnosticReportDelivered to Epic EHRPatient PortalSigned: Dr. A. Patel · 11:47 UTC · TAT: 2d 2h 45m · Audit logged
End-to-End
Test Order to Report Delivery
HIPAA
Compliant by Architecture
FHIR R4
Epic & Cerner Integration
CAP / CLIA
Inspection-Ready Audit Trails

Why Genomics Lab Operations Break Down

The failure modes are predictable — and entirely avoidable with the right clinical genomics workflow software.

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Test Orders Managed Outside the System

Pre-authorization and payer checks live in email threads with no integration to lab operations. Every order entry is a manual hand-off.

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Sample Tracking Done in Spreadsheets

Lab teams manually update sample status in a LIMS built for chemistry, not genomics. Accessioning errors go undetected until a report is already late.

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Clinical Reports Assembled by Hand

Variants copy-pasted from analysis tools into Word documents. No structured output, no version control, no automated delivery to EHR or provider portals.

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Lab and Clinic Operating in Silos

LIMS, sequencing instruments, interpretation platforms, and EHRs exchange data through manual exports and emails. Every handoff introduces delay and risk.

What We Build: End-to-End Clinical Genomics Workflow Software

We engineer every layer of the clinical genomics workflow — from the first test order through to the final report in the clinician’s hands. Six capabilities. One connected system.

01 · LIMS

LIMS Development & Customization for Genomics Labs

A generic LIMS was not built for genomic testing. We develop purpose-designed lab informatics software for genomics — and customize existing LIMS platforms when you already have an investment to protect. Whether it is a ground-up build or a customization of LabWare, STARLIMS, or a comparable platform, we add the genomics-specific workflows, instrument interfaces, and downstream integrations that off-the-shelf LIMS cannot support.

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  • Sample login, accessioning, and chain-of-custody tracking with assay-specific QC thresholds and automated hold logic at each workflow stage
  • Multi-site sample management with configurable routing rules and inter-lab transfer tracking
  • Direct instrument interface modules for sequencer data ingestion and QC analyser integration
  • Immutable audit trail — every sample state change, user action, and system event timestamped and query-able for CAP/CLIA inspection and regulatory review
02 · Order Management

Test Order Management System for Genomics

The front end of the clinical genomics workflow is where most delays begin. Our test order management system for genomics handles the full pre-analytic cycle — before a sample ever arrives in the lab.

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  • Clinician-facing order entry with configurable test menus, clinical indication logic, and role-based ordering rules
  • Pre-authorization and payer eligibility verification — automated against payer rules with exception workflows for manual review
  • Requisition generation, patient consent capture, and kit dispatch management for send-out programmes
  • Real-time order status tracking from submission through accessioning — visible to ordering clinicians without EHR login, with direct Epic and Cerner EHR integration to eliminate duplicate data entry
03 · Sample Tracking

Sample Tracking Software for Clinical Labs

Between receipt and sequencing, samples pass through dozens of state transitions. Our sample tracking software for clinical labs automates that chain so nothing gets lost, nothing gets processed out of sequence, and every team member has live visibility into where every sample stands.

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  • Barcode and QR-driven receipt, labelling, and accessioning with configurable acceptance criteria by sample type
  • Automated sample routing to the correct assay workflow based on test order, sample type, and available instrument capacity
  • Automated TAT monitoring with configurable alerts when samples approach SLA thresholds — before they breach
  • Storage management: plate mapping, freezer location, long-term biobank inventory, and chain-of-custody for stored specimens
04 · Report Generation

Clinical Report Generation & Structured Delivery

The clinical report is the product your lab delivers. We engineer report generation systems that produce structured, clinician-readable outputs automatically — with no copy-paste, no version ambiguity, and no manual formatting step between variant classification and report issuance.

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  • Configurable report templates by assay type, clinical indication, and provider organisation — automated variant-to-report population with no manual re-entry from interpretation tools
  • Structured data output alongside PDF: HL7 v2 ORU messages and FHIR R4 DiagnosticReport resources for direct EHR ingestion — supporting EHR genomics integration with Epic, Cerner, and equivalent systems
  • Amendment and addendum workflow: tracked changes, approval routing, and version history for every report issued
  • TAT compliance tracking — generation timestamp, approval timestamp, and delivery confirmation recorded per order for SLA and accreditation reporting
05 · Tertiary Analysis

Tertiary Analysis Tooling & ACMG Variant Classification Workflow Software

Between variant calls and a clinical report sits the most time-intensive step in genomic medicine: variant interpretation. We build workflow software that makes tertiary analysis structured, scalable, and auditable — turning ACMG variant classification from a bottleneck into a governed, repeatable process.

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  • ACMG/AMP classification framework with configurable rule sets per assay type, structured evidence capture at the variant level, and complete audit trail through sign-off
  • VUS (Variant of Uncertain Significance) management: tracked review schedules, reclassification triggers on new evidence, and automated notification to ordering clinicians on reclassification
  • Somatic variant tiering per AMP/ASCO/CAP guidelines for oncology panels — with configurable evidence tiers and clinical actionability levels
  • Knowledge base integration: ClinVar, ClinGen, OMIM, and lab-internal interpretation history surfaced at the variant level — supporting defensible, evidence-backed classification at scale
06 · Portals

Provider & Patient-Facing Portal Development

We build secure, purpose-designed portals that deliver genomic test results to the right person in the right format. Both portals are built on HIPAA-compliant architecture with encryption at rest and in transit, MFA, and complete access logging.

🏥 Provider Portal

Clinician-facing interface for order placement, real-time status tracking, result review, and report access — integrated with Epic and Cerner via HL7 FHIR so genomic results surface inside the provider’s existing EHR workflow.

  • Order placement and tracking
  • Result and variant detail review
  • FHIR R4 EHR integration
  • Role-based access and audit logging
👤 Patient Portal

Consumer-grade patient interface for result delivery, educational content, follow-up pathway guidance, genetic counseling scheduling, and cascade screening workflow support — built to engagement standards patients expect from modern digital health.

  • Plain-language result summaries
  • Genetic counseling integration
  • Cascade screening workflows
  • Consent management and data privacy
Ready to connect your lab and clinic?
Discuss your lab and clinical workflow requirements with our team.
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Who We Build Clinical Lab Software For

Our clinical genomics workflow platforms and LIMS development services serve organizations at the intersection of genomics and patient care.

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Clinical & Reference Genomics Labs

CAP/CLIA-accredited labs running complex genomic test menus that need lab informatics software purpose-built for genomics — not repurposed from chemistry or haematology workflows.

  • LIMS built for panels, WES, WGS
  • Pre-auth & order management
  • Automated report generation
  • HIPAA-compliant architecture
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Health Systems & Academic Medical Centres

Integrated delivery networks building in-house genomics programmes — needing clinical workflow software that connects to Epic or Cerner and integrates genomic findings into existing care pathways.

  • EHR genomics integration Epic/Cerner
  • Provider and patient portals
  • FHIR R4 DiagnosticReport delivery
  • Variant interpretation workflows
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Genomics & Diagnostics Startups

Early-stage diagnostic companies launching novel genomic tests who need a clinical genomics platform that can pass regulatory scrutiny, impress enterprise customers, and scale from Day 1.

  • Clinical platform from scratch
  • Investor-ready architecture
  • ACMG classification tooling
  • Flexible engagement models

Platforms That Power Your Clinical Genomics Workflow

Our clinical workflow engineering feeds directly into these NonStop platforms:

⚕️
Clinical Genomics Platform

The full-lifecycle platform: test ordering, sample tracking, pipeline execution, variant interpretation, report generation, and EHR delivery in one governed system.

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Patient & Provider Portal

Consumer-grade result delivery, genetic counseling integration, cascade screening support, and consent management — HIPAA-compliant and EHR-connected.

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AI Genomic Data & Analytics Platform

AI-accelerated variant classification and VUS re-analysis sitting directly on top of your interpretation workflow layer.

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FAQ

Frequently Asked Questions

Do you build custom LIMS for genomics labs or customize existing platforms?

We do both. For labs needing purpose-built lab informatics software, we develop custom LIMS from the ground up — designed around your specific assay types, genomic workflows, and compliance requirements. For labs that already have a LIMS investment, we deliver LIMS customization services for genetic testing labs — extending existing platforms with genomics-specific modules, instrument interfaces, and the downstream integrations that off-the-shelf systems cannot support. The right approach depends on your current system, your volume, and your five-year roadmap. We help you make that decision during scoping, not after contract signing.

How does clinical genomics workflow automation reduce errors and improve TAT?

Most errors in genomics lab operations happen at handoff points between disconnected systems. Clinical genomics workflow automation eliminates those handoffs: sample receipt triggers accessioning automatically, QC pass triggers pipeline execution, pipeline output populates the interpretation queue, and completed variant classification populates the report template. The result is shorter turnaround time, fewer transcription errors, a complete digital audit trail, and measurable TAT reduction against your baseline. Every workflow automation we deliver is benchmarked against a pre-implementation measurement so the improvement is quantified, not assumed.

How do you integrate genomic reporting with Epic or Cerner EHR systems?

We build HL7 v2 and FHIR R4 integrations for full bidirectional data exchange between your clinical genomics platform and Epic or Cerner. Inbound: patient demographics, orders, and clinical context flow from the EHR into your genomic workflow, eliminating duplicate entry and ensuring accurate patient matching. Outbound: completed reports are delivered as HL7 v2 ORU messages or FHIR R4 DiagnosticReport resources directly into the EHR result flow, surfacing genomic findings in the clinician’s existing view without a separate portal login. We manage the Mirth Connect configuration, HL7 message design, FHIR resource mapping, and end-to-end validation.

What is the difference between a standard LIMS and a clinical genomics platform?

A standard LIMS manages samples and tracks test status. A clinical genomics platform connects that to bioinformatics pipelines, ACMG variant classification workflow software, tertiary analysis tooling, clinical report generation, FHIR-based EHR delivery, and patient-facing portals — in one governed, HIPAA-compliant system with an audit trail across every layer. Most labs start with a LIMS and bolt disconnected tools around it. We build the integrated clinical genomics platform that replaces that patchwork — or connect your existing LIMS to the rest of the stack through a clean integration layer. The distinction matters most at inspection time and at scale: an integrated platform holds up under both.

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Ready to Replace Your Lab Workflow Patchwork with a Platform That Actually Scales?

Tell us your assay menu, your current system stack, and your biggest operational bottleneck. We will scope a build tailored to your lab.