PRAEDIGENE

Clinical-Grade Dry Lab Platform for Genomics Automation, Analysis and Reporting

PraediGene standardizes variant analysis, interpretation, reporting, and governance across oncology, germline, infectious disease, cytogenetics, and PGx. Turn raw sequencing data into clinician-friendly, EMR-ready results. PraediGene is built for enterprise labs and health systems that need consistency and speed at scale.

  • Interpretation you can stand behind: grounded in ACMG/AMP guidance
  • Calls you can trust: evidence-linked, reproducible, and traceable
  • Reporting you can use: consistent outputs across domains and laboratory sites
  • Governance that holds up: built for validation and change control

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What is PraediGene?​

PraediGene is a clinical-grade platform for genomics analysis and reporting. It automates and standardizes dry lab processes from raw sequencing data to clinician-friendly, EMR-ready results, with versioned interpretation and reporting logic that supports change control across clinical domains.

PraediGene focuses on interpretation, governance, and reporting, and is designed to fit into existing lab environments without requiring a single change to existing wet lab workflows.

Why PraediGene Exists

As genomic testing scales, the bottleneck shifts downstream. Sequencing is only the start. The hard part is producing consistent, clinically reviewable calls and reports across specialties, sites, and teams, while meeting audit and validation expectations.

Many organizations end up with tool sprawl, fragmented rule sets, and manual evidence assembly for every report. That drives variability, slows turnaround time, and increases risk when a clinician or auditor asks, “Why did you call this?”

PraediGene standardizes that work by bringing variant analysis, interpretation, reporting, and governance into one platform, so labs can scale without sacrificing confidence.

Inspection-Ready: Variant Analysis and Interpretation

In clinical genomics, labs must be able to explain and support how a variant call was made. When a clinician challenges a call or an auditor reviews a process, teams need to show their work quickly and consistently.

PraediGene is built for inspection-ready variant analysis and interpretation. It links each call to the underlying evidence, rules, and inputs, so interpretation is transparent, reviewable, and reproducible across teams and sites.

  • Traceable: Every call is linked to supporting evidence, applied rules, and the underlying inputs
  • Reproducible: Versioned logic and configurations support consistency across time, teams, and sites
  • Auditable: A complete decision trail supports validation documentation, reviews, and audits
  • PraediGene supports validation and change control expectations through versioned governance and an auditable interpretation trail.

Clinical Domains Supported

PraediGene supports the modern clinical genomics menu with consistent interpretation and standardized reporting as volumes grow and new domains are added.

Across domains, PraediGene applies the same governance-first approach so labs can scale without multiplying tools, rule sets, or reporting formats.

Enterprise Readiness

Enterprise labs depend on more than product features. They must be able to validate workflows, govern changes, and stand behind results under clinical and regulatory scrutiny. PraediGene is designed to support enterprise review with governance-first workflows and clear decision trails.

Audit Trail and Traceability

Every step is recorded, and decisions are explainable with a complete interpretation trail.

Governance and Change Control

Versioned policies and configurations support reproducibility and controlled updates over time.

Validation
Support

Outputs and workflows are designed to support verification and validation documentation expectations.

Security and Access Controls

Role-based access controls and audit logging aligned to enterprise expectations.

PraediGene supports enterprise review by making audit readiness and change control visible from day one.

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Frequently Asked Questions

PraediGene supports the full lifecycle of LDTs by streamlining the entire dry lab workflow, from raw data ingestion to final clinical reporting. Whether you’re developing targeted pharmacogenomics panels, cancer risk assays, or rare disease pipelines, PraediGene helps your lab move faster, stay compliant, and scale with confidence.

Key areas of support include:

  • Validation: Built-in tools for data processing, quality control, variant analysis, and structured reporting support. PraediGene helps ensure your test performs as intended and your results are reproducible and traceable.
  • Regulatory: PraediGene supports dry lab compliance with major regulatory frameworks including CLIA and institutional compliance frameworks. With built-in audit trails, role-based access controls, and structured data outputs, PraediGene aligns with best practices for LDT oversight and documentation.
  • Commercialization: Custom-branded reports, EHR/LIMS integration, and streamlined reporting workflows help labs monetize new tests quickly and efficiently
With flexible configuration options and proven deployment in both clinical and research settings, PraediGene helps labs bring LDTs online without the operational complexity.
PraediGene supports MRD testing by extending the clinical value of the Bio-Rad QXDx™ BCR-ABL %IS assay with a streamlined digital workflow that simplifies result tracking, enhances reporting, and improves lab efficiency.
MRD (Measurable or Minimal Residual Disease) testing detects trace levels of cancer cells that remain after treatment – even when a patient is in “clinical remission.” This level of sensitivity, especially using digital droplet PCR (ddPCR), enables earlier detection of disease recurrence in conditions like chronic myeloid leukemia (CML), where MRD monitoring guides therapy adjustments and supports treatment-free remission (TFR) planning.

PraediGene enables a complete MRD workflow with:

  • Longitudinal tracking of BCR-ABL1 test results for individual patients, supporting quarterly CML monitoring and treatment response assessment.
  • Standardized, provider-friendly clinical reports with optional interpretive comments for oncologists and hematologists.
  • Secure EMR integration, allowing test results to flow directly into clinical systems to support timely, informed decisions.
  • Full audit trails and compliance tools that align with CLIA and institutional regulatory frameworks.

Whether you’re scaling an MRD program or bringing it in-house for the first time, PraediGene helps labs deliver precise, compliant, and efficient MRD testing without reinventing your digital infrastructure.

MRD for solid tumors (ctDNA): PraediGene can also support workflows where MRD is tracked via circulating tumor DNA (ctDNA) results. Key capabilities include support for ddPCR or NGS outputs, longitudinal result tracking to visualize trends over time, customizable provider-friendly reports with interpretive context, EMR and LIMS integration patterns, and audit-ready infrastructure aligned with oncology research protocols and clinical regulations.

PraediGene supports MRD testing for solid tumors by enabling labs to track and report circulating tumor DNA (ctDNA) results with the same clarity, consistency, and regulatory compliance used in hematologic workflows. As MRD becomes increasingly valuable alongside neoadjuvant therapies in cancers like breast, colorectal, and lung, PraediGene helps labs operationalize ctDNA analysis through digital integration and longitudinal reporting with clinical clarity and regulatory confidence.

Key capabilities for solid tumor MRD workflows include:

  • Support for digital droplet PCR (ddPCR) or Next-Generation Sequencing (NGS) results: PraediGene accommodates ctDNA-based MRD assays that rely on ddPCR or other high-sensitivity detection methods.
  • Longitudinal result tracking: Capture and display serial ctDNA results over time to visualize molecular response trends across pre-, peri-, and post-treatment intervals.
  • Customizable clinical reports: Generate provider-friendly MRD reports that include interpretive comments, trend graphs, and therapeutic context.
  • EMR and LIMS integration: Deliver results directly to clinicians and link back to molecular test data for lab traceability.
  • Audit-ready infrastructure: Role-based access controls, secure data handling, and structured outputs help maintain compliance with oncology research protocols and clinical regulations.

As MRD testing evolves beyond hematologic malignancies, PraediGene ensures your lab is ready to support precision oncology for both blood-based and tissue-based solid tumor workflows.

PraediGene is designed to integrate seamlessly with most modern Laboratory Information Management Systems (LIMS) and Electronic Health Record (EHR) platforms. Our team works directly with your technical and clinical stakeholders to configure secure, automated data flows that reduce manual entry, eliminate silos, and ensure timely result delivery.

Integration capabilities include:

  • Bidirectional LIMS connectivity for automated sample tracking, result posting, and audit traceability.
  • EHR result delivery through HL7 or API-based interfaces, supporting timely access to MRD, PGx, and other genomics reports.
  • Custom mappings for test codes, patient identifiers, and report fields to ensure alignment with your existing systems.
  • Support for multi-site implementations with configurable permissions and access controls.
PraediGene enhances lab efficiency by working within your existing digital ecosystem.
PraediGene accepts a wide range of industry-standard data formats used in genomic testing, allowing labs to upload, process, and report results without reformatting or workflow disruption.
Supported input formats include:
  • FASTQ – Raw sequencing reads directly from NGS instruments
  • BAM/CRAM – Aligned sequence files for downstream variant analysis
  • VCF – Variant Call Format files for annotated or unannotated genomic variants
  • FASTA – Consensus sequences for alignment-based workflows
  • JSON/HL7 – Structured data formats for system integration and report delivery
  • CSV/TSV – Delimited formats for metadata uploads, test manifests, or batch processing
PraediGene’s flexible architecture allows labs to start at any point in the analysis pipeline, whether you’re submitting raw reads or preprocessed variant calls, and integrates easily with upstream and downstream systems such as LIMS, EMRs, or commercial analysis tools.
PraediGene fully supports major regulatory body compliant workflows and is designed to align with the operational and documentation standards required for inspections and lab accreditation.

Compliance-supporting features include:

  • Full audit trails to track user activity, test processing, and report generation. Role-based access controls for secure and segmented system usage.
  • CLIA and CAP compliant: software version control, KB management, integrated release notes, etc.
  • Structured reporting workflows that support LDT validation and regulatory documentation.
  • Customizable SOP-aligned outputs to meet the needs of individual certified labs.
  • Secure data handling and transmission in accordance with HIPAA and institutional policies.
PraediGene is actively deployed in CLIA and CAP-certified environments and supports the compliance needs of both clinical testing and translational research labs. For labs pursuing additional certifications or accreditations, our team works closely to ensure alignment with lab-specific quality and regulatory frameworks.

PraediGene supports a broad range of clinical genomics assays by providing the interpretation, reporting, and governance layer that sits downstream of sequencing and molecular testing workflows. Rather than being limited to a single test type, PraediGene is designed to standardize how results are analyzed and interpreted, how reports are generated, and how changes are governed across a laboratory’s menu.

PraediGene is commonly used to support workflows across major clinical domains, including pharmacogenomics (PGx), molecular oncology (somatic), molecular genetics (germline and hereditary testing), molecular infectious disease, and cytogenetics-related reporting needs. This platform approach helps labs reduce tool sprawl, improve consistency across programs and sites, and produce clinically defensible results that are easier to review and audit.

PraediGene accepts common industry data formats (including FASTQ, BAM/CRAM, and VCF) and is designed to fit into existing laboratory environments. If you have a specific assay type or workflow in mind, our team can review your requirements and outline the best-fit configuration.

PraediGene is designed to support defensible variant analysis and interpretation by making the decision pathway visible and reviewable. In clinical genomics, labs are often asked to justify a call by clinicians, auditors, payors, or internal quality teams. PraediGene helps teams respond quickly and consistently by providing traceability from the reported classification back to the underlying inputs and logic used.

Key capabilities include:

  • Evidence traceability: Variant calls can be linked to the supporting evidence signals and the rules applied during interpretation, enabling “show your work” review.
  • Reproducibility: Versioned configurations and interpretation policies help ensure results are consistent across teams, sites, and time, even as workflows evolve.
  • Audit readiness: Complete decision trails support validation documentation, quality review, and audit workflows, reducing the burden of reconstructing decision logic after the fact.

This approach enables labs to scale interpretation while maintaining clinical scrutiny, governance, and confidence in reported results.

BIAS-2015 is a peer-reviewed, published algorithm designed to automate variant classification using the ACMG 2015 framework. In practical terms, it applies structured evidence criteria and rule-based logic to support consistent, standards-based classification decisions.

Within PraediGene, BIAS-2015 is used as the classification engine across multiple pipelines, including germline, somatic, and pharmacogenomics workflows. It helps teams scale review by producing consistent preliminary classifications and associated evidence signals that can be reviewed, confirmed, and finalized by qualified personnel in accordance with your laboratory’s policies and interpretation practices.

Read the full publication: https://rdcu.be/eUOZy

Contact us to discuss how BIAS-2015 and PraediGene can fit into your validation, review, and reporting workflow.

Intended use: PraediGene is intended for use by qualified personnel in CLIA- and CAP-accredited clinical laboratories (or equivalent regulated environments) to support laboratory workflows for genomic analysis, interpretation, and reporting. Validation and clinical decisions remain the responsibility of the laboratory.