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General Questions

Virtual Geneticist® is an AI-powered genomic interpretation platform consisting of different modules developed by Breakthrough Genomics. The different Virtual Geneticist modules help clinical laboratories, healthcare organizations, children’s hospitals, researchers, and pharmaceutical companies analyze genomic data, prioritize potentially disease-causing variants, evaluate scientific evidence, and support clinical interpretation at scale.

Virtual Geneticist is designed for:

  • Clinical genetic testing laboratories
  • Hospitals and healthcare systems
  • Children’s Hospitals
  • Newborn-screening and population-genomics programs
  • Research institutions
  • Pharmaceutical and biotechnology companies
  • Government and public-health genomics programs

 

Virtual Geneticist is most commonly used by:

  • Medical geneticists
  • Variant scientists
  • Laboratory Directors
  • Genetic Counselors
  • Bio-informatic Teams
  • Translational Scientists
  • Research geneticists
  • Computational Biologists

Virtual Geneticist helps address several major challenges in genomic medicine:

  • Scaling interpretation for high-volume exome and genome programs
  • Large numbers of variants requiring review
  • Time-consuming literature searches
  • Inconsistent or incomplete variant interpretation
  • Re-analysis of previously negative cases
  • Integration of genomic analysis into existing laboratory workflows
  • Limited availability of experienced genomic scientists

The current suite includes VG Variant, Virtual Geneticist, Virtual Geneticist Plus, and the AI Genetic Research Agent. Together, the modules span focused variant review, case-level rare-disease interpretation, end-to-end NGS analysis and reporting, and interactive genomic research.

VG Variant starts with an individual variant and helps users review its classification, evidence, and literature. Virtual Geneticist starts with a patient case and uses phenotype and genomic data to prioritize the variants most likely to explain the patient’s condition.

Virtual Geneticist focuses on rare-disease case interpretation from VCF and phenotype information. Virtual Geneticist Plus expands the workflow upstream and downstream by adding secondary analysis from FASTQ or BAM files, sequencing quality control, advanced filtering, broader test support, and integrated clinical reporting.

The AI Genetic Research Agent provides conversational access to genomics evidence. It complements the structured interpretation modules by helping teams investigate scientific questions, synthesize literature, explore related genes and diseases, and assess emerging or therapeutically relevant evidence.

The best starting point depends on the workflow gap. Choose VG Variant for focused variant intelligence, Virtual Geneticist for scalable rare-disease case interpretation, Virtual Geneticist Plus for end-to-end NGS analysis and reporting, and the AI Genetic Research Agent for interactive genomics research and evidence synthesis.

Sequencing platforms generate genomic data. The Virtual Geneticist suite and the different Virtual Geneticist modules help turn that data into interpretable evidence and clinically relevant findings.

Depending on the module, BTG can support variant-level review with VG Variant, case-level interpretation with Virtual Geneticist, or a more complete workflow—including secondary analysis, advanced filtering, interpretation, and reporting—with Virtual Geneticist Plus.

These modules are used after sequencing to evaluate relevant evidence such as patient phenotype, inheritance patterns, disease associations, population frequency, scientific literature, and computational predictions.

Virtual Geneticist uses AI to organize, analyze, and prioritize large volumes of genomic and scientific information. AI-supported functions may include:
  • Variant prioritization
  • Phenotype matching
  • Literature identification and curation
  • Evidence extraction
  • Gene-disease association analysis
  • Variant classification support
  • Case summarization
  • Re-analysis
  • High-volume workflow automation
The system is designed to support, rather than replace, qualified clinical and scientific professionals.

Clinical and Scientific Capabilities

Virtual Geneticist is sequencer agnostic and works with a wide variety of sequencing data and instruments and can support interpretation workflows involving:

  • Whole-genome sequencing
  • Whole-exome sequencing
  • Rare-disease testing
  • Inherited Risk Assessment
  • Carrier screening
  • Newborn screening
  • Targeted gene panels
  • Single-gene testing
  • Population genomics
  • Re-analysis of previously tested cases

Support for specific variant types and workflows depends on the selected configuration and validated use cases

Yes, all Virtual Geneticist modules support application of ACMG/AMP and relevant ClinGen classification guidance by organizing and evaluating evidence associated with variant classification.

The platform can help automate the evidence review process while preserving expert oversight. Final classification decisions should be reviewed and approved by appropriately qualified laboratory professionals.

All Virtual Geneticist modules can generate classification recommendations and assemble supporting evidence based on the proprietary curated literature database. However, clinical laboratories and other users remain responsible for reviewing, approving, and reporting final classifications according to their validated procedures, regulatory obligations, and professional standards.

Yes. Virtual Geneticist can help re-evaluate variants of uncertain significance (VUS) by identifying new scientific publications, updated disease associations, population data, functional evidence, clinical observations, in-silico scores, and other evidence used in classification.

This can support periodic reanalysis of previously reported variants and unresolved cases.

Yes. Virtual Geneticist can be used to re-analyze previously negative or unresolved exome and genome cases.

Re-analysis may identify:

  • Newly established gene-disease relationships
  • Newly published pathogenic variants
  • Updated phenotype associations
  • Previously overlooked inheritance patterns
  • Improved variant annotations
  • New evidence affecting variant classification

A successful re-analysis is not guaranteed, but updated evidence and the proprietary diagnosis ranking AI modes may increase the likelihood of identifying a clinically relevant finding.

Virtual Geneticist can work with commonly used genomic and clinical data formats, including:

  • Fastq files, Bam files or VCFs
  • Annotated variant files
  • Patient phenotype information
  • Human Phenotype Ontology terms
  • Pedigree and family information
  • Test-specific gene lists
  • Structured clinical information
  • Data submitted through an API

 

The different Virtual Geneticist Modules have distinct file requirements and data workflows, including:

VG Variant

Users can enter a variant directly through the web interface using HGVS nomenclature or an RSID. Organizations can also connect VG Variant to an existing bioinformatics or interpretation workflow through an API, allowing variant intelligence to be delivered without replacing the systems they already use.

Virtual Geneticist

Users can upload VCF files individually or in batches and add patient information through clinical notes, HPO terms, or PDFs. The platform uses natural-language processing and phenotype confirmation to help convert clinical information into a more complete and usable case profile.

Virtual Geneticist Plus

Users can begin with FASTQ, BAM, or VCF files. The secondary-analysis pipeline is sequencer agnostic and supports a range of data types, including short- and long-read whole genomes, whole exomes, RNA data, and specialty gene panels.

AI Genetic Research Agent

Users do not need to upload a data file. The AI Genetic Research Agent is a genomics-focused research and translational-medicine assistant for biopharma, clinical genomics, and specialty interpretation teams. Users can ask complex questions in natural language and receive synthesized answers supported by clear reasoning and cited literature.

Specific input requirements can be configured based on the institution’s workflow and module selection.

Virtual Geneticist Plus can analyze raw and intermediate sequencing files, including FASTQ and BAM files. It supports a broader end-to-end workflow that may include quality control, alignment and variant calling, annotation, prioritization, automated ACMG classification, interpretation, and report generation.

The standard Virtual Geneticist module generally begins with a VCF file after the laboratory has completed secondary analysis. It focuses on case-level variant prioritization, evidence review, classification, interpretation, and reporting.

Organizations can therefore connect Virtual Geneticist to an existing sequencing and bioinformatics pipeline or use Virtual Geneticist Plus when secondary analysis is also required.

Yes, Virtual Geneticist Plus provides an end-to-end solution from FASTQ to clinical report, but it is also fully compatible with data from your existing secondary analysis pipelines (such as DRAGEN or Sentieon). You can also choose to process FASTQ to VCF internally and only use the Virtual Geneticist platform for variant annotation, prioritization, and reporting from the VCF files.

Yes. Virtual Geneticist can use patient phenotypes, including Human Phenotype Ontology terms, to prioritize genes and variants associated with the patient’s clinical presentation.

Virtual Geneticist Plus can also support phenotype-independent analysis when phenotype information is unavailable, which may be useful for newborn screening and other screening tests, population genomics, and other high-volume applications.

Yes. Both Virtual Geneticist and Virtual Geneticist Plus can analyze cases with detailed, limited, or unavailable phenotype information.

When phenotype data are available, both modules use them to strengthen disease and variant prioritization. When phenotype information is limited, they can rely more heavily on genomic evidence, known disease associations, inheritance patterns, population frequency, pathogenicity evidence, and other relevant findings. 

VG-Variant can also incorporate phenotype information into its analysis and uses that information to help limit the appropriate literature evidence and ACMG  scoring that is presents.

Yes. Both Virtual Geneticist and Virtual Geneticist Plus can incorporate pedigree, family relationships, and inheritance information to support trio and family-based analysis, including:

  • De novo variants
  • Recessive inheritance
  • Compound heterozygous variants
  • X-linked inheritance
  • Dominant inheritance
  • Segregation among family members

Depending on the workflow, the platform may evaluate:

  • Peer-reviewed scientific literature
  • Gene-disease relationships
  • Variant-disease relationships
  • Functional studies
  • Case reports and case series
  • Population-frequency databases
  • Clinical databases
  • In-Silico Scores and Computational predictions
  • Inheritance patterns
  • Phenotype associations
  • Disease mechanism
  • Penetrance and age of onset
  • ClinGen and ACMG guidance

No. Virtual Geneticist is a decision-support and workflow-automation platform.

It helps professionals review evidence more efficiently, reduce repetitive work, and manage larger case volumes. Final clinical interpretation, classification, reporting, and patient-care decisions remain the responsibility of qualified professionals.

Literature and Knowledge Base

Yes. Virtual Geneticist connects genomic findings with relevant scientific literature and structured evidence.

This can reduce the amount of time analysts spend manually searching publications and help users identify evidence that may otherwise be difficult to find.

Breakthrough Genomics uses AI-assisted processes to identify and structure relevant genomic evidence from scientific literature. Evidence may then be reviewed and incorporated into the platform’s knowledge system.

The goal is to provide users with traceable evidence that can be reviewed during clinical interpretation.

Yes. Virtual Geneticist is designed to provide transparent and reviewable evidence rather than only producing a final score or conclusion.

Users can review the information supporting variant prioritization, disease association, and classification recommendations.

The knowledge base is updated as new scientific evidence, database information, and genomic knowledge become available.

The update frequency and availability of particular data sources may vary by platform version and configuration.

Workflow and Integration

Yes. Virtual Geneticist can be incorporated into an existing laboratory workflow through configurable data exchange, APIs, file-based workflows, and other integration methods.

It may be connected with:

  • Bioinformatics pipelines
  • Laboratory information management systems
  • Electronic health record systems
  • Reporting systems
  • Case-management platforms
  • Data warehouses
  • Internal laboratory applications

Not necessarily. Virtual Geneticist and the different modules can be used as standalone platforms and intelligence layers or integrated directly into existing workflow.  Virtual Geneticist Plus provides end-to-end capabilities from data ingestion and variant calling all the way through to variant interpretation and clinical reporting.

A laboratory, healthcare system or other institution may retain its current sequencing, variant-calling, annotation, reporting, or laboratory information systems while using Virtual Geneticist and the different Virtual Geneticist modules for selected and complementary interpretation and variant annotation functions.

Yes. API integration is available for organizations that want to automate data submission, analysis, result retrieval, and workflow management.

The specific API configuration depends on the customer’s technical environment and intended use.

While Virtual Geneticist’s API is highly efficient for high-throughput automated analysis and can export basic variant and gene information, it currently cannot return complex graphical evidence available in the platform’s UI, such as protein graphs, multi-paper citations, ClinVar comments, or interactive visual elements.  API customization is available upon request and can incur additional costs.

Cloud-based and private-environment deployment options may be available depending on the customer’s requirements, geography, security policies, and agreement with Breakthrough Genomics.

Yes. Virtual Geneticist can be deployed in different environments depending on customer requirements, including an on-premises environment using containerized deployment.

This option may be appropriate for organizations with strict security, privacy, data-residency, or data-localization requirements.

Yes. Breakthrough Genomics can provide Virtual Geneticist in a containerized deployment model for installation on an approved local or private server environment.

Technical requirements, maintenance responsibilities, upgrades, security controls, and support arrangements are defined during implementation.

Yes. Breakthrough Genomics can provide:
  • Workflow assessment
  • Technical integration support
  • User training
  • Validation assistance
  • Configuration support
  • Scientific consultation
  • Ongoing technical support
The scope of support depends on the customer’s needs

Validation, Quality, and Clinical Use

Virtual Geneticist has been evaluated through customer, collaborator, and comparative testing activities.

Organizations considering clinical use should review the relevant validation data, intended-use documentation, platform version, study design, and performance metrics applicable to their workflow.

Virtual Geneticist has demonstrated strong performance in independent benchmarking and real-world clinical evaluations.

In a head-to-head whole-genome sequencing benchmark conducted by Baylor Genetics, Virtual Geneticist ranked first among the evaluated genomic analysis platforms. A separate evaluation at BC Children’s Hospital demonstrated improved diagnostic performance and supported the use of Virtual Geneticist for efficient analysis and reanalysis of pediatric rare-disease cases.

Results may vary depending on the patient population, disease area, variant types, workflow, software version, evaluation methodology, and performance criteria. Organizations should review the supporting evidence and validate the platform using representative cases before clinical implementation.

Yes. A clinical laboratory should validate or verify the platform for its intended use before implementing it in a clinical workflow.

Validation should reflect the laboratory’s:

  • Specimen types
  • Test types
  • Variant types
  • Patient population
  • Reporting procedures
  • Regulatory requirements
  • Quality-management system

Virtual Geneticist can support clinical interpretation and reporting workflows. Whether it is used directly in report generation depends on the laboratory’s configuration, validation, regulatory status, and quality procedures.  Report templates for rare disease diagnosis and select gene panels are available and will depend on the specific configuration of the platform and module chosen.

Final reports should be reviewed and authorized by appropriately qualified personnel.

Does Virtual Geneticist support Pharmacogenomics (PGx) analysis and reporting?

Yes, with Virtual Geneticist Plus PGx reports can be generated automatically upon data upload. The platform utilizes PharmGKB and CPIC guidelines for interpretation and provides standard star allele nomenclature (e.g., 2C19, 2C9).  PGx customization is available upon request.

Regulatory classification may depend on the software configuration, intended use, jurisdiction, deployment model, and how the platform is used within a clinical workflow.

Customers should review the applicable product documentation and consult their regulatory and quality teams before implementation.

Virtual Geneticist provides analytical and interpretive support. It does not independently establish a medical diagnosis or replace evaluation by a qualified healthcare professional.

Diagnostic conclusions should be based on the complete clinical context, laboratory findings, family history, and professional medical judgment.

Privacy and Security

Virtual Geneticist can be configured with security controls appropriate to the deployment model and customer requirements.

These may include:

  • Encryption
  • Access controls
  • User authentication
  • Audit logging
  • Role-based permissions
  • Secure data transfer
  • Private or on-premises deployment
  • Data-retention controls

Specific safeguards should be documented in the customer agreement and technical implementation plan.

The permitted use of customer data should be defined in the applicable agreement, privacy documentation, and deployment configuration.

Customers should confirm how data are processed, stored, retained, de-identified, and used before implementation.

Yes. On-premises or approved local deployment may allow genomic and patient data to remain within the customer’s controlled environment or required geographic region.

This can support organizations subject to data-localization or data-residency requirements.

Virtual Geneticist may be configured for use in environments subject to HIPAA and other privacy requirements. The customer and Breakthrough Genomics should establish the necessary agreements, security controls, responsibilities, and deployment conditions.

Virtual Geneticist can support traceability of analysis activities, evidence review, user actions, and interpretation decisions.

Specific audit-trail capabilities depend on the platform version, module, configuration, and workflow.

Specialized Variant Types

Yes. Virtual Geneticist can analyze CNVs (typically focusing on filtering those larger than 100kb for WGS, and smaller regions for WES) and includes an IGV tool to visually compare samples and validate calls. However, FastQ or BAM files are strictly required to process CNV data; they cannot be processed using only VCF files.

Yes. Virtual Geneticist and Virtual Geneticist Plus can identify and interpret trinucleotide repeats and come integrated with specific tools specific to the analysis of these types of variants.

Yes. Virtual Geneticist and Virtual Geneticist Plus provides comprehensive analysis for the SMN1, PMS2, CYP2D6, GBA, RCCX, HBA1, HBA2 and other high-homology loci—enabling rare disease and oncology labs to accurately detect copy number changes, variants, gene conversions, and complex star alleles that conventional pipelines often miss.

The platform identifies UPD events and provides visualization and interpretation support.

Yes. A specialized mitochondrial variant pipeline is included on the platform.

Intronic variants are filtered using SpliceAI with a score threshold above 0.5.  This can be adjusted according to the specific needs of each customer.

Newborn Screening and Population Genomics

Yes. Virtual Geneticist can support genomic newborn-screening programs by prioritizing clinically important findings and helping manage large case volumes.

Program design should consider:

  • Disease actionability
  • Age of onset
  • Penetrance
  • Inheritance
  • Reporting criteria
  • Confirmatory testing
  • Consent
  • Follow-up care
  • Local policy and regulation

Yes. This capability is relevant to newborn screening, carrier screening, preventive genomics, and population genomics, where participants may not have a known phenotype.

The platform can prioritize findings using gene-disease validity, pathogenicity, inheritance, penetrance, actionability, and other program-specific criteria.

Yes. Virtual Geneticist is designed to help organizations scale genomic interpretation across large sample volumes.

The platform may be configured for:

  • Automated data intake
  • High-throughput prioritization
  • Program-specific gene lists
  • Standardized classification rules
  • Review queues
  • Batch analysis
  • API integration
  • Structured result export

Yes. Customers may configure analysis according to:

  • Test-specific gene lists
  • Disease panels
  • Actionable-gene lists
  • Newborn-screening programs
  • Secondary-findings policies
  • Population-specific requirements
  • Research protocols

The platform has been trained and validated on diverse population datasets, reducing ancestry bias and improving diagnostic equity in newborn screening and rare disease analysis.

Pharmaceutical and Research Applications

Yes. Pharmaceutical and biotechnology companies may use Virtual Geneticist to support:

  • Genotype-phenotype analysis
  • Patient stratification
  • Biomarker discovery
  • Rare-disease research
  • Natural-history studies
  • Clinical-trial recruitment
  • Variant interpretation
  • Gene-disease evidence assessment
  • Literature review
  • Drug-target research

Yes. Virtual Geneticist may be used for translational, clinical, and genomic research.

Research use should be clearly distinguished from validated clinical use, and all applicable institutional, ethical, privacy, and regulatory requirements should be followed.

Yes. Breakthrough Genomics can work with customers on customized analysis, evidence-generation, cohort review, literature curation, and integration projects.

Project scope, deliverables, timelines, data requirements, and intellectual-property terms are defined separately.

AI Genetic Research Agent

The AI Genetic Research Agent is a genomics-focused conversational research assistant that returns evidence-backed answers, explanations, and cited scientific sources.

The AI Genetic Research Agent is a genomics-focused research and translational-medicine assistant for biopharma, clinical genomics, and specialty interpretation teams. Users can ask complex questions in natural language and receive synthesized answers supported by clear reasoning and cited literature.

The Agent can help explore gene- and variant-disease relationships, clinical phenotypes, therapeutic relevance, emerging evidence, rare variants, biomarkers, and related biological or medical questions. It is designed for questions that require genomics-specific context rather than a generic web summary.

Depending on the question, an answer can include direct explanations, evidence summaries, functional information, gene and variant details, supporting citations, related genes or disease associations, intelligent follow-up opportunities, and suggestions for additional research.

The Agent is based on Breakthrough Genomics’ proprietary database of more than 15 million interpreted scientific publications. Its value comes from combining conversational access with genomics-focused evidence organization and traceable literature support.

The Agent can support biopharma research and translational teams, clinical genomics groups, geneticists, variant scientists, and specialty interpretation teams that need to search, synthesize, and interrogate genomic evidence more efficiently.

VG Variant and Virtual Geneticist are structured interpretation tools centered on variants and patient cases. The AI Genetic Research Agent is question-driven: it helps users investigate broader genomic relationships, scientific evidence, therapeutic relevance, and emerging research through an interactive conversational workflow.

No. The Agent is a research and decision-support resource. Its answers and citations should be reviewed by qualified professionals and considered alongside validated clinical workflows, laboratory procedures, and other relevant evidence before any diagnostic or patient-management decision is made.

Pricing and Access

Pricing depends the Virtual Geneticist modules and also on the customer’s use case and may be based on:
  • Number of samples
  • Annual testing volume
  • Number of users
  • Selected modules
  • Deployment model
  • Integration requirements
  • Support level
  • Customization
  • Research or clinical use
Customers can request a quotation based on their expected workflow and volume.

Per-sample pricing may be available for certain workflows and customer arrangements.

Enterprise, annual-license, project-based, or minimum-volume pricing may also be offered.

Trial or evaluation access may be available for qualified organizations. The evaluation may include representative cases, defined performance criteria, user training, and a limited evaluation period.

Yes. Prospective customers may be able to evaluate the platform using de-identified or appropriately authorized cases.  If not available, Breakthrough Genomics can also provide some sample data for evaluation purposes.

The evaluation process should define:

  • Case selection
  • Ground truth
  • Expected outputs
  • Evaluation metrics
  • Data-transfer method
  • Confidentiality
  • Timeline
  • Success criteria

Individuals and organizations can request a Virtual Geneticist demonstration through the Request a Demo button or by emailing info@BTGenomics.com.  Depending on the module and institutional requirements, an NDA may need to be signed.

To prepare an appropriate demonstration, prospective customers should provide:

  • Organization type
  • Intended use
  • Current testing volume
  • Data format
  • Existing workflow
  • Deployment preference
  • Integration needs
  • Target implementation timeline

Support and Training

Yes. Training may include:

  • Platform navigation
  • Case submission
  • Phenotype entry
  • Variant review
  • Evidence evaluation
  • Classification workflows
  • Reporting
  • Administrative functions
  • API and integration workflows

Support options may include:

  • Email support
  • Scheduled technical meetings
  • Implementation assistance
  • Scientific consultation
  • Troubleshooting
  • Software updates
  • Workflow optimization

Support levels are defined in the applicable agreement.

Yes. Breakthrough Genomics can provide technical documentation, training, example workflows, and assistance with validation planning.

The laboratory remains responsible for approving its validation protocol, evaluating results, documenting conclusions, and determining whether the platform is suitable for clinical use.

Getting Started

The first step is usually a discovery meeting to understand the organization’s workflow, technical environment, scientific objectives, current challenges, timeline, and evaluation criteria.

Breakthrough Genomics can then recommend a demonstration, pilot study, technical assessment, or implementation plan.

Click on the Contact Us tab in the upper right of the page or you can request a Virtual Geneticist demonstration by clicking on the Request a Demo button.

Important Notice

Virtual Geneticist is intended to support genomic analysis and interpretation by qualified professionals. Platform outputs should be reviewed in the context of validated laboratory procedures, applicable regulations, patient history, clinical findings, and professional judgment.
Features, supported workflows, regulatory status, deployment options, and performance may vary by software version, jurisdiction, customer configuration, and intended use.