Congenica
Congenica is a Cambridge-based clinical genomic interpretation platform provider, serving 190+ laboratories across 35+ countries with AI-powered NGS analysis for rare disease and oncology diagnostics. Founded in 2012 from the Wellcome Sanger Institute and now part of SeqOne S.A.S., the company processes 200,000+ patient analyses annually.
- Company typePrivate
- Founded2012
- HeadquartersCambridge, United Kingdom
- Headcount51–100
- GTM typeB2B
- OfferingSoftware
What Congenica does
Congenica is a clinical genomic interpretation platform company founded in 2012 and born from the Wellcome Sanger Institute. The company provides a CE-IVDR Class C certified cloud-based SaaS platform that transforms raw next-generation sequencing (NGS) data into actionable clinical reports for rare disease diagnosis, oncology, and infectious disease applications. Its core technology stack combines automated bioinformatics pipelines with proprietary AI models — notably the UP² (Universal Pathogenicity Predictor) variant scoring engine and PhenoGenius phenotype matching — to accelerate variant interpretation and improve diagnostic accuracy for clinical laboratories.
The platform operates on a modular architecture: the core Congenica Platform handles germline and somatic interpretation workflows, augmented by specialized modules including DiagAI (explainable AI variant ranking with Score, ShortList, SmartPick, and HPO extraction from clinical notes via LLMs), GenomeAlert! (automated monthly reevaluation against ClinVar), SomaHRD (HRD biomarker testing for PARP inhibitor selection in ovarian cancer), SomaLBx/SomaMethyl (liquid biopsy), SomaHemato (hematology IGHV analysis), and germVar (Oxford Nanopore long-read interpretation). Revenue is generated through annual or multi-year enterprise SaaS subscriptions to hospital networks, genomic laboratories, and national health systems, complemented by usage-based licensing for high-volume operations and a self-serve free-trial entry point for smaller labs. A Clinical Interpretation Services layer — NHS-trained genomic experts — provides paid variant analysis support alongside the software.
In September 2025, Congenica was acquired by SeqOne S.A.S., a France-based genomics software company, creating a combined entity serving 160-190+ laboratories across 30-35+ countries and processing over 200,000 patient analyses annually with a 125+ person team. The company is headquartered at the Wellcome Genome Campus in Cambridge, UK, with engineering/R&D in Montpellier, sales operations in Paris, and U.S. operations via SeqOne Inc. in New York. Trust by NHS Genomic Medicine Services and Genomics England anchors its market position in UK national genomic medicine.
Congenica firmographics
Firmographics- Name
- Congenica
- Legal name
- SeqOne S.A.S.
- Website
- https://congenica.com
- Company type
- Private
- Founded year
- 2012
- Operating status
- Acquired
- Headcount range
- 51–100 employees
- Short description
- Congenica is a Cambridge-based clinical genomic interpretation platform provider, serving 190+ laboratories across 35+ countries with AI-powered NGS analysis for rare disease and oncology diagnostics. Founded in 2012 from the Wellcome Sanger Institute and now part of SeqOne S.A.S., the company processes 200,000+ patient analyses annually.
- Ownership category
- akta.pro rank
Congenica industry classification
Industry- Product category
- Clinical Genomic Interpretation Software
- NAICS
- Software Publishers (5132)
- SIC
- Services-Prepackaged Software (7372), Services-Computer Programming, Data Processing, Etc. (7370)
- akta.pro primary industry
- Genomics & Next-Generation Sequencing (NGS) Services (HLAGANAA)
- akta.pro secondary industry
- FHIR/HL7 Data Repositories & Canonical Data Models (HLACAIAI)
Keywords
Where Congenica is headquartered
LocationHeadquarters
- HQ city
- Cambridge
- HQ country
- United Kingdom
- HQ region
- Europe
Offices3 records
Markets served
Congenica business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure, Others
Revenue model
- Cloud-based SaaS Subscription: Annual or multi-year subscription model for accessing the clinical genomic interpretation platform via cloud deployment. Includes software updates, customer support, and regulatory compliance maintenance.
- Platform Usage Licensing: Usage-based licensing potentially available for high-volume laboratory operations processing large numbers of patient samples annually.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Subscription | Annual | Enterprise subscription for large laboratory networks and healthcare systems |
| Freemium | Pay-as-you-go | Self-serve/free trial entry point for smaller laboratories |
Go-to-market motion3 records
Distribution channels4 records
Marketing channels5 records
Congenica product offering
Product offeringCore offering
Congenica provides a cloud-based clinical genomic interpretation platform that transforms raw next-generation sequencing (NGS) data into actionable clinical reports for rare disease, oncology, and infectious disease applications. The CE-IVDR Class C certified platform is augmented by AI-powered modules for variant pathogenicity scoring, phenotype matching, automated re-evaluation, and homologous recombination deficiency testing, and is supported by NHS-trained clinical interpretation services.
Product overview
Congenica operates as a cloud-based clinical genomic interpretation platform (a platform-plus-modules architecture) now part of the SeqOne family. The core product is the Congenica Platform (CE-IVDR Class C certified), which provides AI-powered genomic analysis transforming raw NGS data into clinical insights across rare disease, oncology, and infectious diseases. This core platform is augmented by specialized modules: DiagAI (explainable AI variant ranking suite including Score, ShortList, SmartPick, and HPO/Notes2HPO); GenomeAlert! (automated monthly variant reevaluation against ClinVar); SomaHRD (clinically validated HRD test for ovarian cancer PARP inhibitor selection); CGH Array Interpretation (CNV annotation from Agilent Cytogenomics); germVar (ONT whole genome interpretation); and SomaLBx/SomaMethyl (liquid biopsy with epigenetic signatures) and SomaHemato (hematology IGHV analysis). The product line is rounded out by Clinical Interpretation Services — NHS-trained genomic experts providing variant analysis and reporting support. The platform supports both germline (rare diseases, inherited disorders, carrier screening) and somatic (solid tumors, liquid biopsy, hematology, hereditary cancers) workflows on a unified interface.
Differentiator
Problem solved
Functional benefit
Brands
- Congenica RD: An In Vitro Diagnostic medical device in Europe, CE marked as a Class C IVD under Regulation (EU) 2017/746, used for clinical decision support by trained medical staff.
Products and services
- Congenica Platform (Next-Generation Platform) Cloud-based AI-powered genomic analysis platform that transforms raw NGS sequencing data (FASTQ/VCF) into fast, actionable clinical insights across rare disease, oncology, and infectious diseases. Supports both germline (rare diseases, inherited disorders, carrier screening) and somatic (solid tumors, liquid biopsy, hematology, hereditary cancers) workflows with variant annotation, ACMG classification, and clinical reporting. Used by clinical laboratories, hospital networks, and national genomic medicine programmes.
- Congenica RD (Heritage CE-IVDR Class C Platform) CE-IVDR Class C certified In-Vitro Diagnostic medical device for clinical decision support used by trained medical staff, clinical scientists, and genetic scientists. Built on 13 years of clinical excellence from the Wellcome Sanger Institute and trusted by NHS Genomic Medicine Services.
- DiagAI Explainable AI-powered variant ranking suite comprising DiagAI Score (0–100 pathogenicity ranking), DiagAI ShortList (shortlisted candidate variants), SmartPick (top candidate suggestion), and HPO integration. Powered by UP² (Universal Pathogenicity Predictor trained on 2.5M+ ClinVar variants, 97% accuracy) and PhenoGenius (phenotype matching model outperforming alternatives by 42%). Used by clinical genomic interpreters to accelerate variant interpretation.
- DiagAI HPO (Notes2HPO) AI tool that automates extraction of HPO terms from unstructured clinical notes, referral letters, and free-text clinical descriptions using large language models fine-tuned to the HPO ontology. Supports multi-language input, returns structured HPO terms with positions in the source text, and includes an anonymisation layer for health data regulation compliance. Used by clinical scientists to convert clinical narrative into structured phenotype inputs for variant interpretation.
- GenomeAlert! Automated variant reevaluation agent that monthly reanalyzes all historical patient cases against the latest ClinVar database updates, generates actionable reports identifying candidates for new or revoked diagnoses, and provides one-click access to source information. Used by clinical laboratories to ensure patients benefit from the latest scientific knowledge without manual re-review.
- SomaHRD (Homologous Recombination Deficiency Test) Clinically validated HRD biomarker test for identifying ovarian cancer patients likely to respond to PARP inhibitors, based on shallow whole genome sequencing (sWGS) and targeted gene panel. Validated against the PAOLA-1 cohort with 95% concordance to Myriad myChoice CDx and 96% concordance in independent validation by North West GLH. Used by oncology and molecular pathology laboratories for therapy selection.
- SeqOne CGH Array Interpretation CGH microarray interpretation solution enabling direct import of CNV data from Agilent Cytogenomics software (IntervalBasedReport files), with AI-powered CNV annotation, ACMG automated classification, and seamless historical data migration from Cartagenia Bench Lab. Used by cytogenomic laboratories replacing legacy CGH interpretation workflows.
- SomaLBx Comprehensive liquid biopsy analysis solution covering both somatic variants and epigenetic signatures in a single workflow for oncology applications. Used by molecular pathology laboratories to deliver liquid biopsy testing in-house.
- SomaMethyl Liquid biopsy module integrated within SomaLBx for analyzing epigenetic signatures alongside somatic variants in oncology testing. Used together with SomaLBx by molecular pathology laboratories for comprehensive liquid biopsy analysis.
- SomaHemato Hematology analysis module providing robust, validated IGHV mutational status analysis for CLL prognosis, overcoming NGS short-read limitations for precise clinical insights. Used by hematology and molecular pathology laboratories for chronic lymphocytic leukemia prognostics.
- germVar AI-enhanced whole genome variant interpretation application for Oxford Nanopore EPI2ME workflows, supporting CNV, SNP, INDEL, SV, and STR analysis with an advanced interpretation hub (phasing display, in-silico panels, advanced viewers). Research use only. Used by laboratories deploying Oxford Nanopore long-read sequencing for whole genome interpretation.
- SeqOne Flow Premium Customer-facing automation engine built on N8N workflow orchestration enabling LIMS connectors, file transfer automation, analysis triggering APIs, and HL7/FHIR interfaces for healthcare interoperability. Transforms one-off integrations into reusable, self-service modules. Used by laboratory IT teams to automate integration of the genomic interpretation platform into clinical workflows.
- SeqOne Public API Public REST API enabling customer IT teams to integrate the platform autonomously, supporting file upload/download, analysis triggering, LIMS connectors, and HL7/FHIR interfaces. Also exposes the DiagAI Text2HPO API and the DiagAI PhenoGenius API for in-house pipeline integration. Includes a Python SDK. Used by laboratory IT and bioinformatics teams to embed interpretation capabilities into their own pipelines.
- Clinical Interpretation Services NHS-trained genomic expert team providing fast, rigorous variant analysis and clinical reporting alongside the software platform. Used by laboratories that require additional interpretive support or lack sufficient in-house clinical scientist capacity for genomic case review.
Quantifiable outcome
- 200,000+ patient analyses annually across the platform
- +2 more outcomes
Companies that use Congenica
Customer profileNamed customers7 records
Segments5 records
Ideal customer profiles4 records
Congenica technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- Yes
- API docs
- API detail
Core technology
AI maturity
App detail
Integration11 records
AI capability10 records
Feature6 records
Congenica partnerships and signals
Strategic signalPartnerships
Three partnerships are on record, tiered core and flagship.
- Agilent TechnologiescorePartnership announced June 2025 for liquid biopsy applications, combining Agilent's targeted NGS enrichment chemistry with Congenica's AI-powered interpretation platform for improved cancer diagnostics.
- MGI TechcoreStrategic technology partnership announced June 2024, integrating Congenica's interpretation platform with MGI's sequencing technology for enhanced genomic analysis workflows in clinical settings.
- Oxford Nanopore TechnologiesflagshipTechnology partnership integrating Congenica's genomic interpretation platform with Oxford Nanopore's long-read sequencing technology. The partnership includes germVar, a pipeline specifically optimized for Oxford Nanopore whole genome variant interpretation, enabling seamless workflow from long-read sequencing to clinical report.
Scale indicators7 records
Recent moves6 records
Expansion highlights7 records
Congenica competitors and assessment
Company assessmentDirect peers
- SOPHiA GENETICS: Public clinical genomics interpretation platform used by hospitals and labs worldwide for rare disease, oncology, and hereditary cancer testing. Direct overlap with Congenica across use cases, customer base (hospital networks, genomic labs), and AI-driven interpretation model.
- Fabric Genomics (formerly Omicia): Clinical NGS interpretation platform focused on rare disease and oncology, used by hospital systems and reference labs. Closest direct peer to Congenica in AI-driven variant interpretation, ACMG classification, and clinical reporting workflows.
- DNAnexus: Cloud-based clinical genomics data platform serving pharma, clinical labs, and hospitals for NGS analysis and interpretation. Comparable in cloud-native SaaS delivery, enterprise GTM, and clinical-grade security/compliance positioning.
- Golden Helix: Clinical genomics interpretation and reporting software (VSClinical, SVS) used by molecular diagnostic labs for rare disease and cancer testing. Direct overlap on variant annotation, ACMG/AMP classification, and clinical reporting.
- PierianDx (now part of Intermountain Healthcare): Clinical genomic interpretation platform for rare disease, oncology, and hereditary cancer testing used by hospital systems. Direct peer in clinical-grade NGS interpretation, with comparable customer base of integrated delivery networks.
Broad incumbents
- QIAGEN Digital Insights (QCI): QIAGEN's clinical NGS interpretation portfolio (QCI Interpret, QCI Precision Insights) competes directly with Congenica in variant interpretation and clinical reporting. A much larger incumbent with broader life-sciences portfolio, deeper US sales force, and integrated reagent-instrument-software stack.
- Illumina Connected Software (including DRAGEN, Emedgene): Illumina's tertiary-analysis software portfolio (including Emedgene) competes directly with Congenica in clinical NGS interpretation. A much larger incumbent leveraging the dominant sequencer installed base to bundle interpretation software.
Regional players
- WuXi NextCODE (Genomics Institute): Clinical genomics interpretation and sequencing services platform with strong presence in Asia (China) and the US. Comparable in germline and oncology interpretation offerings, but with deeper Asia footprint and a service-plus-software model.
Emerging players
- BlueBee (now part of Hesperos): Cloud-based bioinformatics and clinical genomics platform serving diagnostic labs and hospitals. Comparable cloud-native interpretation model, with a focus on regulated clinical workflows in Europe.
- GenomOncology: Clinical oncology genomics interpretation platform focused on somatic variant curation, molecular tumor boards, and therapy matching. Partial overlap with Congenica's oncology modules (SomaHRD, SomaLBx, SomaHemato).
Market position
Strengths5 records
Weaknesses5 records
Competitive moat6 records
Key risks5 records
Key highlights6 records
Customer concentration
Congenica social profiles
Digital presenceCongenica compliance and trust
Trust signalCompliance6 records
Congenica financial estimates
Financial estimateRevenue estimate
Valuation estimate
Congenica leadership team
Management profileNumber of profiles
Profiles17 records
Congenica funding detail
Funding detailFunding overview
Funding rounds7 records
Investors14 records
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
Congenica M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about Congenica
What does Congenica do?
Congenica provides a cloud-based clinical genomic interpretation platform that transforms raw next-generation sequencing (NGS) data into actionable clinical reports for rare disease, oncology, and infectious disease applications. The CE-IVDR Class C certified platform is augmented by AI-powered modules for variant pathogenicity scoring, phenotype matching, automated re-evaluation, and homologous recombination deficiency testing, and is supported by NHS-trained clinical interpretation services.
Is Congenica a public or private company?
Congenica is a private company. It is classified as corporate owned and is currently acquired.
When was Congenica founded?
Congenica was founded in 2012. It employs 51 to 100 people.
Where is Congenica based?
Congenica is headquartered in Cambridge, United Kingdom, in the Europe region.
How does Congenica make money?
Two revenue lines are on record. Cloud-based SaaS Subscription is the primary driver. The others are platform Usage Licensing.
Who are Congenica's main competitors?
Direct peers on record are SOPHiA GENETICS, Fabric Genomics (formerly Omicia), DNAnexus, Golden Helix and PierianDx (now part of Intermountain Healthcare). Broad incumbents are QIAGEN Digital Insights (QCI) and Illumina Connected Software (including DRAGEN, Emedgene). WuXi NextCODE (Genomics Institute) is listed as a regional player. Emerging players are BlueBee (now part of Hesperos) and GenomOncology.
Does Congenica have an API?
Yes. SeqOne (parent) operates a Public API gateway enabling customer IT teams to integrate autonomously. The API supports file upload/download, analysis triggering, LIMS connectors, and HL7/FHIR interfaces. The platform also exposes the DiagAI Text2HPO API for converting unstructured clinical notes into HPO terms, and the DiagAI PhenoGenius API for phenotype-genotype matching — both offered for in-house pipeline integration. Developer documentation is at www.congenica.com/platform.
What industry is Congenica in?
Congenica's product category is Clinical Genomic Interpretation Software. Its primary akta.pro industry code is HLAGANAA, Genomics & Next-Generation Sequencing (NGS) Services, with a secondary code of HLACAIAI, FHIR/HL7 Data Repositories & Canonical Data Models. Its NAICS code is 5132 and its SIC code is 7372.