Congenica

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.

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

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

• Clinical genomic interpretation
• NGS data analysis software
• Rare disease diagnostics
• Oncology genomic testing
• AI variant prioritization

Headquarters

HQ city

Cambridge

HQ country

United Kingdom

HQ region

Europe

Offices3 records

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure, Others

Revenue model

1. 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.
2. Platform Usage Licensing: Usage-based licensing potentially available for high-volume laboratory operations processing large numbers of patient samples annually.

Pricing tiers

Go-to-market motion3 records

Distribution channels4 records

Marketing channels5 records

Core 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

Named customers7 records

Segments5 records

Ideal customer profiles4 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration11 records

AI capability10 records

Feature6 records

Partnerships

Three partnerships are on record, tiered core and flagship.

• Agilent TechnologiescoreTechnology or Integration · 1 June 2025Partnership 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 TechcoreTechnology or Integration · 1 June 2024Strategic 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 or Integration · 1 March 2024Technology 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

Direct 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

• Xx.com/congenica

Compliance6 records

Revenue estimate

Valuation estimate

Number of profiles

Profiles17 records

Funding overview

Funding rounds7 records

Investors14 records

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Congenica