What Flagship Biosciences does

Flagship Biosciences is a privately held, US-based contract research organization that delivers spatial biology, genomics, and histopathology services to pharmaceutical and biotechnology companies conducting drug development and clinical trials. Founded in 2009 and headquartered in Broomfield, Colorado, with a second laboratory in Morrisville, North Carolina acquired from Interpace Pharma Solutions in 2022, the company operates CLIA-certified, CAP-accredited, and New York State-permitted facilities. Its service catalog spans immunohistochemistry, multiplex immunofluorescence, in situ hybridization, digital spatial profiling, RNA sequencing, whole-exome and whole-genome sequencing, targeted NGS panels, gene expression analysis, qPCR/Sanger sequencing, flow cytometry, and anatomical pathology, sold through Statement-of-Work engagements on a custom-quote basis.

The company's technical backbone is its proprietary Flotilla image analysis platform, which applies machine learning algorithms to clinical tissue samples, performing tissue segmentation, cell identification, and spectral unmixing while collecting thousands of features per cell to build cellular databases. Expert board-certified pathologists and computational scientists guide this AI through quality control and artifact detection, and the company has published validated digital assays such as Tissue Insight 22C3 NSCLC in Scientific Reports. Flagship also integrates third-party sequencing and spatial profiling instruments — Illumina NovaSeq, NanoString nCounter and GeoMx, Leica whole-slide scanners — into its workflow, and partners with Genomenon, Paige, and Offspring Biosciences to extend its genomic interpretation, immuno-oncology software distribution, and transatlantic assay development footprint.

Flagship generates revenue through professional-services CRO engagements with enterprise pharma and biotech clients, with pricing driven by project scope, assay complexity, sample volume, regulatory requirements, and turnaround time on multi-year Statement-of-Work contracts. The company sells directly through enterprise field sales supported by a conference-heavy marketing program (AACR, ASCO, World CDx, Spatial Biology summits), scientific content, and a quarterly newsletter, and is recognized via the Frost & Sullivan 2023 North American Customer Value Leadership Award in AI-enabled digital pathology.

Name

Flagship Biosciences

Legal name

Flagship Biosciences, Inc.

Website

https://flagshipbio.com

Company type

Private

Founded year

2009

Operating status

Operating

Headcount range

51–100 employees

Short description

Flagship Biosciences is a privately held CRO delivering AI-powered spatial biology, genomics, and histopathology services to pharmaceutical and biotech companies for clinical trials and companion diagnostic development. It operates CLIA-CAP-accredited laboratories in Colorado and North Carolina.

Ownership category

akta.pro rank

Product category

Contract Research Organization (Biomarker and Spatial Biology Services)

NAICS

Medical and Diagnostic Laboratories (6215), Medical Laboratories (621511), Research and Development in Biotechnology (except Nanobiotechnology) (541714), Research and Development in the Physical, Engineering, and Life Sciences (54171)

SIC

Services-Medical Laboratories (8071), Services-Commercial Physical & Biological Research (8731), In Vitro & In Vivo Diagnostic Substances (2835)

akta.pro primary industry

Specialty & Biomarker Laboratory Services (Immunoassays/Flow/Cytometry) (HLAGAEAB)

akta.pro secondary industries

Molecular Pathology & Tissue Biomarkers (IHC/ISH, digital pathology-linked markers) (HLAAAMAI), Biomarker Assay & Reagent Development (LDT/IVD assay design, antibodies/standards/controls) (HLAAAMAL), Transcriptomics & Gene Expression Profiling Services (HLAGANAE), Translational Medicine & Biomarkers (HLAIALAF)

Keywords

• Spatial biology services
• Biomarker analytics
• Digital pathology
• Companion diagnostics
• Tissue imaging analysis

Headquarters

HQ city

Broomfield

HQ country

United States

HQ region

North America

Offices2 records

Markets served

GTM type

B2B

Offering type

Services

Cost components

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

Revenue model

1. Biomarker and Spatial Biology Laboratory Services: Flagship Biosciences generates revenue through providing contract research organization (CRO) services including spatial biology, genomics, histopathology, and biomarker analytics to pharmaceutical and biotech companies for clinical trials. Revenue is project-based and service contract driven, typically scoped as Statement of Work agreements for specific assay development, testing, and analysis projects. The company operates CLIA-certified and CAP-accredited laboratories.
2. Regulatory and Companion Diagnostics Development Services: Provides end-to-end regulatory strategy and companion diagnostic development services from early discovery through commercialization, including FDA interaction support, assay validation, and regulatory submission planning. Revenue generated through consulting and laboratory service engagements.

Pricing tiers

Go-to-market motion1 record

Distribution channels2 records

Marketing channels5 records

Core offering

Flagship Biosciences provides AI-powered spatial biology, genomics, histopathology, and biomarker development services for pharmaceutical and biotech companies through CLIA-certified and CAP-accredited laboratories. Core offerings include immunohistochemistry (IHC), multiplex immunofluorescence (mIF), digital spatial profiling, in situ hybridization (RNAscope ISH), RNA sequencing, whole exome and whole genome sequencing, and regulatory support for companion diagnostic development, all powered by the proprietary Flotilla image analysis platform and supported by expert pathologist consultation.

Product overview

Flagship Biosciences is a technology-driven spatial biology and biomarker services company offering a comprehensive portfolio of laboratory and analytical services. The core offerings include Spatial Biology services (IHC, multiplex immunofluorescence, digital spatial profiling, and ISH), Genomics services (RNASeq, WES, WGS, targeted NGS panels, gene expression analysis, qPCR/Sanger sequencing), and Histopathology. These are supported by proprietary AI-powered image analysis technology (Flotilla platform), Computational Biology for data analysis, Biomarker Development, Regulatory Support for companion diagnostics, and Flow Cytometry. All services are delivered through a CLIA-certified, CAP-accredited laboratory with expert scientific consultation.

Differentiator

Problem solved

Functional benefit

Products and services

• Spatial Biology Services Comprehensive spatial biology services combining multiplexed in situ RNA detection (RNAscope), multiplex immunofluorescence (mIF), digital spatial profiling (NanoString GeoMx), and IHC with AI-powered image analysis. Sold to pharmaceutical and biotech companies for biomarker discovery, assay development, and clinical trial support.
• Genomics Services CLIA-certified, CAP-accredited DNA sequencing and gene expression services including RNASeq, Whole Exome Sequencing, Whole Genome Sequencing, targeted NGS panels, gene expression analysis (NanoString nCounter), and qPCR/Sanger sequencing. Supports biomarker discovery, oncology research, and precision medicine programs.
• Histopathology Services Histopathology services combining board-certified pathologist expertise with digital pathology and AI-powered analysis, including H&E, IHC, multiplex immunofluorescence, and special stains. Includes GLP and clinical trial support for pharma and biotech clients.
• Image Analysis Services Cutting-edge imaging and proprietary image analysis software for tissue sample analysis at transcriptomics and proteomics levels, including multiplexed in situ RNA detection and multiplex immunohistochemical staining with AI and machine learning coupled with expert pathologist consultation.
• ISH (In Situ Hybridization) Services RNA detection service using the RNAscope platform enabling highly sensitive, single-cell RNA detection within tissue samples for precise visualization of gene expression in native tissue context.
• mIF (multiplex immunofluorescence) Services Advanced spatial biology service enabling simultaneous detection of multiple biomarkers on a single slide for immune profiling, biomarker co-localization, and pathway exploration. Combines custom panel development with proprietary image analysis and AI-driven quantification.
• Digital Spatial Profiling (DSP) Services High-resolution biomarker expression analysis using the NanoString GeoMx platform, combining multiplexed RNA or protein quantification with precise spatial localization to uncover insights into tumor microenvironment, immune infiltration, and cellular heterogeneity.
• Biomarker Development Services Assay development, validation, and operationalization services for rare diseases, oncology, and other therapeutic areas. Includes a robust library of fit-for-purpose and validated singleplex, duplex, and multiplex panels using IHC, ISH, and multiplex IF modalities.
• Regulatory Support Services End-to-end regulatory support for biomarker development from early discovery through commercialization, including gap analysis, assay development strategies, FDA interface, LDT development, cutoff determination, and regulatory submission planning for companion diagnostics.
• Computational Biology Services Data science services leveraging advanced analytical techniques for deriving insights from complex tissue image analysis and genomics data. Includes custom analysis using Bioconductor tools, StarAligner for RNA alignment, and DESeq2/GLMMer for differential expression models.
• RNASeq Service RNA sequencing service for transcriptome analysis providing insights into gene expression, alternative splicing, and RNA editing across various sample types using the NovaSeq X Plus platform.
• Whole Genome Sequencing (WGS) Service Comprehensive whole genome sequencing service using NovaSeq X Plus for high-quality sequencing data to support biomarker discovery, oncology research, and precision medicine.
• Whole Exome Sequencing (WES) Service Protein-coding variant detection service providing high-depth coverage for precise identification of genetic mutations associated with disease, therapeutic response, and inherited conditions.
• Targeted NGS Panels Service High-quality targeted next-generation sequencing panels optimized for accuracy, sensitivity, and comprehensive genomic coverage, enabling identification of clinically significant mutations across solid tumors and hematologic malignancies.
• Gene Expression Analysis Service Multiplexed gene expression quantification using the NanoString nCounter platform, enabling analysis without amplification for biomarker discovery, pathway analysis, and immune profiling.
• qPCR / Sanger Sequencing Service Targeted molecular analysis using Applied Biosystems ViiA 7 Real-Time PCR system for biomarker validation and gene expression profiling, and gold-standard Sanger sequencing using Applied Biosystems 3730xl Genetic Analyzer for validation of deep sequencing results.
• Flow Cytometry Service Cell analysis service for enumerating and phenotyping cells using a comprehensive library of CLIA-validated test panels, supporting full work-up on lymphoid and myeloid malignancies, with panels available for apoptosis and immuno-oncology exploration.
• Anatomical Pathology Services Digital pathology services including pathologist-directed image analysis, whole-slide brightfield and fluorescent scanning, multispectral imaging, and AI-powered image analysis using the proprietary Flotilla platform.
• Tissue Insight (TI) 22C3 NSCLC Digital Assay Digital assay for quantifying PD-L1 in non-small cell lung cancer, validated and published in Scientific Reports as a technology to streamline the PD-L1 IHC quantification process.

Quantifiable outcome

• Proprietary digital assay Tissue Insight (TI) 22C3 NSCLC published in Scientific Reports for streamlining PD-L1 IHC quantification in NSCLC

Named customers3 records

Segments2 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

AI capability4 records

Feature4 records

Partnerships

Three partnerships are on record, tiered core.

• Offspring BiosciencescoreStrategic or Co-development Partner · 23 January 2024Flagship Biosciences and Offspring Biosciences formed a strategic partnership to provide complete global assay development services from target identification to companion diagnostics. The partnership combines Offspring's innovative pre-clinical biomarker assay solutions with Flagship's clinical trial data-driven assay solutions, providing a full end-to-end solution with a North American and European footprint. Flagship CEO Trevor Johnson expressed confidence that the combined offerings would bring unique and valuable translational and clinical capabilities to development partners.
• GenomenoncoreTechnology or Integration · 7 February 2023Flagship Biosciences partnered with Genomenon to advance precision medicine development. Genomenon's genomic landscapes (Master Genomic Database and AI-powered genomic interpretation) are integrated with Flagship's biomarker services and companion diagnostic development solutions, enhancing Flagship's ability to provide comprehensive genomic insights for rare disease and oncology research.
• PaigecoreTechnology or Integration · 17 February 2022Paige, the global leader in AI-based diagnostic software in pathology, partnered with Flagship Biosciences to expand access to Flagship's AI-aided software for quantifying PD-L1 IHC stains across various tissue types. The partnership provides broader market access for Flagship's image analysis tools in immuno-oncology biomarker analysis.

Scale indicators3 records

Recent moves6 records

Expansion highlights6 records

Direct peers

• NeoGenomics Laboratories: NeoGenomics operates a Pharma Services division that provides biomarker, IHC, ISH, and molecular testing to support oncology clinical trials and companion diagnostics. It is one of the most direct competitors to Flagship in the biomarker CRO segment serving pharma and biotech sponsors.
• CellCarta (formerly HistoGeneX): CellCarta is a specialty biomarker and histopathology CRO focused on IHC, multiplex immunofluorescence, ISH, and flow cytometry for clinical trials and companion diagnostics. Its menu, multi-site lab footprint, and customer base overlap closely with Flagship's spatial biology and biomarker development services.
• Akoya Biosciences: Akoya Biosciences develops spatial biology platforms (PhenoCycler, PhenoImager) and offers clinical research services including multiplex immunofluorescence and AI image analysis. It competes directly with Flagship in spatial profiling and digital pathology readouts for pharma and academic clients.
• Paige.AI: Paige develops AI-based diagnostic software for pathology and partners with pharma on AI-aided tissue image analysis, including PD-L1 IHC quantification alongside Flagship. Paige and Flagship are both partners and competitors in AI-enabled digital pathology services for clinical trials.
• Personalis: Personalis provides molecular diagnostics and biomarker services for oncology clinical trials, including whole-genome sequencing, ImmunoID Next, and ctDNA assays. It overlaps with Flagship's genomic and biomarker service offering for pharma drug development and companion diagnostic programs.

Emerging players

• Bio-Techne: Bio-Techne offers spatial biology reagents (RNAscope, GeoMx partnership), proteomics, and ExoDx diagnostics, with services and tools that intersect Flagship's spatial biology and biomarker development workstreams. The overlap is partial — more on the reagent/kit side than pure services — but increasingly competitive on assay offerings.

Broad incumbents

• Q² Solutions (IQVIA): Q² Solutions is IQVIA's central lab and biomarker services business, offering global clinical trial lab testing, genomics, flow cytometry, and anatomic pathology. It is a much larger incumbent competing with Flagship for biomarker and central lab work on enterprise pharma trials.
• Fortrea (formerly LabCorp Drug Development): Fortrea is a large global CRO spun out of LabCorp with central labs, biomarker services, and clinical trial capabilities that overlap with Flagship's CRO offerings. It competes on enterprise pharma programs requiring end-to-end clinical lab support at much larger scale.
• Charles River Laboratories: Charles River provides a broad portfolio of CRO and research services including discovery, safety assessment, and CDx/biomarker support through its research models and services segment. Its biomarker and CDx capabilities overlap with Flagship's clinical-stage assay development work, though at much broader scale.

Regional players

• Eurofins Genomics: Eurofins Genomics is a global provider of genomic services (sequencing, genotyping, gene expression, bioinformatics) headquartered in Europe. It competes with Flagship's genomics offering and has a stronger European footprint, though it is less focused on spatial biology and tissue biomarker services.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/flagshipbio
• LinkedInlinkedin.com/company/flagship-biosciences

Compliance4 records

Revenue estimate

Valuation estimate

Number of profiles

Profiles12 records

Funding overview

Funding rounds3 records

Investors

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

M&A1 record

Investments

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

Frequently asked questions about Flagship Biosciences