The right assay for your target

Innovation in discovery, translational research, and clinical trials

As with everything we do at Flagship, our assays ensure that you surpass your development objectives. We focus on the right biomarker for the most intricate insights in the appropriate regulatory setting. Whether your path is a companion diagnostic (CDx) or a better understanding of contextual biology, we provide optimal assays for all of your biomarker needs.

Flagship’s College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified lab develops and validates assays for your target of interest. We custom develop or optimize existing monoplex and multiplex assays for client-specific biomarkers. We can perform full CLIA validations for your assay, or you can choose from our off-the-shelf options for common biomarkers.

RUO Assays

Choose from an extensive list of more than 70 Flagship validated and ready-to-go assays.

Multiplex Immunofluorescence (mIF)

Make the most of your available tissue by characterizing complex cellular interactions with multiplexed immunofluorescent assays.

  • Investigate up to 6 markers of interest in the same tissue for whole-slide analysis
  • Investigate up to 8 markers of interest in the same tissue using ROI analysis (ROI not recommended for spatial profiling)
  • Create custom immunofluorescent panels of interest
  • Analyze biomarker expression, cellular colocalization, spatial analyses, cellular phenotyping, etc., using Flagship’s Image Analysis platform

Immunohistochemistry (IHC)

Offering custom or off-the-shelf IHC assays tailored to your intended use.

  • Optimize commercial or proprietary antibodies to get the best IHC staining
  • Ensure your IHC assay will stand up to regulatory and clinical scrutiny in our CAP/CLIA certified labs:
    • Validate IHC Assays for retrospective analysis of clinical samples (RUO validation)
    • Validate IHC Assays for prospective diagnostic use (CLIA/clinical validation)
  • Process clinical trial samples to run validated IHC assays
  • Multiplex IHC assays to assess multiple markers in the same tissue
  • Utilize Flagship’s Image Analysis platform to get the most data out of your IHC slides


Flagship Biosciences is a CLIA-certified biopharma partner of ACD to utilize their RNAscope CISH assay in support of clinical trials. https://acdbio.com/biopharma-partners

  • Multiplex CISH assays with IHC or other CISH markers
  • Leverage Flagship’s image analysis services to provide accurate, reproducible quantification of RNAscope signals on a per-cell basis
  • Utilize Flagship’s downstream analytics to stratify RNAscope signals in the tumor and tumor microenvironment, or gain new insights via spatial analysis of cell populations and expression patterns
  • Validate RNAscope assays for prospective clinical use in Flagship’s CAP/CLIA-certified laboratory
  • Clinically validate image analysis reads and cutoffs of RNAscope signals for your indication and use case


We now offer full FISH assay services through our partnership with Empire Genomics. Empower your study with an expansive option of FISH probes with Empire Genomics and get the highest quality clinical information and support from Flagship Biosciences.

  • Through Empire Genomics, Flagship offers a full expansive list of FISH assays that are compatible and optimized to run on Flagship’s image analysis platforms
  • Flagship’s spatial biology services provide clinical grade analysis 
  • Multiplex FISH assays with IHC or other FISH markers
  • See the full list of biomarkers here
  • Custom development and selection of FISH probes are offered through Empire Genomics
Custom Assay Development

Work with Flagship’s immunohistochemical (IHC) / immunofluorescent (IF) / in situ hybridization (ISH) assay development experts to create and validate a unique assay.

  • Flagship can custom develop and optimize IHC, CISH, IF, and/or fluorescent in situ hybridization (FISH) monoplex and multiplex assays for unique client-specific biomarkers
  • Flagship can perform full CAP/CLIA validations for assays that are developed by the client or by Flagship
The support you need through every step of the process