FFPE-Based Oncology Target Discovery
Generating data you can trust from FFPE tissues
Explicyte helps biotech and pharma teams discover and prioritize oncology targets in FFPE tissues — the standard archival format for solid tumors.
We build discovery campaigns around your objectives: assembling clinically annotated cohorts, designing fit-for-purpose studies, and applying data science workflows to nominate and rank your targets.
Recent FFPE-based papers
FFPE-based oncology target discovery
A modular FFPE target discovery workflow
Human normal & tumor FFPE samples
Building the right FFPE cohort
We source clinically annotated FFPE specimens through regulatory-compliant French biobanks, design stratified cohorts aligned with your scientific question, and prepare samples to platform-ready specifications.
Transcriptomic profiling & data science
Identifying and ranking targets
We run FFPE transcriptomic campaigns across whole-transcriptome, single-cell, focused-panel, and spatial approaches — paired with in-house data science to nominate and rank candidates.
Tissue validation & de-risking
Validating target expression in situ
We confirm target expression in larger FFPE cohorts — prevalence, protein localization, heterogeneity, and normal tissue distribution — using digital pathology workflows (multiplex IF or IHC).
Dedicated expertise in immuno-oncology targets & biomarkers
Unlocking insights from the tumor microenvironment
In this interview, Jean-Philippe Guégan, PhD, who leads the of Spatial Biology & Data Science teams at Explicyte, explains how we combine access to human FFPE tissue cohorts, spatial transcriptomics, digital pathology, and advanced data science to support oncology discovery programs.
MultiOmics servicesSponsor stories
Target & biomarker discovery testimonials
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
Contact our team
Discuss your discovery project and request a quote
Whether you start from FFPE blocks, an existing dataset, a shortlist of candidate targets, or a specific indication, we can help design the right discovery study and define the next validation steps.
Frequently asked questions
What makes Explicyte different for oncology target discovery?
Explicyte combines deep FFPE expertise, clinically annotated biospecimen access, certified technology and histology workflows, and in-house data science within a single oncology-focused team. Based at Institut Bergonié Comprehensive Cancer Center, our scientists work alongside oncologists and pathologists, with expertise supported by 40+ peer-reviewed publications in oncology and immuno-oncology.
What is oncology target discovery?
Oncology target discovery is the process of identifying and prioritizing therapeutic targets and biomarkers using evidence from human tumor biology, then confirming the most promising candidates through fit-for-purpose validation to support confident go/no-go decisions.
Do you work only with FFPE tissues?
FFPE is a core strength because it provides access to clinically annotated, real-world cohorts and supports both transcriptomic profiling and tissue-based validation. However, we can also source and analyze fresh tissues and peripheral samples when the project requires it.
I already have a target candidate. Which service should I start with?
If you already have a target candidate and need to assess prevalence, localization, heterogeneity, or normal tissue distribution, the best starting point is usually target expression profiling.
I have FFPE blocks but no transcriptomics data. Where should I start?
If your goal is to nominate and prioritize targets or biomarkers from patient tissues, a good starting point is FFPE transcriptomic profiling, especially when comparing tumor subtypes, clinical strata, or responder groups.
I don’t have access to samples yet. Can you help?
Yes. If access to clinically relevant cohorts and metadata is the main bottleneck, we can start with custom biospecimen sourcing so the study design and sample specifications are defined before data generation begins.
How do you select the right discovery approach?
The optimal strategy depends on the biological question, available samples, required resolution and downstream decision. We define a fit-for-purpose approach during project scoping and select the appropriate profiling and validation methods accordingly.
Can you integrate clinical metadata and outcomes?
When available, we integrate clinical and pathological variables to support subgroup analyses, enrichment hypotheses, and decision-oriented statistics, while keeping all data de-identified and handled in line with applicable requirements.
How do you help teams decide what to do next after target nomination?
After nomination, we help teams determine the next validation step based on the strength of the biological signal, cohort-level prevalence, expression heterogeneity, and normal tissue distribution. This may involve tissue-level confirmation, orthogonal validation, or progression toward a more focused follow-up study.
What does a typical target discovery deliverable look like?
A target discovery campaign typically ends with a ranked shortlist of candidates, a summary of the evidence supporting each, key cohort-level figures, and a recommended validation roadmap (which often includes tissue-level expression confirmation).
Can you start from our existing data or public datasets?
Yes. We can start from sponsor-provided datasets, public resources, or both, and build a harmonized analysis, prioritization strategy, and validation plan aligned with your program goals.
What information do you need to scope a discovery project?
To scope a study efficiently, we typically need your indication of interest, the type and availability of samples, the main biological or translational question, and any constraints around timeline, budget, or downstream validation.
