Project-based FFPE cohort sourcing for oncology discovery
Starting from your indication and scientific question, we design clinically annotated FFPE cohorts through regulatory-compliant tumor biobanks, with histopathological review by expert pathologists built in.
Each cohort is quality controlled and processed in-house, then analyzed end-to-end on our own platforms — digital pathology (IHC, mIF), single-cell and spatial transcriptomics (Chromium X, Visium HD, Xenium), and AI-assisted image and data analysis. One project, from sample to dataset.
FFPE sourcing is provided as part of an Explicyte analytical project; specimens are not supplied as standalone products.
Recent FFPE-based papers
FFPE cohort sourcing & analysis
Sourcing major and rare oncology indications
Urothelial carcinoma (non-muscle invasive), Urothelial carcinoma (muscle invasive), Squamous cell carcinoma, Adenocarcinoma, Small cell carcinoma, Upper tract urothelial carcinoma
Invasive ductal carcinoma (IDC), Invasive lobular carcinoma (ILC), DCIS, Triple-negative (TNBC), HER2-positive, Hormone receptor-positive (HR+), Inflammatory breast cancer, Metaplastic carcinoma
Colon adenocarcinoma, Rectal adenocarcinoma, Mucinous adenocarcinoma, Signet ring cell carcinoma, MSI-high / dMMR, KRAS/NRAS/BRAF-mutated, Hereditary (Lynch syndrome, FAP)
Adenocarcinoma (intestinal type), Adenocarcinoma (diffuse type), Signet ring cell carcinoma, GEJ adenocarcinoma, GIST, Mucinous adenocarcinoma, HER2-positive, MSI-high
NSCLC — adenocarcinoma, Squamous cell carcinoma, Large cell carcinoma, SCLC, Mesothelioma, Carcinoid tumors, EGFR-mutated NSCLC, ALK-rearranged NSCLC, KRAS-mutated NSCLC
High-grade serous carcinoma, Low-grade serous carcinoma, Endometrioid carcinoma, Clear cell carcinoma, Mucinous carcinoma, Germ cell tumors, Sex cord-stromal tumors, BRCA-mutated
PDAC, Acinar cell carcinoma, Neuroendocrine tumors (PanNETs), IPMN, Mucinous cystic neoplasm, Ampullary carcinoma
Leiomyosarcoma, Liposarcoma, Synovial sarcoma, Rhabdomyosarcoma, GIST, Osteosarcoma, Ewing sarcoma, Chondrosarcoma, Undifferentiated pleomorphic sarcoma
Liver, Kidney, Lung, Heart, Brain, Spleen, Pancreas, Stomach, Colon, Small intestine, Breast, Ovary, Prostate, Skin, Lymph node, Bone marrow, Thyroid, Adrenal gland, Tonsil
Our FFPE tissue sourcing workflow
Expert cohort design and QC for robust downstream analysis
Project scoping & cohort design
The right cohort starts with the right scientific question
Each project is scoped with a PhD-level study director to translate your scientific question into a cohort that can answer it — indication, treatment stratification, controls, normal tissue panels, sample size, and clinical metadata requirements.
Key outputs
- Cohort design aligned with your scientific objective and decision points
- Inclusion/exclusion criteria with target sample numbers
- Clinical metadata requirements specification
- Sourcing strategy across our biobank partner network
Sourcing & histopathological review
Regulatory-compliant sourcing with pathology review built in
We source clinically annotated FFPE specimens through regulatory-compliant tumor biobanks, with full chain-of-custody documentation and anonymized metadata. Each cohort is reviewed by consulting pathologists to confirm diagnosis, assess tumor content, and verify tissue suitability for the intended analyses.
Key outputs
- FFPE specimens sourced under regulatory-compliant biobank processes
- De-identified clinical and histopathological metadata
- Chain-of-custody documentation for every specimen
- Histopathological review by consulting pathologists
Marie Brevet, MD, PhD
- Pathologist at Technipath, Synlab.
- CEO of Biwako, French company dedicated to medical research.
- Areas of expertise: biomarkers in oncology, AI, molecular pathology, biobank, clinical research.
Lucile Vanhersecke, MD, MSc
- Pathologist at the Institut Bergonié Cancer Center.
- Expert for the French national sarcoma review network.
- Areas of expertise: AI, solid tumors, predictive markers of immune response, immunotherapy, TLS.
Sample QC & preparation
In-house QC and processing for downstream analytical platforms
Every sample cohort passes through in-house QC and processing before downstream analysis — designed to preserve sample integrity, minimize batch effects, and ensure data reliability across the project.
Key outputs
- Sample QC and pathology suitability confirmation
- In-house sectioning with harmonized thickness and annotation
- Managed storage conditions for blocks and slides
- Platform-ready preparation for downstream digital pathology, single-cell, or spatial transcriptomic analysis
OUR FFPE-COMPATIBLE PLATFORMS
From sourced FFPE cohort to in-house analysis
Spatial transcriptomics
Atera
High-throughput spatial whole transcriptomics with single-cell resolution
Explore platform
Spatial transcriptomics
Xenium (×2)
Single-cell spatial transcriptomics with
5K or 300-500-plex focused panels
Explore platform
Spatial transcriptomics
Visium HD
Whole-transcriptome mapping at high resolution, co-registration to H&E or IF
Explore platform
Digital pathology
PhenoImager HT (×2)
Singleplex and multiplex IHC & IF panels for protein-level target validation
Explore platform
Spatial transcriptomics
GeoMx
Whole-transcriptome spatial profiling for compartment-level questions
Explore platform
scRNA-seq
Chromium X
High-throughput single-cell gene expression profiling, compatible with fixed tissues
Explore platform
Bulk RNA-seq
NovaSeq X
High-throughput, whole-transcriptome coverage across large sample cohorts
Explore platform
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 have a target indication, a candidate biomarker, or a specific scientific question, we can scope the right cohort and propose next steps. Within 3 business days, a PhD-level study director will reach out to discuss your project, propose the right cohort and analytical strategy, and provide pricing.
Frequently asked questions
Frequently asked questions about FFPE cohort sourcing
What is project-based FFPE cohort sourcing?
Project-based sourcing means Explicyte scouts and processes FFPE sample cohorts as part of a scientific project we run end-to-end — not as standalone biospecimens delivered to the sponsor. The cohort is custom-designed for your scientific question, sourced through regulatory-compliant biobanks, processed in-house, and analyzed on our platforms (digital pathology, single-cell and spatial transcriptomics). One project, one study director, one team handling everything from cohort design to dataset.
Do you sell biospecimens?
No. Explicyte is not a biospecimen vendor. We don’t deliver tissue samples to sponsors or to other CROs. FFPE specimens are sourced through accredited biobank partnerships as part of an end-to-end Explicyte project — the analysis happens on our platforms, with our study directors, under our quality framework. Sponsors looking for standalone biospecimen purchase should work with dedicated biobank vendors.
Which indications can you source for?
We’ve designed sample cohorts across most major and many rare oncology indications — including lung, breast, colorectal, gastric, pancreatic, ovarian, bladder, sarcomas, and normal tissues. For rare or specific indications not on our standard list, we can usually source through our biobank partner network. The first step is a scoping conversation about your target indication and feasibility.
Can you source normal tissues alongside tumor cohorts?
Yes. Normal tissue panels are a core part of our sourcing capability — particularly important for target expression profiling, on-target/off-tumor risk assessment, and biomarker specificity studies. Normal tissue panels can be standardized or custom-designed around specific toxicity hypotheses for your target’s biology.
What clinical metadata is available with sourced cohorts?
Available de-identified clinical and histopathological metadata may include indication, treatment history, pathological diagnosis, tumor grade and stage, and outcome data where available. Specific data fields depend on the biobank source and what was collected at the time of consent. We confirm metadata availability during scoping so the cohort matches your stratification and analysis needs.
What makes Explicyte different for FFPE cohort sourcing?
Three things that distinguish us from biospecimen vendors and from generalist CROs. First, our sourcing is integrated with the analytical work — same project, same study director, same quality framework from cohort design to final dataset. Second, our biobank partnerships in France and our in-house pathology review give us flexibility to design cohorts around your scientific question, not around an off-the-shelf catalog. Third, our in-house analytical platforms (digital pathology, Chromium X, Visium HD, Xenium) and ISO-certified digital pathology workflows mean the cohort is processed by the team that will analyze it.
Can I source samples through Explicyte and analyze them at another CRO?
No — sourcing happens as part of an end-to-end Explicyte project. We don’t act as a sample supply chain for external analytical providers. This is by design: the value of our sourcing is the alignment between cohort design, pathology review, sample QC, and the analytical platforms that will run on the cohort. For sponsors who already have FFPE samples and want analysis only, we can run our analytical workflows on sponsor-provided cohorts.
Can we provide our own FFPE samples in addition to sourced ones?
Yes. Many projects combine sponsor-provided samples with sourced cohorts — particularly when sponsors have access to specific clinical trial samples or research collections but need additional controls, normal tissues, or comparator cohorts. We handle intake, QC, and processing for both sponsor-provided and sourced material under the same workflow.
How do you ensure ethical sourcing and patient consent?
FFPE specimens are sourced through biobank partners operating under applicable ethical and regulatory requirements and documented quality procedures. Depending on the source, these may include quality systems aligned with standards such as ISO 20387. Samples and associated clinical data are handled under the applicable consent or non-opposition framework, with appropriate de-identification and traceability throughout the project
How long does sourcing take, and what's a typical project timeline?
Sourcing timelines depend on indication availability and cohort size. For common indications and standard cohort sizes, sourcing typically takes 4 to 8 weeks; rare indications or large cohorts can take longer. End-to-end project timelines (sourcing + analysis) typically range from 3 to 6 months depending on the analytical workflow. We confirm timelines in writing during the scoping phase before any commitment.
