Introduction to
CDx Assay Development Cohorts
Purpose-Built Cohorts for Companion Diagnostic Assay Development
CDx Assay Development Cohorts are important resources for oncology companion diagnostic and biomarker programs because developers need representative human specimens that reflect the biological variability encountered in real clinical populations. Carefully selected cohorts can support feasibility, assay optimization, analytical characterization, comparator studies, cut-off development, and translational research. Depending on the program, specimens may include FFPE tumor blocks, unstained slides, tissue curls, extracted DNA or RNA, plasma, serum, whole blood, or matched materials.
Samples can be selected by diagnosis, histological subtype, stage, grade, tumor percentage, biomarker status, treatment history, or other available clinical variables. Molecular characterization using IHC, FISH, ISH, PCR, NGS, or another appropriate method can help sponsors start with a known biological reference. This reduces unnecessary screening and enables pharmaceutical, biotechnology, CRO, and diagnostic teams to focus on assay performance and clinically relevant questions.
Assay Development Cohorts for IHC, FISH, PCR, and NGS CDx Platforms
For CDx Assay Development Cohorts, biomarker stratification is especially valuable because a robust assay must perform across strong-positive, low-positive, borderline, heterogeneous, and negative specimens rather than only ideal cases. Cohorts can be enriched for actionable biomarkers such as HER2, EGFR, ALK, ROS1, KRAS, BRAF, MET, RET, NTRK, BRCA1/2, PIK3CA, MSI, or PD-L1 when appropriate to the indication and study design. Samples near the intended clinical decision threshold can help investigators assess analytical sensitivity, specificity, scoring stability, reproducibility, and potential discordance.
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Orthogonal data may also support comparison between technologies, for example IHC versus FISH or PCR versus NGS. By deliberately including biologically challenging cases, developers can identify assay limitations earlier and design stronger verification or validation plans for subsequent stages of a companion diagnostic program.
Biomarker-Enriched Cohorts for Targeted Therapy Diagnostic Programs
Clinically annotated CDx Assay Development Cohorts can provide substantially greater research value than specimens without context. Depending on availability, associated information may include diagnosis, histology, anatomical site, stage, grade, specimen type, collection date, age, sex, prior therapy, response, recurrence, progression, and relevant molecular or pathology findings. These variables allow sponsors to construct cohorts that more closely resemble the intended-use population and to perform meaningful subgroup analyses.
Where available, matched H&E slides, digital pathology images, pathology reports, IHC scores, FISH findings, PCR data, or NGS results can further strengthen the dataset. Structured annotation can support retrospective studies, biomarker prevalence work, concordance analysis, treatment-response research, and clinical validation planning. The exact fields provided should be defined prospectively so that sourcing, pathology review, and data curation remain aligned with the study protocol.
Custom CDx Cohort Design Based on Sponsor-Specific Criteria
Custom sourcing of CDx Assay Development Cohorts allows pharmaceutical and diagnostic developers to define project-specific inclusion and exclusion criteria instead of relying on generic inventory. A sponsor may specify cancer indication, biomarker status, specimen type, minimum tumor content, necrosis limits, block age, treatment exposure, disease stage, reference-testing methodology, and required clinical annotation. Large pathology or biospecimen archives can then be screened to identify qualifying cases, including rare molecular subsets that would otherwise require substantial pre-screening.
Additional specimen preparation, pathology review, or molecular confirmation can be incorporated where appropriate and material is sufficient. A targeted cohort-building strategy helps reduce internal screening burden, improve biological relevance, and create sample sets aligned with the intended assay, therapeutic mechanism, or regulatory development plan. Regulatory suitability ultimately depends on the specific protocol, jurisdiction, documentation, and quality requirements defined by the sponsor and its regulatory team.
General Questions
Frequent Asked Questions!!
FFPE blocks for genomics are formalin-fixed, paraffin-embedded tissue samples used for DNA, RNA, and biomarker analysis. They are widely used in cancer genomics, molecular pathology, translational research, and retrospective studies.
FFPE tissue blocks are valuable because they preserve tissue architecture and molecular material for long-term storage. Researchers can use them for sequencing, mutation analysis, biomarker discovery, and validation studies.
Yes. DNA can be extracted from FFPE blocks using validated extraction kits and optimized laboratory protocols. DNA quality depends on fixation time, block age, tissue type, tumor content, and storage conditions.
Yes. RNA can be extracted from FFPE tissue, although it is often fragmented because of formalin fixation. Specialized FFPE RNA extraction methods can provide material suitable for targeted RNA sequencing, gene expression studies, and fusion analysis.
Yes. High-quality FFPE blocks are commonly used for next-generation sequencing, including targeted sequencing panels, whole-exome sequencing, RNA sequencing, and selected whole-genome applications.
Tumor content requirements depend on the study design and testing method. Many molecular and NGS studies require at least 20% tumor content, while some projects may require 30%, 50%, or higher tumor percentage. Pathologist review can be performed to confirm tumor content before shipment
FFPE blocks can support mutation testing, copy number analysis, gene fusion detection, microsatellite instability testing, tumor mutational burden analysis, methylation studies, and targeted DNA or RNA sequencing.
Yes. FFPE cancer tissue blocks are extensively used to study genomic alterations in lung, breast, colorectal, prostate, ovarian, pancreatic, liver, kidney, and other tumor types.
Researchers can purchase FFPE blocks from qualified biospecimen suppliers, biobanks, pathology laboratories, hospitals, and research networks that provide ethically sourced and clinically annotated human tissue samples.
Researchers should confirm diagnosis, tissue type, tumor percentage, necrosis percentage, fixation details, block age, specimen size, available clinical data, pathology review, consent status, and intended research-use permissions.
Yes. Clinically annotated FFPE blocks may include donor age, sex, diagnosis, grade, stage, TNM classification, treatment history, pathology report, mutation status, and clinical outcome data.