Introduction to
FFPE Blocks Screened by TSO500
FFPE Tumor Blocks Characterized Using TSO500 Workflows
FFPE tumor samples screened through TruSight Oncology 500-based workflows can provide researchers with extensive genomic information across cancer-related genes and biomarker categories. Depending on the performed analysis and available reporting, results may include sequence variants, copy-number alterations, gene fusions and broader genomic biomarkers such as tumor mutational burden or microsatellite instability. These characterized FFPE blocks can support pharmaceutical research, molecular-diagnostic development and precision-oncology studies that require known genomic features.
Rather than screening large numbers of uncharacterized samples, investigators can prioritize specimens containing molecular alterations relevant to their study. Physical FFPE tissue can then be used for additional validation, histology, immunohistochemistry or alternative molecular testing. TSO500-screened specimens therefore provide a useful bridge between comprehensive genomic profiling and downstream translational research.
TSO500-Screened FFPE Samples for Targeted Oncology Research
Targeted therapy research depends on the ability to identify tumors carrying molecular alterations relevant to specific drug mechanisms. FFPE samples previously screened using a broad oncology NGS panel such as TSO500 can help researchers identify mutation-positive, fusion-positive or amplification-positive cases more efficiently. This allows cohorts to be enriched for defined molecular subgroups and reduces the cost and time required for initial screening.
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Researchers may use these specimens for biomarker studies, assay comparison, drug-response research or development of novel molecular diagnostics. Depending on sample availability, TSO500 information may be combined with histological review, tumor percentage, disease stage and clinical annotation. Such integrated datasets can help investigators design more biologically focused studies and explore how genomic characteristics interact with pathology features and therapeutic response.
NGS-Characterized FFPE Blocks for Assay Development and Benchmarking
Developers of oncology assays require clinically realistic reference specimens with known molecular characteristics. FFPE blocks screened by TSO500 can provide broad genomic datasets that may serve as comparison points for newly developed sequencing panels, PCR assays or computational pipelines. Researchers can evaluate whether their technology detects alterations previously identified through a comprehensive NGS workflow and investigate discordant findings using orthogonal methods where needed. These samples can also help optimize extraction, library preparation and bioinformatics processes using formalin-fixed tissue rather than idealized synthetic controls.
Because FFPE material presents real-world challenges such as variable DNA quality, tumor heterogeneity and fixation effects, it provides an important environment for analytical testing. TSO500-characterized specimens can therefore contribute to robust assay-development and benchmarking programs.
TSO500 Genomic Data Combined with Pathology and Clinical Annotation
Genomic information becomes more useful when researchers can interpret it within the context of histology and patient characteristics. TSO500-screened FFPE blocks can be linked, where available, with pathology diagnosis, tumor subtype, stage, grade, tumor percentage and selected clinical variables. This allows investigators to examine associations between molecular alterations and histological or clinical features.
Such datasets are useful for biomarker discovery, retrospective translational studies and development of multimodal artificial-intelligence models. Digital H&E images may also be paired with genomic labels to investigate whether specific alterations produce recognizable morphological patterns. By combining broad NGS profiling with the original tumor tissue and structured annotation, researchers can create data-rich cohorts that support a wide range of precision-oncology research applications.
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.