{filename}

Publications

Categories

Filter by Topics

ADCC Gene Alteration ALK Angiogenesis Anti-TNF Alpha Therapy Apoptosis Asthma Autocrine Signaling Autoimmune Disorder Biofluid Biology of neoplasia Biomarker Analysis Biomarker Validation Biomarkers Bladder Brain Breast Cancer CDKN2A mutation Cells Cerebrospinal Fluid Childhood Atopic Dermatitis Chronic Obstructive Pulmonary Disease Circulating miRNAs cMET Colorectal cancer Comparison study Core Needle Biopsy Custom mRNA Cytokines Developmental Immunotherapy Developmental Therapeutics Diabetes Differential Gene Expression Analysis DLBCL Drug Response Drug Safety Drug Targets Drug-induced Liver Injury Efficacy EGFR Muatations EMT Encephalophy Epstein-Barr ERBB3 Esophageal Cancer Exosomes Extracellular Vesicles Fabry Disease FFPE FGF Ligand Trap FGFR Fibrous Tumors Follicular lymphoma Gene Expression Profiling Gene Fusions Genetic Polymorphism Genitourinary cancer Glioblastoma Tumors Head and Neck Cancer Heart HER2 Histone Deacetylase Inhibitors HLA-E HPV HTG EdgeSeq ALKPlus Assay EU HTG EdgeSeq Custom Assays HTG EdgeSeq DLBCL Cell of Origin Assay HTG EdgeSeq DLBCL Cell of Origin Assay EU HTG EdgeSeq EGFR KRAS and BRAF Mutation Assay HTG EdgeSeq Immuno-Oncology Assay HTG EdgeSeq Lung Fusion Assay HTG EdgeSeq miRNA Whole Transcriptome Assay HTG EdgeSeq Mouse mRNA Tumor Response Panel HTG EdgeSeq Oncology Biomarker Panel HTG EdgeSeq PATH Assay HTG EdgeSeq Precision Immuno-Oncology Panel HTG EdgeSeq System HTG EdgeSeq System Oncology Biomarker Panel Immune Checkpoint Inhibitors Immune Related Genes Immune Response Immune Tolerance Immune-related Colitis Immuno-Oncology Immunotherapy Inflammation Juvenile Arthritis Kidney Liposarcoma Liquid Biopsy Liver Lung Lupus Lymph Node Metastasis Lymphoma Mechanism of Action Melanoma Mesothelioma MET Microenvironment miRNA Molecular Characterization Mouse mRNA custom mTOR pathway Multiple Myeloma Muscle Mutations MYC NAFLD Nash and Fibrosis Natural Killer Cells Neoantigens Neuroendocrine Tumor Neurologic non-Hodgkin Lymphoma Novel Therapeutic Targets NTRK1 Oesophageal Adenocarcinoma Oncology Oral Cancer Osteoclast Ovarian cancer Pancreas Paralysis Parkinson's Disease Pathogenesis Pathway Analysis PBMCs PCA Cell Lines PIK3CA mutation Placenta Plasma Platform Comparison Predictive Modeling Programmed cell death protein 1 Progression free-survival Prostate qNPA qPCR Radioimmunotherapy Rearrangements Response rate RET Reveal Rheumatoid Arthritis Risk Score ROS1 safety Sarcoma Serum Signaling Inhibitors Signatures Sinonasal Carcinoma SPECS Lung Consortium Squamous cell carcinoma Sub-typing Surveillance Survival Outcomes Survival plots Synovial Fluid Therapeutic Response Therapeutic targets TMB Toxicity TP53 mutation Translational Medicine Transplantation Treatment Outcome Treatment Stratification Treatment Targets Tumor Biology Tumor Heterogeneity Tumor Immunobiology Tumor infiltrating lymphocytes Urothelial carcinoma VEGFR Xenograft Tissue

FFPE Tissue and the HTG EdgeSeq Oncology Biomarker Panel

The overwhelming majority of archival samples of cancer tissue are formalin-fixed, paraffin-embedded (FFPE).  Many FFPE samples, especially pre-treatment biopsy specimens, are too small to reliably extract sufficient RNA for gene expression analysis.  HTG Molecular recommends 12.5 mm2 of tissue from one 5 μm FFPE section with no RNA extraction necessary for gene expression data from their HTG EdgeSeq nuclease-protection assay.

HTG EdgeSeq Oncology Biomarker Panel covers 2,560 genes.  This pilot study examined different amounts of tissue input from 3 colorectal and 2 breast tumors down to 3.1 mm2, representing ¼ the recommended input.

During this webcast you will learn/our speaker(s) will address:

  • The HTG EdgeSeq Oncology Biomarker Panel provides a solid platform to obtain gene expression data from FFPE samples far too small for reliable RNA extraction. 
  • Reproducibility was robust, with technical replicates correlating >0.98, and small areas of the tumor correlating very well with each other, and reasonably well with NanoString and TaqMan data from extracted RNA.
  • The lower limit for tissue input for this assay was not reached in this experiment, but most FFPE biopsy samples of interest will not be smaller than 3.125 mm2

Speaker

Katherine Pogue-Geile, Ph.D., NSABP

Speaker Biography

Dr. Katherine (Kay) Pogue-Geile is Associate Director of MicroArray/Molecular Profiling at the National Surgical Breast and Bowel Project (NSABA) in Pittsburgh, PA.  She has 30 year’s experience in cancer research using a variety of molecular techniques to elucidate molecular mechanisms involved in cancer.  At the NASBP, Dr. Pogue-Geile has developed methodologies for profiling DNA and RNA utilizing formalin fixed paraffin embedded tissue (FFPE) samples collected in clinical trials to identify and validate biomarkers for prognosis and prediction of response to therapy in colon and breast cancer.

Return To List