Enabling Multi-Analyte Analysis of Lung Cancer FFPE Samples with 3D Biology™ Technology

 Worldwide, lung cancer is the most commonly diagnosed form of cancer with a survival rate among the lowest. Somatic mutations (in the form of SNVs and InDels) and gene fusions account for the majority of clinically interpretable and actionable genomic alterations. Biomarkers for lung cancer and identification of molecular drug targets are also actively sought through protein analysis methodologies. Multi-analyte analysis of DNA, RNA, and protein is often hindered by limited amounts of FFPE-preserved specimens. When enough sample is available, each analyte is typically profiled on different instrument platforms, which requires complex workflows and specialized data analysis expertise. To provide a unified and simpler alternative, NanoString’s molecular barcoding technology has been adapted to permit simultaneous digital measurement of biologically-relevant targets that span DNA, RNA, and protein, known as 3D Biology™ technology. This approach has several advantages over other analytical methods. Direct, single-molecule digital counting allows detection over a broad dynamic range with high reproducibility, often >98% concordance between technical replicates. SNV probes enable sensitive and specific identification of ≤ 5% DNA mutant allele sequences from 5 ng of FFPE-extracted genomic DNA. Fusion transcripts are detected with 5’/3’ imbalance probes and toehold-mediated junction probes. Protein and phospho-protein expression is measured via DNA-labeled antibodies and a single antigen retrieval step. The 3D Biology workflow requires just two 5-10 µM sections of FFPE tissue; RNA/DNA extracted from one section and multiplex digital protein profiling from the second.

In this webinar, the speakers will discuss 3D Biology technology and the application of this novel approach in the study 75 lung cancer FFPE samples. These samples were assayed simultaneously with an SNV panel targeting 104 solid tumor somatic mutations in 25 genes, a lung cancer fusion gene panel targeting ALK, RET, ROS1 and NTRK1 transcripts, and a protein panel measuring 26 total and phospho-protein targets, including key members of the EGFR, PI3K, and MAPK signaling pathways. Combined with previous profiling of these samples utilizing 770-plex RNA profiling of key cancer pathways and 770-plex immune gene expression analysis, this multidimensional dataset points the way to a new generation of molecular biomarker-based signatures of disease and true multi-analyte analysis of limited FFPE samples.

Disclaimer: For Research Use Only. Not for use in diagnostic procedures.

Join the webinar to learn how 3D Biology Technology can enable your multi-analyte analysis of FFPE samples.

Speakers

A. McGarry Houghton, MD, Associate Member, Clinical Research Division, Fred Hutchinson Cancer Research Center

Dr. Houghton is a pulmonologist and specializes in critical care, pulmonary complications of malignant disease, and lung cancer. His research focuses on the role of inflammatory cell derived proteinases in diseases occurring within the lungs. To date, this has included novel findings for many disease processes including lung cancer, acute lung injury, pulmonary infections, and pulmonary fibrosis. More recently, his focus has shifted to the tumor microenvironment. Dr. Houghton is currently investigating the role of innate immune cells within the tumor microenvironment in a comprehensive fashion.

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Joseph M. Beechem, PhD, Senior Vice President of Research and Development, NanoString Technologies

Joseph M. Beechem, Ph.D. has served as Senior Vice President of Research and Development, since April 2012. Prior to joining our company, Dr. Beechem held various positions at Life Technologies, a publicly-traded biotechnology tools company, most recently as Vice President, Head of Advanced Sequencing and Head of Global Sequencing Chemistry, Biochemistry and Biophysics from January 2010 to April 2012. From December 2007 to December 2012, he served as Chief Technology Officer of Life Technologies. During his career at Life Technologies, he led the design and development of multiple genetic analysis technologies, the latest advanced SOLiD sequencing technology and the single molecule nano-DNA sequencing technology.

Prior to joining Life Technologies, Dr. Beechem was Chief Scientific Officer at Invitrogen, a publicly-traded biotechnology company that acquired Applied Biosystems in November 2008 to form Life Technologies, from August 2003 to December 2007 and Director of Biosciences at Molecular Probes, a biotechnology company acquired by Invitrogen in 2003, from August 2000 to August 2003. Prior to his industry experience, Dr. Beechem led an NIH-funded research laboratory for 11 years as a tenured associate professor at Vanderbilt University. He has authored or co-authored more than 100 peer-reviewed papers in diverse fields such as biomathematics, physics, chemistry, physiology, spectroscopy, diagnostics and biology. Dr. Beechem is also named on nearly 30 U.S. patents or patent applications and has served on a number of editorial and scientific advisory boards. He received a B.S. in Chemistry and Biology from Northern Kentucky University and a Ph.D. in Biophysics from The Johns Hopkins University.

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