An innovative multi-dimensional NGS approach to understanding the tumor microenvironment and evolution

Transcription

1 An innovative multi-dimensional NGS approach to understanding the tumor microenvironment and evolution James H. Godsey, Ph.D. Vice President, Research & Development Clinical Sequencing Division (CSD) Life Science Solutions For Research Use Only. Not for use in diagnostic procedures. The world leader in serving science

2 CSD Vision and Strategy Leading the democratization of NGS to accelerate research and clinical applications Lead in oncology Targeted research Expand to applied With fast, simple, and scalable sample to answer workflows Playing to win in targeted applications Bringing the power of NGS to applied markets 2 For Research Use Only. Not for use in diagnostic procedures.

3 Growing Menu Across All Key Applications Diagnostics Routine research Translational Full characterization of oncology samples NSCLC + Oncomine Dx Target Test Solid tumor Oncomine Comprehensive + Heme-oncology Oncomine Myeloid Research + + Liquid biopsy Oncomine cfdna s for Lung, Breast, Colon Immuno-oncology Oncomine Tumor Mutation Load Oncomine Focus Oncomine Childhood Cancer Research Oncomine Lung cftna Research Oncomine Immune Response Research Oncomine BRCA Research Oncomine Breast cfdna Research v2 Oncomine TCR Beta- LR Oncomine Pan- Cancer Cell-Free Oncomine TCR Beta- SR NEW Ion AmpliSeq HD Custom cf s NEW Ion AmpliSeq Designer with Ion AmpliSeq HD for custom panels 3 For Research Use Only. Not for use in diagnostic procedures.

4 Tumor-Immune Interactions are Complex and Warrant a Multi-Dimensional Approach Immune Repertoire Tumor Mutation Load Immune Response 4 For Research Use Only. Not for use in diagnostic procedures. Source: License: Labels were removed.

5 Growing Menu Across All Key Applications Diagnostics Routine research Translational Full characterization of oncology samples NSCLC + Oncomine Dx Target Test Solid tumor Oncomine Comprehensive + Heme-oncology Oncomine Myeloid Research + + Liquid biopsy Oncomine cfdna s for Lung, Breast, Colon Immuno-oncology Oncomine Tumor Mutation Load Oncomine Focus Oncomine Childhood Cancer Research Oncomine Lung cftna Research Oncomine Immune Response Research Oncomine BRCA Research Oncomine Breast cfdna Research v2 Oncomine TCR Beta- LR Oncomine Pan- Cancer Cell-Free Oncomine TCR Beta- SR NEW Ion AmpliSeq HD Custom cf s NEW Ion AmpliSeq Designer with Ion AmpliSeq HD for custom panels 5 For Research Use Only. Not for use in diagnostic procedures.

6 Key Questions in Immuno-oncology Translational Research Biomarkers CAR-T Can characterizing the tumor micro- environment (TME) predict immune response? Can we design superior therapeutic T cells by influencing design and development through TCR sequencing? NGS Can we improve a selection strategy for immune therapy clinical research trials? Cancer Vaccines Can we identify the population predisposed to immune-mediated adverse events? Can we design effective cancer vaccines using the information derived from TCR sequencing? 6 For Research Use Only. Not for use in diagnostic procedures.

7 Interrogating the Tumor Microenvironment A multi-dimensional approach Oncomine Immune Response Research (Targeted RNA-Seq) Oncomine Tumor Mutation Load (Tumor mutation burden) Oncomine TCR Beta-SR (Immune repertoire TCR-Seq) Profile 395 key genes associated with immune response Accurately measure gene expression over wide dynamic range Capture low expressing genes (IFNG) with greater sensitivity Quantifies somatic mutations from 1.7mb across 409 cancer genes for accurate assessment of tumor mutation burden (TMB) Correlates with response to immune checkpoint inhibitors Interrogates CDR3 of the T-Cell Receptor beta chain, for characterization of immune status Enables TCR monitoring of minimal residual disease in the peripheral blood 7 For Research Use Only. Not for use in diagnostic procedures.

8 Ion Torrent Oncomine TCR Beta LR Makes the PBLs in Peripheral Blood an Additional Rich Source of Predictive Dx Information Sequencing Beta Chain of T Cell Receptors to Characterize Immune Status Long Read NGS assay capturing all 3 CDRs (1,2 &3). Uniquely captures germline TRBV polymorphism from blood/tissue to investigate predisposition to adverse events. V-gene polymorphism Clonality / TCR convergence 10ng- 1mg Flexible input/sequencing depth requirements covering samples with low, medium, and high clonal diversity. Leader FR1 FR2 FR3 CDR1 CDR2 CDR3 Variable (V) Diversity(D) AmpliSeq Primers ~ bp Non-FFPE RNA Joining (J) Constant Superior informatics for accurate clonality and β chain sequence assessment without interference from primer bias. Allelic variants alter interaction of CDR1 and 2 with HLA TCRComplex.png used under creative commons license: 8 For Research Use Only. Not for use in diagnostic procedures.

9 TCR Convergence May Be a Hallmark of Chronic Antigen Stimulation Tumor Ag Priming and proliferation of tumor antigen specific T cells. T cells do not destroy tumor. Tumor antigen continues to prime naive T cells with shared antigen specificity. This distinguishes T cell responses to cancer from those following short-term acute antigen challenge typical of responses to infectious disease. Over time, convergent TCR groups become detectable in peripheral blood. 9 For Research Use Only. Not for use in diagnostic procedures.

10 TCR Profiling from Peripheral Blood May Provide the Most Direct Measurement of Tumor Immunogenicity Convergent TCRs are the result of T cell responses to antigen, and thus may serve as a metric for quantifying tumor immunogenicity. We propose that TCR convergence is a T cell repertoire feature which preferentially arises following chronic antigen stimulation rather than the acute but transient antigen challenges elicited by infectious disease. Sequence of Events to Elicit Anti-Tumor T Cell Response Tumor acquires nonsynonymous mutation Non-synonymous mutation is translated Translated protein is broken into peptides Tumor mutation burden profiling (TMB) [indirect measure] Given that tumor antigens may prime T cells over months or years time, measurements of TCR convergence may provide an accurate pretreatment estimate of tumor immunogenicity. Peptide is presented by HLA T cells recognize peptide and proliferate HLA typing measure] Anti-tumor T cell responses TCRβ sequencing of peripheral blood [direct 10 For Research Use Only. Not for use in diagnostic procedures.

11 Improving Liquid Biopsy Through Sequencing of Peripheral Blood T Cells Liquid biopsy is traditionally defined as the analysis of tumor cells, or the products of tumor cells, from peripheral blood. cfdna has been the standard input material for liquid biopsy. Oncomine cfdna s However, signatures of T cell responses to tumor may be evaluated by T cell repertoire analysis of peripheral blood leukocytes. Oncomine TCR Beta LR Image via Wikipedia 11 For Research Use Only. Not for use in diagnostic procedures.

12 Expanding Liquid Biopsy with Custom Panels Diagnostics Routine research Translational Full characterization of oncology samples NSCLC + Oncomine Dx Target Test Solid tumor Oncomine Comprehensive + Heme-oncology Oncomine Myeloid Research + + Liquid biopsy Oncomine cfdna s for Lung, Breast, Colon Immuno-oncology Oncomine Tumor Mutation Load Oncomine Focus Oncomine Childhood Cancer Research Oncomine Lung cftna Research Oncomine Immune Response Research Oncomine BRCA Research Oncomine Breast cfdna Research v2 Oncomine TCR Beta- LR Oncomine Pan- Cancer Cell-Free Oncomine TCR Beta- SR NEW Ion AmpliSeq HD Custom cf s NEW Ion AmpliSeq Designer with Ion AmpliSeq HD for custom panels 12 For Research Use Only. Not for use in diagnostic procedures.

13 Breakout Sensitivity, Standout Customization Introducing Ion AmpliSeq HD technology: New amplicon-based NGS library preparation technology that enables you to design custom ultra high-sensitivity panels for your targets of interest Low limit of detection variant detection down to 0.1%* enabled by unique molecular tags and dual barcodes Customization in your hands flexible panel design customization available at an accessible price Complete 2-day workflow fast targeted NGS workflow from sample to data *For cell-free DNA samples 13 For Research Use Only. Not for use in diagnostic procedures.

14 A Mission We Are Proud Of We enable our customers to make the world healthier, cleaner and safer. 14 For Research Use Only. Not for use in diagnostic procedures.