[PPT] - An innovative multi-dimensional NGS approach to understanding the PowerPoint Presentation

SLIDE 1

The world leader in serving science

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

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

SLIDE 2

2

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

Lead in oncology Targeted research Expand to applied Leading the democratization of NGS to accelerate research and clinical applications With fast, simple, and scalable sample to answer workflows Playing to win in targeted applications Bringing the power of NGS to applied markets

CSD Vision and Strategy

SLIDE 3

3

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

Growing Assay Menu Across All Key Applications

Solid tumor solutions Liquid biopsy solutions Immuno-oncology solutions

+ +

Oncomine™ Focus Assay Oncomine™ Comprehensive Assay Oncomine™ BRCA Research Assay Oncomine™ Pan- Cancer Cell-Free Assay Oncomine™ cfDNA Assays for Lung, Breast, Colon Oncomine™ Tumor Mutation Load Assay Oncomine TCR Beta- LR Assay Oncomine™ Immune Response Research Assay Oncomine™ Lung cfTNA Research Assay Oncomine™ Breast cfDNA Research Assay v2

Heme-oncology solutions

+

Oncomine™ Myeloid Research Assay Oncomine™ Childhood Cancer Research Assay Oncomine™ Dx Target Test

NSCLC solutions

+

Routine research Translational Diagnostics

Ion AmpliSeq™ Designer with Ion AmpliSeq™ HD for custom panels

Oncomine TCR Beta- SR Assay

Full characterization

f oncology

samples

Ion AmpliSeq HD Custom cf Assays

NEW NEW

SLIDE 4

4

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

Tumor-Immune Interactions are Complex and Warrant a Multi-Dimensional Approach

Immune Repertoire

Source: http://www.sciencedirect.com/science/article/pii/S1074761313002963 License: https://creativecommons.org/licenses/by/4.0/ Labels were removed.

Immune Response Tumor Mutation Load

SLIDE 5

5

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

Growing Assay Menu Across All Key Applications

Solid tumor solutions Liquid biopsy solutions Immuno-oncology solutions

+ +

Oncomine™ Focus Assay Oncomine™ Comprehensive Assay Oncomine™ BRCA Research Assay Oncomine™ Pan- Cancer Cell-Free Assay Oncomine™ cfDNA Assays for Lung, Breast, Colon Oncomine™ Tumor Mutation Load Assay Oncomine TCR Beta- LR Assay Oncomine™ Immune Response Research Assay Oncomine™ Lung cfTNA Research Assay Oncomine™ Breast cfDNA Research Assay v2

Heme-oncology solutions

+

Oncomine™ Myeloid Research Assay Oncomine™ Childhood Cancer Research Assay Oncomine™ Dx Target Test

NSCLC solutions

+

Routine research Translational Diagnostics

Ion AmpliSeq™ Designer with Ion AmpliSeq™ HD for custom panels

Oncomine TCR Beta- SR Assay

Full characterization

f oncology

samples

Ion AmpliSeq HD Custom cf Assays

NEW NEW

SLIDE 6

6

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

Key Questions in Immuno-oncology Translational Research

NGS

Can characterizing the tumor micro- environment (TME) predict immune response? Can we improve a selection strategy for immune therapy clinical research trials? Can we identify the population predisposed to immune-mediated adverse events?

Biomarkers

Can we design superior therapeutic T cells by influencing design and development through TCR sequencing? Can we design effective cancer vaccines using the information derived from TCR sequencing?

CAR-T Cancer Vaccines

SLIDE 7

7

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

Interrogating the Tumor Microenvironment – A multi-dimensional approach

Oncomine™ Immune Response Research Assay (Targeted RNA-Seq) Oncomine TCR Beta-SR Assay (Immune repertoire TCR-Seq) Oncomine Tumor Mutation Load Assay (Tumor mutation burden)

Profile 395 key genes

associated with immune response

Accurately measure

gene expression over wide dynamic range

Capture low expressing

genes (IFNG) with greater sensitivity

Interrogates CDR3 of the

T-Cell Receptor beta chain, for characterization of immune status

Enables TCR monitoring
f minimal residual

disease in the peripheral blood

Quantifies somatic

mutations from 1.7mb across 409 cancer genes for accurate assessment

f tumor mutation burden

(TMB)

Correlates with response

to immune checkpoint inhibitors

SLIDE 8

8

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

Constant Leader FR1 FR2 Diversity(D) Joining (J) Variable (V) CDR3 FR3 CDR1 CDR2

Sequencing Beta Chain of T Cell Receptors to Characterize Immune Status

AmpliSeq Primers

~325-400 bp Non-FFPE RNA

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. Flexible input/sequencing depth requirements covering samples with low, medium, and high clonal diversity. Superior informatics for accurate clonality and β chain sequence assessment without interference from primer bias.

10ng- 1mg

Ion Torrent™ Oncomine™ TCR Beta–LR Assay | Makes the PBLs in Peripheral Blood an Additional Rich Source of Predictive Dx Information

Allelic variants alter interaction of CDR1 and 2 with HLA

V-gene polymorphism Clonality / TCR convergence

TCRComplex.png used under creative commons license: https://creativecommons.org/licenses/by-sa/3.0

SLIDE 9

9

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

TCR Convergence May Be a Hallmark of Chronic Antigen Stimulation

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. Tumor Ag

SLIDE 10

10

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

TCR Profiling from Peripheral Blood May Provide the Most Direct Measurement of Tumor Immunogenicity

Tumor acquires non- synonymous mutation Non-synonymous mutation is translated Translated protein is broken into peptides Peptide is presented by HLA T cells recognize peptide and proliferate

Anti-tumor T cell responses Tumor mutation burden profiling (TMB) [indirect measure] HLA typing TCRβ sequencing of peripheral blood [direct measure] Sequence of Events to Elicit Anti-Tumor T Cell Response

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.

Given that tumor antigens may prime T cells over

months or years time, measurements of TCR convergence may provide an accurate pre- treatment estimate of tumor immunogenicity.

SLIDE 11

11

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

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.

However, signatures of T cell

responses to tumor may be evaluated by T cell repertoire analysis of peripheral blood leukocytes.

Oncomine™ cfDNA Assays Oncomine™ TCR Beta – LR Assay

Image via Wikipedia

SLIDE 12

12

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

Expanding Liquid Biopsy with Custom Panels

Solid tumor solutions Liquid biopsy solutions Immuno-oncology solutions

+ +

Oncomine™ Focus Assay Oncomine™ Comprehensive Assay Oncomine™ BRCA Research Assay Oncomine™ Pan- Cancer Cell-Free Assay Oncomine™ cfDNA Assays for Lung, Breast, Colon Oncomine™ Tumor Mutation Load Assay Oncomine TCR Beta- LR Assay Oncomine™ Immune Response Research Assay Oncomine™ Lung cfTNA Research Assay Oncomine™ Breast cfDNA Research Assay v2

Heme-oncology solutions

+

Oncomine™ Myeloid Research Assay Oncomine™ Childhood Cancer Research Assay Oncomine™ Dx Target Test

NSCLC solutions

+

Routine research Translational Diagnostics

Ion AmpliSeq™ Designer with Ion AmpliSeq™ HD for custom panels

Oncomine TCR Beta- SR Assay

Full characterization

f oncology

samples

Ion AmpliSeq HD Custom cf Assays

NEW NEW

SLIDE 13

13

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

Breakout Sensitivity, Standout Customization

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 New amplicon-based NGS library preparation technology that enables you to design custom ultra high-sensitivity panels for your targets of interest Introducing Ion AmpliSeq HD technology:

*For cell-free DNA samples

SLIDE 14

14

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

The world leader in serving science

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

Lead in oncology Targeted research Expand to applied Leading the democratization of NGS to accelerate research and clinical applications With fast, simple, and scalable sample to answer workflows Playing to win in targeted applications Bringing the power of NGS to applied markets

CSD Vision and Strategy

Growing Assay Menu Across All Key Applications

Solid tumor solutions Liquid biopsy solutions Immuno-oncology solutions

+ +

Heme-oncology solutions

+

NSCLC solutions

+

Routine research Translational Diagnostics

Full characterization

samples

NEW NEW

Tumor-Immune Interactions are Complex and Warrant a Multi-Dimensional Approach

Immune Repertoire

Immune Response Tumor Mutation Load

Growing Assay Menu Across All Key Applications

Solid tumor solutions Liquid biopsy solutions Immuno-oncology solutions

+ +

Heme-oncology solutions

+

NSCLC solutions

+

Routine research Translational Diagnostics

Full characterization

samples

NEW NEW

Key Questions in Immuno-oncology Translational Research

NGS

Can characterizing the tumor micro- environment (TME) predict immune response? Can we improve a selection strategy for immune therapy clinical research trials? Can we identify the population predisposed to immune-mediated adverse events?

Biomarkers

Can we design superior therapeutic T cells by influencing design and development through TCR sequencing? Can we design effective cancer vaccines using the information derived from TCR sequencing?

CAR-T Cancer Vaccines

Interrogating the Tumor Microenvironment – A multi-dimensional approach

Oncomine™ Immune Response Research Assay (Targeted RNA-Seq) Oncomine TCR Beta-SR Assay (Immune repertoire TCR-Seq) Oncomine Tumor Mutation Load Assay (Tumor mutation burden)

associated with immune response

gene expression over wide dynamic range

genes (IFNG) with greater sensitivity

T-Cell Receptor beta chain, for characterization of immune status

disease in the peripheral blood

mutations from 1.7mb across 409 cancer genes for accurate assessment

(TMB)

to immune checkpoint inhibitors

Constant Leader FR1 FR2 Diversity(D) Joining (J) Variable (V) CDR3 FR3 CDR1 CDR2

Sequencing Beta Chain of T Cell Receptors to Characterize Immune Status

AmpliSeq Primers

10ng- 1mg

Ion Torrent™ Oncomine™ TCR Beta–LR Assay | Makes the PBLs in Peripheral Blood an Additional Rich Source of Predictive Dx Information

Allelic variants alter interaction of CDR1 and 2 with HLA

V-gene polymorphism Clonality / TCR convergence

TCR Convergence May Be a Hallmark of Chronic Antigen Stimulation

TCR Profiling from Peripheral Blood May Provide the Most Direct Measurement of Tumor Immunogenicity

Tumor acquires non- synonymous mutation Non-synonymous mutation is translated Translated protein is broken into peptides Peptide is presented by HLA T cells recognize peptide and proliferate

Anti-tumor T cell responses Tumor mutation burden profiling (TMB) [indirect measure] HLA typing TCRβ sequencing of peripheral blood [direct measure] Sequence of Events to Elicit Anti-Tumor T Cell Response

to antigen, and thus may serve as a metric for quantifying tumor immunogenicity.

repertoire feature which preferentially arises following chronic antigen stimulation rather than the acute but transient antigen challenges elicited by infectious disease.

months or years time, measurements of TCR convergence may provide an accurate pre- treatment estimate of tumor immunogenicity.

Improving Liquid Biopsy Through Sequencing of Peripheral Blood T Cells

defined as the analysis of tumor cells, or the products of tumor cells, from peripheral blood.

material for liquid biopsy.

responses to tumor may be evaluated by T cell repertoire analysis of peripheral blood leukocytes.

Oncomine™ cfDNA Assays Oncomine™ TCR Beta – LR Assay

Expanding Liquid Biopsy with Custom Panels

Solid tumor solutions Liquid biopsy solutions Immuno-oncology solutions

+ +

Heme-oncology solutions

+

NSCLC solutions

+

Routine research Translational Diagnostics

Full characterization

samples

NEW NEW

Breakout Sensitivity, Standout Customization

0.1%* enabled by unique molecular tags and dual barcodes

design customization available at an accessible price

workflow from sample to data New amplicon-based NGS library preparation technology that enables you to design custom ultra high-sensitivity panels for your targets of interest Introducing Ion AmpliSeq HD technology:

We enable our customers to make the world healthier, cleaner and safer.