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Oncomine Solutions

Thermo Fisher Scientific Satellite Symposium at European Congress of Pathology, Nice, 9th of September 2019

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Oncomine Solutions- Optimal NGS solution for precision oncology testing

Relevant target

coverage

and key applications

Low sample

requirements

to test as many

small samples as

possible

Complete and

automated

workflow

to enable

streamlined and

fast analysis

Specialised service

& support

to facilitate the testing

implementation

as well

Bioinformatics

and reporting

solution

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In Precision Oncology, one size does not fit all

Oncomine Solutions

Provides you with options,

Because every lab, individual, and sample is unique

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

4

Oncomine Portfolio Strategy

To fit your needs for every sample and project

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

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Expansion of the Current Oncomine Portfolio

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

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Oncomine CDx Expansion – New Pharma Partnerships

For In Vitro Diagnostic Use.

Blueprint Medicines Spectrum

Pharmaceuticals

Daiichi Sankyo and

Takeda

Pharmaceuticals

Agreement to expand

Oncomine Dx Target

Test with RET fusion

markers to treat non-

small cell lung cancer

patients

Spectrum

Pharmaceuticals Enters

into a Next-Generation

Sequencing Companion

Diagnostic Partnership

with Thermo Fisher

Scientific

Daiichi Sankyo and

Takeda

Pharmaceuticals to

leverage FDA-approved

test for clinical trials

and drug development

programs

Agios

Pharmaceuticals

Thermo Fisher

Scientific Signs

Development

Agreement with Agios

Pharmaceuticals for

Next-Generation

Sequencing Oncology

Companion Diagnostic

in Cholangiocarcinoma

2015 - 2019

Pfizer, GSK, Novartis

Agreement to expand

Oncomine Dx Target Test

with RET fusion markers to

treat non-small cell lung

cancer patients

Lilly Oncology

Lilly Oncology

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A comprehensive solution for tumor profiling

Oncomine Comprehensive Assay Plus

500+ Genes

DNA and RNA

Immuno-oncology

Research Targets

Sequencing

Success

Comprehensive

genomic profiling

Tumor Mutational

Burden (TMB)

Foundational Ion

AmpliSeq technology

SNVs, Indels, CNVs,

Fusions, splice variants

Microsatellite Instability

(MSI)

Up to 99% sequencing

success rate

Designed for detection of known and novel targeted and immuno-oncology biomarkers, this new

broad, pan-tumor assay spans over 500 unique genes, including driver genes across all solid tumors

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

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

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Oncomine Comprehensive Assay Plus

A comprehensive solution

500+

Categorized by somatic alteration type Categorized by relevant evidence

169

333

227

>50

15

22

181

Genes with hotspot mutations

Genes with focal CNV gains or loss

Genes with full-coding DNA sequence (CDS)

for deleterious mutations

Gene-fusion drivers

Genes on labels

Genes in guidelines

Genes are used in global clinical trials

genes

Oncomine Reporter v4.3

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

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

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On-target rates

Oncomine Comprehensive Assay Plus

A comprehensive solution

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

Read depth & coverage

Samples

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

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Oncomine Comprehensive Assay Plus

A comprehensive solution

Microsatellite instability (MSI) and tumor mutational burden (TMB) allow for profiling of key biomarkers for precision

oncology and immuno-oncology research in a single assay

Most up-to-date targeted fusion detection with comprehensive fusion targets

Compatible with Oncomine informatics, high quality data, prioritizes and annotates driver variants, and

completes with linking to relevant biomarkers to labels, guidelines, and clinical trials.

Ion AmpliSeq™ technology for a low number of FFPE slides across different sample types (fine needle aspirates or

cytology samples); Input tested down to 1 ng of DNA/RNA or single slide; enables very low QNS, and allows for up to

99% sequencing success; library preparation automatable on Ion Chef™ instrument

Oncomine value: end-to-end sample-to-report automated workflow; inclusive of full customer service and support,

including installation and training

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

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

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A focused solution

Oncomine Tumor Specific Panels

End to end

workflowSmall sample input

As low as 10ng of DNA

Robust performance on FFPE

tissue

Designed for testing of alterations of interest in specific tumors to maximize their detection rate

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

10 Individual tumor specific panels

15-30 highly relevant genes

Relevant Content

IonTorrent Chef & GeneStudio

Bioinformatics and reporting

solution

Specialised

Support

Sequence Variant

and CNV baseline provided for IR

analysis on 530 chip

Verification on clinical research

samples

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

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Oncomine Tumor Specific Panels Phase 1 Overview

Ion Torrent™ Oncomine™

Lymphoma Panel

Ion Torrent™ Oncomine™

BRCA Expanded Panel

Ion Torrent™ Oncomine™

Colorectal Cancer Panel

Ion Torrent™ Oncomine™

Gynecological Cancer Panel

Ion Torrent™ Oncomine™

Gastric Cancer Panel

Ion Torrent™ Oncomine™

Kidney Cancer Panel

Ion Torrent™ Oncomine™

Prostate Cancer Panel

Ion Torrent™ Oncomine™

Bladder Cancer Panel

Ion Torrent™ Oncomine™

Melanoma Panel

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

Ion Torrent™ Oncomine™

Liver Cancer Panel

The content provided herein may relate to products that have not been officially released and is subject to change without notice

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• 10 samples/530 chip (DNA only)

• GeneStudio 530 and 540 chips supported

• Dual barcode supported

• Customizable with genes from inventory

• Ordered on Ampliseq.com Designer

BRCA Expanded • Homologous Repair (HR) pathway

15 genes (1001 amplicons)

Lymphoma Panel (B-Cell) • Diffuse large B-cell lymphomas (DLBCL)

• Follicular lymphoma

• Mantle cell lymphoma

• Marginal zone lymphomas (ie.

Waldenstrom’s macroglobulinemia)

25 genes (946 amplicons)

Focused solution

Focused solution - Oncomine tumor specific panels

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

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

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Focused solution - Oncomine BRCAness

Coming soon 2

15

Categorized by somatic alteration type Categorized by relevant evidence

7

15

15

2

2

15

Genes with hotspot mutations

Genes with focal CNV gains or loss

Genes with full-coding DNA sequence (CDS)

for deleterious mutations

Genes on labels

Genes in guidelines

Genes are used in global clinical trials

genes

Oncomine Reporter v4.3

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

15

Focused solution - Oncomine Lymphoma

Coming soon 2

25

Categorized by somatic alteration type Categorized by relevant evidence

7

24

18

1

2

12

Genes with hotspot mutations

Genes with focal CNV gains or loss

Genes with full-coding DNA sequence (CDS)

for deleterious mutations

Genes on labels

Genes in guidelines

Genes are used in global clinical trials

genes

Oncomine Reporter v4.3

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

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Focused solution

Focused solution - Oncomine tumor specific panels

On avg. for FFPE samples:

• On-target ~ 70%

• Uniformity ~ 96%

Validation Lot #1 Data Not Final

The content provided herein may relate to products that have not been officially released and are subject to change without notice.

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

0,0%

20,0%

40,0%

60,0%

80,0%

100,0%

Core Panel On-Target and Uniformity - 530 Chip - DUAL BCs

OT_FFPE OT_NA12878 Uni_FFPE Uni_NA12878

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1

1

1

Focused solution

Hematology-Oncology Solutions: Simplify Your Journey to Answers

Everything you need to expedite your path to hematology-oncology insights is in one place

Oncomine Myeloid Research Assay

Oncomine Myeloid MRD Assay*

Oncomine BCR IGH-LR Assay*

Oncomine BCR IGH-SR Assay*

Oncomine Lymphoma Assay*

Oncomine Childhood

Cancer Research Assay

* Denotes assays coming soonOncomine TCR Beta-SR

The content provided herein may relate to products that have not been officially released and is subject to change without notice

Focused solution

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

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Oncomine BCR IGH LR & SR Assays

The Oncomine™ BCR IGH assays are 2 powerful and sensitive BCR repertoire assays that allow you to

identify, assess and track malignant B-cell clones with superior sensitivity, ease, and confidence

Identify TrackMeasurethe dominant malignant

clone and determine its

unique CDR3 sequence for

subsequent tracking

the frequency of somatic

hypermutation (SHM) in

the IGHV genes

the malignant clone in

subsequent samples for

measurable residual disease

(MRD) research

The content provided herein may relate to products that have not been officially released and is subject to change without notice

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

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Oncomine Lymphoma Assay

Targets all B-cell lymphomas,

including:

• Diffuse large B-cell

lymphomas (DLBCL)

• Follicular lymphoma

• Mantle cell lymphoma

• Marginal zone lymphomas

such as Waldenstrom’s

macroglobulinemia

Highly curated tumor-specific

content:

• 25 unique genes

• Option to customize with

additional gene targets in

inventory

Robust performance with

minimal sample input

requirement (10ng)

• End to end workflow

including bioinformatics

and reporting solution

• Specialized support for

assay verification

The content provided herein may relate to products that have not been officially released and is subject to change without notice

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

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Constant Leader FR1 FR2

Diversity (D) Joining (J)Variable (V)

CDR3

FR3

CDR1 CDR2

Somatic Hypermutation (LR) Clonality / Monitoring Isotype (LR)

~410 bp

Non-FFPE RNA

OncomineTM BCR IGH-LR* Assay for SHM Analysis | Assay Design

B cell heavy chain (IGH)• Long amplicon design = ~410bp

• Covers CDR1, 2 and 3 and CH1 domain of isotype

• Enables accurate quantification of somatic

hypermutation (SHM), measurement of clonal

expansion, and tracking of clonal lineages.

• Constant region primers designed against all B cell

isotypes

• Flexible input requirements ranging from 25 ng to 2 µg

• Accepts total RNA from whole blood, bone marrow,

peripheral blood leukocytes (PBL), peripheral blood

mononuclear cells (PBMC), or fresh frozen specimens

*LR: Long Read

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

The content provided herein may relate to products that have not been officially released and is subject to change without notice

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OncomineTM BCR IGH-SR* Assay for MRD | Assay Design

• Short amplicon design = ~110bp covering the CDR3

region.

• Enables the detection and longitudinal tracking of

residual or re-emerging malignant B-cell clones with

high capture efficiency and low LoD (10-6).

• Clonal lineage analysis allows for identification of

subclones deriving from ongoing SHM (e.g. follicular

lymphoma)

• Flexible input requirements ranging from 25 ng to 2 µg

• Compatible with RNA or DNA input from whole blood,

bone marrow, PBL, PBMC, fresh frozen and FFPE

preserved samples.

~110 bp

RNA or gDNA

*SR: Short Read

Constant Leader FR1 FR2

Diversity (D) Joining (J)Variable (V)

CDR3

FR3

CDR1 CDR2

Somatic Hypermutation (LR) Clonality / Monitoring Isotype (LR)

B cell heavy chain (IGH)

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

The content provided herein may relate to products that have not been officially released and is subject to change without notice

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Oncomine Myeloid MRD Assay

New amplicon-based NGS library preparation technology for ultra high-sensitivity

• Low limit of detection — variant detection targeting

0.1%-0.01% enabled by unique molecular tags and dual

barcodes

• Validated MRD panel — First assay targeted for routine

use with actionable gene set compatible with whole blood,

or bone marrow

• Complete 2-day workflow — fast targeted NGS workflow

from sample to data

• Content — Curated gene and fusion transcript targets for

comprehensive myeloid coverage

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

The content provided herein may relate to products that have not been officially released and is subject to change without notice

23

In Precision oncology, one size does not fit all

Oncomine Solutions provide you with option,

Because every lab, individual, and sample is unique

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

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property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified