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Enabling New Markets for Growth

Empowering the Genomics Revolution

2013 NGS User Forum Tokyo, Japan

June 27, 2013

Peter Fromen Sr. Director, Product Marketing &

Market Development

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Technology Revolutions

Industrial Revolution 1750 Maximise Production

Digital Revolution 1950 Maximize Intellectual Output Biological Revolution 2003 Maximise Biological Output

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From: Venturebeat.com, 1/27/13 commenting on the 12/24/12 Time magazine cover story

“We are at an inflection point.”

“…Companies to watch: Illumina.”

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Lancet Infect Dis.: E-pub ahead of print

Outbreak Monitoring & Public Health

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Microbiology & Food Pathogen Testing

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Metagenomics & Environmental

The benefits of shotgun metagenomics and metatranscriptomics

Single cell genome sequencing of unculturable organisms

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NextGen Forensics

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Cancer Research & Treatment

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Non-Invasive Prenatal Testing

T21 Down syndrome T18 Edwards syndrome T13 Patau syndrome XO Turner syndrome XXX Triple X XXY Klinefelter syndrome XYY Jacobs syndrome

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Rapid Diagnosis of Newborns HiSeq 2500 WGS – from DNA to Disease in ~50hrs

Neonate at 5 mo - developmental regression &

seizures

Samples prepared, sequenced and

analyzed (HiSeq 2500)

Identified novel variant in gene

linked to copper metabolism

Confirmed diagnosis of

Menkes disease

Courtesy of Stephen Kingsmore, Children’s Mercy Hospital, Kansas City

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The Platform of Choice for High Impact Studies

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We are in the very early phases of a transformative period

A View on Current State

Genetics Cancer

Consumer

Reproductive Health Forensics

BioPharm

Infectious Disease Agriculture

Research 40%

30%

10%

5%

10%

30%

20%

30%

5%

0

% penetration

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We are in the very early phases of a transformative period

Essential to continue to drive down sequencing costs (true total costs)

A View on Current State

http://www.genome.gov/sequencingcosts/

Sanger Sequencing

HiSeq Systems

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We are in the very early phases of a transformative period

Essential to continue to drive down sequencing costs (true total costs)

Upstream & downstream processes to the sequencer need to become less of a bottleneck

A View on Current State

Sample Prep Sequencing Analysis

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We are in the very early phases of a transformative period

Essential to continue to drive down sequencing costs (true total costs)

Upstream & downstream processes to the sequencer need to become less of a bottleneck

Educating clinicians, doctors, regulators, and ultimately patients is essential to responsibly broadening use of NGS

A View on Current State

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Customer Driven Development

Gen

eric

Tec

hnol

ogy

Customer

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Dx Diagnostics

(IVD) Molecular Biology

and PCR Genomic Solutions

Translational & Consumer Genomics

Business Unit Structure

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Customer Focus: – Research – Applied Markets

Assay development for emerging sequencing applications and methods

– eg. Nextera – RNA & Regulation – Purification, isolation assays

Ezymes & Proteomics – Internal development for existing kit

components – Novel or emerging products

qPCR – NuPCR assays for low complexity GEx – ECO System

Molecular Biology & PCR Business Unit

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Customer Focus: – Basic Research – Translational Research – Applied Markets – Emerging Markets

Develops all major technology platforms – Sequencing systems – Core Sequencing chemistry and FC technology – Sequencing sample prep – Microarrays and Array Systems – Primary & Secondary bioinformatics solutions – BaseSpace

Focused on system development and end-to-end solutions to enable robust workflows

– Extend to market specific needs

Genomic Solutions Business Unit

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Customer Focus – Translational/Clinical Labs – Consumer

Focus on enabling LDT solutions for clinical labs – Targeted content sets – Optimized reagents set – Clinical market education on NGS and genomic utility

Understand Your Genome – Enabling Clinical Informatics

MyGenome, GeneInsight, Nexus Copy Number, VariantStudio

Enable custom array content into Consumer Genomics

– 23andMe, Ancestry.com, Family Tree

Translational & Consumer Genomics Business Unit

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Translational & Consumer Genomics Business Unit TrūSight Clinical Panels

TruSight Tumor

Familial Cancer

Clinical Exome

Cardio-myopathy

Autism

Inherited Disease

48 genes ~100 genes ~3000 genes ~80 genes ~100 genes ~300 genes

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TruSight Tumor Workflow Go from Extracted Genomic DNA to Data in Two Days with the MiSeq System

► Extract DNA from FFPE ► qPCR QC and DNA titration

► Amplicon-based library prep ► Content developed in partnership with experts ► 7 hours DNA library prep ► 2.5 hours Hands on time

► 2 x 121 PE Sequencing Run ► 22 hours ► Somatic Variant Calling ► Filtering and Annotation

Pre-Screen Samples Assay Biochemistry Sequencing and Analysis

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Alignment and Variant

Calling Annotation Filtering/

Analysis Clinical

Interpretation Reporting

The Illumina Informatics Workflow

MiSeq Reporter or HiSeq Analysis

Illumina Annotation and Filtering Tool

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TG Consumables Increased Productivity; Reduced Operational Costs

TG parts are shipped with a minimum of 6-months shelf life. Extended Shelf Life

TG parts are shipped with kits all from the same lot. Single Lot Shipments

TG parts provide at least a 6 month notice prior to discontinuation. Change Notification

License for use in life science applications. Life Sciences Rights*

Kit Lot Testing Lot Testing performed on all kit components together as a unit.

* Standard parts include a license only for research use purposes

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Customer Focus: – Clinical Labs – Regulated products – 510k, CE/IVD

Reproductive Health – Blue Gnome Acquisition for IVF - PGS/PGD

development – Verinata NIPT market

Cytogenetics – Pre & Post Natal screening and Dx – Hematological malignancies

Regulatory Submissions

Diagnostics Business Unit

Dx

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Certifications and FDA Submissions Strong Partnership with the FDA

2010 2011 2012 2013

Apr, 2010 Veracode Factor V/II BeadXpress Cleared

Certifications

FDA Submissions

Jan, 2011 ISO13485 San Diego Singapore, ISO13485 Hayward

Sep, 2012 ISO13485 Eindhoven

Dec 20, 2012 MiSeqDx Platform

De novo 510(k) EU Launch 2013

Dec 22, 2012 MiSeqDx CF Assay 510(k) EU Launch 2013

Feb 2013 iScan instrument Infinium HD Cyto Abnormality De novo 510(k)

Mar, 2013 Verifi IVD Pre-submission

Dx

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Illumina’s Clinical Vision

Preconception

Carrier Screening

Cystic Fibrosis MiSeqDx

IVF

BlueGnome

Prenatal

Verinata

Cardio- vascular

Birth Death

$400K

Years

Health Care Costs

Cancer

Early Life

Autism Cardiomyopathy

Inherited Conditions

TruSight Panels

Cancer Mutation

Detection

TruSight Tumor Panel

Postnatal

Cytogenetics (Autism, Mental

Retardation, Dev. Delay)

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What Will the Technology Enable? Sequencing Alters the Landscape

1. Sequencing begins to directly save lives

2. Radical acceleration in rate of genomic discovery/insights

3. Tumor samples routinely sequenced and become Standard of Care

4. Nations begin sequencing their populations

5. Complete human sequence under $1000

6. Infants routinely sequenced at birth

7. Cancer “succumbs” to new technology tools

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Time Frame (years)

Human Health

Genetics

Infectious Disease

Research Reproductive Health

Forensics

Consumer

Cancer

BioPharm

Agriculture

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Thank You