© 2014 Illumina, Inc. All rights reserved.

Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DesignStudio, Epicentre, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate,

HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect, ForenSeq, MiSeq, MiSeqDx, MiSeqFGx, NeoPrep, Nextera, NextBio, NextSeq, Powered by Illumina, SeqMonitor, SureMDA, TruGenome, TruSeq,

TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or

other countries. All other names, logos, and other trademarks are the property of their respective owners.

Illumina’s VeriSeq™ NIPT Solution

Fast, Accurate, Accessible Non-Invasive Prenatal Testing (NIPT)

Caroline Thureau

Ass. Dir. Clinical Business Illumina

Izmir, 5th of May 2018

For In Vitro Diagnostic Use. Not available in all countries or regions.

2

Presentation Outline

Introducing the VeriSeq NIPT Solution and workflow

VeriSeq NIPT technical innovations

VeriSeq NIPT clinical accuracy study results

Q&A – visit the Incekaralar booth

3

The VeriSeq NIPT Solution

A Revolution for “In-lab” NIPT Testing

Streamlined

Easy to run

PCR-Free Assay

Fast

26 Hour turn around*

96 or 48 Spls/Batch

Confidence

Highly accurate results

Report on more samples

Automated NIPT for detection of aneuploidy of chromosomes 21, 18, 13, X & Y

For In Vitro Diagnostic Use. Not available in all countries or regions

*From accessioned sample to clinical report

CE-IVD marked CE-IVD marked

4

Sample Preparation

VeriSeq NIPT Sample Prep CE-IVD marked Kits

Two CE-IVD marked kit options: 96 & 48 Sample

Versions

Include reagents and consumables for preparing

cfDNA sequencing libraries from plasma

PCR-Free

For In Vitro Diagnostic Use. Not available in all countries or regions.

VeriSeq NIPT SolutionAutomated Laboratory Workflow

VeriSeq NIPT Microlab STAR

Blood to prepared library ~8 hours/batch

– ~2 hours of user hands on time

5

VeriSeq NIPT SolutionAutomated Laboratory Workflow

Sequencing Analysis Clinical Report

Assay software installed on

on-site server

Analysis performed on-site

Evaluation of fetal fraction

and chromosomal ratios for

chromosomes 21, 18, 13, X,

and Y

CE-IVD marked software

Aneuploidy classifications

for chromosomes 21, 18 ,13,

X, and Y

Individualized Fetal

Aneuploidy Confidence

Test (iFACT)

Fetal Fraction Estimate

Other QC metrics

2 x 36 base pair sequencing

48 sample multiplex

~13 hour run (overnight)

For In Vitro Diagnostic Use. Not available in all countries or regions

Batch Analysis and Report

6

VeriSeq NIPT SolutionAutomated Laboratory Workflow

Key Technical Innovations

For In Vitro Diagnostic Use. Not available in all countries or regions

Paired-

end

sequencing

Fetal

fraction

estimatorLLR

iFACT

QC

7

Fetal Fraction Estimation Methods in Illumina NIPT

The Coverage Profile Method

Fragment Size Distribution1

Some genomic regions are enriched,

and some depleted with higher fetal

fraction

Training data from 20K CLIA samples

used to create a model to estimate FF

based on coverage profile

1 The VeriSeq NIPT Solution software uses both coverage profiling and fragment

size information in the estimation of fetal fraction

Fragment size distribution,

determined from the analysis of PE

sequencing data, can be used in the

estimation of fetal fraction

FF from Chr Y

FF

fro

m f

rag

siz

e

Fetal Maternal

All charts: Illumina internal data on file

Comparison of maternal and fetal size distribution

of cfDNA fragments

Numerous studies have shown that

cfDNA of fetal origin is shorter than

cfDNA of maternal origin. Therefore,

fetal signal is higher in shorter

fragments.

For In Vitro Diagnostic Use. Not available in all countries or regions

8

Analysis of Sequence Output: Alignment

CGATTTAACT

…ACCACGATTTAACTGGAGTAAAGACTTCCAGGTACCGATCTAGCCT…

Millions of “counts” per sample

GACTTCCAGG

Count:

AGGTACCGAT

Human Genome

Alignment

CGATTTAACT

9

CountingFetal

cfDNA

Maternal

cfDNA

Chromosomes: 1 2 3

……

Trisomy 2121

10% more Chr21

cfDNA in T21

VS

Analysis of Sequence Output: Counting by Sample and chromosome scoring

Not to Scale

10

Log Likelihood Ratio (LLR)Incorporates aneuploidy score and fetal fraction information

Fetal fraction

An

eu

plo

idy s

co

re

Expected distribution of

affected samples

Expected distribution of

unaffected samples

LLR incorporates the

estimated fetal fraction of a

sample when assessing

the probability of being

affected.

Likely unaffected sample

(closest to unaffected

distribution)

For In Vitro Diagnostic Use. Not available in all countries or regions

11

Log Likelihood Ratio (LLR)Incorporates aneuploidy score and fetal fraction information

Fetal fraction

An

eu

plo

idy s

co

re

Expected distribution of

affected samples

Expected distribution of

unaffected samples

LLR incorporates the

estimated fetal fraction of a

sample when assessing

the probability of being

affected.

Equivalent aneuploidy

signals are more likely to

be affected for lower fetal

fractions

Likely affected sample

(closest to affected

distribution)

For In Vitro Diagnostic Use. Not available in all countries or regions

12

iFACTIllumina’s innovative approach to ensuring excellent results

even at low fetal fraction

individualized Fetal Aneuploidy Confidence Test

iFACT1 is a dynamic threshold that is assessed for each sample.

For samples with low fetal fraction, iFACT determines whether there is

enough sequencing coverage to make a call.

– Results can be determined even for samples with low fetal fraction.

– iFACT allows results to be determined on the maximum number of

samples.

– Samples that do not pass this quality metric threshold do not provide

a call.

1 The VeriSeq™ NIPT Solution Assay Software has iFACT, which uses sequencing coverage and fetal fraction. The VeriSeq™

NIPT Analysis Software (16 Samples) uses a QC metric based on sequencing coverage alone.

For In Vitro Diagnostic Use. Not available in all countries or regions

13

Total Plasma Aliquots Available, n 3,107

Total Quality Control Failure, n(%) 21 (0.68)

Failed iFACT 11

Data Outside Expected Range 8

Fragment Distribution Outside of Normal Range 2

Total Reported 3,086

With Clinical Reference for Autosomes 3,057

With Clinical Reference for Sex Chromosomes 3,082

The Clinical Accuracy StudySample Exclusion

Data on file. Illumina, Inc. February 2017.

For In Vitro Diagnostic Use. Not available in all countries or regions

14

VeriSeq NIPT Solution ResultsOverall Performance Metrics for Autosomes

a CI based on Wilson’s score method.

Trisomy 21 Trisomy 18 Trisomy 13

Sensitivity, % (n/N) 98.9% (90/91) 90.0% (18/20) 100.0% (8/8)

2-Side 95% CIa (94.0%,99.8%) (69.9%,97.2%) (67.6%,100.0%)

Specificity, % (n/N)>99.9%

(2965/2966)

99.9%

(3034/3037)

99.9%

(3045/3049)

2-Side 95% CIa (99.8%,100.0%) (99.7%,100.0%) (99.7%,99.9%)

Data on file. Illumina, Inc. February 2017.

For In Vitro Diagnostic Use. Not available in all countries or regions

15

Percent Concordance of VeriSeq NIPT Solution Results

For Fetal Sex Classification with

Clinical Reference Standard Outcome

a Percent concordance is calculated as the number of samples in which the VeriSeq™ NIPT Solution fetal sex classification is consistent with the clinical

reference standard classification, divided by the total number of samples with the same clinical reference standard classification and valid VeriSeq™ NIPT

Solution results. Outcomes are based on 3,082 samples, as 4 did not have a clinical reference.b Represents monosomy X. c 1 sample was 49, XXXXY, classified as “Sex chromosome not reportable”.

Newborn Physical Exam

Outcome

[No Cytogenetic Results]

Cytogenetic Results

Female Male XX XY MXb XXX XXY XYY Otherc

Percent Concordanta99.9%

(1371/1373)

99.9%

(1420/1422)

97.4%

(147/151)

100.0%

(118/118)

100.0%

(6/6)

80.0%

(4/5)

100.0%

(5/5)

100.0%

(1/1)

Not

Applicable

Data on file. Illumina, Inc. February 2017.

For In Vitro Diagnostic Use. Not available in all countries or regions.

16

VeriSeq NIPT Solution Clinical Accuracy Study Implications

Data on file. Illumina, Inc. February 2017.

The observed sensitivities and specificities for VeriSeq NIPT in determining fetal

aneuploidy for chromosomes 21, 18, 13, X and Y are vastly superior to

traditional serum screening.

The VeriSeq™ NIPT Solution utilizes iFACT, a quality metric which enables

detection of fetal aneuploidy at fetal fraction estimations of 4% or less.

The VeriSeq™ NIPT Solution demonstrated fewer false positive results which

may result in fewer invasive diagnostic tests compared to serum screening. This

may lead to fewer procedure-related pregnancy losses.

For In Vitro Diagnostic Use. Not available in all countries or regions

17

Thank You!Questions?

• Easy to implement, Automated, PCR-free workflow

• Integrated, CE-IVD marked sample preparation and analysis

• Hands-on training and support from Illumina

• Fastest sample accession to report time (~26 hours total)

• 2 hours “hands on time” per batch of 48 or 96 samples

• High-throughput

• Industry leading low failure rate

• Large (>3k sample) clinical accuracy study

• Reduce invasive procedures and patient anxiety

Streamlined

Fast

Confidence

Automated NIPT for detection of aneuploidy of chromosomes 21, 18, 13, X & Y

For In Vitro Diagnostic Use. Not available in all countries or regions