Rob Kelley, MBA Global Sales Manager Translational Genomics September 27, 2011

1. © 2010 Illumina, Inc. All rights reserved.
Illumina, illuminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro, GenomeStudio, Genetic Energy, and HiSeq
are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
Rob Kelley, MBA
Global Sales Manager
Translational Genomics
September 27, 2011
Next Generation Diagnostics:
Potential Clinical Applications
of Illumina’s Technology

2. 2
HiScanSQ
Unique
combination
of
sequencing
and arrays
Provider of Genomic Analysis Tools
That Advance the Understanding of Genetics and Health
From Genome-Wide Discovery to Targeted Validation and Screening
Sequencing Arrays qPCR
HiSeq
1000
Powerful,
Flexible,
Scalable

3. 3
Markets Served
Life Sciences
~$2.8B
Consumer
Molecular Dx
~$3B
Applied
Markets
~$1B

4. 4
Dx Strategy
Risk HighLow
Oncology
Discovery
Platforms
Objectives
Strategies
Venue
Low
High
Return
Partnering
Internal
Development
Build Installed Base
Oncology Discovery
Create a novel dx
Sequencing
Services
Sequencing Services
Accelerate Revenue
Vision To be the leader in translational diagnostics
Platforms ApplicationsServices

5. 5
Platforms
BeadXpress
FDA cleared instrument & Factor II/V assay Q2 10
FDA approved GPR beads Q2 10
CE Mark Q4 11
iScan
Cytogenetics Post-Natal Q4 11
Cytogenetics Cancer TBD
Cytogenetics PGS TBD
Cytogenetics Pre-Natal TBD
MiSeq
Pre-IDE submission to FDA Q2 11
Carrier screen 2012
Somatic Mutation Panel 2012

6. 6
Molecular Cytogenetics

7. 7
Cytogenetic Technologies and Resolution
Genome-wide analysis
Targeted/focused analysis
HiScanSQ
Infinium HD Beadchips

8. 8
ISCA (International Standards for Cytogenetic Arrays)
Consensus Statement: AJHG, May 2010

9. 9
ACMG (American College of Medical Genetics) revised
guidelines: Arrays recommended first line

10. 10
Large & Growing Opportunity in Array-Based
Cytogenetics
10
A technology substitution is underway
ILLUMINA IS POSITIONED FOR GROWTH
$-
$50
$100
$150
$200
$250
$300
$350
$400
2009 2010 2011 2012
Revenue(Millions)
Array-based cytology market growing
double digits (CAGR = 16–20%)
Molecular Cytogenetics Revenue
Forecasts by Market Segment (US)
90
100
80
70
60
50
40
30
20
10
0
2007 2008 2009 2010 2011 2012 2013 2014 2015
PercentofRevenues(%)
z
Microarray-Based
FISH

11. 11
Detection of a Wide Range of Aberrations
For Research Use Only

12. 12
HumanCytoSNP-12 BeadChip:
Optimized for Efficient Cytogenetic Analysis
► Streamlined, most informative set of targeted and whole-
genome SNP and non-polymorphic markers
► Uniform picket fence of entire genome (including ~92% of
RefSeq genes)
– 300,000 markers, mostly SNPs
– 6.2kb median marker spacing yields ~30kb resolution
► Higher density in cyto high-value regions (~250 for ~40% of
genome)
– All pericentromeres and subtelomeres
– Sex chromosomes
– Common regions of interest (e.g., associated with known
syndromes)
– Regions contain ~9000 genes
► Higher density in ~400 “disease genes”
For Research Use Only

13. 13
BeadArrayTM Technology
Oligo Mfg 2 μm Silica
~18-fold Redundancy Decoding = 100% QC
Bead Identifier
(30base nt)
Specific Probe
(50 base nt)
Population in wells

14. 14
The Infinium HD Assay
► Unconstrained Marker Design
– Freedom to select the best, most
informative SNPs then fill-in with
intensity-only probes
► Well-proven
– High reproducibility (> 99.9%)
– High call rates (> 99%)
► Streamlined, automatable
► PCR-free protocol
► No need to run a reference
sample
► High locus selectivity and allele
specificity
– Two-step enzymatic
discrimination

15. 15
Copy-Neutral Cytogenetic Aberrations
Forms of copy-neutral cytogenetic aberrations
► Uniparental disomy
– Case in which individual receives two copies of a chromosomal region from one
parent, none from the other
► Copy-neutral loss of heterozygosity (or “acquired uniparental disomy”)
– Case in which one allele of a gene in a heterozygote is already inactivated and
the second, “good” allele is lost without a net change in copy number. This can
occur through a gene conversion event in which the chromosome region
containing the inactivated allele is used as a template to repair a gap occurring
in the corresponding region of the other chromosome
In either case, the absence a functional allele leaves the individual
vulnerable to phenotypes that may be associated to the effected gene(s)
For Research Use Only

16. 16
SNPs Provide More Information to Detect Copy Number
► Also can detect:
– Amplification
– Unbalanced aberration
– Aneuploidy
– Mosaicism
Normal (diploid)
Deletion (loss of one copy)
Duplication (gain of one copy)
Genotypes
Copy-Neutral LOH (UPD)
Log R Ratio B Allele Frequency
Intensity
For Research Use Only

17. 17
B allele frequency data
(AAB genotype)
A shift in the LogR value is
detectible, but the integration
of B allele data improves the
signal to noise ratio
Detected duplication
A profile of chromosome 3 of a cell line derived
from a breast tumor.
SNP-based Detection Provides More Information and
Enables Better Characterization of Chromosomal
Aberrations
For Research Use Only

18. 18
Copy-Neutral Features Are Missed by Array CGH
IlluminaAgilent Agilent Illumina
Chromosome Zoom to position

19. 19
KaryoStudioDx:
Illumina’s custom‐designed Cytogenetics Software

20. 20
KaryoStudioDx Features Highlights
► Accepts data from any Infinium HD array*
► Automated data importation
► Automated scanning for aberrations
► User permissions and authentication
– Input validation
► Mosaic detection
► Inheritance confirmation (non‐paternity)
► UPD parent of origin / inheritance calculation
► % consanguinity
► Quality metric: Pass or Fail
► Integrated Chromosome Browser
► Ability to filter CNV polymorphisms
► Cross‐matching capabilities to the most popular cytogenetic databases
* Certain computer requirements must be met

21. 21
Found Regions Displayed in KaryoStudioDx
User‐defined
Known Regions track
Found RegionsFound RegionsFound Regions
Samples table with QC score
Found regions table
Link out to databases:
UCSC, DGV, ENSEMBL, DECIPHER, etc.

22. 22
Diagnostic PDF Report Generated From Aberrations
Report Includes:
• Sample and product information
• Aberration display
• Information on found region
• Cross‐matches to user‐defined Known
Regions list
• Custom info fields
• ISCN nomenclature

23. 23
HumanCytoSNP‐12
Optimized for
cytogenetics
Plans for FDA Submission: iScan Platform
Package includes Q4 ’09 Illumina submitted Pre‐IDE for Cytogenetics, followed by
additional discussions with FDA
iScan platform, arrays, reagents and software
Intended use
Post‐natal
DD/ID/MCA
Broad, genome‐wide coverage
Simultaneously pursuing CE‐IVD marking (ISO 13485) – 2011/2012
23
iScan/KaryoStudioDx

24. 24
Molecular Diagnostics

25. 25
Load
MiSeq –
Finally a sequencer designed with Dx customers in mind
Go
Workflow
Fully integrated system
On-board cluster generation and data visualization
Preloaded reagent cartridge
1 flow cell lane per run
Performance
Up to 5M clusters
2 x 150 bp in under 28 hours
RFID reagent & flow cell tracking
Auto flow cell positioning
Walk-away automation

26. 26
MiSeq – Prep, Run, Analyze
Sample to Data in as Little as Eight Hours*
08:00:00
MiSeq is the Only Personal Sequencing System Capable of
an 8 Hour Sample to Data Workflow
Amplicons
Clones
gDNA
*1x36bp run – 3 hr sequencing

27. 27
TruSeq Exome Enrichment
Targets = 100,000s
TruSeq Custom Enrichment
Targets = 1000s
TruSeq Custom Amplicon
Targets = 100s
TruSeq Targeted Resequencing
The simplest and most scalable targeted resequencing solutions
Nextera PCR Amplicons
Targets = 10s

28. 28
► Rapid & Economical
– Up to 384 amplicons per sample, 96 samples per
plate (36,864 reactions)
– Plate based processing
– <8 hrs from DNA to sequencing‐ready library
– No gels, no fragmentation – uses standard lab equipment
► Fully customized target probes and capture
– Extension and ligation based assay
► Interactive probe design and ordering
– Personalized and easy to use design tool
– Rapid design turnaround – as little as 10 days from
design to assay shipment
►
Coming soon! TruSeq Custom Amplicon Sequencing
Unprecedented amplicon and sample multiplexing

29. 29
Assay
Biochemistry
TruSeq Custom Amplicon Assay Time
96 samples & 384 targets: from DNA to called variants in ~2 days
8am – Day 1
Hybridization
Setup
Oligos,
universal
reagents
Extension &
Ligation, PCR
with index
Library
Normalization
Create pooled
library,
normalize
Cluster Gen &
Sequencing
Pre-kitted
sequencing
reagents
Real-time
Analysis
Alignments,
variant calling
2pm – Day 1 5pm – Day 2
<8 hr assay with <3 hr hands-on time
No fragmentation required
No gel purification steps
No additional hardware

30. 30
► Coverage Uniformity spec: >80% bases covered at 0.2x mean coverage
– e.g. if mean coverage is 100x, then >80% bases covered at 20x
► Users need to carefully plan how many samples are sequenced together
based on number of amplicons, to achieve desired coverage
TSCA throughput and coverage on MiSeq
How many samples can be run together?

31. 31
MiSeq - Comparison to CE Sequencing
Example: TruSeq Custom Amplicon with 96 Samples x 384 TargetsTSCA
Assay
biochemistry
CE
One plate of gDNA+oligos
for all 384 amplicons
Quant
96 x 384 well
plates
3730xl
5-6 weeks
~$3/amplicon
96-wellplate
TruSeq Custom
Amplicon
•Highly multiplexed
•Integrated sample indexing
•Standard lab equipment
Dispense, PCR, Cleanup
Assay Biochemistry Pool Libraries and
Sequence
Dye-terminator sequencing,
cleanup
96 x 384 well
plates
MiSeq
4 days
<$0.75/amplicon

32. 32
MiSeq Applications
A huge variety of applications can be done on MiSeq*
Application Read Length Kit Config. Sample Prep Kit
TruSeq Custom Amplicon 2 x 150 300PE TSCA
Nextera Amplicon 1 x 36 50PE NXT
Standard Amplicon 2 x 150 300PE TS DNA or HB
Small Genome - De Novo 2 x 150 300PE TS DNA
Small Genome - Reseq., plasmids 1 x 36, 2 x 150 50PE / 300PE TS DNA or NXT
16S Metagenomics (amplicon) 2 x 150 300PE TS DNA, NXT, HB
Library QC 2 x 25 50PE Open
Small RNA 1 x 36 50PE TS smRNA
RNA-Seq (human, mammalian) 2 x 50 50PE TS RNA
RNA-Seq (bacterial, viral) 2 x 150 300PE RZ + TS RNA
TruSeq Custom Enrichment 2 x 50 300PE TS DNA
ChIP-Seq 1 x 50 50PE TS DNA
TSCA = TruSeq Custom Amplicon TS DNA = TruSeq DNA Sample Prep NXT = Nextera
TS RNA = TruSeq RNA Sample Prep TS smRNA = TruSeq Small RNA Sample Prep HB = Homebrew
RZ + TS RNA = RiboZero + TruSeq RNA Sample Prep
*Applications can be performed, but MiSeq platform may not be the most optimal solution for a particular application. There will be situations where
HiSeq, GA or HiScan SQ are better suited to a particular application.

33. 33
MiSeq
Characterization of Genetic Variations in Tumor Tissues
► Deep sequencing of cancer samples to
detect somatic mutations, gene
amplifications and germline variants
that influence patient treatment
decisions
► Genes under consideration include
AKT1, ALK, BRCA1, BRCA2, BRAF,
COMT, CYP17A1, CYP2A6, CYP2C8,
CYP2D6, CYP3A4, DPYD, EGFR,
ERBB2, FGFR2, GNAQ, KIT, KRAS,
MET, MTHFR, NRAS, PDGFRA,
PDGFRB, PIK3CA, PTEN, TP53,
TPMT, TYMS, UGT1A1, VEGFA,
VEGFR

34. 34
MiSeq FFPE Amplicon Data
KRAS Exon 2 – 76 Base Amplicon
1.1% variant in
normal adjacent
tissue > Assay
LOD of 0.5%
Rectal
Normal
Ovarian
Tumor
Gastric
Tumor
No-FFPE
Control
Gastric
Normal
Rectal
Tumor
Sample
Coverage 178667 X151695 X 176530 X 179630 X 161866 X 178900 X
27.5% G C
variant at Chr12:
25398284 in rectal
tumour

35. © 2010 Illumina, Inc. All rights reserved.
Illumina, illuminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro, GenomeStudio, Genetic Energy, HiSeq and
HiScan are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
Illumina Experiment
Manager
September 2011

36. 36

37. 37

38. 38

39. 39

40. 40

41. 41

42. 42

43. 43
How to Generate Library Plates

44. 44

45. 45

46. 46

47. 47

48. 48

49. 49

50. © 2010 Illumina, Inc. All rights reserved.
Illumina, illuminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro, GenomeStudio, Genetic Energy, HiSeq and
HiScan are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
Run
Starting and Monitoring a MiSeq Run

51. 51
How to Start a MiSeq Run
The MiSeq Control Software (MCS) is a streamlined push-button user
interface designed to quickly start a sequencing & analysis run
► Minimal user input required to start a run
► A sample sheet is required to initiate a run
► User has the option to save data locally or to a BaseSpace (cloud) account

52. 52
MiSeq Instrument User Interface
Begin sequencing by selecting “SEQUENCE” button

53. 53
[OPTIONAL] Log on to BaseSpace
BaseSpace is a cloud option to store, analyse, and share your MiSeq data.

54. 54
[OPTIONAL] First Time BaseSpace User
If this is the first time user is using BaseSpace, they must agree the to terms &
conditions of BaseSpace use.

55. 55
Animation Instructions to Load Flow Cell

56. 56
Instructions to Load Reagent Cartridge and Waste Bottles

57. 57
Sample Sheet Required for MiSeq Run
Sample Sheet is required for each MiSeq run
► Contains instructions on how to perform sequencing chemistry
► Also contains instructions on how to perform bioinformatics secondary
analysis:
– Resequencing
– amplicon resequencing
– de novo
– small RNA
– Metagenomics
– library QC
► By default, MiSeq will use the Sample Sheet (in Sample Sheet repository)
that matches the reagent cartridge RFID
► User may override MCS to select a user-specified Sample Sheet

58. 58
[OPTIONAL] User-specified Sample Sheet
User may select sample sheet from alternate folder or attached USB key

59. 59
Review of MiSeq Run
User has opportunity to review parameters of run before submitting

60. 60
MiSeq Performs Pre-Run Check
MCS checks for dependencies to ensure run success
Click here
to start run

61. 61
MiSeq Performs Sequencing Run
Current status
of run
Output to current
BaseSpace
account
Name of run
Realtime run
metrics
Connectivity status
With BaseSpace

62. 62
MiSeq Reporter
► MiSeq Reporter (MSR) is the onboard bioinformatics engine that
automatically processes MiSeq primary analysis (image and basecall) data.
► At launch, MSR supports the following reports:
– Resequencing
– Amplicon resequencing
– de novo assembly (using Velvet)
– Small RNA
– 16S metagenomics
– Library QC
► MSR contains a webserver so users may point browser to MiSeq
instrument to view reports.
► MSR outputs may be stored on the instrument or on network folders.

63. 63
MiSeq Reporter

64. © 2010 Illumina, Inc. All rights reserved.
Illumina, illuminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro, GenomeStudio, Genetic Energy, HiSeq and
HiScan are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
MiSeq Reporter
Screenshots

65. 65
Start Up Page
Currently run and progress
List of past runs
Run completion status
Area for Illumina messages
and updates

66. 66
General Summary Report

67. 67
Resequncing Details Report
Coverage and error
Q score
SNP/indel +
annotation
Table of samples/
variants
Zoom in/outScope of view

68. 68
Amplicon Detail Report

69. 69
De Novo Details Report
Syntenic dot plot
De novo metrics

70. 70
Small RNA Summary Page
Trimmed read
lengths

71. 71
Small RNA Details Report
Distribution of
RNA species
Top 10 most
abundant species
Tabular information

72. 72
Metagenomics Summary Page

73. 73
Metagenomics Details Report

74. 74
Run Status

75. 75
Run Sample Sheet

76. 76
Run Log

77. 77
Run Errors

78. 78
Change Repository

79. 79
Requeue Run

80. 80
Questions

81. 81

82. 82
Clinical
Whole
Genome
Sequencing
Illumina
CLIA Lab
2009
>30 Whole
genomes

83. 83
• A patient treated with Erlotinib but lung
metastases are unresponsive
• Whole genome and transcriptome
sequencing of the cancer on the GA
reveals that
• The drug target was mutated, hence the
unresponsiveness
• 17 genetic disruptions of a key cancer
pathway
• A target for the alternative FDA
approved drug sunitinib was over-
expressed
• Sunitinib treatment was successful and
the tumours regressed.
Jones et al. Genome Biology 2010, 11:R82
http://genomebiology.com/2010/11/8/R82
Sequencing Informs Therapy

84. 84
Acute Promyelocytic Leukemia (APL)
Most APL patients have a characteristic translocation between
chromosomes 15 and 17 that fuses the PML1 and RARA genes
– These patients respond well to treatment with ATRA but treatment requires prior
demonstration of the translocation or fusion gene
► A targeted PCR test of the patient’s DNA did not reveal the characteristic
fusion gene
► Whole genome sequencing (in just 1 week) revealed a novel 77 kb insertion
that recapitulates the translocation
► Rearrangement event confirmed by PCR
► ATRA treatment prescribed
Mardis, E, Wilson R et al. unpublished

85. 85
Nextera DNA Sample Prep
Sequencing’s fastest and easiest sample prep
► 90 min sample prep
► No Covaris required
► High throughput
► Super low 50ng input unlocks access
to precious samples
► Enables a range of CE applications:
amplicons, plasmids, small genomes
~1.5 hours
~12 hours
Enables effective use of single
36bp reads

86. 86
Overall positioning of Targeted Resequencing on MiSeq
PCR amplicons through TruSeq Custom Enrichment
Application
Target
Sequence
Number samples
/ project
Price / sample
(Prep and Seq)
Key Benefit
CE +
Amplicons
< 10 kb <100 $50
Small sample/content
projects
Nextera +
Amplicons
< 20 kb 100s $80
Long contiguous
amplicons and speed
TSCA 10 – 96 kb 100s – 1000s $50 - 300
Multiplexing and
speed
TSCE 700 kb – 2 Mb 100s – 1000s $260 - 800 More target content

87. 87
TSCA
TSCE
CE
Nextera
Samples
96
1000s
50
Target Sequence (kb)
20 70010 Mb’s2001 100
Positioning of Targeted Resequencing products

88. 88
Nextera and MiSeq
Sequencing’s fastest time to answer for rapid variant analysis
08:00:00
15:00:00
*Based on 1 x 36 bp reads
1 – 8 samples
1 – 96 samples

89. 89
Ovarian Cancer
Deadly
Incurable
Difficult Dx
Patients present with a suspicious/palpable mass
Less than 40% are cured
204,449 New cases annually; 124,860 deaths
Early Dx is Key
Five year survival is good if diagnosed early,
but most patients are diagnosed late stage
Illumina Solution
Develop a diagnostic assay which will diagnose
ovarian cancer at an early stage
19%
22%
30%
33%
37%
40%
47%
54%
72%
100%
92%
85%
82%
69%
56%
51%
39%
26%
17%
12%
-10%
10%
30%
50%
70%
90%
110%
Ia Ib Ic Iia Iib Iic IIIa IIIb IIIc IV
Cum % of Cases
5 Yr Survival

90. 90
TruSeq Targeted Resequencing
A broad suite of tools for discovery or validation experiments
Option
Amount of
sequence
Best for Availability
TruSeq Exome
Enrichment
~62 Mb
Mendelian disease:
case-control exome studies, rarer
variants, causal variants
exome-wide linkage analysis
Now!
TruSeq Custom
Enrichment
~1 to ~10 Mb
GWAS follow-up: validation of
variants, variant discovery, pathways
Now!
TruSeq Custom
Amplicon
Sub-500 Kb
Amplicon sequencing: high-
throughput CE experiments, ultra
deep seq, variant disc, screening
2H2011
Nextera + PCR
Amplicons
100’s of bp
targets
Amplicon sequencing: ultra-deep
sequencing, validation, screening, CE
replacement
Now!

91. 91
Meet MiSeq
52.3 cm
12 cm

92. 92
Oncology Biomarker Discovery
Targeted Seq
300
FFPE Tumors
Frozen
25
Tumor/Normals
WGS, Gex, Methyl
25
Tumor/Normals
10 Cases/20 Controls
Blood, Tumor, Pap,
Proximal Fluids
CLIA Lab Service
for
Early Detection
IVD
Diagnostics
25/25 40 Biomarkers
20 Novel
10 @ 1,000X
58 @ 300X
Ovarian
23/23 141 Biomarkers
Gastric
25/25 6/6 Sequenced
30 by Q1
Colon
Samples Discovery Validation Translation Dx Service Dx Product

93. 93
Options for Targeted Resequencing with Illumina
From specific, customized regions of interest to the complete coding region
Option
Amount of
sequence
Best for Availability
TruSeq Exome
Enrichment
~62 Mb
Mendelian disease:
case-control studies, rarer variants,
causal variants, linkage analysis
Now!
TruSeq Custom
Enrichment
~700Kb to ~15
Mb
GWAS follow-up: validation of variants,
variant discovery, pathways
Now!
Nextera + PCR
Amplicons
100’s of bp
targets
Amplicon sequencing: ultra-deep seq,
validation, screening, CE replacement
Now!
TruSeq Custom
Amplicon
~100 Kb
Amplicon seq: high-throughput CE,
ultra deep seq, variant disc, screening
2H2011
The only company with the complete end-to-end TRS workflow solution.

94. 94
Simplest Sequencing Workflow
Integrated workflow from sample to analyzed data
TruSeq Chemistry
Clustering & Sequencing
TruSeq DNA
Simple, scalable and cost
effective
TruSeq RNA
Optimized, gel-fee, low input
TruSeq Small RNA
Hi throughput miRNA
discovery & profiling
TruSeq Exome
Lowest cost and most
scalable exome sequencing

95. 95
MiSeq Workflow Guide
Pre-defined data analysis workflows
Targeted
Resequencing
TruSeq Custom
Amplicon
Nextera PCR
Amplicon
Metagenomics
16S rRNA
Clone Checking
TruSeq Custom
Enrichment
ChIP-Seq
Small Genome
Sequencing
De novo
Resequencing
Plasmids
RNA
Sequencing
Small RNA
RNA-Seq
Library QC
Library QC
Primary
workflows
Secondary
workflows
Automated
Semi-Automated

96. 96
MiSeq Applications
A huge variety of applications can be done on MiSeq*
Application Read Length Kit Config. Sample Prep Kit
TruSeq Custom Amplicon 2 x 150 300PE TSCA
Nextera Amplicon 1 x 36 50PE NXT
Standard Amplicon 2 x 150 300PE TS DNA or HB
Small Genome - De Novo 2 x 150 300PE TS DNA
Small Genome - Reseq., plasmids 1 x 36, 2 x 150 50PE / 300PE TS DNA or NXT
16S Metagenomics (amplicon) 2 x 150 300PE TS DNA, NXT, HB
Library QC 2 x 25 50PE Open
Small RNA 1 x 36 50PE TS smRNA
RNA-Seq (human, mammalian) 2 x 50 50PE TS RNA
RNA-Seq (bacterial, viral) 2 x 150 300PE RZ + TS RNA
TruSeq Custom Enrichment 2 x 50 300PE TS DNA
ChIP-Seq 1 x 50 50PE TS DNA
TSCA = TruSeq Custom Amplicon TS DNA = TruSeq DNA Sample Prep NXT = Nextera
TS RNA = TruSeq RNA Sample Prep TS smRNA = TruSeq Small RNA Sample Prep HB = Homebrew
RZ + TS RNA = RiboZero + TruSeq RNA Sample Prep
*Applications can be performed, but MiSeq platform may not be the most optimal solution for a particular application. There will be situations where
HiSeq, GA or HiScan SQ are better suited to a particular application.

97. 97
ILMN vs. Moore’s Law

98. 98
Illumina’s First FDA Cleared In-Vitro Diagnostic Device
► The BeadXpress System is an FDA 510(k) cleared In-Vitro Diagnostic
Device
► FDA Cleared BeadXpress System includes:
– BeadXpress Reader
– VeraScan Software
► The Intended Use Statement:
– The BeadXpress® System is an In-Vitro Diagnostic
Device intended for the simultaneous detection
of multiple analytes in a DNA sample utilizing
VeraCode holographic microbead technology.
The BeadXpress System consists of the
BeadXpress Reader and VeraScan software.
– It is cleared for use only with FDA cleared
VeraCode tests.
BeadXpress Reader and
VeraScan Software

99. 99
Comprehensive VeraCode product portfolio
Research
Use Only
VeraCode ADME
Core Panel
VeraCode Universal
Capture & Carboxyl
Beads
Custom GoldenGate
Genotyping,
48, 96, 144, 192 &
384-plex
DASL Custom Gene
Expression,
32 to 384-plex
Custom GoldenGate
Methylation,
48 to 384-plex
Regulated
Products
VeraCode GPR
Universal Capture
Beads
VeraCode GPR
Carboxyl Beads
VeraCode PGx Panel
(in development)
VeraCode GI Panel
(in development)

100. 100
Fixed Content: VeraCode ADME Core Panel
► VeraCode ADME include184 polymorphisms (34 genes)
– >95% Pharma ADME Core List www.pharmaadme.org
ADME Core (34 genes, 184 markers)
ABCB1 CYP2C9 NAT1 SULT1A1
ABCC2 CYP2D6 NAT2 TPMT
ABCG2 CYP2E1 SLC15A2 UGT1A1
CYP1A1 CYP3A4 SLC22A1 UGT2B15
CYP1A2 CYP3A5 SLC22A2 UGT2B17
CYP2A6 DPYD SLC22A6 UGT2B7
CYP2B6 GSTM1 SLCO1B1 VKORC1
CYP2C19 GSTP1 SLCO1B3
CYP2C8 GSTT1 SLCO2B1
For Research Use Only

101. 101
Sequencing Services
Illumina Clinical Services Lab
Somatic Mutation Panel
Somatic Mutation Panel launch Q4 11
Content will include genes with proven/anticipated clinical utility:
KRAS EGFR BRAF TP53 VEGF-A
ERBB2 ESR1 PGR TYMS UGT1A1
TPMT COMT CYP2D6 NRAS EML4/ALK
WGS
30+ Whole genomes sequenced Q4 10
First clinical case reimbursed Q4 10
Cancer, genetic diseases, SCID cases
Infrastucture
CLIA certified for high complexity molecular diagnostics Q1 09
CAP Accredited Q2 09
CA State CLS training program Q1 10

102. 102
Individual Genome Sequencing: Workflow
o Initial discussion & genetic counseling
o Informed Consent and Service Agreement
o Saliva and blood sample taken (DNA possible)
o Cooling-off period (7+ days); order confirmed
o Barcode samples for confidentiality
o Saliva and blood genotype for ID match
o Whole genome sequencing of blood DNA
o Analyze and QC sequence and called variants
o Check sequence and genotype ID match
o Archive full dataset
Physician orders IGS for patient
Genome sequencing and QC
Clinical lab delivers data to physician

103. 103
Innovative Genotyping Approach
Make Target
Add Oligos
Extend/Ligate
PCR
Make ssDNA
Hyb VBS
[A/B]
b
B
A
Cy
Cy
Cy
c
b
b

104. 104
► Summary Report
► Consensus sequence with quality scores of calls
► SNPs report, with dbSNP designation or novel
► All individual reads, aligned to the human genome reference sequence
► GenomeStudio genome browser installed on an encrypted hard drive with variants
annotated
Delivery of Individual Genome Sequence

105. 105
Illumina Sequencing Workflow
Fragment DNA
Repair ends
Add A overhang
Ligate adapters
Purify
Library Preparation1
Cluster Generation Hybridize to flow cell
Extend hybridized template
Perform bridge amplification
Prepare flow cell for sequencing
2
Sequencing
Perform sequencing
Generate base calls
3
Data Analysis
Images
Intensities
Reads
Alignments
4

106. 106
Sample Prep Workflow
DNA RNA

107. 107
DNA
(0.1-1.0 ug)
Sample
preparation Cluster growth
5’
5’3’
G
T
C
A
G
T
C
A
G
T
C
A
C
A
G
T
C
A
T
C
A
C
C
T
A
G
C
G
T
A
G
T
Illumina Sequencing Technology
Robust Reversible Terminator Chemistry Foundation
Sequencing

108. 108
Simplest Sequencing Workflow
Parallel sample
processing
Automated cluster
generation
Automated
sequencing
SIMPLIFIED
SAMPLE PREP
cBot CLUSTER
GENERATION
SEQUENCING DATA PROCESSING
& ANALYSIS
Simple, efficient data
analysis

109. 109
MiSeq FFPE Cancer Sequencing
Summary
• MiSeq and SBS Chemistry is capable of generating high depth of
coverage sufficient enough to detect rare variants even in highly
degraded DNA
• The limit of detection for these types of assays is approximately
0.5%, MiSeq was able to easily detect a variant close to the limit of
detection
• MiSeq has the bandwidth to cover 48 amplicons from 48 samples
at an average coverage depth of over 2000x

110. 110
Competitive Environment
TruSeq Custom
Amplicon
Fluidigm Access
Array
HaloPlex PCR PCR/Homebrew
Number of Amplicons 48 – 384 48 ‐ 480[1] < 2,000 1 ‐ 5
Target Genomic
Sequence
< 96 kb < 120 kb < 400 kb < 3 kb
Panel Design DesignStudio FLDM service Design Wizard Primer3/Manual
Total Assay Time
(hands on)
7 hr (2.5 hr) 5 hr (<1 hr) 24 hr (2.5 hr est) 2 hr (0.5 hr)
Manual Batch Size
(samples)
192 48 48 < 384
Order to Ship Time 10 days 3 weeks < 3 weeks[2] < 5 days
Special Hardware None $75K ??? ‐
Price per amplicon < $1.00 $0.50 ‐ 0.70 $0.50 – 1.10 $0.50 – 1.00
Input DNA 0.25 µg 0.05 µg 0.9 µg < 0.25 µg
End to end solution Yes No No No
llumina supported
assay
Yes No No No
[1] Promising 10‐plex PCR [2] Estimated