2011 course on Molecular Diagnostic Automation - Part 3 - Detection. This is from early 2011. Prices and Specifications of instruments may have changed a lot. Part 3 of 3

1. Patrick Merel
Biomedical Innovation Platform (PTIB), Pessac, France
pmerel@mac.com
Post-PCR Procedures Automation
in Molecular Diagnostic
part 3
1

2. 2 Options for Post-PCR procedures
• Fluorescence based detection
• Realtime PCR procedures
• New possibilities in automation
Gel Electrophoresis
Difficult
Automation through Capillary Electrophoresis (CE)
Microfluidics progress, CE chips
Sequencing
Complete automation: difficult but almost possible
Automation through CEquencing

3. Former options for Post-PCR
3 procedures
Reverse Dot-Blot
most popular approach
favorite commercial procedure
Microtiterplate compatible
Automation of Reverse Dot-Blot
Few solutions, Roche, Abbott, …
MicroArrays, Chips automation
Generic Robotic Workstations for simple automation of reverse dot-blot
protocols

4. HLA Typing by PCR/SSO on strip
4 REVERSE-DOT-BLOT on membrane: ‘Strip Assay’

5. Automation of HLA-Typing by Reverse Slot-Blot
Invitrogen-Dynal, HLA RELI-SSO with the AutoRELI-48 and the RELI-Scan.
Innogenetics, HLA, HPV, CFTR with the Auto-Lipa48.
Automates Probe Hybridisation and Strip Detection
Eliminates Strip Handling and Manual Data Entry
Easy to Use Interpretation Software Combined with a comprehensive
Results Management Package
5

6. Automation of reverse hybridization procedures
6

7. Automation of hybridization procedures
7 Dedicated PCR+Post-PCR workstation:
the Roche Cobas Amplicor

8. Perspective for Hybridization
8 Procedures
MicroArray-based Technologies
Liquid Arrays
Solid surfaces Arrays
Affymetrix and alike DNA Chips technology
New generation of IVD microarrays
The in-house way
What about automation?

9. Hybridization on Beads: the future of hybridization procedures?
❖ Luminex technology
❖ Beads of various colors
❖ Different probes on each color coded beads
❖ Multiple colors combination detection
❖ Nanoparticules and alike
❖ Quantum Dots, Nanosphere, …etc
❖ new: Digital particules
9

10. Luminex based Technologies
I. Multiplex PCR
xTag Technology
Numerous applications from
II. Multiplex ASPE/TSPE various vendors and partners
Asuragen
The PCR reaction is then subjected to a
primer extension step that is specific for Applied Cytometry Systems
the allele or the infectious agent that is BMD
being analyzed. The 5’ end of the ASPE Bio-Rad Diagnostics
primer is attached to an xTAG universal Bio-Rad Life Science
tag sequence. EraGen Biosciences
Fisher Healthcare
INOVA Diagnostics, Inc.
Invitrogen
MICROBIONIX GmbH
Marligen Biosciences, Inc.
IV. Universal Array Sorting Millipore Corporation (LINCO & Upstate)
The 5’ universal tag sequence is MiraiBio
hybridized to the complementary anti-tag Multimetrix GmbH
sequence coupled to a particular xMAP One Lambda, Inc.
bead set. Panomics
PerkinElmer
QIAGEN
Radix
Tepnel Lifecodes
Zeus Scientific, Inc.
V. Detection
The hybridized beads are read
by the Luminex System Directly from LuminexCorp
10

11. Luminex based
11 Technologies
The Luminex 100/200 System are
flexible analyzers based on the
principles of flow cytometry.
Multiplexing: Up to 100 analytes per
well.
The Luminex High Throughput Screening System
(HTS) is designed to perform hundreds of
thousands of individual bioassays per day.
The FLEXMAP 3D and MagPix are the Supports 96 or 384 well plates; Compatible with
latest multiplexing systems launched by front-end plate handling robotics; Uses the 64
Luminex. bead set, not the 100 bead set; For Research use
only, not for use in Diagnostic procedures
Increased Multiplexing: from 50 to 500
analytes per well.

12. Progress in Luminex Technology Automation
The following Products for the BioPlex 2200 are
Available:
Syphilis IgG
Epstein-Barr Virus (EBV)
IgG and IgM
ANA MDSS
Currently in Development:
Syphilis IgM*
ToRC IgG*
ToRC IgM*
Lyme IgG/IgM*
Immunity IgG*
HSV 1/2*
Vasculitis*
Gastrointestinal (GI)*
12
Anti-Phospholipid Syndrome*
Rheumatoid Arthritis*
The Biorad, BioPlex 2200: A Fully-Automated, Random Access, Multiplex Platform. EIA based until now.

13. Nanosphere Technology
The Verigene System consists of two instruments: the
Auto Processing System (APS) and the Verigene ID,
which makes it easier than ever to run a variety of
13
assays on nucleic acids and proteins with the
simplicity of a sandwich assay.
❖Ultra-sensitive detection of multiple
proteins and nucleic acids
simultaneously
❖Direct genomic detection without
The assay involves a 2-step process similar to an amplification or enzymes
ELISA sandwich assay:
❖5-6 orders of magnitude more
After isolation from a sample, DNA is hybridized to sensitive than ELISA based
both nanoparticle probes and capture strands methods for proteins
Silver is catalyzed on the gold resulting in six
orders of magnitude amplification of signal

14. Nanosphere Technology
Step 1
Enter patient ID and test requisition (duration: 1 minute)
Start with the Verigene ID by entering sample identification (manually or via
barcode).
Scan the assay barcode on the slide with the integrated wand.
Intuitive Touchscreen and Software
･Guides the user step-by-step through the testing process
･Uses simple, icon-based instructions that minimize data entry
･Tracks the samples, slides and reagent packs via barcode throughout the
assay process
Step 2
Pipette sample into test cartridge (duration: 1 minute)
No PCR is necessary for DNA or RNA. Just pipette the prepared sample into the
self-contained test cartridge.
Test Cartridge
･Eliminates sample contamination
･Maintains consistency of assay process through microfluidics
･Minimizes tech-to-tech variability by reducing manual pipetting
Step 3
Insert test cartridge into Verigene APS (duration: ~90 minutes)
Once the prepared sample is in the test cartridge, insert it into the Verigene
APS. This automates the ClearRead nanoparticle detection method through
integrated fluid processing.
Verigene Auto Processing System (APS)
･Operated, monitored and verified by the Verigene ID
･Contains reagent pack required for processing The Verigene System consists of
･Simple load and run capability two instruments: the Auto
Processing System (APS) and the
14
Step 4 Verigene ID, which makes it easier
Insert processed test cartridge unit into Verigene ID (duration: 3 than ever to run a variety of assays
minutes) on nucleic acids and proteins with
Remove the slide from the test cartridge and insert it into the Verigene ID. the simplicity of a sandwich assay.
Through the touch-screen, simply select and print the results.
Total duration: <95min for F2, F5, MTHFR, CFTR, HFE
for Warfarin, CYP2C19
for multiplex A/B Flu+RSV

15. Nanosphere latest automated platform: The Verigene SP
The Verigene® SP is a bench top, free-
standing instrument with a single,
independent sample processing module.
Random access, multifunctional test
processing, including nucleic acid extraction,
reverse transcription (if necessary), target
amplification (if necessary), and target
15
identification and analysis in a Verigene® Test
Cartridge.

16. 16 Nanostring Molecular Barcodes
The technology uses
molecular "barcodes" and
single molecule imaging to
detect and count hundreds of
unique transcripts in a single
reaction.
Each color-coded barcode is attached
to a single target-specific probe
corresponding to a gene of interest.
Mixed together with controls, they
form a multiplexed CodeSet.
The Reporter Probe carries the
signal; the Capture Probe allows the
complex to be immobilized for data
collection.
Gene Expression CodeSets for the
nCounter Analysis System offer a
cost-effective way to analyze the
expression levels of up to 800 genes
simultaneously with sensitivity
comparable to qPCR. +miRNA + CNV

17. 17 Applied BioCode: digital arrays
Applied BioCode, Inc. (ABC) has combined
photolithographic digital barcodes with immuno- and
molecular chemistry to create a new, patented
Barcoded Magnetic Bead (BMB) technology.
Barcoded Magnetic Bead has one of the highest
multiplex capacities available (up to 1,024 targets/
assay). Optically bar-coded beads are mass
produced at low cost by well established
semiconductor processes. These beads are
functionalized with nucleic acids, proteins or other
probe molecules, allowing highly multiplexed assays
to be carried out in homogeneous or heterogeneous
media.
The BMBs' barcode patterns give a high-contrast
transmitted signal and no fluorescence background,
allowing the barcode to be identified easily and
accurately, with near 100% decoding accuracy.

18. 18 MicroArrays in Diagnostic
Pathogens characterization
Water-born virus, bacteria, genotyping
Gene Expression monitoring
Oncology
Genotyping
SNP detection
Pharmacogenetics/Pharmacogenomics
Disease predisposition, drug metabolism, drug design and
development

19. DNA Chips :
19 from synthesis to commercial products
Affymetrix GeneChip :
For genotyping and
expression monitoring
GeneChip Probe Array
HIV PRT GeneChip, an array with more than 15,000 different probes
« Wafer-scale chemical synthesis » GeneChip Probe Array synthesis principle

20. Affymetrix
20 GeneChip
GeneChip Fluidics Station
GeneChip Probe Array GeneChip Software
GeneArray Scanner
Proprietary GeneChip software controls the Affymetrix fluidics station and scanner functions, captures
the fluorescent image from the probe array, extracts data from the image and provides subsequent
data analysis.

21. Affymetrix HIV
21 GeneChip
The GeneChip® HIV PRT assay used in conjunction with the GeneChip analysis system enables rapid,
high accuracy sequence analysis on the HIV-1 protease and reverse transcriptase (codons 1242) genes.

22. AmpliChip CYP450 from Roche
Molecular Diagnostics a partnership IVD DNA
22 with Affymetrix
Array

23. Automated robotics for microarrays
23 NanoChip® Loader
4 NanoChip ® Cartridges per Loader
Nanogen’s CF ASR
Single sample per six test sites
Genotype for ∆F508 on initial run
Screen for 24 other mutations
15 patients per cartridge
60 patients per run (4 chips)
Also available as ASR: ASPA, ApoE, HFE,
NanoChip ® Electronic Microarray
Factor V/Prothrombin, Assay ToolBox 15 samples X 4 cartridges = 60 sample per Loader
run

24. Multi-Processing of individual arrays: Osmetech
Osmetech eSensor (previously CMS division
from Motorola)
At the core of the eSensor detection
technology are DNA fragments attached to
electrodes on the surface of a small circuit
board.
This DNA microarray is the basis of detection
by the eSensor System for any DNA
sequence. Each electrode is electronically
active and detects a different DNA sequence.
Finding the complimentary sequence in the
target DNA generates a characteristic
electrical signal.
Each eSensor DNA Detection System
cartridge can detect several different DNA
targets at once, providing a cost-effective
platform for complex analysis.
24
eSensor CF test: 23 mutations tested for in the ACOG/ACMG-recommended cystic fibrosis carrier screening panel.

25. Osmetech XT-Technology
§ Modular design–expandable from 1
to 3 towers (8 to 24 slots)
§ Improved software with touch-
screen interface
§ On-chip mixing for rapid
hybridization
§ Random access
§ 4-label discrimination capability
25 CYP 450 2C9 and VKORC1 polymorphisms IVD assays
New eSensor® XT-8 System

26. Osmetech Key Technology Features
• Homogeneous assay
– No post-PCR sample purification
– No post-hybridization wash steps
– Insensitive to interferences from sample matrix
• Complex samples (whole blood, tissue extracts)
• Redox-active compounds (ascorbate, acetaminophen)
• Electronic detection
– Simple, inexpensive instrumentation
– No optics or mechanical parts
26
– Inherent ratiometric data analysis eliminates need for calibration

27. 27 Autogenomics Technology
The INFINITI™ Analyzer is an automated, multiplexing,
continuous flow, random access microarray platform that
integrates all the discrete test processes such as sample handling,
reagent management, hybridization, stringency and detection for
the analyses of DNA into a totally self-contained system.
The BioFilmChip™ Microarray is a novel, film based microarray,
which consists of multiple layers of hydrogel matrices about 8-10
µm thick on a polyester solid support.

28. 28 Autogenomics Menu
The BioFilmChip microarray is based on polyester film that is coated with a proprietary
multi-layered technology for DNA and protein analysis.
Arrays will have densities of less than 100 spots/chip and will be primarily assay
specific.
Analysis can be performed utilizing:
Hybridization assay, Primer Extension assay, In situ hybridzation, Immunoassay (Competitive /
Sandwich)
Available RUO Menu: Available CE Menu: Available IVD Menu:
Factor II
Factor V Leiden
Ashkenazi Jewish Panel Factor II-V Leiden Panel
CYP450 2C19 MTHFR
Warfarin Assay
CYP450 3A4 FII-FV-MTHFR Panel
CYP2C19
CYP450 3A5 CFTR31
MDR-1 CYP450 2C9-VKORC1
HPV Genotyping CYP450 2D6
HPV Quad UGT1A1 (Irinotecan)
NAT-2 HPV Genotyping
CHEK-2 HPV Quad
EGFR, 5-FU (mutations) FLU A-sH1N1
MTB-DR (Drug Resistance)
Respiratory Viral Panel
STD Panel
NTM

29. 29 Clondiag Technology
ArrayTube, ArrayStrip, Assay Processor
Unique feature of the AT platform is the combination of probe array chip
and micro reaction vial into one single platform, allowing easy and
reliable array handling with conventional lab equipment.
The probe arrays are made up of a transparent glass chip supporting a filter
membrane like coating with the embedded probe molecules.
Probe deposition is performed by applying state-of-the-art spotting techniques
(for the fabrication of oligonucleotide, polynucleotide and protein arrays) and
by oligonucleotide in-situ synthesis using CLONDIAG's proprietary micro wet
printing process (µWP).
With the ArrayStrips, CLONDIAG'S reliable ArrayTube platform is now
available in a 96 well microplate compatible format.
The AP cartridge is integrating target amplification, hybridization and signal
detection in a single device.
part of Inverness Medical Innovation

30. Clondiag AT Procedure
30
The ArrayTube Workstation ATS is designed for fast and accurate detection and analysis of all ArrayTube Tests.
In combination with CLONDIAG's robust colorimetric detection method, ATS allows the analysis of the test specific interaction pattern on the AT-array carrying multiple
diagnostic features wit

31. Clondiag Platform by Genomica
1-This microarray (3x3 mm) includes 120 cDNA spots immobilised
on a polymer-coated slide which hybridise with specific DNA
sequences from the sample.
2-Amplified DNA is marked with biotin and added to the Array Tube
3-These labelled products recognize the specific probes on the
microarray during hybridisation, and are immobilised
4-The microarray is incubated with a streptavidin-peroxidase
conjugate which binds to the amplified products via a reaction
between the streptavidin and the biotin label
5-In the presence of tetramethylbenzidine (TMB), the peroxidase
activity of the conjugate induces the appearance of an insoluble
31
product which precipitates at the hybridisation sites on the
microarray.
6-Final image. Dark spots indicate hybidization.

32. Genomica middle high throughput platform
With the CAP (Clinical Array Processor) and the CAR (Clinical Array Reader) Up to 12
ArrayStrips can be inserted into one microplate frame allowing the parallel testing of up
to 96 samples.
In contrast to common microplate test formats, each well containing a microarray
enables the analysis of one sample for multiple parameters in parallel.
32

33. Clondiag Assay Processor
The size of a test strip the AP cartridge is integrating target amplification,
hybridization and signal detection in a single device. Central part of the reaction
cartridge is a high quality micro probe array enabling the parallel analysis of
multiple test parameters in a single step reaction.
The AssayProcessor Station is designed for easy and rapid AP
testing in the doctor's office or in the routine lab. After
sample injection, the AP is placed into the Station, and the
test is started via simple touch screen command. All assay
steps run automatically controlled without any further user
interaction.
APS Features
- fully automated AP test processing for both nucleic
acid and serological AP assay formats
- robust fluorescence detection concept for qualitative
and quantitative measurements
- integrated data matrix reader for automated
identification of test and test parameters
33
- integrated PC and built-in touch screen, interface for
external data transfer and printing
- ease of operation
- complies with current IVD guide
APS control unit with 4 processing modules in parallel

34. 34 Genomica clondiag-based Menu
PneumoVir - Respiratory Virus Panel MetaBone HPV
(17)
COLLAGEN TYPE1 - SpI 35 HPV genotypes
Influenza A VITAMIN D RECEPTOR – FokI y BsmI
Influenza B ESTROGEN RECEPTOR - PvuII y XbalI predisposition to suffer endocrine system
RSV A CALCITONIN RECEPTOR – AluI pathologies, rheumatological alterations and
RSV B osteophatologies.
Influenza C predisposition to suffer endocrine system
pathologies, rheumatological alterations and
Parainfluenza 1
osteophatologies.
Rhinovirus
Adenovirus
Parainfluenza 2
Parainfluenza 3
Parainfluenza 4a
Parainfluenza 4b
Echovirus
Bocavirus
Coronavirus
Metapneumovirus A
Metapneumovirus B
All products, CE-IDV

35. Greiner Bio-One
Technology
The HTA™Slide is a standard 25 x 75 mm glass slide
partitioned into 12 flat compartments, each with a printable
surface of 6 x 6 mm. Therefore 12 samples can be
processed simultaneously.
Greiner Bio-One’s HTA™Plate is an innovative and reliable
platform for diagnostic applications of microarrays.
•96 x 36 mm2 printable area
•4 individual sections with 24 wells each
•Removable wash collars
•Low autofluorescence
•Barcode labeling
35

36. Greiner Bio-One Procedure
1. Sample collection 2. DNA extraction 3. PCR
10 mins 30 mins 120 mins
36 4. Hybridisation
15 mins at RT
5. Washing
2 mins
6. Scanning
10 mins
7. Evaluation
5 mins

37. CheckScanner™
37 Fast and Reliable Analysis
Automatic analysis of four HTA™Slides (or one HTA™Plate under
development) with barcode identification
Data analysis and reporting with CheckReport™Software

38. PapilloCheck®
Orientation Control
for optimised analysis OC OC OC OC OC PC PC PC PC PC PCR Control
6 6 6 6 6 45 45 45 45 45
11 11 11 11 11 51 51 51 51 51
16 16 16 16 16 52 52 52 52 52 • Type-specific
18 18 18 18 18 53 53 53 53 53 HPV DNA probes
31 31 31 31 31 56 56 56 56 56 in replicates of 5
33 33 33 33 33 58 58 58 58 58
35 35 35 35 35 59 59 59 59 59 • Print Control
39 39 39 39 39 66 66 66 66 66 • Negative Control
40 40 40 40 40 68 68 68 68 68
42 42 42 42 42 70 70 70 70 70
43 43 43 43 43 73 73 73 73 73
44 44 44 44 44 82 82 82 82 82
Hybridisation Control HC HC HC HC HC SC SC SC SC SC
Sample Control
38

39. 39 Greiner Bio-One Menu
ParoCheck®: Inflammation of the gums and the
paradontium are among the most frequent human
diseases. ParoCheck® is the first biochip approved as an
“In-Vitro-Diagnostic” (IVD), and with it up to 20 different
characteristic indicative pathogens can be detected.
CarnoCheck®: With this biochip 8 different animal
species can be unequivocally identified in foods or other
products.
PapilloCheck®: Early recognition of human
papillomaviruses (HPVs). With this newly developed •PapilloCheck DNA chip comprises 12 wells, A1
biochip PapilloCheck® a total of 18 of the “high risk” – B6 defined by elevated rims.
•Each well contains one PapilloCheck
HPV types and 6 “low risk” HPV types can be identified.
microarray with 28 probes, each in 5 replicate
spots.
coming: CF chip (>50 mutations) •These 140 spots are arranged in an array of
10 by 14 spots distributed over an area of
about 10 mm2.

40. 40 Asian Market Development
Hybribio, HongKong
Flow-through biochip [HPV (21), HBV (rtPCR), HPV (rtPCR)]
Dr Chip, Taiwan
Polymer Biochip [enterovirus, RVP (10), milk pathogens (7), food pathogens (7)]
Guilin Immunetech Co, Ltd, GIMT, China
rtPCR, ELISA biochip [CMV]
BioCore, Seoul, Korea
Slide Chip, gelPCR [HPV (32), HCV(10) - CT, NG, MP, CMV, EBV, HSV, MT]
LGLife Sciences, Seoul, Korea
Slide Chip, rtPCR [HPV (32)- HPV, TB
Seegene, Seoul, Korea
CEPCR [Sepsis, RVP (18), HPV (18), TB, HBVgeno]
GelPCR [JAK2, FLT3, BCR-ABL, PML, AML, MTHFR, CYP2C9, ApoE, Food]

41. 41 European Market Development
Attomol, Germany
DNA-LINA [VZV, HSV, B19, bacteria]
AID, Germany
CEPCR [STD(6), HPV (5)], StripPCR [ HLA, F2-F5-MTHFR, Hfe, ApoE-B,
Osteop,CYP2C9, HFI]
Greiner Bio-One, Germany
CE-IVD BioChips [HPV (24), CF (49), ParoCheck, CarnoCheck, MycoDtect]
Vircell, Spain
Speed-Oligo (stripPCR) [Mycoplasma-Legionella-Chlamydia Pnemonia]
Progenika, Spain
LIPOchip, BLOODchip, PHARMAchip

42. 42 European Market Development
Innogenetics, Belgium
4-Mat technology, 3D porous microarray
Eppendorf, Germany
BioChip System, SilverQuant detection, DualChip GMO assay, Gene Expression
on-demand assays

43. 43 Italian Market Development
Ab Analitica, Padova, Italy
PCR [B19, CMV, EBV, HCV, HCVgeno strip, HHV6, HSV, HBV, HPV strip (32)]
rtPCR [CMV, EBV, HSV, HHV6, HHV8, HPV (8)]
Ce-Gel-PCR [col.cancer, CPIG clonality, KRAS, BCR-ABL, AZF, DDK, APoE, COL1A1, VDR, STR,
VNTR]
strip-PCR [F2-F5-MTHFR, Hfe]
BCS Biotech, Cagliari, Italy
rtPCR [Scrapie], ProDect Chip [ceivd HPV (25), RVP(8), Pan-Entero, L-C-M pneumoniae, Milk(8),
Food(10)]
ELISA-PCR [HPV(19), HCV, HCVgeno, HBV, HBVgeno, HAV, HGV, HDV, HSV, CMV, VZV, HHV6, HHV8,
EBV, Rub, JC/BK, Entero, B19, HIV, HTLV, SARS, MT, MBhsp65, BA, HP, MP, MG, TC, CP, BP, BB,
ToxoB1, ToxoP30, SMA, F2, F5, MTHFR, F8, Hfe, BCR-ABL, K-Ras, GMO]
EuroClone, Siziano, Italy
CE-IVD stripPCR [F2-F5-MTHFR, Infertility, Hfe]

44. 44 Making Your Own Array Tests
Choose your probes (oligos, cDNA)
Choose the way for spotting them
Hybridization experiments
Scanner Detection
Biocomputing Analysis

45. Array Construction
45

46. Array Hybridization
46

47. Semi Automation for Array Hybridization
The TECAN HS 4800 Pro and HS 400 The systems are designed for
Pro Hybridization Stations full automation, from pre-
47
represent the very latest technology hybridization and on-board
for performing fully automated, denaturation up to automatic
highly sensitive and reproducible slide drying with OSND™
microarray processing on slides. technology.

48. Semi Automation for Array Hybridization
BioMicro’s MAUIs are
Systems for automating
the fluid processing of
microarray samples in
low-to-high-throughput
laboratories.
The MAUI System
integrates and optimizes
the sample processing
performed on microscope
slide arrays via its
patented instrument and
MAUI Mixer hybridization
chambers.
48
Also from Advalytix.de, the ArrayBooster, SlideBooster, and
PlateBooster

49. Array Detection
Affymetrix
Agilent Technologies
Alpha Innotech
Applied Biosystems
Applied Precision
Biomedical Photometrics
Inc.
Bio-Rad
Genetix
Illumina
Invitrogen
Molecular Devices
PerkinElmer
Tecan
Telechem-ArrayIt
VIDAR Sys. Corp.
etc...
49

50. 50 Arrays Competitor: realtime PCR
Combination of NA extraction platforms + QPCR instrument
most popular : Roche MagnaPure LC
then Qiagen EasyOne, Biomerieux EasyMag
In France, 30% Roche LightCycler, 30% AB-Prism, 30%
Cepheid (IL) SmartCycler
QPCR average cost in France 12€ (in house - including NA
extraction @4-5€) or 18-45€ (CE-IVD)
Clondiag, Greiner, Innogenetics like arrays: 40-65€

51. Gene Expression Assays: from
51 array to pcr and back
the rapid development of PCR arrays for gene expression analysis
SABiosciences (acquired by Qiagen) PCRarrays
Roche Applied Sciences, a development of the UPL products, RealTime Ready arrays
Fluidigm Digital PCR and LifeTechnologies/BioTrove OpenArray
Pathway Focused: Profile the expression of a panel of genes relevant to a pathway or disease state.
Simple and Accurate: Simple real-time PCR method provides high sensitivity and wider dynamic range.
Requires as little as 1 ng total RNA.
Pre-aliquoted primer set plates and Master mix formulation enable the PCR Array to amplify 96 or 384
different gene-specific products simultaneously for a single patient, or series of genes for multiple patients
on a single 96 or 384 PCR plate.

52. Gene Expression made simple
52 with realtime PCR arrays
Choose an array list from
your provider or make
your configure your own
array.
Extract RNAs
Make cDNA
Dispense patient’s cDNA
into
pre filled PCR plates
Qiagen PCR arrays: Sybr
Green
Roche PCR arrays: UPL
(hydrolysis) probes with
LNA

53. 53 Gene Expression, Arrays, RT PCR
Realtime PCR may have found an appropriated way to directly
compete with moderate complexity arrays in MDx
realtime PCR more familiar to MDx users
instrumentation and automation ready in numerous MDx labs
ready-to-go assays
easy customization, online tools...etc
PCR arrays still expensive but just starting
384 well plate compatible instrument recommended

54. 54 And what about electrophoresis?
Automation of conventional electrophoresis
The CE switch
CEquencing
Mass-spectrometry

55. Automation of gel loading
Robotic workstation
+
MT compatible gel box
Biomek 2000 + OneLambda gel box
55

56. Automation of gel loading
E-Gel 96 from Life Technologies
SBS design.
56
Beckman Coulter Biomek script available

57. 57 Automating Gel Electrophoresis
With Capillary Electrophoresis

58. Electrophoresis Automation: Capillary Electrophoresis (CE)
Fluorescence (530 nm)
200 bp
500 bp
Multiplex STR Analysis
after PCR
0 5 10 15 20
Electrophoresis time (minutes)
CE is simply electrophoresis
in a very thin capillary, under
58
high voltage. Gel and samples
are automatically injected for
each run.

59. MicroFluidics and CE chips, the next automated instruments for MDx?
Agilent LabChip 2100
BioAnalyzer
1 PC + 1 Analytical Station
Single Use Chip
90 s run/sample
12 samples / 30 min
The first available LabChip based
instrument, from Agilent, in
association with Caliper Life
59
Sciences

60. 60 LabChip Pros and Cons
Pros Cons
Automation of electrophoresis Low throughput (actually)
process
Dedicated reagents
Fast
Still a lot hands on time
Quantitative
Sensibility and accuracy
Cost of instrument vs conventional
Standardized electrophoresis electrophoresis

61. LabChip automation
61 from Caliper LifeSciences
LabChip 90
The LabChip 3000 is dedicated to drug-discovery and immunoassays: Serine/
Threonine Kinases;Tyrosine Kinases; Phosphatases; Proteases; Lipid-
modifying Enzymes; and G-protein coupled receptors (GPCRs).
LabChip 3000

62. Bencntop Labchip instrument for High
62 Throughput DNA and RNA Analysis
Caliper LabChip GX/GXII instruments with LabChip GxP Software are
computerized systems designed to automate the analysis of DNA, RNA
or proteins using Caliper Sipper Chip technologies.
With sample acquisition time less than a minute the instrument can
thoroughly analyze 96 samples in less than an hour.
Caliper LifeSciences LabChip GX

63. The end of Agarose Gel: Qiagen QIAxcel
The QIAxcel System is
based on a proprietary
multiplexed fluorescence
detection with
inexpensive solid-state
light sources and micro-
optical collector.
It uses a multiple usage
and disposable multi-
capillary-gel cartridge.
High resolution
separation is provided
for 12 samples, every
5-7min.
Resolution is 3-5 bp in
DNA fragment sizes
between 15-5000 bp.
Sensitivity is 0.1 ng/µl
of diluted PCR product
solution.
63
Now the QIAxcel from Qiagen

64. Development of automated
64 sequence based diagnostic
with Capillary Electrophoresis

65. Sequencing by CE: CEquencing
The AB Prism
310 a pioneer
65

66. Sequencing Instrumentation
Company Amersham Biosciences Beckman Coulter Licor
Instrument MegaBace MegaBace MegaBace MegaBace CEQ 8000 CEQ 8800 4200 4300
500 1000 4000 750/1500
Technology capillaire capillaire capillaire capillaire capillaire capillaire Gel plat Gel plat
type/lanes 48 non 96 non 384 non 8 coated 8 coated 0,25mm/
16-32-48- 64/96 lanes
nber coated coated coated capillaries capillaries 32/48/64/9
(96)/
capillaries capillaries capillaries 1x96 2x96 6 lanes
16-32-48-96
non coated samples samples
Lanes length 40 cm 40 cm 40 cm 40 cm 33 cm 33 cm 41/66 cm 25/41/66
(75µm) (75µm) (75µm) (75µm) (75µm) (75µm) cm
Pyrosequencing AB / Visible Applied Biosystems
MJ-Research,
Biotage Genetics
BaseStation PSQ 96 PSQ 96 Long-Read Prism 310 3730 3500
3100/Avant 3730xl
100 HS/HSA MA Tower
gel ultra plat pyrosequencing gel Plat capillaire capillaire capillaire capillaire capillaire
75µm/100 10x 96 well 96 well Microcell 1 capillary 16 or 4 48 to 96 96 capillaries 8-24
lanes plates plate 0,5µm capillaries capillaries 16x96/384 capillaries
16 lanes 16x96/384 plates
plates
N.A. N.A. 14, 21, 28 47/61 cm 22/36/80 36/50 cm 36/50 cm xx
20, 30,40 cm
cm (50µm) cm (50µm) (50µm) (50µm)
66

67. Low Cost multicapillary systems for sequencing based diagnostic automation
8 to 24 capillary systems made available
Applied BioSystems new 3500 Genetic Analyzer
Beckman Coulter CEQ 2000/8000/8800
Eight-capillary array
Four-wavelength fluorescence detection/
capillary
96-well microplate format for samples
96-well microplate format for buffer
Automatic gel replenishment
Automatic sample denaturation and
injection
67

68. CEquencing for HIV genotyping
• HIV extraction
• RT/PCR
• nested PCR
• Cycle sequencing reactions
• Electrophoresis onto a CEquencer
• Sequence Confirmation
• Resistance profile assignment
CEquencing HIV Protease gene
50min protocol
8 capillary system
4 patients/ 50min
CEquencing HIV RT gene
68
1hr50 protocol
8 capillary system
4 patients/ 1hr50
4 patients RT+Prot
CEquencing/2.6hours
24 patients/16hrs

69. 69 Estimating CEquencing Cost
Sequencing: 3+1+(0.4+4.5+0.4 €)x2=$19 per 700b sequence
CEQuencing with 8 capillaries: 33.000b per 24h (48x2x700b)
CEquencing cost for ds33.000 bases: $892
CEquencing cost for ds1Mb: $27.000
BioIT, sequence confirmation: 5min/1000b ; 7hrs/33.000b

70. Sequencing based diagnostic and BioInformatics
70

71. Sequence confirmation with CEQuence Investigator
71

72. Major and Minor HIV mutations
Protéase Reverse Transcriptase
1 31 61 1 31 61 91 121 Q151M Y181C 211 241
2 V32i 62 2 32 A62V 92 122 152 182 212 242
3 L33 63 3 33 63 93 123 153 183 213 243
4 34 64 4 34 64 94 124 154 M184V 214 244
5 35 65 5 35 K65R 95 125 155 185 T215Y/F 245
6 M36i 66 6 36 66 96 126 156 186 216 246
7 37 67 7 37 D67N/E/S 97 127 157 187 217 247
8 38 68 8 38 68 98 128 158 Y188C/H/L 218 248
9 39 69 9 39 T69D/N 99 129 159 189 K219Q/E 249
L10i 40 70 10 40 K70R L100i 130 160 G190A/S 220 250
11 41 A71V/T 11 M41L 71 K101E 131 161 191 221 251
12 42 72 12 42 72 102 132 162 192 222 252
13 43 G73S 13 43 73 K103N 133 163 193 223 253
14 44 74 14 E44A/D L74V 104 134 164 194 224 254
15 45 75 15 45 V75M/S/A/T 105 135 165 195 P225H 255
16 M46i/L 76 16 46 76 V106A 136 166 196 226
17 i47V V77i 17 47 F77L 107 137 167 197 227
18 G48V 78 18 48 78 V108i 138 168 198 228
19 49 79 19 49 79 109 139 169 199 229
K20R i50V 80 20 50 80 110 140 170 200 230
21 51 81 21 51 81 111 141 171 201 231
22 52 V82A/F/S/T 22 52 82 112 142 172 202 232
23 53 83 23 53 83 113 143 173 203 233
L24i i54V/L/T i84V 24 54 84 114 144 174 204 234
25 55 85 25 55 85 115 145 175 205 235
26 56 86 26 56 86 F116Y 146 176 206 P236L
27 57 87 27 57 87 117 147 177 207 237
28 58 N88D/S/T 28 58 88 118 148 178 208 238
29 59 89 29 59 89 119 149 179 209 239
D30N 60 L90M 30 60 90 120 150 180 L210W 240
mutations primaires
mutations secondaires
mut majeure ANRS : pas JAMA
mut mineure JAMA : pas ANRS
72

73. LIMS Solutions for Genomic Applications
73
Genologics, SCC soft computer, SoftGenetics, GenomeQuest, web Genomatix, GGA,
Soft Lab, SoftMolecular, Nextgene based platform ChipInspector, ..etc
Biorepositories, SoftCytogenetics,
BioChronicles, SoftHLA CLC bio, DNA BiotiqueSystems, InteRNA, Intess
Workbench, Genomics BLIS
Geneus, Omix...etc Geospiza, GeneSifter Workbench

74. Molecular Diagnostic IT
Sequence Databases
Mutation Databases
SNP Databases
Journal References
74

75. IDNS modules for research,
clinical diagnostics,
epidemiology
Actionable § Microbial identification: bacteria,
mycobacteria
§ Fungal identification
§ Veterinary and food pathogens
§ HIV drug-resistance: genotyping
and resistance assessment
§ HCV genotyping and HBV resistance
testing
§ Epidemiological genotyping of
bacteria and viruses: MLST for
meningococci, Campylobacter,
Influenza, others
§ HLA typing Interface (XML, HL7)
Integrated analysis
Public databases
Expert board Reference Database
Sequence profiles Algorithms
Data management
IDNSTM
Intranet Internet
Lab-Data
Laboratory
Complex Data
75
© 2006

76. An Alternative To Sequencing
76 Instrumentation
Mass Spectrometry

77. 77 MALDI-TOF-MS for DNA analysis
• DNA consists of a four-letter alphabet: A, C, G, T and each letter has defined molecular mass:
• dAMP = 313.2 Da - dCMP = 289.2 Da - dGMP = 329.2 Da - dTMP = 304.2 Da
• Matrix-assisted laser desorption ionization time-of flight mass spectrometry (MALDI-TOF-MS) has been
mainly commercialized by Sequenom Inc. (San Diego, CA) and has emerged as a strong contender in the
high throughput genotyping field. In this technology, the PCR products serve as templates for an optimized
primer extension reaction, generating allele-specific oligonucleotide products.
• High resolution resolves non-specific background from signal => the very high sensitivity
• Large mass window allows multiplexing many analyses into a single spectrum
• Absolute concentration can be measured with higher precision than other methods
• Full automation and data interpretation means no mass spec expertise required
courtesy of Dr Charles Cantor, Sequenom

78. 78 MALDI-TOF-MS for SNP Genotyping
Multiplex up to 40 SNPs/reaction, 150,000 genotypes/day
courtesy of Dr Charles Cantor, Sequenom iPlex Gold from Sequenom

79. MALDI-TOF MS sensivity for CNV
analysis
79 Analysis of Copy Number Variation using Quantitative Interspecies Competitive PCR
Nigel M. Williams, Hywel Williams, Elisa Majounie Nadine Norton, Beate Glaser, Huw R. Morris, Michael J. Owen and Michael C.
O’Donovan. Nucleic Acids Research, 2008.
Relative SNP Allele Copy Number Variation
Ratio
Requires Well-characterized SNPs for CNV Flexibilit Doesn’t rely upon a SNP, Can use heterozygote or homozygote
region and Heterozygote samples Provides Absolute copy number, Highly quantitative, informative data
Provides Relative copy number and Minimal quantitative informative data Useful for Fine mapping of specific CNV regions, Copy number
Useful for Post-array validation, Fine mapping of specific CNV regions, Potential association studies, Post-array validation of uncharacterized regions
CNV discovery from genotyping experiments
courtesy of Dr Charles Cantor, Sequenom

80. 80 Numerous applications for MALDI-TOF MS
Detection of low pourcentage mutations (>20% by sequencing,
1-3% by MS)
Detection of low abundance transcripts
ie, Sequenom SEQureDX T21 test
DNA methylation measurements
Resequencing
Signature sequence identification
bacteria typing, HCV quasispecies analysis, respiratory virus
surveillance...etc

81. 81 The major players in MDx
Ibis Biosciences,
T5000 Biosensor
System
(an Abbott Company) Sequenom, Inc., MassArray

82. 82 Sequence based diagnostic
Is getting highly automated
With microtiterplate compatible operation and multicapillary throughput
New area to take care with: bioinformatics
Lot of time required for analysis
Informatics skilled technicians needed
Collection of data
Integration with LIS
megaBase, gigaBase and full genome sequencing may be the next
molecular tool revolution after realtime PCR
MALDI-TOF MS a serious alternative to sequencing instrumentation

83. 83 From Sequencing to Genotyping: SNPs
Interest in SNPs is increasing in the diagnostic field
pharmacogenomics, pharmacogenetics, personalized medicine
Disease risk prediction
Disease predisposition
Many options to analyze SNPs with a high throughput
Sequencing, PyroSequencing, Real-time PCR, Invader, MassArray,
OLA, BeadArray, SBE…etc

84. 1, 0 0
15,000,000
SNP
2 haploid genomes differ at 1 nucleotide every 1331 bp
84

85. 5,000,000
SNPs have been identified so far
85

86. 99%
SNPs have no biological effect.
Over 60.000, however, are within genes, and some are
associated with disease.
86

87. 87 SNP Genotyping Methods
According Ivo Gut, Human Mutation 17:475-492 (2001)

88. 88 SNP Detection in MDx
Implementing such technologies still requires a lot of effort.
•<10 •the easiest way: realtime PCR approach for a limited number SNP to analyze
per patient
•>10 <96 •while SNPs number increase reasonably, switch to sequencing approach
•>96 •when SNPs to analyze start to be numerous, switch to microarray based
assays
•the complete picture: whole genome sequencing?

89. 89 Real-time PCR for SNP genotyping
The TaqMan assay for SNPs analysis

90. 90 Real-time PCR for SNP genotyping

91. 91 Real-time PCR for SNP genotyping
The Amplifluor assay for SNPs analysis

92. Sequencing for SNP genotyping
92

93. Sequencing for SNP genotyping
With AB-Prism 3700
93

94. Sequencing for SNP genotyping
With Beckman Coulter
CEQ 8000/8800
94

95. 95 PyroSequencing for SNP genotyping
Chaque incorporation de dNTP libère un pyrophosphate
PPI (relation équimolaire)
Chaque PPI est converti en ATP en présence
d’Adénosine 5’ phosphosulfate APS
Grâce à l’ATP, la luciférine est transformée en
oxyluciférine. Cette réaction s’accompagne d’une
émission de lumière (relation proportionnelle aux nbres
de molécules d’ATP utilisées)

96. PyroSequencing for SNP genotyping
The PSQ HS 96A
96
(Pyrosequencing) Biotage, a Qiagen company

97. 97 Major SNP Technology Providers

98. Illumina SNP Technologies
The Golden
Gate Assay
on the Sentrix
Universal-16
BeadChip or
Universal-96 Array
Matrix multi-sample
array formats.
The Illumina
GoldenGate
Genotyping Assay
is a flexible, pre-
optimized assay
that uses a
discriminatory
DNA polymerase
and ligase to
interrogate 96, or
from 384 to
1,536, SNP loci
simultaneously.
98

99. Illumina SNP Technologies
a novel approach to microarrays
Illumina’s BeadArray Technology is
based on 3-micron silica beads that
self assemble in microwells on either
of two substrates: fiber optic bundles
or planar silica slides.
Each bead is covered with hundreds
of thousands of copies of a specific
oligonucleotide that act as the
capture sequences.
The BeadXpress Reader is a high-
throughput, dual-color laser
detection system that enables
scanning of a broad range of
multiplexed assays developed using
the VeraCode digital microbead
technology.
99

100. Beckman Coulter SNPstream Technology
1. Primer Design Autoprimer.com
2. Multiplex PCR
3. PCR Cleanup
4. Single Base Extension SNPware® Reagent Kits
reaction
5. Tag-Array hybridization
6. Image Scanning
7. Automated Genotype SNPstream Software Suite
Calling
100

101. Final Step: Interpretating the results
250 SNP/patient for 3000 patients
DNA extraction campaign = 10 days
PCR setup = 10 days
DNA PCRs = 11 nights
Primer extension reactions and readings = 12 days
Project duration ≈ 32 days (1 month)
101

102. Pre-PCR Setup (1)
✓ Beckman Coulter, Inc. (BCI) Biomek Nx sp8 for DNA
extraction, PCR setup and PCR plate loading
✓ Roche LightCycler 480 for robotic PCR
102

103. Post-PCR Setup (2)
✓ BCI Biomek Nx sp8 for primer extension reaction setup, hybridization
setup, plate washes, PCR product purif., sequencing reaction setup,
sequence reaction purif. ...etc
✓ BCI SNPstream scanner
✓ BCI CEQ 8000
103

104. High Throughput SNP detection:
104 portable to routine MDx?
Screening for a large set of SNP is still high end and technical
demanding
Large set of SNP studies more related to research and clinical studies
rather than routine MDx
However, more and more SNP are related with disease-associations. So
still a high potential for MDx developments.
How these technologies will face the $100 full genome sequencing era?
Technologies for 1m SNPs vs Full genome sequence with >5m SNPs?

105. Virus: 3500 to 8 x
Basics
105 bases
1 kilobase
1kb Bacteria >1Mb
(Escherichia coli =
1 000 bases 4,7 Mb)
Eucaryotes
10-3.105 Mb
1 megabase
1Mb yeast
1,3 Mb
1 000 000 bases
drosophila
1 million 165 Mb
Homo sapiens
1 gigabase 3400 Mb
1 Gb 3Gb
20 000-25 000
1000 Mb genes
1 billion Transcriptome
2% Genome
105

106. AB Solid, PGM,
AB & BCI
Illumina HiSeq,
2nd Generation CE Sequencing
Roche FLX, Jr
PacBio
Sequencing:
routine MDX tools?
AB 96 capillaries: Roche:
NextGen Sequencers - NextGen 2,8 Mb/24h 0,5 GB/10hrs
Sequencing - NGS 400b/read Illumina:
BCI 8 capillaires: 200 GB/8days
Whole Genome Sequencer - Whole 45KB/24h AB/LT:
Genome Sequencing - WGS 700b/read 210 GB/7days
106

107. 107
Sanger vs NextGen

108. The Polonator G.007 is the first
"open source" gene sequencing
instrument to hit the lab market
in which the instrument's
Other Players software (Web ware) and
specifications are freely
available to the public.
At $150,000, the Polonator is the
cheapest instrument on the
The HeliScope™ market
Single Molecule
Sequencer is the first
genetic analyzer to
harness the power of
direct DNA
George Church Lab. + Danaher measurement, enabled
Motion: Polonator G.007 by Helicos True Single
Molecule Sequencing
(tSMS)™ technology.
Helicos BioSciences Corp.:
HeliScope SMS
Upcoming 3rd generation
sequencers
108

109. Roche Applied-Science
(454)
GS-20, GS-FLX, GS-FLXti
GS-junior
109

110. Roche GS-FLX
technology
110

111. Roche New Instrument 111
The GS Junior Launch Nov. 2009
GS FLX ti GS junior
Throughput 0.7 GB / day 35 MB / day
Read
4-500b 4-500b
Length
Reads per
> 1million 70-100,000
run
Instrument
~$648,000 ~$100,000
price
Potential applications shown:
HIV drug resistance testing, 8 patients @ 1500X
HLA class 1+2 full sequencing

112. NextGen Sequencers Roche GS-FLX:
Workflow
112
Workflow 3-4 days (setup) + 1 day (run) IT steps:
1. Generation of a single-stranded template DNA library (~8-16 hours)
2. Emulsion-based clonal amplification of the library (~8 hours) GS-FLX Software
3. Data generation via sequencing-by-synthesis (9 hours)
4. Image and Base calling analysis (~8 hours)
▪GS Reference Mapper
5. Data analysis using different bioinformatics tools
•Long Single Reads / Standard Shotgun (required input = 3–5μg,5μg recommended)
▪GS De Novo Assembler
~1,000,000 single reads with an average read length of 400 bases
▪GS Amplicon Variant Analyzer
•Paired End Reads (required input = 5μg @25 ng/μl or above, in TE; >10kb)
◦3K Long-Tag Paired End Reads. Sequence 100 bases from each end of a 3,000 base span on Third Party Software
a single sequence read (Figure). Co-assemble GS FLX Titanium shotgun reads with 3K Long-
Tag Paired Ends reads from Standard series runs.
•Sequence Capture (required input = 3–5μg)
◦Roche NimbleGen Sequence Capture using a single microarray hybridization-based
enrichment process.
•Amplicon Sequencing (1-5ng or 10-50ng)

113. NextGen Roche GS-FLX:
Sequencers add-
ons
not included
- Nebulizers + nitrogen tank
Nebulization is required to shear fragments for DNA >70-800bp
- emPCR Breaking Kit
This device is required for the preparation of consistently sized reactors
for emulsion PCR.
- Magnetic Concentrator IVGN +€5000
- MT plate centrifuge BCI +€15.000
- Multisizer™ 3 COULTER counter +€15.000
The most versatile and accurate particle sizing and counting analyzer
available today. Using The Coulter Principle, also known as ESZ (Electrical
Sensing Zone Method), the Multisizer 3 COULTER COUNTER provides
number, volume, mass and surface area size distributions in one
measurement, with an overall sizing range of 0.4 µm to 1,200
- Agilent BioAnalyzer +€20.000
- Titanium cluster station +€29.000
113

114. The REM e System, is a
liquid handler accessory
designed to fully automate
the emPCR enrichment and
sequence primer annealing
Automating the
steps in the Genome
Sequencer FLX System
workflow.
process
The Fluidigm Access
Still required
Array System to automate
preparation of 48 samples
•MT plate centrifuge BCI +
€15.000
with up to 48 amplicons in
one run — then sequence
•M u l t i s i z e r 3 B C I
counter +€15.000
all 2,304 unique amplicons in
a single Roche GS Junior
•Agilent BioAnalyzer +
€20.000
System run.
114

115. 115
illumina
Genome Analyzer
(Solexa)

116. Illumina-Solexa Technology
116
The approach relies on attachment of randomly fragmented genomic DNA to a planar, optically transparent surface
and solid phase amplification to create an ultra-high density sequencing flow cell with >10 million clusters, each
containing ~1,000 copies of template per sq. cm. These templates are sequenced using a very robust four-color
DNA sequencing-by-synthesis technology that employs reversible terminators with removable fluorescence.

117. Illumina new instruments 117
Genome Analyzer IIx
HiSeq 2000 HiSeq 1000
HiSeq 2000 HiSeq 2000 GA IIx
Throughput 200 Gb / 8 days 100 Gb / 8 days 85 Gb / 14 days
Capacity 25 Gb / day 12,5 Gb / day 85 Gb / 14 days
Read Length 2 x 100bp 2 x 100bp 2 x 150bp
cBot Cluster System Paired-End Module Genomes 2/run @ $10,000 1/run 1/run
Instrumentation Accessories Instrument price ? 828 000 $ ? 600 000 $ ? 564 000 $

118. Redefining NGS workflow 118

119. NextGen Illumina GA2:
Sequencers add-
ons
not included
- Cluster Station +$50.000
The Cluster Station is a standalone, software-
controlled system for the automated generation of
clonal clusters from single molecule fragments on
Illumina Genome Analyzer flow cells.
- Paired-End Module +$45.000
The Paired-End Module provides fully automated
template preparation for the second round of
sequencing in a paired-end sequencing run.
- IPAR +$60.000
IPAR is a bundled hardware and software solution
that provides real-time quality control and integrated
online processing of primary data during sequencing
runs
- Agilent BioAnalyzer +€20.000
Total: €126.000
119

120. 120
Life Technologies
Applied BioSystems
SOLID systems

121. AB SOLID high throughput
121
How it Works
Start with a fragment or mate-paired library depending on
the application and information you need.
Prepare clonal bead populations in microreactors containing
template, PCR reaction components, beads and primers.
After PCR, you denature the templates and perform a bead
enrichment step to separate beads with extended templates
from undesired beads.

122. Illumina new instruments 122
New Microfluidic FlowChip
5500xl 5500
Throughput 200 Gb / 7 days 100 Gb / 7 days
Capacity 30 Gb / day 15 Gb / day
Read Length 75 +35 75 +35
Genomes 2/run @ $3,000 1/run
Instrument price 595,000 $ 349,000 $

123. Redefining NGS workflow 123
Fragment library
preparation
workflow with
the steps
performed on
the Tecan
Freedom EVO 75
or others
The SOLiD EZ Bead System automates
the SOLiD System work flow from
emulsion PCR (ePCR) to templated bead

124. 124
Ion Torrent/Life Technologies
$50k benchtop inst.
<$500 10Mb run
or
Pacific Biosciences
Single Molecule Sequencer
30Gb/day >1000b frag.
The Challengers?

125. 125 2nd Generation Sequencers and MDx
1.Cost of instrumentation 1.Massive amount of useful data
2.Cost of reagents 2.Genome, Transcriptome,
Microbiome applications
3.Procedure time
3.Reagent cost decreasing
4.BioIT requirements
4.$3-10K full genome access

126. The $100 Full Genome sequence and
126 its impact on the Mdx market
The new era of personalized medicine (P4 medicine)
The DTC-Genomics market
The 3rd generation sequencing technology breakthrough
What 3rd gen. sequencers will provide and how it will change
the MDx market?

127. 127 The DTC-Genomics Players
-23AndMe $1000->$499->$99 (111)
-Athleticode
> 40 players and growing
-deCODEme
-DNAancestry $99 (mtDNA)
-DNAdirect
-DNAVision
-EthnoAncestry $129-299 (Y/mtDNA)
‣ Illumina (everygenome)
-Genebase $448 (mtDNA+91) ➡ full genome @ $48k -> $19k->14k
-GeneEssence $1195 (84) ‣ Knome
-Genelex ➡ full genome @ $100k->$68k->$25k?
-GeneLink
-GenePartner ‣ Complete Genomics
-GeneTonix ➡ full genome @ $12k - 7k
-GeneWize
-MatrixGenomics
-Medomics
-MyredhairGene
-Navigenics $2500->$999 (28) ‣ Life Technologies
-Pathway Genomics (USA) $249 (77) ➡ full genome @ $3k
-ScientificMatch ‣ illumina
-TruGenetics ➡ full genome @ $10k
socialcompare.com DTC-Genomics Players http://t.co/60acprd

128. Upcoming 3rd generation sequencing
128 technology breakthrough
-Complete Genomics -Mobious Biosystems > 20 upcoming players
-Pacific BioSciences -NaBsys
-Life Technologies -Netbio
-ZS Genetics -Population Genetics
-Ion Torrents -Seirad
-Oxford Nanopore -U.S. Genomics
-BioNanometrix ...and growing
-Lightspeed Genomics
-IBM
-Reveo et ReVase
-Genome Corp.
-GenoVoxx
-Halcyon Molecular
-Base4Innovation
-Intelligent BioSystems
-LaserGen

129. Upcoming 3rd generation sequencers:
129 the promise
Instrument target price $10k
$500k in 2010 then down to $10k by 2015
compared to >$600k today
Full genome target price $100 before end of 2012?
$10k end 2009, $3000 end of 2010, $1000 by 2011?
compared to $50k in 2009 (or $20-10k reagents)
1 day assay for full genome sequence at 40X
compared to 10-15 days today

130. Upcoming 3rd generation sequencing
130 revolution?
If (1 NA extraction + 1 3rd gen. test) = full genome at 40X in > 8hrs
then MDx for genetic marker, mutation, deletion, SNP, VNTR, STR = in silico
diagnostic?
if 3rd gen. seq. capable of full transcriptome and epigenome analysis
then what about array based diagnostics, what about gene expression
technologies?
if 3rd gen. seq. capable of >100X sequencing for the microbiome
then what about PCR based assays for infectious diseases?
if 3rd gen. seq. deliver the promise
then shall we enter into the new era of P4 medicine?
(personalized, predictive, preventive and participative)

131. What is the Future of Molecular
131 Diagnostic Procedures?
More automation needed
For sample preparation (higher throughput, larger vol.)
For Fast-PCR (in 96 well format)
Links to be improved
Between sample preparation and PCR
Between molecular diagnostic and clinical chemistry
Between molecular diagnostic and pre-analytical steps
Full Integration

132. What is the Future of Molecular
132 Diagnostic Procedures?
Evolution through RealTime PCR
entering the ‘array’ gene expression business
New Genotyping and Pharmacogenetics era
Technologies development in the SNP field
Evolution of Sequence Based Diagnostics
The $100 full genome sequence: the upcoming revolution
The MDx future: in silico diagnostic?

133. Any Question?
P. Merel 133