Illumina

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22 Φεβ 2013 (πριν από 4 χρόνια και 5 μήνες)

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Dx
, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Inf
ini
um, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro,
GenomeStudio, Genetic Energy, HiSeq, and HiScan are registered trademarks or trademarks of Illumina, Inc. All other brands an
d n
ames contained herein are the property of their respective owners.

MiSeq
TM

System


Overview and Applications

for Public Health

.

.

Susan Knowles

Sr. Market Manager

Product Marketing

October, 2012

2

Agenda



Introduction to
Illumina

Sequencer Portfolio and
MiSeq

Overview

MiSeq

Applications


Applications for Public Health

US Food and Drug Administration (FDA) Award

3

Introduction to
Illumina

4

Illumina

Founded in 1998

Initial Public Offering on July 27, 2000

Headquarters in San Diego, CA

More than
600,000
square ft. of facility

space in
7
countries

>2,000
employees

IP portfolio of 159 issued

patents and 171 pending applications

Ranked
#1 on Forbes


list of Fastest Growing

Technology Companies in 2009 & 2007

2010
: Fortune 100 Fastest
-
Growing Companies
(#27)






5

Global Organization

Multi
-
site Manufacturing, R&D, Sales, Service & Support

Commercial

Mfg/R&D

Partners

Illumina KK (Tokyo)

Jinan, China

Chengdu, China

Korea

India

Malaysia

Vietnam

Shanghai

New Zealand

Thailand

Taiwan

Illumina BV

(The Netherlands)

Illumina China

(Beijing)

Illumina

Cambridge

Illumina

Singapore

Illumina Hayward

(Hayward, CA)

Illumina Global
Headquarters

(San Diego, CA)

Australia

South Africa

Greece

Turkey

Russia

Middle East

Israel

Illumina
Sao Paulo
(Brazil)

Epicentre


(Madison, WI)

6

Sequencer Portfolio and
MiSeq

Overview


7

300
Gb

95Gb

Illumina

Sequencing Portfolio

HiScanSQ

Genome
Analyzer
IIx

HiSeq
1000/
1500

HiSeq
2000/
2500

1000
Gb





100
Gb





10
Gb





1
Gb

600
Gb

150Gb

7 Gb



1.5Gb

Generating 90%

of world’s

sequencing

data

MiSeq

8

Technology Spanning the Spectrum of Needs

Making sequencing more accessible

Small
Genomes

and
Targeted
Tests

$150

9

Meet the
MiSeq

Instrument

My
Samples. My Study.
MiSeq


52.3 cm

12 cm

Included On
-
Instrument:

Cluster Generation (amplification)

Paired
-
End Fluidics

Computing for Primary and Secondary Analysis

10

Load

MiSeq

Instrument

Next
-
Gen Made Simple: Load & Go


Go

DESIGNED FOR THE WAY YOU WANT TO WORK

Preloaded single use reagent cartridge

Positive consumables tracking

Auto flow cell positioning

Walkaway automation

11

MiSeq

Sequencing Kits for Different Throughput Needs

Chemistry Improvements
-

66% increase in read lengths, 3x increase in number of
clusters per run

Up to 4 M clusters/run

Up to 2 x 250
bp

read length

New reagents

ETA: late Q4 2012

100’s Mb

7.5


8.5
Gb

1.0
-

1.5
Gb

Gb

15
-
17 M clusters/run

2 x 250
bp

read length


4.5
-

5.1
Gb at 2 x 150

<5 min cycle time

New v2 reagents

5
-
7 M clusters/run

2 x
150
bp

read length


5 min cycle time

12

Nextera XT DNA Sample Prep

The fastest & easiest prep for small
genomes,
PCR amplicons
and plasmids

Rapid
Prep


90 min prep, only
15
min
of hands on time

Optimized for small genomes, PCR amplicons
and
plasmids

Innovative
sample
normalization


No library quantification needed

Fastest time to
results


DNA
to analyzed data in
<8
hours with
MiSeq

Ultra low
input


only
a single
nanogram

(1
ng
) of
input DNA
needed

High Throughput, High Indexing


Prepare up to 96 samples per batch


Automation
-
friendly reagent configurations


96 indices supported on all
Illumina

sequencers


13

MiSeq

Applications

14

MiSeq

Applications

Application Flexibility for Every Lab

RNA
-
SEQ

Small RNA

Microbial RNA
-
S
eq

Mammalian RNA
-
Seq

REGULATION

Chip
-
S
eq

TARGETED RESEQUENCING

Amplicons

(
Nextera
, Tailed
-
PCR)

TruSeq

Custom
Amplicon

(up to 600Kb)

TruSeq

Custom Enrichment (up to 2 MB)

SMALL GENOME
RESEQUENCING

SMALL GENOME
DE NOVO
SEQUENCING

LIBRARY QC

15

Public Health 1.0


Public Health
2.0

Coordinated real time prevention, diagnosis, response and information
sharing

Faster diagnosis and response times


detection, identification and containment

Updated methods (including NGS)


accurate, high throughput, automated

Crowd
-
sourced, cloud
-
based data storage/exchange and sharing

Functional and geographic
connectivity for analysis and communications


16

Tracking MRSA Hospital Outbreaks in Real Time

Koser

et al., (NEJM, June 2012)

Investigated putative MRSA
outbreak in a neonatal ICU
with a clinically relevant
turnaround time

Retrospectively sequenced
the DNA of 7 isolates
associated with the outbreak
and another 7 MRSA isolates
associated
w
ith carriage of
MRSA or bacteremia in the
hospital

17

Tracking MRSA Hospital Outbreaks in Real Time

Koser

et al., (NEJM, June 2012)

Results:

Constructed a phylogenetic tree
comparing SNPs of the core
genome to a reference genome

ID outbreak vs. non
-
outbreak
isolates and defined the
transmission pathway

Demonstrated ability to use NGS
info to prevent transmission
events between patients carrying
different strains

Took 1.5 days from genome DNA
to data

Rest of hospital

Outbreak
isolates

18

Microbial Outbreak Surveillance

Eyre et al., (BMJ, May 2012)

Goal:
Investigate prospect of
benchtop

sequencers to provide rapid
WGS data in routine clinical practice

Goal:
Investigate the potential of this
technology for identification of
transmission events of healthcare
-
associated pathogens

26 MRSA and 15
C.
difficile

isolates
were sequenced and analyzed within
5 days of culture

MiSeq

sequencing can enhance
hospital infection control, providing
additional genetic resolution over
existing genetic typing techniques



19

Microbial Outbreak Surveillance

Eyre et al., (BMJ, May 2012)

MRSA clusters were identified
as outbreaks, with most
sequences in each cluster
indistinguishable.

20

Genomic Epidemiology of 2011 E. Coli Outbreak

Grad et. al., (PNAS, December 2011)

Isolates were indistinguishable
by standard tests.

German outbreak
-

remarkably
little diversity (2 SNP)

French outbreak
-

much greater
diversity (19 SNPs)

German isolates a
clade

within
the more diverse French
outbreak strains.

21

Conclusions

MiSeq is a powerful tool in clinical
microbiology/public health


Ability to distinguish between cases that are part of a putative outbreak, and those
that are
not


Predict antibiotic resistance


Simple to use, accurate


Data is generated in clinically relevant
timescale

Sequencing data has far greater discrimination power than traditional tests


PFGE, MLST, Spa typing

We are deploying sequencing on real clinical samples to build our
knowledge,
understand customer needs and develop better tools


Faster results


Sample prep for complex samples


Secondary data analysis that delivers actionable report


22

US Food and Drug Administration (FDA)
Selects
MiSeq

23

FDA Selects
MiSeq

for Next Generation Sequencing to
Identify
Foodborne

Pathogens

Customer: FDA Center for Food Safety and Applied Nutrition (CFSAN)


Mission: To promote and protect the public's health by ensuring that the
nation's food supply is safe, sanitary, wholesome, and honestly labeled, and
that cosmetic products are safe and properly labeled.

Some of CFSAN functions


Food safety surveillance and compliance


Cooperative programs with state, local and tribal governments


Regulatory and research programs to address health risks of contaminants


Safety of food developed through biotechnology

FDA
-
CFSAN is part of a global initiative to define how to deploy next
-
generation genomic typing tools for public health and clinical disease
cluster detection on a global scale.




24

FDA CFSAN Project/RFP Goals


Provide national and state field labs with WGS
capability to generate sequences from historical
enteric pathogens collections and from isolates
collected from produce sources across the country.

Build a
reference
database


Across these labs, establish proof

of concept
for
rapid networking of using a WGS approach to
pathogen detection, identification and
traceback
.

Train /equip
national and
state labs


Accurate
subtyping

and clustering of isolates for
investigating
foodborne

outbreaks and
traceback

to food or environmental source.

Technical
accuracy


Piloting transition to

NGS from
PFGE (FDA
standard for >20 years). PFGE has limited ability
to provide clear genetic differentiation of highly
clonal strains/tightly linked isolates (particularly
common with Salmonella bacteria).

Upgrade
technology

25

Why is
MiSeq

a good choice?

FDA Consideration

Performance comparison
MiSeq

v.
PGM using real samples

Data quality


total output, read
length and Q
-
scores


Easy workflow


reduced training
requirements


Cost per sample


library prep and
sequencing


Field service and support


on
-
site, online and phone

Illumina

Offering

Illumina

sequenced 20 salmonella
genomes

MiSeq

generates read lengths of
2 x 250
bp
, and >70% of bases at
≥Q30 quality at that length

With
Nextera

XT users can
prepare samples in <90 minutes
with 15 minutes hands on time

Nextera

XT combined with
MiSeq

can sequence whole genomes in a
single day

Comprehensive support package



26

MiSeq

at the Olympics, August 8
th

Genome Web Article

Sequencing pathogens for disease outbreaks during the Olympics

27

MiSeq Applications Portfolio

Integrated. Optimized. Simplified.

Amplicon

Sequencing

Custom

Amplicon

De novo

sequencing

Resequencing

16S

Metagenomics

RNA
-
Seq

ChIP
-
Seq

Targeted

Resequencing

Custom

Enrichment

Library QC

Small

genome

Plasmid

Clone

checking

Regulation

Small RNA

sequencing

RNA

sequencing

Thank You!

Questions?