The Future is Here:
Ion PGM™ and Ion Proton™ Product Roadmap
October 2012
1
1
2
3
Ion PGM™ System
Rapidly growing community
400 base read length
99.99+% accuracy
Ion AmpliSeq™ Kits
10 ng input, single tube amp
Thousands of amplicons
100% coverage demonstrated
Ion Proton™ System
Routine exome sequencing
99.99+% accuracy
Same day sample to interpretation
2
1
2
3
Ion PGM™ System
Rapidly growing community
400 base read length
99.99+% accuracy
Ion AmpliSeq™ Kits
10 ng input, single tube amp
Thousands of amplicons
100% coverage demonstrated
Ion Proton™ System
Routine exome sequencing
99.99+% accuracy
Same day sample to interpretation
3
>1,000 Ion PGM™ Systems Installed
4
>13,000 Users on Ion Community
Datasets
Applications and Protocols
Discussions
Programs and Events
RecognitION
Chip
User
Q20 bases
Submission Date
314
Lindsay Vang (aka lindsayvang)
135,446,449
September 21st
316
Matt Shudt (aka corebotz)
785,531,874
September 28th
318
Kai Wataru (aka wtr)
1,270,839,192
October 1st
5
Cumulative Per-Base Accuracy
Read Length and
Accuracy for Finding Point Mutations
100.0%
99.5%
Q3:2011
99.0%
Q3:2012
Q1:2011
98.5%
98.0%
97.5%
97.0%
0
50
100
150
200
250
300
350
Position
400 base chemistry available this quarter!
6
400
Significant Accuracy Enhancements
With the Most Difficult Sequences
100.0%
99.5%
Accuracy
99.0%
Q3:2012
98.5%
98.0%
97.5%
Q2:2011
97.0%
Q1:2011
96.5%
96.0%
95.5%
95.0%
1
2
3
4
Homopolymer Length
7
5
6
Accuracy Experience Verified Externally
0.007
25
0.006
20
0.005
0.004
15
0.003
10
0.002
5
0.001
0
0
v1.4
v1.5
Note: Slide Courtesy of8 Chad Nusbaum/Broad Institute
v2.0
v3.0
Mean Quality (Q score)
30
Mismatches, Deletions &
Insertions
0.008
Accuracy Experience Validated Externally
0.007
25
0.006
20
0.005
0.004
15
0.003
10
0.002
5
0.001
0
0
v1.4
v1.5
Note: Slide Courtesy of9 Chad Nusbaum/Broad Institute
v2.0
v3.0
Mean Quality (Q score)
30
Mismatches, Deletions &
Insertions
0.008
Semiconductor Sequencing Just Gets Better, Faster
Sequence Output per Run
Small
Genome
Genes
Transcriptome
100G
10G
1G
Ion 318™
Ion 316™
100M
Ion 314™
Ion 316™
10M
Ion 314™
10
Ion 318™
1
2
3
Ion PGM™ System
Rapidly growing community
400 base read length
99.99+% accuracy
Ion AmpliSeq™ Kits
10 ng input, single tube amp
Thousands of amplicons
100% coverage demonstrated
Ion Proton™ System
Routine exome sequencing
99.99+% accuracy
Same day sample to interpretation
11
Higher Coverage Uniformity = Lower Cost per Sample
Ion AmpliSeq™ CHPv2
99% coverage uniformity
100000
Reads per amplicon
10000
1000
100
10
1
10000
1000
100
10
1
v1
Attribute
v2
v2
656,260
Total number of reads
639,837
~320,000
3,454
Average coverage
3,091
~1,500
17
Minimum coverage
963
~430
4
Samples per Ion 316™ Chip
4
8
Price per sample
~ $272
€255
$204
~ $272
€255
12
1
1
1
2
3
4
5
6
7
8
9
1
1
1
1
1
1
1
1
1
1
1
1
1
10
19
28
37
46
55
64
73
82
91
100
109
118
127
136
145
154
163
172
181
190
Reads per amplicon
100000
Ion AmpliSeq™ CP (v1)
95% coverage uniformity
AmpliSeq to Support Non-Human Models
13
1
2
3
Ion PGM™ System
Rapidly growing community
400 base read length
99.99+% accuracy
Ion AmpliSeq™ Kits
10 ng input, single tube amp
Thousands of amplicons
100% coverage demonstrated
Ion Proton™ System
Routine exome sequencing
99.99+% accuracy
Same day sample to interpretation
14
Ion Proton™ System
Bringing Rapid Genome-Scale Sequencing to Every Lab
15
€950 for Ion PI™ and PII™ Runs
Sequencing in as little as 2 hours on the Benchtop
Ion PI™ Chip
165 M wells
Up to 10 Gb
60-80M
Filtered Reads
Up to 200-Base Reads
2-4 hours
16
Ion PII™ Chip
660 M wells
Up to 20X human
genome
240-320M
Filtered Reads
Up to 200-Base Reads
Runs in Hours
>100 Ion Protons™ Shipped with
Installations Ramping Up Worldwide in Q4
17
Ion Proton™ System Makes
Human Exome Sequencing Routine
99.996+% consensus accuracy for SNPs & InDels
>100X mean coverage with >90% covered at 20X
18
Ion Reporter™ Software Supports
Multiple Types of Exome Analyses
Simple workflows for one, two, or three exome samples
Single Exome Sample Analysis
– What is different from a reference genome?
Paired Exome Analysis
– How do the variants differ between these two samples?
Somatic Paired Exome Analysis
– What variants exist in a tumor but not the germline sample?
Trio Exome Analysis for Inherited Diseases
– What variants are shared/different across related individuals?
19
Ion Reporter™ Integration with Ingenuity®
to Rapidly Understand Biological Function
• Quickly ID biologically relevant variants
– Focus on important variants via biological
context, genetic, cancer driver and PGx filters
• Interactive, customizable application
– See visualizations such as pathway diagrams
of the potential impact of each variant
• Accurate, evidence-backed insights
– Leverage over 4 million literature findings from
the Ingenuity® Knowledge Base
20
Ion PI™ RNA-Seq Data Routinely Contains
>80M Reads per Run
Ion PI™ Runs with MAQC Universal Human Reference (UHR)
65% Avg
Mapping
Rate
# of refGenes Detected
16,257
16,767
16,525
16,560
16,829
16,629
% of refGenes Detected
75.4%
77.8%
76.6%
76.8%
78.1%
77.1%
Up to 320M reads with Ion PII™ Chip
21

Mean correlation
coefficient >0.999
across data set

Dynamic range
spanning 6 logs
(log10)
TaqMan Expression HBR:UHR
High Sensitivity Across a Wide Dynamic Range with
Results Validated by TaqMan® Gold-Standard


R2 = 0.958
N= 657
Ion Proton™ Expression HBR:UHR
22
We’re striving to make sequencing easier…
23
Ion OneTouch™ 2 System:
Simple, Modular, and Robust Template Prep
 Available now for both the Ion
PGM™ and Ion Proton™ Systems
(upgrade for current users)
 Simple to set-up and use
 Modular
−
Workflow flexibility
−
Enables access by multiple users
 Robust – IVD/Dx version
The content provided herein may relate to products that have not been officially released and is subject to change without notice
24
Ion Chef™ System:
Library In, Loaded Chips Out on a Benchtop
Tip Racks
Chip
Loader
Reagent
Chiller
Thermalcycler
Enricher
Recovery
Modules
Simpler, Higher Throughput, Ultimate Flexibility
The content provided herein may relate to products that have not been officially released and is subject to change without notice
25
Ion Avalanche™ Chemistry
30-Minute, Non-Emulsion, Long-Read Template Prep
Sequencing Metrics on 318
Total Number of Bases
Longest Alignment
Mean Coverage Depth
AQ20
543 Mb
384 bases
117x
Perfect
408 Mb
384 bases
88x
>625-base perfect reads achieved since 2 weeks ago!
The content provided herein may relate to products that have not been officially released and is subject to change without notice
26
Ion Avalanche™ Enables Higher Densities and Ion PIII™
First 18 Months
Next
PIII
100 Gb
PII
PIII
10 Gb
PI
PI
1 Gb
Ion 318™
Ion 316™
100 Mb
Ion 314™
Ion 316™
10 Mb
27
Ion 314™
Ion 318™
PII
All products mentioned in this presentation are for research
use only and not for use in diagnostic procedures.
Unless noted, all data shown in this presentation was
generated by Life Technologies
28