1. The State of the Art - Ion RoadMap Update
ESHG - Life Technologies Workshop
Andy Felton Ph.D
Head Product Management – Ion Torrent

2. Wide Adoption of Ion Semiconductor Sequencing >150 Peer Reviewed Publications
2012
2013

3. Accuracy and Workflow Improvements

4. Improving Ion Sequencing
2) Beads
Amplification capacity
Uniformity
Library Prep
Uniformity
Speed
Simplicity
Ampliseq Coverage
RNASeq Simplicity
3) Template Amplification
Template length
Copy number
Uniformity
8) Software
Signal Processing Phase Correction
Accuracy
Variant Calling
Speed
4) Chips
Number of sensors
Wells & Surfaces
Sensitivity
Speed
Noise reduction
7) Fluidics
Flow profile
Efficiency
Speed
5) Loading
Percentage loaded
Simplification
6) Sequencing Biochemistry
Completeness, Speed, Read Length

5. PGM Performance Improvements over the last 12 months

6. Ion Chef™ System: Simple, High Throughput, Modular Benchtop Sequencing Preparation
Simple fully automated workflow – 15 mins of Hands-on-Time
Input 2 Libraries and output 2 chips
Supports sequencing preparation for the Ion PGM™ and Proton™ systems and chips
Ion Chef combines multiple components in a compact benchtop footprint. Ion Chef is only ~6 inches wider than Ion Proton.
Proton
Width: 21.3 in/54.2 cm
Depth: 30.5 in/77.5 cm
Height: 18.7 in/47.4 cm
Chef
Width: 28in
Depth: 28in
Height: 22in

7. Modular Workflow Allows Flexibility
1 run (16-20 samples/run):
Cancer hotspot panel V2 + Ion Chef™ System + Ion 318™ 200bp chip
Ion Chef™ System
Initialization
Ion PGM™ Sequencer
Torrent
Server (TS)
Ion AmpliSeq™ Panel+ Equalizer™ Kit
23 hours total
1 hour hands-on time
library prep
template prep
sequencing
analysis
Detailed analysis of PGM and MiSeq workflow shows that PGM workflow is much faster. It starts with the library preparation, continues with the template preparation and chip loading and culminates with sequencing and analysis. Ion utilizes separate instruments for template prep, sequencing and analysis thus allowing for parallel utilization of them. This approach substantially increases capacity utilization.
Library preparation for MiSeq’s workflow takes much longer than AmpliSeq, and what is even more important MiSeq combines cluster generation, sequencing and analysis in a single instrument thus making this instrument unavailable for a long time. 4 8 12 16 20 24 28 32 36

8. Ion AmpliSeq DNA & RNA Panels
Cancer Hotspot Panel v2
50 genes
>2,800 COSMIC Mutations
207 Amplicons
RNA Cancer Panel
50 genes
Corresponds to genes in Ion AmpliSeq™ Cancer Hotspot v2
Comprehensive Cancer Panel
409 Genes
16,000 Amplicons
RNA Apoptosis Panel
267 genes
TaqMan® validated
Inherited Disease Panel
700 Diseases
328 Genes
10,000 Amplicons
RNA Custom Panel
Target any gene
300 genes in single tube

9. Ion AmpliSeq Community Panels
BRCA 1&2 Panel
2 genes
167 amplicons
Colon and Lung Cancer Panel
22 genes
90 amplicons
available now
AML Panel
Coding regions of known mutations
21 genes
CFTR Panel
All exons, intron-exon boundaries, and UTRs
1 gene
coming soon
Cardio Panel
All exons and UTRs
62 genes
TP53 Panel
All exons and UTRs
1 gene

10. Ion Reporter™ Software 1.6
What’s new in Ion Reporter 1.6
Oncomine®
Copy Number Analysis
Visualize the impact of your variants across 1000’s of cancer samples
Enabled for all oncology workflows
Detect CNVs in your paired Ion AmpliSeq workflows
Visualize with Broad’s IGV
Aneuploidy Workflow
Ingenuity Variant Analysis
Broad’s IGV
Identify biologically relevant variants
Shortlisted variants can be returned to Ion Reporter
Identify biologically relevant variants
Shortlisted variants can be returned to Ion Reporter
One click access to data visualization (SNPs, InDels, CNVs, etc)
Customized karyotype view
No charge for Ion Reporter™ Software, Compendia Oncomine™, or Ingenuity® Variant Analysis™ till August 2013

11. Ion Proton

12. Proton exomes are comparable to other platforms Joe Boland National Cancer Institute
Proton  vs. SNP chip
Proton vs. HiSeq
NA12889
0.9920
0.9856
NA12890
0.9923
0.9868
Notes from Joe’s talk
This is NA12878 data
Proton is TargetSeq v2 Exome capture HiSeq is Nimblegen. Comparing data in overlapped regions
Goal was to compare side by side
ILMN only most in segmented duplicated regions
Proton only SNPs due are mostly FPs due to HPs but TSS 3,4 improved this dramatically
Indels- platforms are comparable

13. Rapidly Improving PI Performance
Gb of Aligned Ouput
Mean
Readlength
95 bp
114 bp
162 bp
191 bp
Filtered Reads
62 million
89 million
94 million

14. Enables Two Exomes Per Ion PI Chip
Library
Run ID
G BC10
G BC16
Number of mapped reads
42,916,142
44,355,204
Percent reads on target
75.7%
77.1%
Total aligned base reads
5,889,106,971
6,275,436,198
Total base reads on target
3,131,870,050
3,370,195,602
Average base coverage depth
67.8
72.9
Uniformity of base coverage
90.4%
90.5%
Target base coverage at 1x
97.4%
97.5%
Target base coverage at 20x
86.0%
87.3%
Target base coverage at 100x
20.5%
23.9%
Run G on Library L8045

15. Continued Scaling to PII Chip
PI 1.68 um pitch
165 M Sensors
PII 0.84um pitch
660 M Sensors

16. All products mentioned in this presentation are For Research Use Only
All products mentioned in this presentation are For Research Use Only. Not for use in diagnostic procedures.
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