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The State of the Art - Ion RoadMap Update

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Presentation on theme: "The State of the Art - Ion RoadMap Update"— Presentation transcript:

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. © 2013 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation and/or its affiliate(s) or their respective owners.

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