Ion Torrent Systems Research Applications and Developments for PGM and Proton Sequencers

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1 Ion Torrent Systems Research Applications and Developments for PGM and Proton Sequencers Mathieu Larivière Life Technologies Field Application Scientist Next Generation Sequencing 1

2 Introduction to PGM and Proton Sequencers 2

3 Ion Proton and Ion PGM Instruments Ion PI Chip Ion 314 Chip Ion 316 Chip Ion 318 Chip 3

4 Direct Detection of Hydrogen Ions and Conversion to an Electrical Signal Read by a Transistor Substrate dntp H + ph Q Sensing Layer Sensor Plate V Bulk Drain Source Silicon Substrate To column receiver Rothberg J.M. et al Nature doi: /nature

5 Sequence Output per Run Superior Scalability 10,000-Fold From Ion 314 to Ion PIII Chip* Small Genome Small to Large Gene Panels Transcriptome Exome Human Genome 100G Ion PIII 10G Ion PII Ion PI 1G Ion M Ion M Ion From 1.2 Million Sensors to 1.2 Billion Sensors *The content provided herein may relate to products that have not been officially released and is subject to change without notice

6 Ion AmpliSeq Technology 6

7 Ion AmpliSeq Workflow Overview Learn more at *The content provided herein may relate to products that have not been officially released and is subject to change without notice 7

8 Ion AmpliSeq Porfolio Ready-to-use Panels Off-the-shelf panels to transform cancer and inherited disease research Custom Designs Power of ampliseq.com to customize your own gene panels with Ion AmpliSeq technology Community Panels Design and Verification with leading researchers Ion AmpliSeq Technology As low as 10 ng of input DNA for FFPE compatibility 3.5 hours for targeted library construction Up to 6144 amplicons in one tube with simple PCR Flexibility and cost-effectiveness with different chips to match throughput needs 8

9 Ion AmpliSeq Ready-to-Use DNA Panels Cancer Hotspot Panel v2 50 genes >2,800 COSMIC Mutations 207 Amplicons 10 ng DNA input Comprehensive Cancer Panel 409 Genes 16,000 Amplicons 40 ng DNA input Inherited Disease Panel 700 Diseases 328 Genes 10,000 Amplicons 30 ng DNA input 9

10 Ion AmpliSeq Community Panel Designs BRCA 1&2 Panel 2 genes 167 amplicons available now Colon and Lung Cancer Panel 22 genes 90 amplicons AML Research Panel Coding regions of known mutations 21 genes Cardio Research Panel All exons and UTRs 62 genes coming soon CFTR Research Panel All exons, intron-exon boundaries, and UTRs 1 gene TP53 Research Panel All exons and UTRs 1 gene 10

11 Ion AmpliSeq Designer 3.0 DNA Pipeline Up to 6144 amplicons per pool (up to 5Mb submission) User selectable padding around exons Improved coverage Mouse DNAPanels Target your mouse genes of interest The same proven DNA pipeline Start with mouse gene symbols or mm10 coordinates Human RNA Panels Relative quantification of your transcripts of interest From 12 to 1200 amplicons in a single pool Coverage Analysis plugin quantifies amplicon abundance 11

12 Ion AmpliSeq RNA Panels RNA Cancer Research Panel 50 genes Corresponds to genes in Ion AmpliSeq Cancer Hotspot v2 RNA Apoptosis Panel 267 genes TaqMan validated 12 RNA Custom Panels Over 20,000 human genes with thorough coverage of the coding genome 1200 genes in single tube 5ng FFPE or 500pg unfixed RNA Custom pools are designed using Ion AmpliSeq Designer

13 Ion AmpliSeq Exome 13

14 Ion AmpliSeq Exome ~294,000 primer pairs across 12 primer pools >24,500-plex PCR! ~2.4 M PCRs per plate of 8 exomes!! Total DNA input as low as 50 ng Covers >97% of CCDS (Release 12) >19,000 coding genes, >198,000 coding exons, no UTRs, mirnas, or ncrnas ~85% of human disease-causing variants found in coding regions or splice junctions 1 Amplicon size range bp Average insert size is ~202 bp 14

15 Ion AmpliSeq Exome Library Workflow Amplify target Digest primers Ligate adapters Amplify library (optional) Simplest, fastest exome enrichment workflow Total DNA input as low as 50 ng 6 hours for exome library 12 pools collapse to 1 well / sample for all steps after amplification qpcr is recommended method of quantitation for best barcode balancing High uniformity 90% at 20% of the mean High specificity 90% bases on-target 15

16 Ion AmpliSeq Exome Dataset NA12878 sample sequenced on half Ion PI Chip v2 16

17 Ion AmpliSeq Exome Certified Service Provider Edge/GeneDx Maryland Sick Kids Toronto, Canada Roswell Park Cancer Institute Buffalo Claritas Genomics Boston Selah Genomics South Carolina Memorial Sloan Kettering Cancer Center New York Cedars Sinai Los Angeles University of British Columbia, Vancouver, Canada 17

18 Ion AmpliSeq Data Flow and Analysis 18

19 The Bottleneck 19

20 Ion Reporter Software Simple push button informatics enables any lab to do next generation sequencing Direct integration with the sequencer Automated analysis from data generation to annotated variants Bioinformatics expertise not required 20 Two solutions optimized to fit your needs

21 Ion Reporter Software Workflows Preconfigured analysis workflows for your most common experimental designs. Single Sample Analysis What s different from a reference genome? Paired Analysis How do the variants differ between these two samples? Somatic Paired Analysis What variants exist in a tumor but not the germline sample? Trio Analysis for Inherited Diseases Explore variation across families. 21

22 Design, Sequence, Report Complete workflow taking you from design to interpretation & confirmation Your Sample Ion AmpliSeq Designer Torrent Suite Software Ion Reporter Software > > > Explore your SNPs, InDels, and CNVs Every variant is richly annotated dbsnp COSMIC OMIM SIFT / Polyphen Gene Ontology Pfam Custom Annotations and more. 22

23 Ion Reporter Software CNVs Detect copy number changes in paired AmpliSeq and low-pass whole genome applications acgh: -5,-22 Ion Reporter Software: Ion AmpliSeq Panel Paired sample analyses enable you to detect SNPs, Indels, and CNVs in one analysis workflow Detect CNVs of 100Kb or larger Low-pass whole-genome Detect large chromosomal abnormalities with just 0.05X coverage Detect CNVs of 20Mb or larger 23 Ion Reporter Software allows you to detect copy number changes with up to 100% sensitivity when compared to acgh

24 What s coming next? 24

25 Ion Chef System 25 The content provided herein may relate to products that have not been officially released and is subject to change without notice

26 Ion Chef System* Simple, High Throughput, Modular Benchtop Sequencing Preparation 15 minutes total hands on HEIGHT 22 in (55 cm) Minimizes sources of user-introduced variability Helps save time and labor Library to Loaded Chips for Ion PGM and Proton systems WIDTH 28 in (71 cm) DEPTH 28 in (71 cm) *The content provided herein may relate to products that have not been officially released and is subject to change without notice 26

27 Ion Chef System: Workflow Semi-automated Ion OneTouch 2 System Post Library Prep Fully-automated Ion Chef System Post Library Prep OneTouch 2 Ion Chef ES PGM PGM Start Run Start Run 27

28 Ion Chef System: Simple Workflow Ion Chef Samples in Loaded Chips Data Template Prep & Chip Loading Ion PGM Sequencing Data 28 Start Run

29 Ion Chef System Availability Dec 2013 Early Access PGM 200bp Kits March 2014 Broad commercial release PGM 200bp Kits Ion PI v3 kits 2013 Q Q Q2 29 The content provided herein may relate to products that have not been officially released and is subject to change without notice

30 Ion Hi-Q Chemistry *The content provided herein may relate to products that have not been officially released and is subject to change without notice 30

31 Systematic Errors Reduced by 90% SysEr=0.224% SysEr=0.027% 31

32 Dramatic Improvement as seen in IGV Kit New 32

33 Accurate for more bases New Hi-Q Chemistry for a 420 bp run on the Ion PGM System Q Score Q30 Download data today at Ion Community 33

34 Hi-Q Chemistry Availability New Highly Accurate Sequencing Enzyme Nov 2013 Technology Access Launch Register at Ion Community Web Site 2013 Q Q Q2 New Highly Accurate Sequencing Enzyme July 2014 Commercial Launch 34

35 Ion Rapid Isothermal Template Prep The content provided herein may relate to products that have not been officially released and is subject to change without notice 35

36 Template Preparation Matched to the Speed of Ion Sequencing 36

37 Template Preparation Matched to the Speed of Ion Sequencing Up to 75% reduction in template prep time* Reaction Setup 1. Rehydration buffer 2. ISPs + library 3. Primer Mix 4. Start Solution Post Reaction Clean-Up 1. Stop Solution 2. 2X Wash 3. Ion OneTouch ES Enrichment 40 C for 30 minutes Thermal Cycler/Block Pre-amplification area Post-amplification area 10 min setup 15 min wash & setup + 50 min ES time Total Time < 2 hrs * depending on library size. The content provided herein may relate to products that have not been officially released and is subject to change without notice 37

38 Reproducible, High Quality Templating E. coli DH10b 510bp Insert * Read Length Histogram Clonality Total Number Reads 4,391,892 4,603,216 5,794,279 Total Number of Bases: 1.437G 1.726G 2.305G Mean Read Length: [bp] GC Percentile Proportional Similarity Average Raw Read Accuracy 99.20% 99.31% 99.41% *Ion Torrent R&D data 38

39 The content provided herein may relate to products that have not been officially released and is subject to change without notice. Start sequencing now at lifetechnologies.com/iontorrent For Research Use Only. Not for use in diagnostic procedures. 39

40 The content provided herein may relate to products that have not been officially released and is subject to change without notice. For Research Use Only; Not for use in diagnostic procedures. All data shown in this presentation was generated by Life Technologies 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. The content provided herein may relate to products that have not been officially 40 released and is subject to change without notice

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