Ion Torrent Semiconductor Sequencing for Life. A billion years of evolution meets a trillion dollars of investment

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1 Ion Torrent Semiconductor Sequencing for Life 1 A billion years of evolution meets a trillion dollars of investment

2 Translating Biological to Digital Information DNA Protein Cell X-rays/Light The Monolithic Idea Semiconductor Sequencing A C G His Asp Ser Leu Cys Ile T Biological Information Digital information

3 Sanger Chain Terminating methods 3 Modern Molecular Biology

4 Smith Automated fluorescent Sanger Sequencing 4 Smith 1986 The Human Genome

The Monolithic Idea Applied to Sequencing Planar

Cloning by Limiting Dilution + Solid Phase

Texas Instruments and Robert Noyce of Fairchild

Detection by light on monolithic Substrate Enabled

5 The Monolithic Idea Applied to Sequencing Planar Transistor Jean Hoerni at Fairchild Semiconductor Cloning by Limiting Dilution + Solid Phase Sequencing Early Integrated Circuit Jack Kilby of Texas Instruments and Robert Noyce of Fairchild Semiconductor & Gordon Moore of Moore s law Detection by light on monolithic Substrate Enabled massively parallel sequencing Walt, Lloyd Rothberg 1999 Individual Genomes

6 And the Next-Gen Sequencing Age The box is the Machine Next-Gen Defined

7 Starting with the First Post Sanger Genome This is is going to to be big Richard Richard Gibbs Gibbs I I think doing a whole bacterium will will be be a challenge Edward Edward Rubin Rubin Rothberg 2003

8 And an Explosion in Discovery Microbial Genomes MicroRNAs Metagenomics Ancient DNA Transciptomes and Gene Regulation citations: From Genome Structure to Honey Bees

9 The New Age of Molecular Diagnostics for Microbial Agents : Our Diseases Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Unbiased high-throughput sequencing was proven to be a new tool for the discovery of pathogens. The use of this high-throughput sequencing during an outbreak of disease facilitated the identification of a new arenavirus transmitted through solid-organ transplantation. Rothberg with Ian Lipkin

Samples were collected by USDA and Penn State from a large number of sites over three years.

10 Honey Bee Mystery: Our Ecosystem Colony collapse disorder resulted in a loss of 50-90% of colonies in beekeeping operations. Samples were collected by USDA and Penn State from a large number of sites over three years. Sequencing associated Israeli Acute paralysis Virus (IAPV), an unclassified dicistrovirus with the collapse of the hives. Rothberg with Ian Lipkin 1 0

11 Neanderthal Genome: Our Origins Sequencing of the Neanderthal Genome Identifying the genes that make modern human s unique Rothberg & Paabo

reads Rothberg, Wheeler, Gibbs Diploid Genome 98.

12 Culminating with: First Individual Human Genomes 8 x genome coverage 24.5 Billion Bases 234 Runs (over 2 months) 106 million high quality 230 base long reads Rothberg, Wheeler, Gibbs Diploid Genome 98.7% Coverage 1% of Euchromatic Genome missing from public Databases Good estimate of heterochromatin and genome size Individual Genomes

13 Disruptive Technology Main Frame Mini Computer Personal Computer Sanger Sequencing Next Gen Sequencing Ion Semiconductor Sequencing 13

14 Portal between Chemical and Digital Worlds DNA Protein Cell A C G His Asp Ser Leu Cys Ile T Biological Information Ion Semiconductor Chip The Chip is the Machine Digital information 14 DO NOT DUPLICATE

First Personal Genome Sequencer Complete solution 1. Lowest entry cost 2. Lowest cost per experiment 3. Fastest turn around time 4. High throughput 5. Long reads at high accuracy 6.

15 First Personal Genome Sequencer Complete solution 1. Lowest entry cost 2. Lowest cost per experiment 3. Fastest turn around time 4. High throughput 5. Long reads at high accuracy 6. Simplest operation 7. Compatible with existing libraries & software 8. Ultra-reliable & Upgradable 9. Built with diagnostics in mind 10. And It s all Yours ION inside 15 DO NOT DUPLICATE

16 The History of ION Semiconductor Sequencing First Ion sensitive semiconductor device: P. Bergveld, Development of an ion-sensitive solid-state device for neurophysiological measurements, IEEE Trans. Biomed. Eng. BME-17 (1970) First Detection of Polymerization with Isfet: T. Sakurai, Y. Husimi, Real-time monitoring of DNA polymerase reactions by a micro ISFET ph sensor, Analytical Chemistry, Vol. 64, No. 17. (1 September 1992), pp ISFET using standard CMOS: Bausells J. Cmbina I. Emchid A, Medos A, Ion-sensitive field effect transistors fabricated in a commercial CMOS technology, Sensors and Actuators B: Chemical, vol. 57, no. 1-3, pp , Imaging ph in a small array: K. Sawada, S. Mimura, M. Ishida, et al., Novel CCD based ph imaging sensor, IEEE Trans. ED 46 (9) (1999) Small ISFET Arrays in CMOS for cell based assays: M.J. Milgrew, P.A. Hammond, D.R.S. Cumming, The development of scalable sensor arrays using standard CMOS technology, Sens. Actuators B 103 (2004) ION Chips & Semiconductor sequencing (first large, dense, fast arrays, first de novo DNA sequencing): ION Torrent DO NOT DUPLICATE

17 Isfet - P. Bergveld 17 DO NOT DUPLICATE

18 2007 ION CHIP Ion Torrent 18 The Chip is the Machine DO NOT DUPLICATE

Speed Leverages Trillion dollar investment and $50 billion annual spend on semiconductor

19 Leveraging Semiconductor Technology Scalability CMOS technology 40 years of Moore s law Simplicity Natural nucleotides No lasers No optics No camera No fluorescence No enzyme cascade Speed Leverages Trillion dollar investment and $50 billion annual spend on semiconductor design, manufacturing and packaging technology. 19 Real-time detection of sequence extension DO NOT DUPLICATE

20 Simple Natural Chemistry Eliminate source of sequencing errors: Modified bases Fluorescent bases Laser detection Enzymatic amplification cascades H+ Eliminate source of read length limitations: Unnatural bases Faulty synthesis Protect/de-protect Slow cycle time Sequence is determined by measuring hydrogen ions released (1 per base added per DNA strand) during 2nd strand synthesis when complementary base (A, C, G or T) are sequentially incorporated by DNA polymerase. 20 DO NOT DUPLICATE

21 Fast Direct Detection dntp H + ph Q DNA Ions Sequence Nucleotides flow sequentially over Ion semiconductor chip One sensor per well per sequencing reaction Direct detection of natural DNA extension Millions of sequencing reactions per chip Fast cycle time, real time detection Sensing Layer Sensor Plate V Bulk Drain Source Silicon Substrate To column receiver 21 Confidential and Proprietary DO NOT DUPLICATE

22 Ion Chips Read Themselves Selected pixel Millions of parallel sensors per Ion Chip. Row select register Sensor array Array read at up to 60 times per second never miss a base, unparallel accuracy. Column select register Output driver Column receivers and multiplexer To reader board Moore s law scaling - Chips get denser and arrays get larger, without increase in cost, or time per read. Doubling the number of reads no longer require more reading time The Chip is the Machine. 22 DO NOT DUPLICATE

Wells are in perfect register with sensors 1 read per well.

23 and Unprecedented Scalability Ion 314: Millions of parallel wells 400 fit on the end of a human hair. Wells are in perfect register with sensors 1 read per well. Sensors can be made smaller and arrays can be made larger. 23 DO NOT DUPLICATE

55 million sensor Ion Chip (314). Wash Nucleotide Flow Wash Single well sequencing trace. ~2 seconds per incorporation.

24 Fast Direct Detection: Never Miss a Base Curve Fit to Incorporation Signal Allows lossless compression of data, for the most efficient data collection possible and most accurate base calling. Sigma=0.125s Tau=1.04s Chemical Images of 100 x 100 region of a 1.55 million sensor Ion Chip (314). Wash Nucleotide Flow Wash Single well sequencing trace. ~2 seconds per incorporation. 100 s of observations per incorporation. Eliminate the sources of data overload and major source of error: image collection, storage & analysis. 24 DO NOT DUPLICATE

25 Wafer-level Fabrication 25 DO NOT DUPLICATE

26 Robotic, Low Cost Assembly, Disposable Chips From wafer to finished Ion chip without human contact to meet any demand. Robotic dicing, die attach, and flow cell attachment. Price drops exponentially with volume. 26 DO NOT DUPLICATE

27 Convenient to Use Pin Grid Array Land Grid Array Low cost, convenient, single use device. Easy to sequence: put in chip, load sample, pull lever down, press GO. Match the size of the Ion chip to your application. 27 DO NOT DUPLICATE

28 Personal Computer The chip is the machine Desk top convenience, real-time sequence, semiconductor cost structure. Built with diagnostics in mind: FDA registered facility. ISO Certified. 28 DO NOT DUPLICATE

29 Simplicity, Speed, Scalability Built to last, built to meet any demand. Built with diagnostics in mind: FDA registered facility, ISO Certified. 29 DO NOT DUPLICATE

30 Simple, Reliable, Electronic Chip Reader Non-optical sequencing instrument (11 x 7.5 ). Unparalleled ability to manufacture at low cost. Extreme Reliability, Robustness, Shock resistance. Complete flexibility in form factor, and operating environment. 30 DO NOT DUPLICATE

31 Dial in performance As chips get denser, faster, and more sensitive sequence gets better and better 31 Confidential and Proprietary DO NOT DUPLICATE

32 First Post-Light Genome 34,000 Base pair genome 59x Coverage 100% of Genome % Consensus Accuracy (Q61) 10 Times better than current accuracy standards Adenovirus Post-light Sequencing 32 DO NOT DUPLICATE

coli Experiment Sequence three bacterial genomes with varying GC content to

33 Investigating Systematic Performance Vibrio fischeri Bacterium Percent GC Vibrio fischeri 38% E. coli 51% R. palustris 65% E. coli Experiment Sequence three bacterial genomes with varying GC content to 5X coverage. Analysis Uniform coverage for any GC content. Rhodopseudomonas palustris 33 DO NOT DUPLICATE

34 Escherichia coli K12 Single 314 Run 4.6Mb Genome 8.4x Coverage 99.7% of Genome covered 99.8+% Accuracy 51% G+C 34 Confidential and Proprietary DO NOT DUPLICATE

Rhodopseudomonas palustris - 314 Run 5.5Mb Genome 4.5x Coverage 97.

35 Rhodopseudomonas palustris Run 5.5Mb Genome 4.5x Coverage 97.4% of Genome covered 99++% Accuracy 65% G+C 35 Confidential and Proprietary DO NOT DUPLICATE

Read Number, Quality, Coverage RUN NAME B15 45 B14 40 B6 237 Q17 coverage 99.82 99.67 99.

35,285,919 38,166,121 Q20 coverage 99.51 99.08 99.

36 Read Number, Quality, Coverage RUN NAME B15 45 B14 40 B6 237 Q17 coverage Q17 406, , , Q17 198, , ,802 Q17 bases 39,429,389 35,285,919 38,166,121 Q20 coverage Q20 316, , , Q20 150, , ,892 Q20 bases 32,167,707 28,509,040 30,512, Confidential and Proprietary

37 Consensus Accuracy (Single 314 Run) Qscore of Mean Error Q30 1 error per 1,000 bases Q40 1 error per 10,000 bases coverage 37 Confidential and Proprietary DO NOT DUPLICATE

38 Consensus Accuracy (Two 314 Runs) Qscore of Mean Error Q30 1 error per 1,000 bases Q40 1 error per 10,000 bases Q50 1 error per 100,000 bases coverage 38 Confidential and Proprietary DO NOT DUPLICATE

39 Progress on Read Length April July Oct Q7 Read Q10 Read Q17 Read LQ20 Read Perfect Read Confidential and Proprietary

40 Coming Soon to you $49,000

41 41

42 Small & Fast: 3.5 um wells 400* reads fit on the end of a human hair. Millions of parallel sensors fit on an Ion chip. High Quality Sequence. ~4 Seconds per incorporation *3.5 micron well at 5.1 micron pitch 42 DO NOT DUPLICATE All the data today

43 Smaller & Faster: 1.3 um wells 4000* reads fit on the end of a human hair. 100 s of Millions of parallel sensors fit on an Ion chip. Sequence quality improves sequencing gets faster. <2 Seconds per incorporation *1.3 micron well at 1.5 micron pitch 43 DO NOT DUPLICATE

44 What Does Moore s Law Mean to ION Ion 314/316 Well Ion in new Foundry 454 Well DO NOT DUPLICATE

45 Ion Torrent: Why It s Inevitable 1 Semiconductor devices scale, making larger chip sizes routine, and higher densities inevitable. 2 Semiconductor manufacturing is focused on reducing the cost per chip, ensuring production and assembly at costs not attainable with other manufacturing methods. 3 Direct detection of polymerization (no modified bases, fluorescent modifications, or enzymatic detection) enables fast run times, lowest possible reagent costs, highest completion of the polymerization event, and most linear detection. Highest completion yields most accurate and longest sequencing reads. 4 No optical systems, or external scanners, means lowest instrument costs, highest densities, efficient capture of information, and higher throughput. 5 Doubling the number of reads, or chips no longer require more reading time The Chip is the Machine. 45 DO NOT DUPLICATE 6 In the limit, sequencing is really about moving chemical data to the digital realm. 7 ION Sequencing direct semiconductor sequencing allows the highest bandwidth transfer of this information per unit dollar.

46 46 Gordon Moore James D. Watson

Matthew Tinning Australian Genome Research Facility. July 2012

Next-Generation Sequencing: an overview of technologies and applications Matthew Tinning Australian Genome Research Facility July 2012 History of Sequencing Where have we been? 1869 Discovery of DNA 1909