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Ionseq Genome Sequencing University of Pennsylvania ScholarlyCommons Department of Chemical & Biomolecular Senior Design Reports (CBE) Engineering 4-2013 IonSeq Genome Sequencing Kendrick Chow University of Pennsylvania Tushmit Hasan University of Pennsylvania Gawain Lau University of Pennsylvania Joan Liu University of Pennsylvania Follow this and additional works at: https://repository.upenn.edu/cbe_sdr Part of the Biochemical and Biomolecular Engineering Commons Chow, Kendrick; Hasan, Tushmit; Lau, Gawain; and Liu, Joan, "IonSeq Genome Sequencing" (2013). Senior Design Reports (CBE). 55. https://repository.upenn.edu/cbe_sdr/55 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/cbe_sdr/55 For more information, please contact [email protected]. IonSeq Genome Sequencing Abstract The emergence of advanced DNA sequencing methods has presented disruptive opportunities in biotechnology, establishing the foundation for the personalized medicine industry. Since the completion of the Human Genome Project, the number of genomes sequenced has grown exponentially and the sequencing price has dropped precipitously. To make personalized medicine a reality, there is a need for a large collection of sequenced genomes in order to link specific genes ot diseases. IonSeq seeks to be the leading DNA sequencing service, employing new semiconductor- based sequencing technology offered by Ion Torrent, to help pharmaceutical companies generate these libraries of genomes for their drug- development processes. To support sequencing reliability and throughput, IonSeq will explore such technical details such as chip configuration, insertion kinetics, signal generation, base-calling methods, and accuracy metrics. IonSeq will prove a 40 genome/day output, made possible by the massively parallel procedure employed by the sequencers. IonSeq will sequence each genome at a price of $2,000 while the cost of ‘manufacture’ will only be $645. Series A will consist of a $3,682,886 investment and will yield the investors a MIRR of 102.98% over four years. The Series B investment will total $4,510,491 and result in a 93.43% MIRR over a three period. The NPV by the time of liquidation or acquisition event will be $39,322,347, at a conservative projected growth rate of 5%. Disciplines Biochemical and Biomolecular Engineering | Chemical Engineering | Engineering This working paper is available at ScholarlyCommons: https://repository.upenn.edu/cbe_sdr/55 IonSeq Genome Sequencing Kendrick Chow Tushmit Hasan Gawain Lau Joan Liu Project Advisor: Dr. John C. Crocker Professor Leonard A. Fabiano Department of Chemical and Biomolecular Engineering University of Pennsylvania April 9, 2013 Kendrick Chow Tushmit Hasan Gawain Lau Joan Liu 3300 Walnut St Philadelphia, PA April 9, 2013 Dr. Leonard Fabiano Dr. Warren Sieder Dr. John Crocker University of Pennsylvania, Chemical and Biomolecular Engineering Room 311A Towne Building 220 South 33rd Street University of Pennsylvania Philadelphia, PA 19104-6393 Dear Sirs, The following enclosure is a detailed design of our solution to the proposed problem: “Scalability of DNA Sequencing with Moore’s Law.” As a solution to this problem we have designed a biotechnology start-up company, IonSeq, which sequences whole human genomes as a service. The enclosed report documents our entire design process and decisions that were made during the formulation of this process. The report also contains a competitive analysis, market analysis, and financial models of the start-up company. This report contains all necessary information for hypothetical start-up scientists and engineers, whom could, with the use of this report, design a working prototype for IonSeq as per this project’s specifications. This report also provides all necessary information that a potential investor in IonSeq would require in order to make an investment decision for the company’s future. We submit this report for your review with our strongest recommendations of the success of IonSeq. Sincerely, __________________________________ __________________________________ Kendrick Chow Gawain Lau __________________________________ __________________________________ Tushmit Hasan Joan Liu TABLE OF CONTENTS 1. Abstract ................................................................................................................................................ 1 2. Introduction ....................................................................................................................................... 3 2. A. Purpose of Genome Sequencing ......................................................................................................................... 4 2. B. Basics of Genome Sequencing .............................................................................................................................. 5 2. C. History of Genome Sequencing ........................................................................................................................... 7 2.C.i. First Generation Advancements in Genome Sequencing .................................................................... 7 2.C.ii. Next Generation Genome Sequencing ....................................................................................................... 9 2.C.iii. The Human Genome Project ...................................................................................................................... 10 2.C.iv. The Archon Genomics X Prize ................................................................................................................... 11 2. D. Project Goals and Requirements ...................................................................................................................... 12 2.D.i. IonSeq Report Roadmap ................................................................................................................................ 13 3. Company Background: Creation of IonSeq ............................................................................ 15 3.A. Ion Torrent ................................................................................................................................................................. 15 3.A.i. Overview of Ion Torrent Technology ....................................................................................................... 16 3.A.ii. Ion Technology vs. Everything Else ......................................................................................................... 17 3.A.iii. Customer Needs Analysis ........................................................................................................................... 18 3.A.iv. Technical Requirements .............................................................................................................................. 18 4. Pre-Sequencing................................................................................................................................ 19 4.A. Pre-Sequencing Preparations ............................................................................................................................. 19 4.A.i. DNA Collection ................................................................................................................................................... 20 4.A.ii. DNA Extraction ................................................................................................................................................. 20 4.A.iii. DNA Fragment Library Preparation ....................................................................................................... 21 4.A.iii.1) DNA Fragmentation ............................................................................................................................. 21 4.A.iii.2) End Repair ............................................................................................................................................... 22 4.A.iii.3) Adapter Ligation, Nick Repair, and Barcoding .......................................................................... 22 4.A.iii.4) DNA Purification ................................................................................................................................... 23 4.A.iii.5) Size Selection and Library Quantitation ...................................................................................... 23 4.A.iv. Template Preparation using Emulsion PCR (emPCR) ..................................................................... 24 4.A.iv.1) Clonal Amplification and Sample Recovery ............................................................................... 24 4.B. Pre-Sequencing Results ........................................................................................................................................ 25 5. Chip Configuration, Workflow, and Throughput ................................................................. 27 5.A. Manufacturing Node, Die Size, and Other Chip Specifications .............................................................. 27 5.B. Reverse Engineering Proton II Specifications .............................................................................................. 29 5.C. Chip Flow Processes ................................................................................................................................................ 32 5.C.i. Nucleotide Flow In ............................................................................................................................................ 32
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