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UNIVERSITY of CALIFORNIA, SAN DIEGO The UNIVERSITY OF CALIFORNIA, SAN DIEGO The Genetics and Epigenetics of Induced Pluripotent Stem Cells A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Athurva Jayavant Gore Committee in charge: Professor Kun Zhang, Chair Professor Adam Engler Professor Lawrence S. B. Goldstein Professor Xiaohua Huang Professor Alysson Muotri 2013 Copyright Athurva Jayavant Gore, 2013 All rights reserved. SIGNATURE PAGE The Dissertation of Athurva Jayavant Gore is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ____________________________________________________________________ ____________________________________________________________________ ____________________________________________________________________ ____________________________________________________________________ ____________________________________________________________________ Chair University of California, San Diego 2013 iii DEDICATION For my wife, my parents, and my brother. Thank you for all your support. iv TABLE OF CONTENTS TABLE OF CONTENTS SIGNATURE PAGE..................................................................................................... iii DEDICATION............................................................................................................... iv TABLE OF CONTENTS................................................................................................v LIST OF FIGURES ...................................................................................................... xi LIST OF TABLES .......................................................................................................xiii ACKNOWLEDGEMENTS.......................................................................................... xiv VITA...........................................................................................................................xvii ABSTRACT OF THE DISSERTATION.....................................................................xviii Chapter 1: Introduction .................................................................................................1 1.1 Next Generation Sequencing ...........................................................................1 1.2 Targeted Sequencing.......................................................................................3 1.3 Bisulfite Sequencing.........................................................................................5 1.4 Induced Pluripotent Stem Cells........................................................................7 1.5 Scope of the Dissertation .................................................................................8 Chapter 2: Library-Free Bisulfite Sequencing with Padlock Probes ...........................11 2.1 Abstract ..........................................................................................................11 2.2 Introduction ....................................................................................................11 2.3 Methods .........................................................................................................13 2.3.1 Bisulfite padlock probe production (Agilent) ............................................13 2.3.2 Bisulfite padlock probe production (LC Sciences)...................................14 2.3.4 Sample preparation and capture .............................................................15 v 2.3.5 Capture circles amplification (Library-free protocol, Agilent)...................16 2.3.6 Capture circles amplification (Library-free protocol, LC Sciences)..........16 2.3.7 Primer barcode design for multiplexing ...................................................16 2.3.8 Bisulfite read mapping and data analysis................................................17 2.3.9 Correlation of methylation levels between two samples..........................17 2.3.10 Analysis of differential methylation ........................................................18 2.4 Results ...........................................................................................................18 2.5 Conclusions....................................................................................................23 2.6 Acknowledgements ........................................................................................24 Chapter 3: Identification of Coding Mutations in Induced Pluripotent Stem Cells ......40 3.1 Abstract ..........................................................................................................40 3.2 Introduction ....................................................................................................40 3.3 Methods .........................................................................................................42 3.3.1 CV fibroblast derivation ...........................................................................42 3.3.2 CV-hiPS-B and CV-hiPS-F derivation .....................................................42 3.3.4 CV-hiPS characterization ........................................................................43 3.3.5 dH1F-iPS8 and dH1F-iPS9 derivation.....................................................44 3.3.6 hiPS 11a, 11b, 17a, 17b, 29A and 29e derivation...................................44 3.3.7 HFFxF fibroblast derivation .....................................................................46 3.3.8 FiPS3F1 and FiPS4F7 generation ..........................................................46 3.3.9 FiPS3F1 and FiPS4F7 characterization ..................................................47 3.3.10 CF-Fib, CF-RiPS1.4 and CF-RiPS1.9 derivation ..................................48 3.3.11 FiPS4F2 and FiPS4F-shpRb4.5 plasmid construction ..........................49 3.3.12 FiPS4F2 and FiPS4F-shpRb4.5 retroviral and lentiviral production......49 3.3.13 FiPS4F2P9, FiPS4F2P40 and FiPS4F-shpRb4.5 derivation ................50 vi 3.3.14 FiPS4F2 and FiPS4F-shpRb4.5 characterization .................................50 3.3.15 Preparation of padlock probes ..............................................................51 3.3.16 Multiplex capture of exonic regions .......................................................52 3.3.17 Amplification of capture circles..............................................................52 3.3.18 Shotgun sequencing library construction ..............................................53 3.3.19 Hybridization capture with DNA or RNA baits .......................................54 3.3.20 Consensus sequence generation and variant calling............................54 3.3.21 Sanger validation of candidate mutations .............................................55 3.3.22 Clonal fibroblast experiments ................................................................56 3.3.23 Digital quantification of mutations..........................................................57 3.3.24 Statistical analysis—probability of mutations occurring naturally ..........59 3.3.25 Statistical analysis—digital quantification..............................................60 3.3.26 Statistical analysis—NS/S mutation ratio ..............................................61 3.3.27 Statistical analysis—pathway and COSMIC gene enrichment..............61 3.4 Results ...........................................................................................................62 3.4.1 hiPS cell lines contain a high level of mutational load.............................62 3.4.2 Reprogramming-associated mutations arise through multiple mechanisms ........................................................................................................64 3.5 Conclusions....................................................................................................68 3.6 Acknowledgements ........................................................................................70 Chapter 4: Functional Consequences of Coding Mutations in Induced Pluripotent Stem Cells ..................................................................................................................79 4.1 Abstract ..........................................................................................................79 4.2 Introduction ....................................................................................................79 4.3 Methods .........................................................................................................81 vii 4.3.1 Cell culture...............................................................................................81 4.3.2 hiPSC generation. ...................................................................................81 4.3.3 Plasmid construction. ..............................................................................82 4.3.4 Retroviral and lentiviral production. .........................................................83 4.3.5 Immunostaining. ......................................................................................83 4.3.6 RNA isolation and real-time PCR analysis. .............................................84 4.3.7 Whole-genome library construction.........................................................84 4.3.8 In-solution hybridization capture with DNA baits. ....................................84 4.3.9 Consensus sequence generation and variant calling..............................84 4.3.10 Sanger validation of candidate mutations. ............................................85 4.3.11 Statistical
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