Next Generation Sequencing Technologies in Medical Genetics

SpringerBriefs in Genetics For further volumes: http://www.springer.com/series/8923 C. Alexander Valencia • M. Ali Pervaiz Ammar Husami • Yaping Qian • Kejian Zhang Next Generation Sequencing Technologies in Medical Genetics C. Alexander Valencia Division of Human Genetics Cincinnati Children’s Hospital Medical Center Cincinnati, OH, USA Ammar Husami Division of Human Genetics Cincinnati Children’s Hospital Medical Center Cincinnati, OH, USA M. Ali Pervaiz WellStar Douglas Hospital WellStar Health System Douglasville, GA, USA Yaping Qian Division of Human Genetics Cincinnati Children’s Hospital Medical Center Cincinnati, OH, USA Kejian Zhang Division of Human Genetics Cincinnati Children’s Hospital Medical Center Cincinnati, OH, USA ISSN 2191-5563 ISSN 2191-5571 (electronic) ISBN 978-1-4614-9031-9 ISBN 978-1-4614-9032-6 (eBook) DOI 10.1007/978-1-4614-9032-6 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2013949287 © C. 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Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface The purpose of this book is to serve as an introduction to those that want to learn about next-generation–sequencing (NGS) and its applications. However, from the middle to end of each chapter a more in-depth approach will be taken to satisfy the curious minds of professionals in the fields of medical genetics and other related disciplines. Most chapters will contain one figure or table illustrating principles or summarizing key findings in the field. A book search on Amazon and Google on “next-generation–sequencing” leads to book hits covering a wide range of topics including (1) NGS methods, (2) NGS informatics, (3) application to microRNA expression profiling, (4) application to personalize medicine, (5) application to plant sciences, and (6) challenges and opportunities of NGS for biomedical research. However, none of these books describes the direct application of NGS to medicine, specifically, laboratory medicine or molecular diagnostics. This book will bridge the gap between research and direct application to patient care. I foresee this book as the first, of many to come, translation medicine books in this field. Moreover, being a part of the Briefs in Genetic series will allow the reader to quickly become familiar with the technologies and most importantly their clinical applications. Furthermore, throughout the book the recent developments are briefly summarized. In this book (Part I), we introduce the reader to the wealth of next-generation technologies followed by their direct applications (Part II) in the diagnosis of genetic disorders in the field broadly known as medical genetics. We will separate Parts I and II equally because this will allow a more in-depth description of the technologies for those that require a more profound understanding of the technologies. The equal space split, Part II, will provide the opportunity to describe the applications of NGS to molecular diagnostics by starting with a comprehensive view of the genetic disorders that have been analyzed by these technologies and then we focus on several of these genetic disorder examples including muscular dystrophy and hearing loss. Within these disorder-based chapters, we will describe the disorder and how NGS has been an excellent tool for reaching a diagnosis of previously undiagnosed patients. Furthermore, we will discuss the additional NGS v vi Preface benefits, namely, increased sequencing throughput and decreased cost that patients can obtain from these tests. It can be speculated that NGS will become an even more popular platform in laboratory medicine and it can be argued that the technology is here to stay to provide better patient care by reaching a diagnosis sooner. Finally, we will end the book by briefly acknowledging the breakthroughs, in light of eight other chapters that describe the triumphs of the technologies, and focus on the challenges that lie ahead and suggest possible solutions to such challenges. Cincinnati, OH Douglasville, GA C. Alexander Valencia Ammar Husami Yaping Qian Kejian Zhang M. Ali Pervaiz Acknowledgements I would like to take this opportunity to thank all contributors of this book. It was a great pleasure and an enjoyable experience working with you on this project. I would like to express my gratitude to the many people who provided support, talked things over, read, offered comments, and assisted in the proofreading. This book is dedicated to our families, who supported and encouraged us in spite of all the time it took me away from them. C. Alexander Valencia, Ph.D. vii Contents Part I Advances in Next-Generation–Sequencing Technology 1 Sanger Sequencing Principles, History, and Landmarks ........................ 1.1 Historical Overview ........................................................................... 1.2 Principle of Sanger Sequencing ......................................................... 1.3 First-Generation Automated Sanger DNA Sequencing ..................... 1.4 Automated Sequencing Factories....................................................... 1.5 Sequencing the Human Genome ........................................................ 1.6 Overview of Next-Generation–Sequencing and Clinical Applications ................................................................... 1.7 Future Trends ..................................................................................... References ..................................................................................................... 3 3 4 6 6 7 2 A Survey of Next-Generation–Sequencing Technologies ......................... 2.1 Introduction ........................................................................................ 2.2 Fundamentals of NGS Platforms ....................................................... 2.3 Roche/454 Life Sciences.................................................................... 2.4 Illumina/Solexa .................................................................................. 2.5 Applied Biosystems/SOLiD ............................................................... 2.6 Benchtop Sequencers ......................................................................... 2.6.1 Personal Genome Machine (PGM) ........................................ 2.6.2 Illumina’s MiSeq.................................................................... 2.7 NGS Analysis Strategies .................................................................... 2.8 Common Sources of Errors in NGS Data .......................................... 2.9 Clinical Applications of NGS ............................................................ 2.10 Summary ............................................................................................ References ..................................................................................................... 13 13 14 15 16 17 18 18 18 19 20 20 21 22 7 8 9 ix x Contents 3 A Review of DNA Enrichment Technologies............................................. 3.1 Introduction ........................................................................................ 3.2 Non-hybridization-Based Enrichment Methods ................................ 3.2.1 Molecular Inversion Probes ................................................... 3.2.2 Highly Multiplex Droplet PCR .............................................. 3.3 Hybridization-Based Enrichment Methods........................................ 3.3.1 Solid Phase Capture ............................................................... 3.3.2 Solution-Based Capture ......................................................... 3.4 Summary ............................................................................................ References ..................................................................................................... Part II Clinical Applications of Next-Generation–Sequencing 4 Application of Next-Generation–Sequencing to the Diagnosis of Genetic Disorders: A Brief Overview .................................. 4.1 Introduction ........................................................................................ 4.2 Congenital Disorders of Glycosylation.............................................. 4.3 Colon Cancer ..................................................................................... 4.4 Mitochondrial Diseases...................................................................... 4.5 Cardiovascular Diseases .................................................................... 4.6 Ophthalmic Disorders ........................................................................ 4.7 Hematological Disorders ................................................................... 4.8 Primary Ciliary Dyskinesia ................................................................ 4.9 Urea Cycle Disorders ......................................................................... 4.10 Summary ............................................................................................ References ..................................................................................................... 5 25 25 27 27 27 28 28 29 30 30 Next-Generation–Sequencing-Based Noninvasive Prenatal Diagnosis....................................................................................... 5.1 Introduction ........................................................................................ 5.2 Trisomy 21, a Common Aneuploidy .................................................. 5.3 Methods for the Detection of cffDNA ............................................... 5.4 Principle of Aneuploidy Detection with Next-Generation–Sequencing .................................................... 5.5 Noninvasive Diagnosis of Fetal Aneuploidy by Shotgun Sequencing DNA ............................................................ 5.6 Noninvasive Prenatal Diagnosis of Fetal Chromosomal Aneuploidy by Next-Generation–Sequencing ................................... 5.7 Noninvasive Prenatal Diagnosis of Fetal Chromosomal Aneuploidy Using Different Next-Generation–Sequencing Strategies and Algorithms .................................................................. 5.8 Single Molecule Sequencing for the Detection of Trisomy 21 .......... 5.9 Factors Affecting Next-Generations–Sequencing for Aneuploidy Determination ........................................................... 5.10 Limitations of Noninvasive Prenatal Screening ................................ 5.11 Summary ............................................................................................ References ..................................................................................................... 35 35 36 37 37 38 39 40 41 41 42 42 45 45 46 46 47 49 50 50 51 52 52 53 53 Contents 6 Diagnosis of Inherited Neuromuscular Disorders by Next-Generation–Sequencing ............................................................... 6.1 Introduction .......................................................................................... 6.2 A Broad Neuromuscular Diseases Panel .............................................. 6.3 Next-Generation–Sequencing Panel for Duchenne and Becker, Congenital, and Limb Girdle Muscular Dystrophies ........................... 6.4 Duchenne and Becker Muscular Dystrophy Diagnosis by Next-Generation–Sequencing ......................................................... 6.5 Congenital Muscular Dystrophies Next-Generation– Sequencing Panel ................................................................................. 6.6 Summary .............................................................................................. References ..................................................................................................... 7 Application of Next-Generation–Sequencing in Hearing Loss Diagnosis .......................................................................... 7.1 Introduction .......................................................................................... 7.2 Hearing Loss Syndromes ..................................................................... 7.3 Nonsyndromic Hearing Loss ............................................................... 7.4 Importance of Hearing Loss Detection and Genetic Testing ............... 7.5 Capture-Based Hearing Loss Panels .................................................... 7.5.1 PCR-Based Hearing Loss Panels ............................................. 7.6 Whole Exome Sequencing ................................................................... 7.7 Summary .............................................................................................. References ..................................................................................................... 8 9 Exome Sequencing as a Discovery and Diagnostic Tool .......................... 8.1 Introduction .......................................................................................... 8.2 Classic Gene Discovery Approaches and Limitations ......................... 8.3 Exome Sequencing Necessity for Gene Discovery ............................. 8.4 Exome Sequencing Gene Discovery Applications .............................. 8.4.1 Sequencing of Unrelated Individuals ....................................... 8.4.2 Sequencing of Family Members .............................................. 8.4.3 Implementation of Family-Based Analysis as a Discovery Tool.................................................................. 8.4.4 Exome Sequencing Diagnostic Applications ........................... 8.4.5 Tiered Clinical Exome Analysis............................................... 8.4.6 Clinical Exome Analysis Guided by Clinical Features ............ 8.4.7 Clinical Laboratories Offering Exome Sequencing ................. 8.4.8 Clinical Exome Data and Interpretation Challenges ................ 8.5 Summary .............................................................................................. References ..................................................................................................... xi 57 57 58 60 61 62 64 64 67 67 67 68 69 69 71 72 73 73 75 75 76 77 77 77 78 79 82 82 82 83 83 84 84 Challenges of Next-Generation–Sequencing-Based Molecular Diagnostics................................................................................. 87 9.1 Introduction .......................................................................................... 87 9.2 Sample Processing and Standardization of Capture and Sequencing Platforms.................................................................... 88 xii Contents 9.3 Data Analysis ..................................................................................... 9.3.1 Base Calling ........................................................................... 9.3.2 Reads Alignment .................................................................... 9.3.3 Variant Calling ....................................................................... 9.3.4 Variant Annotation and Filtering ............................................ 9.4 Testing Validation and Revalidation .................................................. 9.5 Quality Management of Next-Generation– Sequencing Testing ............................................................................ 9.6 Reporting and Interpretation .............................................................. 9.7 Informed Consent and Genetic Counseling ....................................... 9.8 Training and Education ...................................................................... 9.9 Cost and Reimbursement ................................................................... 9.10 Summary ............................................................................................ References ..................................................................................................... 88 89 89 89 89 90 91 92 92 93 93 94 94