Next Generation Sequencing Based Clinical Molecular Diagnosis of Human Genetic Disorders

Next Generation Sequencing Based Clinical Molecular Diagnosis of Human Genetic Disorders

Lee-Jun C. Wong Editor Next Generation Sequencing Based Clinical Molecular Diagnosis of Human Genetic Disorders

Editor Lee-Jun C. Wong Molecular Diagnostic Laboratory Baylor College of Medicine Houston, Texas, USA ISBN 978-3-319-56416-6 DOI 10.1007/978-3-319-56418-0 ISBN 978-3-319-56418-0 (ebook) Library of Congress Control Number: 2017939356 Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface Recent development of high-throughput next generation sequencing (NGS) technology has transformed the way DNA-based molecular diagnostic testing is performed in clinical laboratories. In the past few years, clinically validated NGS has been applied to routine molecular diagnosis of human genetic diseases. In this book, we review the outcome of NGS in clinical practice. Pitfalls of traditional PCR-based Sanger sequencing can be overcome by NGS. This book first reviews the technologies of NGS and their advantages over traditional Sanger sequencing and why NGS has become the new gold standard for clinical molecular diagnosis. In addition, clinically validated deep NGS can accurately detect not only single nucleotide variants (SNVs) but also copy number variants (CNVs). The ability to simultaneously detect and quantify SNVs and CNVs in multiple genes makes NGS an ideal comprehensive approach for molecular diagnosis. Applications of NGS to genetic analysis of various disease areas, such as metabolic disorders, retinal disease, hearing impairment, primary immunodeficiency, bone disorders, hereditary cancer, RASopathies, complex neuromuscular disorders, diabetes, cardiovascular genetic diseases, mitochondrial DNA-related disorders, whole exome sequencing in clinical setting, family-based studies, and carrier screening, are described in individual chapters. The complete coverage of clinical utility of NGS is of course beyond the scope of this book. We hope that through the examples described in this book, readers will have an overview of how NGS is utilized in clinical diagnostic laboratories. I am indebted to contributing authors who have made this book possible. Houston, Texas, USA Lee-Jun C. Wong v

Contents Overview of the Clinical Utility of Next Generation Sequencing in Molecular Diagnoses of Human Genetic Disorders................... 1 Lee-Jun C. Wong Detection of Copy Number Variations (CNVs) Based on the Coverage Depth from the Next Generation Sequencing Data...... 13 Yanming Feng, David Chen, and Lee-Jun C. Wong Next Generation Sequencing (NGS) Based Panel Analysis of Metabolic Pathways........................................... 23 Elizabeth B. Gorman and Lee-Jun C. Wong The Next Generation Sequencing Based Molecular Diagnosis of Visual Diseases............................................... 51 Xia Wang and Richard Alan Lewis Application of Next-Generation Sequencing to Hearing Loss........... 71 Lisa Dyer, Xinjian Wang, Kejian Zhang, John Greinwald, and C. Alexander Valencia Next-Generation Sequencing Based Clinical Molecular Diagnosis of Primary Immunodeficiency Diseases.................... 89 Lijun Wang, C. Alexander Valencia, Rebecca A. Marsh, and Kejian Zhang Next-Generation Sequencing Based Testing for Disorders of the Skeleton................................................. 113 Allison Tam, Victor Wei Zhang, Lee Jun Wong, and Sandesh C.S. Nagamani Diagnosing Hereditary Cancer Susceptibility Through Multigene Panel Testing................................. 123 Holly LaDuca, Shuwei Li, A.J. Stuenkel, Virginia Speare, Jill S. Dolinsky, and Elizabeth C. Chao vii

viii Contents Application of Next-Generation Sequencing in Noonan Spectrum Disorders............................................ 155 Hui Mei, Hongzheng Dai, Jinglan Zhang, Lee-Jun Wong, and Pilar L. Magoulas The Applications and Challenges of Next-Generation Sequencing in Diagnosing Neuromuscular Disorders................. 177 Lijun Wang, Arunkanth Ankala, Hamoud Al Khallaf, Xinjian Wang, Mikhail Martchenko, Biao Dong, Ammar Husami, Kejian Zhang, and C. Alexander Valencia Next-Generation Sequencing for the Diagnosis of Monogenic Disorders of Insulin Secretion.................................... 201 Amy E. Knight Johnson, Siri Atma W. Greeley, and Daniela del Gaudio Application of NGS in the Diagnosis of Cardiovascular Genetic Diseases................................ 243 Guoliang Wang, Vivan Niewiadonski, Jianping Li, Ruirui Ji, Wenxin Zou, Daniel J. Penny, and Yuxin Fan Comprehensive Analyses of the Mitochondrial Genome............... 287 Victor Wei Zhang and Lee-Jun C. Wong Exome Sequencing in the Clinical Setting.......................... 305 Theodore Chiang, Magalie Leduc, Mari Tokita, Teresa Santiago-Sim, and Yaping Yang Family-Based Next-Generation Sequencing Analysis................. 321 Xia Wang, Linyan Meng, and Magalie S. Leduc Next Generation of Carrier Screening............................. 339 Anastasia Fedick and Jinglan Zhang Erratum to:.................................................... E1 Index......................................................... 355