Grand Celebration: 10th Anniversary of the Human Genome Project Volume 3 Edited by John Burn, James R. Lupski, Karen E. Nelson and Pabulo H. Rampelotto Printed Edition of the Special Issue Published in Genes www.mdpi.com/journal/genes John Burn, James R. Lupski, Karen E. Nelson and Pabulo H. Rampelotto (Eds.) Grand Celebration: 10th Anniversary of the Human Genome Project Volume 3 This book is a reprint of the special issue that appeared in the online open access journal Genes (ISSN 2073-4425) in 2014 (available at: http://www.mdpi.com/journal/genes/special_issues/Human_Genome). Guest Editors John Burn University of Newcastle UK James R. Lupski Baylor College of Medicine USA Karen E. Nelson J. Craig Venter Institute (JCVI) USA Pabulo H. Rampelotto Federal University of Rio Grande do Sul Brazil Editorial Office Publisher Assistant Editor MDPI AG Shu-Kun Lin Rongrong Leng Klybeckstrasse 64 Basel, Switzerland 1. Edition 2016 MDPI • Basel • Beijing • Wuhan ISBN 978-3-03842-123-8 complete edition (Hbk) ISBN 978-3-03842-169-6 complete edition (PDF) ISBN 978-3-03842-124-5 Volume 1 (Hbk) ISBN 978-3-03842-170-2 Volume 1 (PDF) ISBN 978-3-03842-125-2 Volume 2 (Hbk) ISBN 978-3-03842-171-9 Volume 2 (PDF) ISBN 978-3-03842-126-9 Volume 3 (Hbk) ISBN 978-3-03842-172-6 Volume 3 (PDF) © 2016 by the authors; licensee MDPI, Basel, Switzerland. All articles in this volume are Open Access distributed under the Creative Commons License (CC-BY), which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. However, the dissemination and distribution of physical copies of this book as a whole is restricted to MDPI, Basel, Switzerland. III Table of Contents List of Contributors ................................................................................................................... V Preface ...................................................................................................................................... IX Erin Sandford and Margit Burmeister Genes and Genetic Testing in Hereditary Ataxias Reprinted from: Genes 2014, 5(3), 586-603 http://www.mdpi.com/2073-4425/5/3/586 ................................................................................. 1 Anke R. Hammerschlag, Tinca J. C. Polderman, Christiaan de Leeuw, Henning Tiemeier, Tonya White, August B. Smit, Matthijs Verhage and Danielle Posthuma Functional Gene-Set Analysis Does Not Support a Major Role for Synaptic Function in Attention Deficit/Hyperactivity Disorder (ADHD) Reprinted from: Genes 2014, 5(3), 604-614 http://www.mdpi.com/2073-4425/5/3/604 ............................................................................... 19 Thiviyani Maruthappu, Claire A. Scott and David P. Kelsell Discovery in Genetic Skin Disease: The Impact of High Throughput Genetic Technologies Reprinted from: Genes 2014, 5(3), 615-634 http://www.mdpi.com/2073-4425/5/3/615 ............................................................................... 29 Bjorn T. Adalsteinsson and Anne C. Ferguson-Smith Epigenetic Control of the Genome—Lessons from Genomic Imprinting Reprinted from: Genes 2014, 5(3), 635-655 http://www.mdpi.com/2073-4425/5/3/635 ............................................................................... 49 Gilberto Paz-Filho, Margaret C.S. Boguszewski, Claudio A. Mastronardi, Hardip R. Patel, Angad S. Johar, Aaron Chuah, Gavin A. Huttley, Cesar L. Boguszewski, Ma-Li Wong, Mauricio Arcos-Burgos and Julio Licinio Whole Exome Sequencing of Extreme Morbid Obesity Patients: Translational Implications for Obesity and Related Disorders Reprinted from: Genes 2014, 5(3), 709-725 http://www.mdpi.com/2073-4425/5/3/709 ............................................................................... 70 IV Stacey Pereira, Richard A. Gibbs and Amy L. McGuire Open Access Data Sharing in Genomic Research Reprinted from: Genes 2014, 5(3), 739-747 http://www.mdpi.com/2073-4425/5/3/739 ............................................................................... 87 Scott D. Boyd, Stephen J. Galli, Iris Schrijver, James L. Zehnder, Euan A. Ashley and Jason D. Merker A Balanced Look at the Implications of Genomic (and Other “Omics”) Testing for Disease Diagnosis and Clinical Care Reprinted from: Genes 2014, 5(3), 748-766 http://www.mdpi.com/2073-4425/5/3/748 ............................................................................... 96 Emma Duncan, Matthew Brown and Eileen M. Shore The Revolution in Human Monogenic Disease Mapping Reprinted from: Genes 2014, 5(3), 792-803 http://www.mdpi.com/2073-4425/5/3/792 ............................................................................. 115 Thomas Mikeska and Jeffrey M. Craig DNA Methylation Biomarkers: Cancer and Beyond Reprinted from: Genes 2014, 5(3), 821-864 http://www.mdpi.com/2073-4425/5/3/821 ............................................................................. 127 Grégory Caignard, Megan M. Eva, Rebekah van Bruggen, Robert Eveleigh, Guillaume Bourque, Danielle Malo, Philippe Gros and Silvia M. Vidal Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives Reprinted from: Genes 2014, 5(4), 887-925 http://www.mdpi.com/2073-4425/5/4/887 ............................................................................. 173 William G. Newman and Graeme C. Black Delivery of a Clinical Genomics Service Reprinted from: Genes 2014, 5(4), 1001-1017 http://www.mdpi.com/2073-4425/5/4/1001 ........................................................................... 214 Donald Freed, Eric L. Stevens and Jonathan Pevsner Somatic Mosaicism in the Human Genome Reprinted from: Genes 2014, 5(4), 1064-1094 http://www.mdpi.com/2073-4425/5/4/1064 ........................................................................... 230 V List of Contributors Bjorn T. Adalsteinsson: Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK. Mauricio Arcos-Burgos: Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia. Euan A. Ashley: Department of Medicine, Stanford University, Stanford, CA 94305, USA. Graeme C. Black: Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester, M13 9WL, UK. Cesar L. Boguszewski: Endocrine Division (SEMPR), Department of Internal Medicine, Federal University of Parana, Avenida Agostinho Leão Junior, 285-Alto da Glória. CEP 80030-110, Curitiba-PR, Brazil. Margaret C.S. Boguszewski: Endocrine Division (SEMPR), Department of Internal Medicine, Federal University of Parana, Avenida Agostinho Leão Junior, 285-Alto da Glória. CEP 80030-110, Curitiba-PR, Brazil. Guillaume Bourque: McGill University and Genome Quebec Innovation Center, Montréal, QC, H3A 1A4, Canada. Scott D. Boyd: Department of Pathology, Stanford University, Stanford, CA 94305, USA. Matthew Brown: University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, 37 Kent Road, Woolloongabba, Brisbane 4102, Queensland, Australia. Margit Burmeister: Molecular & Behavioral Neuroscience Institute/Departments of Human Genetics/Department of Psychiatry/Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA. Grégory Caignard: Complex Traits Group/Department of Human Genetics, McGill University, Montréal, QC H3G 0B1, Canada. Aaron Chuah: Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia. Jeffrey M. Craig: Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3052, Australia. Christiaan de Leeuw: Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; Institute for Computing and Information Sciences, Radboud University Nijmegen, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands. VI Emma Duncan: University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, 37 Kent Road, Woolloongabba, Brisbane 4102, Queensland, Australia; Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Herston 4029, Queensland, Australia. Megan M. Eva: Department of Medicine/Complex Traits Group/Department of Human Genetics, McGill University, Montréal, QC H3G 0B1, Canada. Robert Eveleigh: McGill University and Genome Quebec Innovation Center, Montréal, QC, H3A 1A4, Canada. Anne C. Ferguson-Smith: Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK. Donald Freed: Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD 21205, USA. Stephen J. Galli: Department of Microbiology and Immunology/Department of Pathology, Stanford University, Stanford, CA 94305, USA. Richard A. Gibbs: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Philippe Gros: Department of Biochemistry/Complex Traits Group, McGill University, Montréal, QC H3G 0B1, Canada. Anke R. Hammerschlag: Department