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10Th Anniversary of the Human Genome Project Grand Celebration: 10th Anniversary of the Human Genome Project Volume 1 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 1 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 ............................................................................................................ VII Preface .................................................................................................................................XI Debra J. H. Mathews and Leila Jamal Revisiting Respect for Persons in Genomic Research Reprinted from: Genes 2014, 5(1), 1-12 http://www.mdpi.com/2073-4425/5/1/1 .................................................................................. 1 Vincent Timmerman, Alleene V. Strickland and Stephan Züchner Genetics of Charcot-Marie-Tooth (CMT) Disease within the Frame of the Human Genome Project Success Reprinted from: Genes 2014, 5(1), 13-32 http://www.mdpi.com/2073-4425/5/1/13 .............................................................................. 13 Megan E. Aldrup-MacDonald and Beth A. Sullivan The Past, Present, and Future of Human Centromere Genomics Reprinted from: Genes 2014, 5(1), 33-50 http://www.mdpi.com/2073-4425/5/1/33 .............................................................................. 32 Nathalie Chami and Guillaume Lettre Lessons and Implications from Genome-Wide Association Studies (GWAS) Findings of Blood Cell Phenotypes Reprinted from: Genes 2014, 5(1), 51-64 http://www.mdpi.com/2073-4425/5/1/51 .............................................................................. 49 Jose Russo, Julia Santucci-Pereira and Irma H. Russo The Genomic Signature of Breast Cancer Prevention Reprinted from: Genes 2014, 5(1), 65-83 http://www.mdpi.com/2073-4425/5/1/65 .............................................................................. 63 IV Katsushi Tokunaga Lessons from Genome-Wide Search for Disease-Related Genes with Special Reference to HLA-Disease Associations Reprinted from: Genes 2014, 5(1), 84-96 http://www.mdpi.com/2073-4425/5/1/84 .............................................................................. 82 Hannelore Ehrenreich and Klaus-Armin Nave Phenotype-Based Genetic Association Studies (PGAS)—Towards Understanding the Contribution of Common Genetic Variants to Schizophrenia Subphenotypes Reprinted from: Genes 2014, 5(1), 97-105 http://www.mdpi.com/2073-4425/5/1/97 .............................................................................. 95 Albino Bacolla, David N. Cooper and Karen M. Vasquez Mechanisms of Base Substitution Mutagenesis in Cancer Genomes Reprinted from: Genes 2014, 5(1), 108-146 http://www.mdpi.com/2073-4425/5/1/108 .......................................................................... 104 Muhammad Imran Khan, Maleeha Azam, Muhammad Ajmal, Rob W. J. Collin, Anneke I. den Hollander, Frans P. M. Cremers and Raheel Qamar The Molecular Basis of Retinal Dystrophies in Pakistan Reprinted from: Genes 2014, 5(1), 176-195 http://www.mdpi.com/2073-4425/5/1/176 .......................................................................... 144 Sara L. Pulit, Maarten Leusink, Androniki Menelaou and Paul I. W. de Bakker Association Claims in the Sequencing Era Reprinted from: Genes 2014, 5(1), 196-213 http://www.mdpi.com/2073-4425/5/1/196 .......................................................................... 163 Megan J. Puckelwartz and Elizabeth M. McNally Genetic Profiling for Risk Reduction in Human Cardiovascular Disease Reprinted from: Genes 2014, 5(1), 214-234 http://www.mdpi.com/2073-4425/5/1/214 .......................................................................... 181 David J. Elliott Illuminating the Transcriptome through the Genome Reprinted from: Genes 2014, 5(1), 235-253 http://www.mdpi.com/2073-4425/5/1/235 .......................................................................... 203 V Nicola Whiffin and Richard S. Houlston Architecture of Inherited Susceptibility to Colorectal Cancer: A Voyage of Discovery Reprinted from: Genes 2014, 5(2), 270-284 http://www.mdpi.com/2073-4425/5/2/270 .......................................................................... 222 Dianne F. Newbury, Anthony P. Monaco and Silvia Paracchini Reading and Language Disorders: The Importance of Both Quantity and Quality Reprinted from: Genes 2014, 5(2), 285-309 http://www.mdpi.com/2073-4425/5/2/285 .......................................................................... 237 VII List of Contributors Muhammad Ajmal: Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands. Megan E. Aldrup-MacDonald: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Division of Human Genetics, Duke University, Durham, NC 27710, USA. Maleeha Azam: Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands. Albino Bacolla: Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA. Nathalie Chami: Montreal Heart Institute, Faculté de Médecine, Université de Montréal, 5000 Bélanger Street, Montréal, QC H1T 1C8, Canada. Rob W. J. Collin: Radboud Institute for Molecular Life Sciences/Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands. David N. Cooper: Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK. Frans P. M. Cremers: Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan; Radboud Institute for Molecular Life Sciences/Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands. Paul I. W. de Bakker: Department of Medical Genetics, Institute for Molecular Medicine / Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands. Anneke I. den Hollander: Department of Ophthalmology/Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands. Hannelore Ehrenreich: Max Planck Institute of Experimental Medicine, Hermann-Rein- Str.3, 37075 Göttingen, Germany; DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Hermann-Rein-Str.3, 37075 Göttingen, Germany. David J. Elliott: Institute of Genetic Medicine, Newcastle University, Newcastle, NE1 3BZ, UK. Richard S. Houlston: Division of Genetics and Epidemiology / Molecular and Population Genetics Team, Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK. VIII Leila Jamal: Department of Health Policy and Management, Johns Hopkins Bloomberg School of Health, 615 North Wolfe St., Baltimore, MD 21205, USA; Division of Neurogenetics, Kennedy Krieger Institute, 801 N. Broadway, Rm. 564, Baltimore, MD 21205, USA. Muhammad Imran Khan: Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands. Guillaume Lettre: Montreal Heart Institute, Faculté de Médecine, Université de Montréal, 5000 Bélanger Street, Montréal, QC H1T 1C8, Canada. Maarten Leusink: Julius Center for Health Sciences and Primary Care / Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands; Division of Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University,
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