Genomic Disorders The Genomic Basis of Disease The Genomic Basis of Disease Edited by James R. Lupski, MD , P h D Pawel Stankiewicz, MD , P h D Genomic Disorders Edited by James R. Lupski, MD , P h D Pawel Stankiewicz, MD , P h D G ENOMIC D ISORDERS Edited by JAMES R. LUPSKI, MD, PhD PAWEL STANKIEWICZ, MD, PhD Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX G ENOMIC D ISORDERS The Genomic Basis of Disease / © 2006 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.humanapress.com All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. The content and opinions expressed in this book are the sole work of the authors and editors, who have warranted due diligence in the creation and issuance of their work. 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The fee code for users of the Transactional Reporting Service is: [1-58829-559-1/06 $30.00]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 eISBN 1-59745-039-1 Library of Congress Cataloging-in-Publication Data Genomic disorders : the genomic basis of disease / edited by James R. Lupski, Pawe Stankiewicz. p. ; cm. Includes bibliographical references and index. ISBN 1-58829-559-1 (alk. paper) 1. Genetic disorders Molecular aspects. [DNLM: 1. Genetic Diseases, Inborn. 2. Chromosome Aberrations. 3. Genome Components. 4. Genome. 5. Genomics methods. QZ 50 G3354 2006] I. Lupski, James R., 1957- II. Stankiewicz, Pawe . RB155.5.G465 2006 616'.042 dc22 2005020461 Dedication To our many mentors who have nurtured our intellectual curiosity and to our dedicated families for their love and support. —J. R. L. and P. S. v In Memorium In memory of Carlos A. Garcia (1935–2005) and his passion for medicine, science, and the patients and families for whom he cared. vii Preface ix Uncovering Recurrent Submicroscopic Rearrangements As a Cause of Disease For five decades since Fred Sanger's (1) seminal discovery that proteins have a specific structure, since Linus Pauling's (2) discovery that hemoglobin from patients with sickle cell anemia is molecularly distinct, and since Watson and Crick's (3) elucidation of the chemical basis of heredity, the molecular basis of disease has been addressed in the context of how mutations affect the structure, function, or regulation of a gene or its protein product. Molecular medicine has functioned in the context of a genocentric world. During the last decade it became apparent, however, that many disease traits are best explained not by how the information content of a single gene is changed, but rather on the basis of genomic alterations. Furthermore, it has become abundantly clear that architec- tural features of the human genome can result in susceptibility to DNA rearrangements that cause disease traits. Such conditions have been referred to as genomic disorders (4,5). It remains to be determined to what extent genomic changes are responsible for disease traits, common traits (including behavioral traits), or perhaps sometimes represent benign polymorphic variation. The widespread structural variation of the human genome, alter- natively referred to as large-copy number polymorphisms, large-scale copy number varia- tions, or copy number variants has begun only recently to be appreciated (6–9). High-resolution analysis of the human genome has enabled detection of genome changes heretofore not observed because of technology limitations. Whereas agarose gel electro- phoresis enables detection of changes of the genome up to 25–30 kb in size, and cytoge- netic banding techniques can resolve deletion rearrangements only greater than 2–5 Mb in size, alterations of the genome between more than 30 kb and less than 5 Mb defied detection until pulsed-field gel electrophoresis and fluorescence in situ hybridization became available to resolve changes in the human genome of such magnitude (10–12). Those methods were limited to detection of specific genomic regions of interest and could not evaluate genomic rearrangements in a global way. The availability of a “finished” human genome sequence (13) and genomic microarrays (14) have enabled approaches to resolve changes in the genome heretofore impossible to assess on a global genome scale (i.e., simultaneously examining the entire genome rather than discreet segments). Array comparative genome hybridization (aCGH) is one powerful approach to high-resolution analysis of the human genome. The CGH determines differ- ences by comparisons to a reference “normal genome,” whereas the array enables detec- tion of such changes at essentially any resolution that is desired, limited only by imagination and cost. Furthermore, the application of bioinformatic analyses to the finished human genome sequence and comparative genomic analysis enable information technology approaches to identify key architectural features throughout the entire genome that are associated with known recurrent rearrangements causing genomic disorders. An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. A combination of high-resolution [...]... is a powerful approach to address the question: To what extent are constitutional DNA rearrangements in the human genome responsible for human traits? Such approaches may also yield insights into recurrent somatic rearrangements (15) Genomic Disorders: The Genomic Basis of Disease attempts to survey the subject area of genomic disorders in the beginning of the postgenomic era After a short historical... because of their belief in the research efforts Importantly, we had to perform the electrical studies (NCVs) and collect blood samples from all family members This included unaffected individuals, who were sometimes hesitant, or required further explanation of the need for their samples I often thought of the irony of the situation At these reunion parties, Dr Garcia would oversee the administration of the. .. had the double density of the other There was also no consistency because in one patient it was the upper band and in another patient the lower band revealing the increased dosage intensity After checking and rechecking, I realized that the data could only be explained if one of the alleles was duplicated I reinterpreted the genotypes, and yes, the recombinants had disappeared I can still feel the. .. members called their respective laboratories and, indeed, review of their Southern blots revealed RFLP dosage differences for the appropriate markers The existence of the CMT1A duplication had now almost instantaneously been confirmed around the world FROM EUROPE I started my PhD in October 1988 at the University of Antwerp, Belgium in the laboratory of Christine Van Broeckhoven, currently the scientific... marker from the same locus and noted that often when there were three alleles revealed by RM11-GT (14), a dosage difference could be observed between the two alleles if the affected individual was heterozygous for that RFLP These initial observations suggested that there may be three copies of the genomic region that was being assayed, potentially reflecting genomic duplication at the CMT1A locus The entire... living in the village where they were born Every week Peter De Jonghe and his wife Gisèle Smeyers, at that time the research nurse on the project, made many trips visiting family members of family CMT-A at their homes to collect blood samples Gisèle made the first contact with the patients and relatives to explain the aims of the study and to ask whether she could visit again, but now with the neurologist... identified the CMT1A duplication in Europe, that she had submitted their paper to Science the same month that we submitted our papers There were referees’ and editors’ comments to both of us from a couple of journals that we “had not identified the gene.” This pretty clearly showed that the reviewers completely misunderstood the novelty of our findings, as did the editor handling the manuscript, thus, the. .. Mb in size based on other duplicated markers in the region (pVAW412R3 [D17S125] and pEW401 [D17S61]) and PFGE data We wrote the paper and submitted it to Nature While under editorial review, we continued the work and found the real genetic proof that it was the duplication that caused the disease, namely in one family we observed the duplication appearing de novo together with the disease In this family... Nowadays, the Southern blot method (Fig 3A) has been replaced by PCR methods making use of highly informative short tandem repeat markers in the CMT1A region or specific primers located within the CMT1A-REP region At the second CMT workshop, sponsored by the ENMC in The Netherlands, researchers from several European countries agreed to contribute to a large study with the aim to estimate the frequency of the. .. neuropathies Professor Alan Emery said at the first European CMT workshop: “This is another step towards discovery of the causes of all these disorders, which will open doors to possible treatments in the future.” The CMT1A duplication mechanism is now referred to in many textbooks on Human Molecular Genetics ACKNOWLEDGMENTS I appreciate the help of both Christine Van Broeckhoven and Peter De Jonghe for their . rearrangements (15). Genomic Disorders: The Genomic Basis of Disease attempts to survey the subject area of genomic disorders in the beginning of the postgenomic era Genomic Disorders The Genomic Basis of Disease The Genomic Basis of Disease Edited by James R. Lupski, MD , P h D Pawel Stankiewicz, MD , P h D Genomic Disorders Edited