Molecular Oncology Testing for Solid Tumors

Molecular Oncology Testing for Solid Tumors

Michael Ola Idowu Catherine Isabelle Dumur Carleton Theodore Garrett Editors Molecular Oncology Testing for Solid Tumors A Pragmatic Approach

Editors Michael Ola Idowu, MD, MPH Department of Pathology Virginia Commonwealth University Catherine Isabelle Dumur, PhD Department of Pathology Virginia Commonwealth University Carleton Theodore Garrett, MD, PhD Department of Pathology Virginia Commonwealth University ISBN 978-3-319-16303-1 DOI 10.1007/978-3-319-16304-8 ISBN 978-3-319-16304-8 (ebook) Library of Congress Control Number: 2015942519 Springer Cham Heidelberg New York Dordrecht London Springer International Publishing Switzerland 2015 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. Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com)

Contents Part I Overview of Basic Cellular Biology 1 Molecular Biology Basics in the Omics Era: Genes to Proteins... 3 Carleton T. Garrett 2 Molecular Biology Basics in the Omics Era: Cancer Pathology... 67 Dipti Surve and Michael O. Idowu Part II Standard Nomenclature 3 Standard Nomenclature: Why Bother?... 103 Michael O. Idowu and Shuji Ogino Part III General Principles of Molecular Oncology Testing 4 Pathologists Roles in Molecular Oncology Testing of Solid Tumors... 139 Michael O. Idowu 5 Molecular Methodologies... 153 Catherine I. Dumur 6 General Principles of Validating a Molecular Test... 171 Catherine I. Dumur 7 Application of Chromosomal Microarray... 181 Colleen Jackson-Cook and Shivani Ponnala v

vi Contents Part IV Molecular Testing in Solid Tumors 8 Lung and Mediastinal Tumors... 221 Dhananjay A. Chitale 9 Breast Tumors... 269 Cora G. Uram-Tuculescu and Alida I. Podrumar 10 Head and Neck Tumors... 303 Jennifer Laudadio and Anthony N. Snow 11 Thyroid and Parathyroid Tumors... 341 Adebowale J. Adeniran 12 Gastrointestinal and Pancreatobiliary Tumors... 375 Khalid Matin and Sarah W. Gordon 13 Soft Tissue Tumors... 407 Vickie Y. Jo and Steven Christopher Smith 14 Genitourinary System Tumors... 477 Kenneth A. Iczkowski and Nicholas Harding-Jackson 15 Gynecologic Tumors... 507 Mohamed Mokhtar Desouki and Oluwole Fadare 16 Central Nervous System Tumors... 537 Hope T. Richard, Jason F. Harrison, and Christine Fuller 17 Molecular Oncologic Testing of Skin and Adnexa Tumors... 567 Jyoti P. Kapil and Julie D.R. Reimann 18 Lymphoma and Lymphoproliferative Disorders... 619 Kathryn A. Rizzo 19 Common Hereditary Cancer Syndromes... 645 Heather A. Creswick and John M. Quillin Part V Quality Assurance and Regulatory Affairs 20 Quality Control and Quality Assurance in Solid Tumor Molecular Genetic Testing... 677 Andrea Ferreira-Gonzalez 21 Coding and Reimbursement... 705 David S. Wilkinson Index... 715

Contributors Adebowale J. Adeniran Department of Pathology, Yale University School of Medicine, New Haven, CT, USA Dhananjay A. Chitale Department of Pathology, Henry Ford Hospital, Detroit, MI, USA Heather A. Creswick Massey Cancer Center, Virginia Commonwealth University Heath System, Mohamed Mokhtar Desouki Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA Catherine Isabelle Dumur Department of Pathology, Virginia Commonwealth University, Oluwole Fadare Department of Pathology, University of California San Diego, San Diego, CA, USA Andrea Ferreira-Gonzalez Molecular Diagnostics Laboratory, Virginia Commonwealth University Health Service, Christine Fuller Department of Pathology, Virginia Commonwealth University Medical Center, Carleton Theodore Garrett Department of Pathology, Virginia Commonwealth University, Nicholas Harding-Jackson Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA Department of Pathology, Froedtert Hospital, Milwaukee, WI, USA Jason F. Harrison Department of Neurosurgery, Virginia Commonwealth University, vii

viii Contributors Kenneth A. Iczkowski Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA Michael Ola Idowu Department of Pathology, Virginia Commonwealth University Health System, Colleen Jackson-Cook Departments of Pathology, Human & Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA Vickie Y. Jo Department of Pathology, Brigham and Women s Hospital, Boston, MA, USA Jyoti P. Kapil Miraca Life Sciences, Irving, TX, USA Jennifer Laudadio Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA Khalid Matin Department of Internal Medicine, Virginia Commonwealth University Medical Center, Shuji Ogino Laboratory of Molecular Pathological Epidemiology, Dana Farber Cancer Institute, Boston, MA, USA Sarah W. Gordon Department of Internal Medicine, Virginia Commonwealth University Medical Center, Alida I. Podrumar Department of Hematology/Oncology, Nassau University Medical Center, East Meadow, NY, USA Shivani Ponnala Department of Pathology, Virginia Commonwealth University, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA John M. Quillin Department of Human and Molecular Genetics, Virginia Commonwealth University Health System, Julie D.R. Reimann Molecular Dermatopathology, Miraca Life Sciences, Newton, MA, USA Tufts University Medical Center, Boston, MA, USA Hope T. Richard Department of Pathology, Virginia Commonwealth University Medical Center, Kathryn A. Rizzo Department of Hematopathology, Virginia Commonwealth University, Steven Christopher Smith Department of Pathology, Virginia Commonwealth University Health System, Anthony N. Snow Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA

Contributors ix Dipti Surve Molecular Diagnostics Laboratory, Virginia Commonwealth University Health System, Cora G. Uram-Tuculescu Department of Pathology, Virginia Commonwealth University Health System, David S. Wilkinson Department of Pathology, Virginia Commonwealth University,