Molecular Diagnostics Fundamentals, Methods and Clinical

Applications, 3rd Edition

Visit the link below to download the full version of this book:

https://medipdf.com/product/molecular-diagnostics-fundamentals-methods-and-clini
cal-applications-3rd-edition/

Click Download Now

BOOST YOUR CONFIDENCE
ANYTIME | ANYWHERE
Awesome! I have referred all my classmates to purchase this
excellent resource. Even my instructor was impressed with it.
You will not find a more handy and complete pocket guide.”

Just what I needed. It was exactly what I needed for class.

It has helped through my clinical studies as well. Anytime I
need an answer it has it for me.”
—Amazon Reviewers

This book is great. “This book helped me get an A in anatomy

and physiology, this was my pocket book anywhere. I still use it
after the class. I love it!”

THE BEST!!! “This is the best anatomy book I’ve ever seen!!! Don’t
let the pocket size of it fool you! This anatomy guide is so detailed
and complete!!! Very well done!!! Love it! Love it! Love it!!!”
—Amazon Reviewers

SAVE 20% ORDER TODAY!

FADavis.com
+ FREE SHIPPING
Promotion subject to change without notice. Offer valid for
Use Promo Code: DAVIS20 individual purchases from FADavis.com in the U.S. only.
Molecular
Diagnostics
Fundamentals, Methods,
and Clinical Applications
THIRD EDITION

Lela Buckingham, PhD, MB (ASCP), DLM (ASCP)

College of Health Sciences
Rush University Medical Center
Chicago, Illinois
Acknowledgments

Thanks and gratitude are extended to all who helped This book was originally envisioned by my co-author
in the completion of the third edition of this work. The for the first edition, Dr. Maribeth Flaws. Thanks to her
useful input provided by reviewers who gave their valu- for initiating this project. Thanks to Dr. Herb Miller and
able time to comment on and improve the writing is the Medical Laboratory Science faculty in the Rush Uni-
gratefully acknowledged. Molecular laboratory science versity College of Health Sciences for the opportunity
is an example of innovative technology applied to the to participate in medical laboratory science education. I
ultimate goal of improved patient care. greatly appreciate the guidance and support of the pub-
I owe thanks to my colleagues at Rush University lication staff at F. A. Davis—Christa Fratantoro, Julie
Medical Center, Dr. Wei-Tong Hsu, Dr. Nick Moore, Chase, Roxanne Klaas, and Katharine Margeson—for
Dr. Mary Hayden, Dr. Sivadasan Kanangat, and Dr. Eliz- the illustration and production of the text.
abeth Berry-Kravis, for help and support in their areas of I would like to acknowledge and thank fellow
expertise. I would also like to acknowledge colleagues members of the Association for Molecular Pathology, a
in the Rush University College of Health Sciences, res- vibrant and resourceful organization dedicated to educa-
idents, fellows, students, and laboratory professionals tion and policy in the practice of molecular diagnostics.
who provided suggestions for the third edition, partic- This organization has provided an outlet for contex-
ularly Alexandra Vardouniotis, Dr. Mezgebe Gebrekiris- tual information, training, and sanction to further this
tos, and Adrian Tira, with whom I work and from whom ever-advancing field of study.
I learn every day.

xi
F. A. Davis Company
1915 Arch Street
Philadelphia, PA 19103
www.fadavis.com

Copyright © 2019 by F. A. Davis Company

Copyright © 2019 by F. A. Davis Company. All rights reserved. This product is protected by copyright. No part of it may be
reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying,
recording, or otherwise, without written permission from the publisher.

Printed in the United States of America

Last digit indicates print number: 10 9 8 7 6 5 4 3 2 1

Acquisitions Editor: Christa A. Fratantoro

Director of Content Development: George W. Lang
Content Project Manager: Julie Chase
Art and Design Manager: Carolyn O’Brien

As new scientific information becomes available through basic and clinical research, recommended treatments and drug therapies
undergo changes. The author(s) and publisher have done everything possible to make this book accurate, up to date, and in
accord with accepted standards at the time of publication. The author(s), editors, and publisher are not responsible for errors
or omissions or for consequences from application of the book, and make no warranty, expressed or implied, in regard to the
contents of the book. Any practice described in this book should be applied by the reader in accordance with professional
standards of care used in regard to the unique circumstances that may apply in each situation. The reader is advised always
to check product information (package inserts) for changes and new information regarding dose and contraindications before
administering any drug. Caution is especially urged when using new or infrequently ordered drugs.

Library of Congress Cataloging-in-Publication Data

Names: Buckingham, Lela, author.

Title: Molecular diagnostics : fundamentals, methods, and clinical
applications / Lela Buckingham.
Description: Third edition. | Philadelphia : F.A. Davis Company, [2019] |
Includes bibliographical references and index.
Identifiers: LCCN 2018058583 (print) | LCCN 2018059084 (ebook) |
ISBN 9780803699540 | ISBN 9780803668294 (alk. paper)
Subjects: | MESH: Molecular Diagnostic Techniques—methods | Nucleic
Acids—analysis | Genetic Techniques
Classification: LCC RB43.7 (ebook) | LCC RB43.7 (print) | NLM QY 102 |
DDC 616.9/041—dc23
LC record available at https://lccn.loc.gov/2018058583

Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by
F. A. Davis Company for users registered with the Copyright Clearance Center (CCC) Transactional Reporting Service, provided
that the fee of $.25 per copy is paid directly to CCC, 222 Rosewood Drive, Danvers, MA 01923. For those organizations that
have been granted a photocopy license by CCC, a separate system of payment has been arranged. The fee code for users of the
Transactional Reporting Service is: 978-0-8036-6829-4 / + $.25.
 To our students committed to
service through the practice of Medical Laboratory Science
Preface

Molecular technology continues to grow in importance purpose, principles, and interpretation of the molecular
in the clinical laboratory. Training of health-care pro- diagnostic tests that they will be ordering and assessing
fessionals routinely includes molecular biology, from for their patients.
laboratory techniques to therapeutic decisions. This text- Students who are first learning about molecular-based
book was written to provide fundamental knowledge of assays will find the text useful for explaining the funda-
molecular biology, current methods, and their clinical mental principles. Practitioners who are performing and
applications. interpreting these assays can use this text as a resource
The primary audience for this text is students enrolled for reference and troubleshooting and to drive the imple-
in Clinical/Medical Laboratory Science programs at all mentation of additional molecular-based assays in their
levels. It explains the principles of molecular technol- laboratories.
ogy that are used for diagnostic purposes. Examples of An Instructor ’s Resource package has been devel-
applications of molecular-based assays are included in oped for educators who adopt this text for a course.
the text, along with case studies that illustrate the use These resources, including PowerPoint presentations, a
and interpretation of these assays in patient care. test-item bank, and additional case studies, are available
This text is also appropriate for those in other on DavisPlus at http://davisplus.fadavis.com.
health-related disciplines who need to understand the
Lela Buckingham

vii
Reviewers

Catherine E. Bammert, MS, CT, MB (ASCP)CM Rachel Hulse, MS, MLS (ASCP)CM
Associate Professor Program Director
Program Director, Diagnostic Molecular Science Medical Laboratory Sciences
Clinical Laboratory Sciences Idaho State University
Northern Michigan University Pocatello, Idaho
Marquette, Michigan
Marisa K. James, MA, MLS (ASCP)CM
Katie Bennett, PhD, MB (ASCP), NRCC-CC Program Director
Assistant Professor and Laboratory Director School of Clinical Laboratory Science
Laboratory Sciences and Primary Care North Kansas City Hospital
Texas Tech University Health Sciences Center North Kansas City, Missouri
Lubbock, Texas
Jacqueline Peacock, PhD, MB (ASCP)CM
Tammy Carter, PhD, MT (ASCP), MB (ASCP) Assistant Professor and Program Coordinator
Assistant Professor, CLS Program Director Clinical Laboratory, Respiratory Care, and Health
Laboratory Science and Primary Care Administration Programs
Texas Tech University Health Sciences Center Ferris State University
Lubbock, Texas Grand Rapids, Michigan

Kristen Coffey, MS David Petillo, PhD, MT (ASCP)CM, MB

Visiting Instructor Clinical Coordinator/Assistant Professor
Medical Laboratory Sciences College of Health Professions
University of West Florida Molecular Diagnostics Program
Pensacola, Florida Ferris State University
Grand Rapids, Michigan
Daniel Harrigan, MS, MB (ASCP)CM
Professor
Laboratory Sciences
Blackhawk Technical College
Monroe, Wisconsin

ix
x Reviewers

Linda M. Ray, MS (ASCP)CM EDITORIAL REVIEWERS

Assistant Professor
Medical Laboratory Science We especially thank our editorial reviewers for assisting
University of North Dakota, School of Medicine & with page proof review.
Health Sciences
Grand Forks, North Dakota Mezgebe Gebrekiristos, PhD, MS, MT (ASCP)
Clinical Laboratory Scientist
Barbara Sawyer, PhD, MLS (ASCP), MB Molecular Oncology Laboratory
Professor Pathology Department
Lab Sciences and Primary Care Rush University Medical Center
Texas Tech University Health Sciences Center Chicago, Illinois
Lubbock, Texas
Lenny K. Hong, M.S., MLS (ASCP)CM, MB (ASCP)CM
CM
Ebot Sahidu Tabe, BMLS, MS, PhD, MB (ASCP) PhD Graduate Student - Department of Pathology
Instructor University of Illinois at Chicago - College of Medicine
Basic and Clinical Sciences Chicago, Illinois
Albany College of Pharmacy and Health Sciences
Albany, New York Adrian Tira, MSc., MT (ASCP)
Department of Pathology
Geoffrey Toner, MS, MB (ASCP)CM Rush University Medical Center
Instructor/Education Coordinator Chicago, Illinois
Medical Laboratory Sciences and Biotechnology
Jefferson College of Health Professions Alexandra Vardouniotis MS, MLS (ASCP)CM SBBCM
Thomas Jefferson University Medical Laboratory Scientist
Philadelphia, Pennsylvania Rush University Medical Center
Chicago, Illinois
Contents

Transfer RNA 33
Section I Other RNAs 35
Fundamentals of Molecular Biology: RNA POLYMERASES 35
OTHER RNA-METABOLIZING ENZYMES 36
An Overview 1
Ribonucleases 36
1 Nucleic Acids and Proteins 2 RNA Helicases 37
PROTEINS AND THE GENETIC CODE 37
DNA 3
Amino Acids 38
DNA STRUCTURE 4
Genes 43
Nucleotides 4
The Genetic Code 43
Nucleic Acid 8
TRANSLATION 46
DNA REPLICATION 9
Amino Acid Charging 46
Polymerases 11
Protein Synthesis 47
ENZYMES THAT METABOLIZE DNA 14
Restriction Enzymes 14 2 Gene Expression and Epigenetics 57
DNA Ligase 17 TRANSCRIPTION 58
Other DNA Metabolizing Enzymes 17 Transcription Initiation 58
RECOMBINATION IN SEXUALLY REPRODUCING ORGANISMS 19 Transcription Elongation 58
RECOMBINATION IN ASEXUAL REPRODUCTION 21 Transcription Termination 59
Conjugation 21 REGULATION OF TRANSCRIPTION 60
Transduction 23 Regulation of Messenger RNA Synthesis at Initiation 60
Transformation 23 Post-Transcriptional Regulation 64
PLASMIDS 25 Post-Translational Regulation 64
RNA 27 EPIGENETICS 65
Transcription 27 Histone Modification 65
Transcription Initiation 28 Nucleic Acid Methylation 66
Transcription Elongation 28 CLASSIFICATION OF EPIGENETIC FACTORS 69
Transcription Termination 29 NONCODING RNAs 69
TYPES/STRUCTURES OF RNA 29 MicroRNAs 70
Ribosomal RNA 29 Small Interfering RNAs 70
Messenger RNA 29 Other Small RNAs 70
Small Nuclear RNA 33 Long Noncoding RNAs 71
xiii
xiv Contents

Protein Probes 124

Section II Probe Labeling 126
Common Techniques in Molecular Nucleic Acid Probe Design 126
HYBRIDIZATION CONDITIONS, STRINGENCY 128
Biology 77
DETECTION SYSTEMS 129
3 Nucleic Acid Extraction Methods 78 INTERPRETATION OF RESULTS 132
ISOLATION OF DNA 79 ARRAY-BASED HYBRIDIZATION 133
Preparing the Sample 79 Dot/Slot Blots 133
DNA Isolation Chemistries 81 Genomic Array Technology 134
ISOLATION OF RNA 87 SOLUTION HYBRIDIZATION 138
Total RNA 87 6 Nucleic Acid Amplification 142
Specimen Collection 87 TARGET AMPLIFICATION 143
RNA Isolation Chemistries 87 Polymerase Chain Reaction 143
MEASUREMENT OF NUCLEIC ACID QUALITY AND QUANTITY 90 Transcription-Based Amplification Systems 164
Electrophoresis 90 Genomic Amplification Methods 165
Spectrophotometry 92 PROBE AMPLIFICATION 168
Fluorometry 93 Ligase Chain Reaction 168
Microfluidics 94 Strand Displacement Amplification 169
4 Resolution and Detection of Nucleic Qβ Replicase 170
Acids 97 SIGNAL AMPLIFICATION 172
ELECTROPHORESIS OF NUCLEIC ACIDS 98 Branched DNA Amplification 172
Hybrid Capture Assays 173
GEL SYSTEMS 99
Cleavage-Based Amplification 173
Agarose Gels 99
Cycling Probe 174
Polyacrylamide Gels 101
CAPILLARY ELECTROPHORESIS 102 7 Chromosomal Structure and Chromosomal
BUFFER SYSTEMS 104 Mutations 179
Buffer Additives 105 CHROMOSOMAL STRUCTURE AND ANALYSIS 181
ELECTROPHORESIS EQUIPMENT 106 Chromosomal Compaction and Histones 181
Gel Loading 108 Chromosome Morphology 183
DETECTION SYSTEMS 109 Visualizing Chromosomes 184
Fluorescent Dyes 109 DETECTION OF GENOME AND CHROMOSOMAL MUTATIONS 186
Silver Stain 110 Karyotyping 186
Fluorescence In Situ Hybridization 190
5 Analysis and Characterization of Nucleic COMPARATIVE GENOME HYBRIDIZATION (CGH) 195
Acids and Proteins 112
RESTRICTION ENZYME MAPPING OF DNA 113
8 Gene Mutations 199
TYPES OF GENE MUTATIONS 200
CRISPR ENZYME SYSTEMS 115
DETECTION OF GENE MUTATIONS 201
HYBRIDIZATION TECHNOLOGIES 116
Biochemical Methods 201
Southern Blots 117
Nucleic Acid Analyses 207
PROBE HYBRIDIZATION 121
GENE VARIANT NOMENCLATURE 218
Northern Blots 122
GENE NAMES 219
Western Blots 122
PROBES 123 9 DNA Sequencing 223
DNA Probes 123 DIRECT SEQUENCING 224
RNA Probes 124 Manual Sequencing 224
Other Nucleic Acid Probe Types 124 Automated Fluorescent Sequencing 229
 Contents xv

PYROSEQUENCING 235 QUALITY ASSURANCE 305

BISULFITE DNA SEQUENCING 236 Controls 305
RNA SEQUENCING 237 Quality Control 305
NEXT-GENERATION SEQUENCING 238 Selection of Sequence Targets for Detection
Gene Panels 240 of Microorganisms 307
NGS Library Preparation 240 MOLECULAR DETECTION OF MICROORGANISMS 308
Targeted Libraries 241 Bacteria 309
Sequencing Platforms 243 Viruses 313
Sequence Quality 246 Mycology 323
Filtering and Annotation 247 Parasites 324
BIOINFORMATICS 248 ANTIMICROBIAL AGENTS 324
THE HUMAN GENOME PROJECT 250 Resistance to Antimicrobial Agents 325
Variant Associations With Phenotype 253 Molecular Detection of Resistance 327
MOLECULAR EPIDEMIOLOGY 329
Molecular Strain Typing Methods for Epidemiological
Section III
Studies 330
Techniques in the Clinical Comparison of Typing Methods 336
Laboratory 259
12 Molecular Detection of Inherited
10 DNA Polymorphisms and Human Diseases 344
Identification 260 THE MOLECULAR BASIS OF INHERITED DISEASES 345
TYPES OF POLYMORPHISMS 261 CHROMOSOMAL ABNORMALITIES 345
RFLP TYPING 262 PATTERNS OF INHERITANCE IN SINGLE-GENE DISORDERS 346
Genetic Mapping With RFLPs 264 MOLECULAR BASIS OF SINGLE-GENE DISORDERS 349
RFLP and Parentage Testing 264 Lysosomal Storage Diseases 349
Human Identification Using RFLPs 265 Factor V Leiden 349
STR TYPING BY PCR 266 Prothrombin 349
STR Analysis 268 Methylenetetrahydrofolate Reductase 352
Y-STR 278 Hemochromatosis 352
LINKAGE ANALYSIS 282 Cystic Fibrosis 353
Cytochrome P-450 354
BONE MARROW ENGRAFTMENT TESTING USING DNA
SINGLE-GENE DISORDERS WITH NONCLASSICAL PATTERNS
POLYMORPHISMS 283
OF INHERITANCE 355
PSTR Testing 285
Mutations in Mitochondrial Genes 356
Post-Transplant Engraftment Testing 287
Nucleotide-Repeat Expansion Disorders 357
QUALITY ASSURANCE FOR SURGICAL SECTIONS
Genomic Imprinting 362
USING STR 289
Multifactorial Inheritance 363
SINGLE-NUCLEOTIDE POLYMORPHISMS 289
LIMITATIONS OF MOLECULAR TESTING 363
The Human Haplotype Mapping (HapMap) Project 290
MITOCHONDRIAL DNA POLYMORPHISMS 291 13 Molecular Oncology 369
OTHER IDENTIFICATION METHODS 293 CLASSIFICATION OF NEOPLASMS 370
Protein-Based Identification 293 MOLECULAR BASIS OF CANCER 371
Epigenetic Profiles 294
ANALYTICAL TARGETS OF MOLECULAR TESTING 372
11 Detection and Identification GENE AND CHROMOSOMAL MUTATIONS IN SOLID TUMORS 372
of Microorganisms 301 Human Epidermal Growth Factor Receptor 2, HER2/neu/erb-b2 1
SPECIMEN COLLECTION 302 (17q21.1) 372
SAMPLE PREPARATION 304 Epidermal Growth Factor Receptor, EGFR (7p12) 373
xvi Contents

Kirsten Rat Sarcoma Viral Oncogene Homolog, K-ras (12p12); HLA Test Discrepancies 436
Neuroblastoma ras, N-ras (1p13); and Harvey Rat Sarcoma Coordination of HLA Test Methods 437
Viral Oncogene Homolog, H-ras (11p15) 375 ADDITIONAL RECOGNITION FACTORS 437
Ewing Sarcoma, EWS (22q12) 376 Minor Histocompatibility Antigens 437
Synovial Sarcoma Translocation, Chromosome 18—Synovial Nonconventional MHC Antigens 437
Sarcoma Breakpoint 1 and 2, SYT-SSX1, SYT-SSX2 t(X;18) Killer Cell Immunoglobulin-Like Receptors 437
(p11.2;q11.2) 377 MHC DISEASE ASSOCIATION 438
Paired Box-Forkhead in Rhabdomyosarcoma, PAX3-FKHR, SUMMARY OF LABORATORY TESTING 439
PAX7-FKHR, t(1;13), t(2;13) 378
Tumor Protein 53, TP53 (17p13) 378 15 Quality Assurance and Quality Control
Ataxia Telangiectasia Mutated Gene, ATM (11q22) 379 in the Molecular Laboratory 446
Breast Cancer 1 Gene, BRCA1 (17q21), and Breast Cancer 2 Gene, SPECIMEN HANDLING 447
BRCA2 (13q12) 380 Collection Tubes for Molecular Testing 448
Von Hippel–Lindau Gene, VHL (3p26) 380 Precautions 450
V-myc Avian Myelocytomatosis Viral-Related Oncogene, Holding and Storage Requirements 451
Neuroblastoma-Derived, MYCN or n-myc (2p24) 381 TEST PERFORMANCE 451
V-Ros Avian UR2 Sarcoma Virus Oncogene Homolog 1 (ROS1) Next-Generation Sequencing 456
Proto-Oncogene (6q22.1) and Rearranged During Transfection Calibrators and Method Calibration 456
(RET) Proto-Oncogene (10q11) 381 Controls 457
Anaplastic Lymphoma Receptor Tyrosine Kinase (ALK) QUALITY CONTROL 458
Proto-Oncogene, 2p23.1 382 QUALITY ASSURANCE 458
V-Kit Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog, INSTRUMENT MAINTENANCE 459
KIT, c-KIT (4q12) 382 Instrument Calibration 463
Other Molecular Abnormalities 382 REAGENTS 463
Microsatellite Instability 382 Reagent Categories 464
Loss of Heterozygosity 385 Chemical Safety 465
Liquid Biopsy 386 Reagent Storage 466
MOLECULAR ANALYSIS OF LEUKEMIA AND LYMPHOMA 387 Reagent Labeling 466
Gene Rearrangements 387 PROFICIENCY TESTING 468
Mutations in Hematological Malignancies 397 DOCUMENTATION OF TEST RESULTS 468
Mutation Spectra 405 Gene Nomenclature 469
Gene Sequencing Results 469
14 DNA-Based Tissue Typing 417 REPORTING RESULTS 469
THE MHC LOCUS 418
HLA POLYMORPHISMS 420 Appendix A Study Question Answers 473
HLA Nomenclature 420
MOLECULAR ANALYSIS OF THE MHC 425
Appendix B Answers to Case Studies 501
Serological Analysis 427 Glossary 505
DNA-Based Typing 430
Combining Typing Results 436 Index 529