Contents

Dedication v

Foreword vii

Preface ix

Color Plates xv

Contributors xvii

Value Added eBook Instructions xix

Part I. Introduction

1 An Historical Perspective on the Clinical Diagnostic Laboratory 3

Robert E. Moore

Part II. Basic Molecular Biology

2 An Overview of Nucleic Acid Chemistry, Structure, and Function:

The Foundations of Molecular Biology 13

William B. Coleman

3 Extraction of Nucleic Acids 25

Paul N. Bogner and Anthony A. Killeen

4 Nucleic Acid Blotting Techniques: Theory and Practice 31

Terry Amiss and Sharon Collins Presnell

5 The Polymerase Chain Reaction 47

William B. Coleman and Gregory J. Tsongalis

6 Bioinformatics: Computer-Based Approaches to Genetic Analysis 57

Sharon L. Ricketts

Part III. Molecular Diagnostic Technologies

7 PCR-Based Methods for Mutation Detection 65

Ian M. Frayling, Emma Monk, and Rachel Butler

8 Alternative Methods for Amplified Nucleic Acid Testing 75

Deborah A. Payne and Laurie E. Sower

9 Electrophoretic Methods for Mutation Detection and DNA Sequencing 85

W. Edward Highsmith, Jr.

10 Single-Nucleotide Polymorphisms: Testing DNA Variation for Disease Association 111

Ulrich Broeckel and Martin J. Hessner

11 Microarray Approaches to Gene Expression Analysis 121

David Neil Hayes and Matthew Meyerson

12 Methods for Analysis of DNA Methylation 149

Alexander Dobrovric

Part IV. Other Clinical Diagnostic Technologies

13 Flow Cytometry 163

Joseph A. DiGiuseppe

14 Medical Cytogenetics 173

Martha B. Keagle

15 Fluorescence In Situ Hybridization: A Major Milestone in Luminous Cytogenetics 189

Suneel D. Mundle and Robert J. Koska

16 Immunohistochemistry 203

John Hunt, Larissa Davydova, Richard W. Cartun, and Maria Baiulescu

17 Laser Capture Microdissection 219

C. Robert Bagnell, Jr.

Part V. Quality Assurance in the Molecular Diagnostics Laboratory

18 Framework for Quality Assurance in Molecular Diagnostics 227

Marlene Sabbath-Solitare, Selwyn J. Baptist, and Teresita Cuyegkeng Redondo

19 Verification of Molecular Assays 237

Brent L. Seaton

20 Standards and Standardization of Molecular Diagnostics 243

John P. Jakupciak and Catherine D. O'Connell

21 Laboratory-Developed Tests in Molecular Diagnostics 247

Andrea Ferreira-Gonzalez and Carleton T. Garrett

Part VI. Applications of Molecular Diagnostics for Genetic Diseases

22 An Overview of Molecular Genetics 259

Elaine Weidenhammer and Gregory J. Tsongalis

23 Genetic Basis of Neurologic and Neuromuscular Diseases 267

Narasimhan Nagan, Christopher J. Klein, D. Brian Dawson, Myra J. Wick, and Stephen N. Thibodeau

Contents xiii

24 Molecular Mechanisms of Endocrine Disorders 281

Amy Potter and John A. Phillips III

25 Molecular Pathogenesis of Cardiovascular Disease 295

26 Molecular Diagnostics in Coagulation 311

Enrique Ballesteros

27 Cystic Fibrosis 321

Eugene H. Lewis III, Myra J. Lewis, Jean A. Amos, and Gregory J. Tsongalis

28 Prenatal Genotyping for Identification of Fetuses at Risk for Immune Cytopenic Disorders 329

Martin J. Hessner and Brian R. Curtis

29 Personalized Medicine 341

Karen McCullough

Part VII. Applications of Molecular Diagnostics for Human Cancers

30 Molecular Pathogenesis of Human Cancer 349

William B. Coleman and Gregory J. Tsongalis

31 Application of Molecular Diagnostics to Hereditary Nonpolyposis

Colorectal Cancer 375

Ian M. Frayling, Lisa Happerfield, Christopher Mattocks, Kim Oakhill, and Mark J. Arends

32 Molecular Genetic Applications to the Diagnosis of Lymphoma 393

William N. Rezuke, Jr. and Gregory J. Tsongalis

33 Molecular Genetic Abnormalities in Acute and Chronic Leukemias 415

Pei Lin and L. Jeffrey Medeiros

Part VIII. Applications of Molecular Diagnostics for Infectious Diseases

34 Molecular Testing for Chlamydia trachomatis and Neisseria gonorrhoeae 437

Alexandra Valsamakis

35 Human Papillomavirus 447

Theresa M. Voytek and Gregory J. Tsongalis

36 Molecular Diagnosis for HIV-1 453

Angela M. Caliendo and Charles E. Hill

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