Diagnostic Molecular Pathology. A Guide to Applied Molecular Testing. Edition No. 2

Table of Contents

Section 1 Introduction to Molecular Testing 1. Introduction to Molecular Testing in Human Disease 2. The Polymerase Chain Reaction and Other Amplification Methodologies 3. Whole-exome and Whole Genome Sequencing in the Molecular Diagnostic Laboratory 4. Long-read Sequencing

Section 2 Molecular Testing in Infectious Disease 5. Molecular Testing for Human Immunodeficiency Virus 6. Molecular Testing in Hepatitis Virus-related Disease 7. Molecular Testing for Human Papilloma Viruses 8. Molecular Testing for Parvoviruses 9. Molecular Testing for Polyomaviruses 10. Molecular Testing for Respiratory Viruses 11. Molecular Testing for Diseases Associated with Bacterial Infection 12. Agents Associated with Sexually-transmitted Infections 13. Molecular Methods for Healthcare-Acquired Infections 14. Molecular Testing in Emerging Infectious Diseases 15. Molecular and Serological Testing in the Setting of a Global Pandemic

Section 3 Molecular Testing in Genetic Disease 16. Non-invasive Prenatal Screening (NIPS) for Fetal Aneuploidies 17. Molecular Testing in Cardiomyopathies 18. Molecular Diagnostics for Coagulopathies 19. Molecular Diagnosis of Cystic Fibrosis 20. Molecular Testing in Hemochromatosis 21. Molecular Testing for Spinal Muscular Atrophy 22. Molecular Testing for Autism Spectrum Disorders

Section 4 Molecular Testing in Oncology 23. Molecular Testing in Breast Cancer 24. Molecular Testing in Lung Cancer 25. Molecular Testing in Colorectal Cancer 26. Molecular Pathology and Testing in Melanocytic Tumors 27. Molecular Testing for Glioblastoma 28. Molecular Testing in Pancreatic Cancer 29. Molecular Testing in Gynecologic Cancer 30. The Emerging Genetic Landscape in Renal Cell Carcinoma 31. Molecular Testing in Thyroid Cancer 32. Molecular Testing for Pediatric Cancers 33. Molecular Pathogenesis of Soft Tissue and Bone Tumors 34. Molecular Pathology of Gastrointestinal Stromal Tumors 35. Molecular Pathology of Liver Cancer

Section 5 Molecular Testing in Hematopathology 36. Molecular Testing in Myeloproliferative Neoplasms 37. Molecular Testing in Myelodysplastic Syndromes 38. Molecular Testing in Acute Myeloid Leukemia 39. Molecular Testing in the Assessment of Bone Marrow Transplant Engraftment

Section 6 Molecular Testing in Personalized Medicine 40. Pharmacogenomics in Cardiovascular Disease 41. Personalized Medicine for Disorders of Hemostasis and Thrombosis 42. Personalized Medicine in Cancer Treatment

Section 7 The Future of Molecular Testing 43. Imaging Mass Spectroscopy in Clinical Pathology 44. Artificial Intelligence and Deep Learning in Molecular Testing 45. Nanotechnology in Molecular Diagnostics 46. Chip-based Nanotechnology in the Molecular Pathology Laboratory and Beyond 47. Translational and Clinical Applications of the GeoMx� Digital Spatial Profiling Platform

Authors

William B. Coleman Executive Officer, American Society for Investigative Pathology, Rockville, MD, USA. William B. Coleman, PhD is the Executive Officer for the American Society for Investigative Pathology (Rockville, MD). Prior to taking this position with the American Society for Investigative Pathology, Dr. Coleman spent 28 years at the University of North Carolina School of Medicine (Chapel Hill, NC), first as a postdoctoral fellow (1990-1995) and then as a faculty member (1995-2018) in the Department of Pathology and Laboratory Medicine. During his time at the UNC School of Medicine, Dr. Coleman served as Director of Graduate Studies for the Molecular and Cellular Pathology Ph.D. Program (2006-2012; now the Pathobiology and Translational Medicine Ph.D. Program), was a co-founder of the UNC Program in Translational Medicine and served as its Co-Director (2006-2015) and then its Director (2015-2018), was affiliated with the Curriculum in Toxicology, the Cancer Biology Training Program, and was a member of the UNC Lineberger Comprehensive Cancer Center. Dr. Coleman was active in teaching biomedical graduate students and is a four-time recipient of the Joe W. Grisham Award for Excellence in Graduate Student Teaching from the Molecular and Cellular Pathology graduate students at the UNC School of Medicine. Prior to becoming an employee, Dr. Coleman was active in the leadership of the American Society for Investigative Pathology, serving in various roles including President (2015-2016). Dr. Coleman was honored with the ASIP Outstanding Investigator Award in 2013 from the American Society for Investigative Pathology. He is also a long-time member of the American Association for Cancer Research. He serves as Senior Associate Editor for The American Journal of Pathology, and is an Associate Editor for BMC Cancer, and PLoS One, and serves on the editorial boards of Clinica Chimica Acta, Experimental and Molecular Pathology, Archives of Pathology and Laboratory Medicine, Laboratory Investigation, and Current Pathobiology Reports, and has served as an ad hoc reviewer for 99 other journals. Dr. Coleman's major research interests are in the molecular pathogenesis of human cancers, with a specific interest in breast cancer epigenetics, liver carcinogenesis, and lung cancer biology. His research was funded by the NIH/NCI, The Susan G. Komen Breast Cancer Foundation, Friends for an Earlier Breast Cancer Test, and the UNC Lineberger Comprehensive Cancer Center. Dr. Coleman is the author of over 140 original research articles, reviews, and book chapters. In addition, Dr. Coleman has co-edited or co-authored ten books on topics related to molecular pathology, molecular diagnostics, and the molecular pathogenesis of human cancer. Gregory J. Tsongalis Laboratory for Clinical Genomics and Advanced Technology (CGAT), Department of Pathology and Laboratory Medicine, Dartmouth, Hitchcock Medical Center and Dartmouth Cancer Center, Lebanon, NH, United States and the Geisel School of Medicine at Dartmouth, Hanover, NH, USA. Gregory J. Tsongalis, PhD, HCLD, CC, FNACB., is the Vice Chair for Research and the Director of the Laboratory for Clinical Genomics and Advanced Technology (CGAT) in the Department of Pathology and Laboratory Medicine at the Dartmouth-Hitchcock Medical Center and Norris Cotton Cancer Center (NCCC) in Lebanon, NH. He is a Professor of Pathology and Laboratory Medicine at the Audrey and Theodor Geisel School of Medicine at Dartmouth in Hanover, NH and a member of the NCCC Molecular Therapeutics Program and the gastrointestinal and breast cancer clinical oncology groups. In 2016 he became a member of Dartmouth College's Program in Experimental and Molecular Medicine (PEMM), and he has served on the advisory board of the Health Care Genetics Professional Science Master's Degree Program and Diagnostic Genetic Sciences Program at the University of Connecticut (Storrs, CT). His area of expertise is in the development and implementation of clinical molecular diagnostic technologies. His research interests are in the pathogenesis of human cancers, personalized medicine and disruptive technologies. He has authored/edited twelve textbooks in the field of molecular pathology, published more than 230 peer reviewed manuscripts, and has been an invited speaker at both national and international meetings. He has served on numerous committees of the American Association for Clinical Chemistry, the American Society for Investigative Pathology, the Federation for American Societies for Experimental Biology, and the Association for Molecular Pathology (where he is a past President). He is active in the Alliance for Clinical Trials in Oncology, the Association for Molecular Pathology, the American Association for Clinical Chemistry, the American Association of Bioanalysts, and the American Society for Investigative Pathology. He serves on the editorial boards of 8 journals including Clinical Chemistry, Experimental and Molecular Pathology, and the Journal of Molecular Diagnostics. In 2016, Dr. Tsongalis received the Norris Cotton Cancer Center Award for Excellence, in 2017 the Association for Molecular Pathology (AMP) Jeffrey A. Kant Leadership Award, and in 2019 the American Society for Investigative Pathology Robbins Distinguished Educator Award. He also serves on numerous corporate scientific advisory boards.