Diagnostic Molecular Pathology - A Guide to Applied Molecular Testing - 신간POD상품

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Editors: William B. Coleman, Gregory J. Tsongalis

ISBN: 9780128228241

Imprint: Academic Press

Published: October 18, 2023

Pages: 844

Hardback

Description

Diagnostic Molecular Pathology: A Guide to Applied Molecular Testing, Second Edition assembles a group of experts to discuss the molecular basis and mechanisms of major human diseases and disease processes and how the molecular features of disease can be harnessed to develop practical molecular tests for disease detection, diagnosis and prognosis. The book explains how molecular tests are utilized in the treatment of patients in personalized medicine, highlights new technologies and approaches of applied molecular pathology, and discusses how this discovery-based research yields new and useful biomarkers and tests. As it is essential to stay up-to-date on new molecular diagnostics in this changing field, this book covers critically important areas in the practice of personalized medicine and reflects our understanding of the pathology, pathogenesis and pathophysiology of human disease.

Key features

• Includes new material on mass spectrometry for infectious diseases, microbiome, homology-directed repair for PARPi, whole genome sequencing for constitutional testing, and much more

• Provides insights on the value of the molecular test in comparison to traditional methods, which include speed, precision, sensitivity and clinical impacts for the patient

• Focuses on the menu of molecular diagnostic tests available in modern molecular pathology or clinical laboratories that can be applied to disease detection, diagnosis and classification in the clinical workup of a patient

• Explains how molecular tests are utilized to guide the treatment of patients in personalized medicine (guided therapies) and for the prognostication of disease

Readership

Fellows, professional clinicians in pathology, laboratory medicine, and across internal medicine subspecialties, and secondary appeal to biomedical researchers

Table of contents

Cover image

Title page

Table of Contents

Copyright

Dedication

List of contributors

Preface

Chapter 1. Introduction to molecular testing in human disease

Abstract

Introduction

Mutations and epimutations

Sources of nucleic acids for molecular testing

Classification of disease

Molecular classification of disease

Molecular testing and companion diagnostics

Molecular detection of disease

Molecular diagnosis of disease

Molecular prognostication of disease

Perspectives

References

Chapter 2. Laboratory approaches in molecular pathology: the polymerase chain reaction

Abstract

Introduction

The polymerase chain reaction

Components of the polymerase chain reaction

Optimization of polymerase chain reaction amplification reactions

Increasing polymerase chain reaction specificity and sensitivity

Polymerase chain reaction contaminants

Inhibitors of polymerase chain reaction

Analysis of polymerase chain reaction products

Variations of the typical polymerase chain reaction amplification reaction

References

Chapter 3. Whole-exome and whole-genome sequencing in the molecular diagnostic laboratory

Abstract

Introduction

Molecular technology in next-generation sequencing

Clinical utility of clinical genome sequencing

Applications of whole-genome sequencing

Optimism surrounding whole-genome sequencing

References

Chapter 4. Long-read sequencing for metagenomics in microbiology

Abstract

Introduction

Summary

Disclosure

References

Chapter 5. Molecular testing for human immunodeficiency virus

Abstract

Introduction

Background on human immunodeficiency virus infection and AIDS

Molecular tools in the diagnosis and follow-up of human immunodeficiency virus infection

Special emphasis on the use of human immunodeficiency virus molecular tools in specific clinical situations

New insights in molecular human immunodeficiency virus testing

Conclusion

References

Chapter 6. Molecular testing in hepatitis virus-related disease

Abstract

Introduction

Hepatitis A virus and hepatitis A virus RNA detection

Hepatitis B virus infection

Hepatitis C virus infection and hepatitis C virus RNA detection

Hepatitis D virus and hepatitis D virus RNA detection

Hepatitis E virus and detection of hepatitis E virus RNA

Hepatitis G virus and its genome

Summary

References

Chapter 7. Molecular testing for human papillomaviruses

Abstract

Introduction

Molecular target

Molecular technologies

Clinical utility

Limitations

References

Chapter 8. Molecular testing for parvoviruses

Abstract

The family Parvoviridae

Parvovirus B19

Molecular target

Molecular technologies

Clinical utility

Other parvoviruses

References

Chapter 9. Molecular testing for polyoma viruses

Abstract

Introduction

Molecular targets

Molecular technologies

Clinical utility

Limitations of testing

References

Chapter 10. Molecular testing for respiratory viruses

Abstract

Introduction

Viral pathogens targeted by molecular testing

Clinical utility of molecular diagnostics for respiratory virus infection

Molecular technologies and limitations of testing

Conclusions

Acknowledgments

References

Chapter 11. Molecular testing for diseases associated with bacterial infections

Abstract

Introduction

Identification of bacteria

Respiratory infections

Gastrointestinal infections

Bloodstream infections

Group B Streptococcus screening

Future perspectives

Acknowledgments

References

Chapter 12. Agents associated with sexually transmitted infections

Abstract

Introduction

Syphilis

Gonorrhea

Genital chlamydia infection

Mycoplasma genitalium infection

Trichomoniasis

Future directions

Concluding remarks

References

Chapter 13. Molecular methods for healthcare-acquired infections

Abstract

Introduction

Methicillin-resistant Staphylococcus aureus molecular diagnostic testing and clinical utility

Methicillin-resistant Staphylococcus aureus molecular typing and clinical utility

Methicillin-resistant Staphylococcus aureus molecular screening/surveillance

Clostridioides difficile

Clostridioides difficile molecular testing and clinical utility

Clostridioides difficile molecular typing and clinical utility

Conclusions

References

Chapter 14. Molecular testing in emerging infectious diseases

Abstract

Background and catalog of emerging infectious agents

Discovery of emerging infectious agents using molecular methods

Molecular epidemiological studies of emerging infectious pathogens

Molecular diagnostics of emerging infectious pathogens

Limitations of current testing and future prospects

References

Chapter 15. Molecular and serological testing in the setting of a global pandemic

Abstract

Introduction

Historical overview

Molecular diagnostic tests for SARS-CoV-2/COVID-19

Serological testing

Surveillance of SARS-CoV-2 variants of concern

SARS-CoV-2 infection in tissues

RNA ISH

Regulation and reimbursement for COVID-19 testing

Vaccine development for management of COVID-19

Summary

References

Chapter 16. Noninvasive prenatal screening for fetal aneuploidies

Abstract

Introduction

The molecular target: approaches using plasma nucleic acids

Molecular technologies and clinical utility: four approaches by four commercial laboratories

Limitations of testing

Conclusions and future directions

References

Chapter 17. Molecular testing in inherited cardiomyopathies

Abstract

Introduction

Major forms of cardiomyopathy

Molecular target

Molecular technologies

Clinical utility

Limitations of testing

Abbreviations

References

Chapter 18. Molecular diagnostics for coagulopathies

Abstract

Introduction

Molecular targets

Coagulopathy-associated genes

Clinical utility

Limitations of testing

References

Chapter 19. Molecular diagnosis of cystic fibrosis

Abstract

Introduction

Molecular target

Molecular technologies

Clinical utility

Limitations of testing

References

Chapter 20. Molecular testing in hemochromatosis

Abstract

Introduction

Background on disease mechanisms

Clinical strategy leading to diagnosis of hemochromatosis

Clinical strategy for molecular testing in family screening

Molecular biology methods and strategy

Perspectives

Conclusions

References

Chapter 21. Molecular genetics of spinal muscular atrophy

Abstract

Introduction

Clinical presentation

Molecular targets

Molecular technologies

Clinical utility

Limitations of testing

Conclusions

References

Chapter 22. Molecular testing in autism spectrum disorder

Abstract

Introduction

Behavioral diagnosis of autism spectrum disorders

Comorbidities associated with autism spectrum disorder including syndromes

Genetic categories of autism spectrum disorder

Genetic investigation of individuals with autism spectrum disorder

Considerations for an autism-relevant gene list

Clinical utility

Limitations of testing

Conclusions

References

Chapter 23. Molecular testing in breast cancer

Abstract

Introduction

HER2 testing by fluorescence in situ hybridization

Breast cancer molecular subtype

Prognostic signatures and prediction of benefit from therapy

References

Chapter 24. Molecular testing in lung cancer

Abstract

Introduction

Molecular targets

Anaplastic lymphoma kinase

Molecular technologies

Limitations of testing

Clinical utility

Acknowledgment

References

Chapter 25. Molecular testing in colorectal cancer

Abstract

Introduction

Molecular targets

Biomarkers for targeted therapies in colorectal cancer

Biomarkers for immune checkpoint inhibitor therapies

Molecular technologies, clinical utility, and limitations of testing

References

Chapter 26. Molecular pathology and testing in melanocytic tumors

Abstract

Introduction

Molecular testing for the diagnostician

Genetic testing for the diagnostician

Molecular pathology of melanoma for the researcher

Genomic alterations in melanoma

Tissue microenvironment changes and melanoma

Important proteins in melanoma and possible directions for future research

Technologies used to interrogate the molecular pathology of melanoma

Conclusion

References

Chapter 27. Molecular testing for gliomas

Abstract

Introduction

Molecular target

Molecular technologies

Clinical utility

Limitations of testing

References

Chapter 28. Molecular testing in pancreatic cancer

Abstract

Introduction

Pancreatic ductal adenocarcinoma biomarkers in serum

Pancreatic ductal adenocarcinoma biomarkers in pancreatic juice

Pancreatic ductal adenocarcinoma biomarkers in stool

Pancreatic ductal adenocarcinoma biomarkers in urine

Pancreatic ductal adenocarcinoma biomarkers in saliva

Summary

References

Chapter 29. Molecular testing in gynecologic cancer

Abstract

Background

Human papilloma virus and uterine cervical cancer

Gestational trophoblastic disease

Endometrial stromal sarcoma

Sex cord stromal tumors: adult granulosa cell tumor and sertoli-leydig cell tumor

Lynch syndrome screening in endometrial cancer

Tumors of the gynecologic tract with switch/sucrose nonfermenting protein family alterations

Future directions in gynecologic cancer: using genomic data and theranostic testing to improve diagnostic classification

References

Chapter 30. The emerging genetic landscape of renal cell carcinoma

Abstract

Introduction

Molecular targets and technologies

Clinical utility

Limitations of testing

Acknowledgment

References

Chapter 31. Molecular testing in thyroid cancer

Abstract

Introduction

Molecular alterations in thyroid cancer

Molecular technologies

Clinical utility of molecular testing

Limitations of testing

References

Chapter 32. Molecular testing in pediatric cancers

Abstract

Introduction

Retinoblastoma

Wilms tumor

Neuroblastoma

References

Chapter 33. Molecular pathogenesis of soft tissue and bone tumors

Abstract

Glossary

Introduction

Selected soft tissue tumors

Selected bone tumors

References

Chapter 34. Molecular pathology of gastrointestinal stromal tumors

Abstract

Introduction

Molecular mechanisms of gastrointestinal stromal tumor

New developments and future directions

References

Chapter 35. Molecular pathology of hepatocellular carcinoma

Abstract

Introduction

Molecular mechanisms of hepatocellular carcinoma

New developments

References

Chapter 36. Molecular testing in myeloproliferative neoplasms

Abstract

Introduction

Clinical features and molecular pathogenesis of myeloproliferative neoplasms

Molecular testing in myeloproliferative neoplasms

Molecular methods for myeloproliferative neoplasm testing

Conclusion

References

Chapter 37. Molecular testing in myelodysplastic syndromes

Abstract

Introduction

Cytogenetic findings in myelodysplastic syndrome

Gene mutations in myelodysplastic syndrome

Clonal hematopoiesis

Role of sequencing in diagnosis of myelodysplastic syndrome

Prognostic markers in myelodysplastic syndrome

Conclusion

References

Chapter 38. Molecular testing in acute myeloid leukemia

Abstract

Abbreviations

Introduction

Diagnostic workup of acute myeloid leukemia

Cytogenetic abnormalities in acute myeloid leukemia

Gene mutations in acute myeloid leukemia

Monitoring residual disease

New horizons

References

Chapter 39. Molecular testing in the assessment of bone marrow transplant engraftment

Abstract

Introduction

Molecular target

Molecular technologies

Clinical utility

Limitations of testing

References

Chapter 40. Pharmacogenomics in cardiovascular disease

Abstract

Introduction

Clopidogrel

Conclusion and future perspective

Warfarin

Statins

Metoprolol

Antiarrhythmics

Conclusion and future perspective

Disclosures

References

Chapter 41. Personalized medicine for disorders of hemostasis and thrombosis

Abstract

Introduction

Bleeding disorders

Thrombotic disorders

Personalizing the care of patient with disorders of hemostasis and thrombosis

Summary

References

Chapter 42. Germline pharmacogenomics in cancer treatment

Abstract

Introduction

Molecular target: fluoropyrimidines and DPYD

Molecular target: irinotecan and UGT1A1

Molecular target: rasburicase and G6PD deficiency

Molecular target: tamoxifen and CYP2D6

Molecular target: thiopurines and TPMT/NUDT15

Other considerations for personalized medicine in cancer treatment

References

Chapter 43. Imaging mass spectrometry in clinical pathology

Abstract

Introduction

Imaging mass spectrometry

Applications to anatomic pathology

Advances in imaging mass spectrometry

Conclusions

References

Chapter 44. Artificial intelligence and deep learning in molecular testing

Abstract

Introduction

Introduction to machine learning

Training and evaluating a machine learning algorithm and example code

Emerging areas of application in molecular pathology

Challenges and opportunities facing the adoption of artificial intelligence technologies in molecular pathology

Conclusion

Acknowledgments

Appendix

References

Chapter 45. Nanotechnology for molecular diagnostics

Abstract

Introduction

Clinical utility of nanotechnology

Nanotechnology for enrichment

Nanotechnology for nucleic acid amplification and detection

Nanotechnology for sequencing

Nanotechnology for multiplexed cell and tissue profiling

Advantages and limitations of nanotechnology

Conclusion

References

Chapter 46. Chip-based nanotechnology in the molecular pathology laboratory and beyond

Abstract

Introduction

Today’s diagnostic workhorses

A lesson learned from COVID-19: the need for point-of-care testing

Nanoparticle-driven detection modalities

Applications of electrochemistry in pathogen detection

Multiplexing

Conclusions and perspective

Acknowledgments

References

Chapter 47. Translational and clinical applications of the GeoMx digital spatial profiling platform

Abstract

List of abbreviations

Spatial biology and introduction to technology

Clinical opportunities

Translational applications

Biomarker discovery in triple-negative breast cancer

Future of Digital Spatial Profiler clinical assays

Panel design

Evaluating assay performance

Assay signature development

Assay procedures and output

Analysis and clinical best practices

Conclusion

Acknowledgments

Funding information

Disclaimer

Conflict of interest

References

Index

About the editors

William B. Coleman

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

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.