Diagnostic Molecular Pathology : A Guide to Applied Molecular Testing / edited by William B. Coleman and Gregory J. Tsongalis.

Format:

Book

Contributor:

Coleman, William B., 1811 or 1812- editor.

Tsongalis, Gregory J., editor.

Language:

English

Subjects (All):

Molecular diagnosis.

Pathology, Molecular.

Molecular Diagnostic Techniques.

Precision Medicine.

Medical Subjects:

Pathology, Molecular.

Molecular Diagnostic Techniques.

Precision Medicine.

Physical Description:

1 online resource (846 pages)

Edition:

Second edition.

Place of Publication:

London, England : Academic Press, [2024]

Summary:

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.- 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

Contents:

Front Cover

Diagnostic Molecular Pathology

Copyright Page

Dedication

Contents

List of contributors

Preface

1 Introduction to molecular testing in human disease

Introduction

Mutations and epimutations

Genetic alterations

Epigenetic alterations

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

2 Laboratory approaches in molecular pathology: the polymerase chain reaction

The polymerase chain reaction

Components of the polymerase chain reaction

DNA template

DNA polymerase enzyme

Oligodeoxynucleotide primers

Polymerase chain reaction buffer

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

Hot-start and nested polymerase chain reaction

Polymerase chain reaction analysis of RNA

Real-time polymerase chain reaction

Digital polymerase chain reaction

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

Molecular technology in next-generation sequencing

Distinguishing whole-genome sequencing from whole-exome sequencing

Limitations of clinical genome sequencing

Design and validation of a genome-scale test

Bioinformatics consideration for clinical genome sequencing

Interpreting variants in clinical genome sequencing.

Variants of uncertain significance in clinical genome sequencing

Secondary findings and the ethical, legal, and social implications of clinical genome sequencing

Clinical utility of clinical genome sequencing

Enhancing our understanding of the noncoding genome

Whole-exome sequencing and whole-genome sequencing for oncology applications

Applications of whole-genome sequencing

Public health screening

Personalized medicine and pharmacogenomics

Optimism surrounding whole-genome sequencing

4 Long-read sequencing for metagenomics in microbiology

Nanopore sequencing

PacBio single molecule, real-time

Clinical applications

Characteristics of metagenomics studies

Potential added utility of long-read techniques

Current applications and examples

Limitations and complications

Potential future applications of metagenomics

Summary

Disclosure

5 Molecular testing for human immunodeficiency virus

Background on human immunodeficiency virus infection and AIDS

Overall epidemiology

Life cycle of human immunodeficiency virus

Transmission of human immunodeficiency virus

Natural history of human immunodeficiency virus infection

Human immunodeficiency virus evolution during treatment

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

Diagnosis of human immunodeficiency virus infection

Follow-up of human immunodeficiency virus-infected subjects

Summary of human immunodeficiency virus molecular testing in the course of human immunodeficiency virus infection

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

Screening of blood products

Screening of organs and tissues from human donors.

Screening human immunodeficiency virus-1 genome in semen in medically assisted procreation

Screening of neonates born to human immunodeficiency virus-infected mothers

Use of human immunodeficiency virus-1 molecular tools in low-income and middle-income countries

New insights in molecular human immunodeficiency virus testing

Improvement of the sensitivity of quantitative human immunodeficiency virus-1 viral load tests

Development of new point-of-care molecular assays for human immunodeficiency virus testing

Present and future of ART resistance determination

Conclusion

6 Molecular testing in hepatitis virus-related disease

Hepatitis A virus and hepatitis A virus RNA detection

Hepatitis B virus infection

Hepatitis B virus DNA and RNA detection

Hepatitis B virus genotyping

Molecular testing for hepatitis B virus antiviral resistance

Hepatitis C virus infection and hepatitis C virus RNA detection

Hepatitis C virus genotyping

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

7 Molecular testing for human papillomaviruses

Molecular target

Pathophysiology of human papillomaviruses

Human papillomaviruses and cervical cancer

Molecular technologies

Digene Hybrid Capture 2

Cervista HPV HR and Cervista HPV 16/18

Aptima HPV and Aptima HPV 16 18/45

Roche cobas HPV

BD Onclarity HPV

Clinical utility

Limitations

8 Molecular testing for parvoviruses

The family Parvoviridae

Parvovirus B19

The virus

Transmission

Infection-early events

Infection-late events

Virus persistence

Fetal infection

Target and samples

B19V genotypes

Molecular technologies.

Technical developments

qPCR assay design

qPCR assay validation

In situ hybridization techniques

Immunological techniques

Diagnostic approach

qPCR result interpretation and relevance

Limitations of testing

Other parvoviruses

Human bocaparvovirus

Human tetraparvovirus

Human protoparvovirus

9 Molecular testing for polyoma viruses

Molecular targets

The BK virus

The JC virus

Other polyoma viruses

10 Molecular testing for respiratory viruses

Viral pathogens targeted by molecular testing

Influenza

Paramyxoviruses

Adenovirus

Enteroviruses-including rhinoviruses and human parechoviruses

Coronaviruses

Clinical utility of molecular diagnostics for respiratory virus infection

Upper respiratory tract infections

The common cold

Influenza-like illness

Lower respiratory tract infections

Croup

Bronchiolitis

Pneumonia

Molecular technologies and limitations of testing

Specimen collection

Timing of disease/virus shedding

Seasonality

Interpretation of nucleic acid amplification test results

Antiviral resistance testing

Conclusions

Acknowledgments

11 Molecular testing for diseases associated with bacterial infections

Identification of bacteria

Probes

Molecular target(s) and technologies

Sequencing

Matrix-assisted laser desorption ionization time of flight mass spectrometry

Respiratory infections

Molecular target(s) and technologies.

Clinical utility

Gastrointestinal infections

Bloodstream infections

Peptide nucleic acid florescence in situ hybridization

Multiplex assays from positive blood cultures

Group B Streptococcus screening

Future perspectives

12 Agents associated with sexually transmitted infections

Syphilis

Overview of the disease and its epidemiology

Current diagnosis of syphilis

Place of syphilis molecular testing

Gonorrhea

Current diagnosis of gonorrhea

Nucleic acid tests specific for gonococcal infection

Genital chlamydia infection

Nonmolecular methods of laboratory diagnosis

Molecular methods of laboratory diagnosis

Mycoplasma genitalium infection

Current diagnosis

Trichomoniasis

Diagnosis based on conventional techniques

Diagnosis based on molecular testing

Future directions

Vaginal microbiome and sexually transmitted infections

Multiplex approach of sexually transmitted infection diagnosis using molecular tools

Point-of-care diagnostics for sexually transmitted infections

Molecular tools dedicated to antimicrobial susceptibility

Concluding remarks

13 Molecular methods for healthcare-acquired infections

Introduction.

Methicillin-resistant Staphylococcus aureus molecular diagnostic testing and clinical utility.

Notes:

Includes bibliographical references and index.

Description based on print version record.

ISBN:

0-12-822993-4