Advances in Molecular Pathology

1st Edition, Volume 6-1 - October 18, 2023
Editor: Gregory J. Tsongalis
Language: English
Hardback ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 0 5 1 - 9
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 0 5 2 - 6

Advances in Molecular Pathology reviews the year’s most important findings and updates within the field in order to provide molecular pathologists with the current clinical… Read more

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Advances in Molecular Pathology reviews the year’s most important findings and updates within the field in order to provide molecular pathologists with the current clinical information they need to improve patient outcomes. A distinguished editorial board, led by Dr. Gregory Tsongalis, identifies key areas of major progress and controversy and invites preeminent specialists to contribute original articles devoted to these topics. These insightful overviews in molecular pathology inform and enhance clinical practice by bringing concepts to a clinical level and exploring their everyday impact on patient care.

Cover image
Title page
Table of Contents
Copyright
Editorial Board
Contributors
Preface
Genetics
The Landscape of Clinical Whole Genome Sequencing and the Emergence of Rapid Genetic Diagnosis in Critical Care
Key points
Introduction
Whole genome sequencing for clinical interpretation
Landscape of whole genome sequencing
Rapid sequencing and genome interpretation
Future projections and summary
Hematopathology
Blastic Plasmacytoid Dendritic Cell Neoplasm: Advances in Molecular Markers and Treatments
Key points
Introduction
Epigenetic dysregulation and modern therapeutic era
The splicing factor ZRSR2 and BPDCN
Karyotyping, FISH and comparative genomic hybridization (CGH)
CD123 (interleukin-3 alpha chain receptor)
Targeting BCL2 and modern therapeutic era
Multiple myeloma-based regimens
Treatment with conventional chemotherapy and stem cell transplant
Cytotoxic chemotherapy in combination with targeted therapy
Future implications
Summary
Disclosure
Clinics care points
Molecular Classification of Diffuse Large B Cell Lymphoma: Impact on Prognosis and Treatment
Key points
Introduction
Classification based on structural genetic a lterations and dark zone gene expression
Discussion and conclusions
Clinics care points
Disclosure
B-Lymphoblastic Leukemia/Lymphoma: Newly Defined Entities and Subtypes by Molecular Methods
Key points
Introduction
B-lymphoblastic leukemia/lymphoma with high hyperdiploidy/B-ALL, hyperdiploid
B-lymphoblastic leukemia/lymphoma with hypodiploidy/B-ALL, low hypodiploid and B-ALL, near-haploid
B-lymphoblastic leukemia/lymphoma with iAMP21/B-ALL with iAMP21
B-lymphoblastic leukemia/lymphoma with BCR::ABL1 fusion/B-ALL with t(9;22) (q34.1;q11.2)/BCR::ABL1
B-lymphoblastic leukemia/lymphoma with BCR::ABL1-like features/B-ALL, BCR::ABL1-like
B-lymphoblastic leukemia/lymphoma with KMT2A rearrangement/B-ALL with t(v;11q23.3)/KMT2A rearranged
B-lymphoblastic leukemia/lymphoma with ETV6::RUNX1 fusion/B-ALL with t(12;21) (p13.2;q22.1)/ETV6::RUNX1
B-lymphoblastic leukemia/lymphoma with ETV6::RUNX1-like features/provisional entity: B-ALL, ETV6::RUNX1-like
B-lymphoblastic leukemia/lymphoma with TCF3::PBX1 fusion/B-ALL with t(1;19) (q23.3;p13.3)/TCF3::PBX1
B-lymphoblastic leukemia/lymphoma with IGH::IL3 fusion/B-ALL with t(5;14) (q31.1;q32.3)/IL3::IGH
B-lymphoblastic leukemia/lymphoma with TCF3::HLF fusion/B-ALL with HLF rearrangement
Other entities in the WHO and ICC defined by recurring genetics
Summary
Disclosure
Clinics care points
Infectious Disease
Molecular Diagnostics for Invasive Fungal Infections: Barriers to Widespread Adoption and Opportunities for Improvement
Key points
Introduction
Key issues
Key issues
Key issues
Key issues
Key issues
Summary
Clinic care points
Disclosure
Recently Updated Sexually Transmitted Infection Screening Guidelines and Impact on Molecular Diagnostics
Key points
Introduction
HIV
Mycoplasma genitalium
Summary
Disclosure
Quantitative Viral Load Monitoring: How far are We from Commutable Results?
Key points
Introduction
Viral load monitoring for specific viruses
Viral load commutability and international standards
Impact of international standards
Reasons for persistent assay to assay variation
Other strategies for commutability
Clinics care points
Pharmacogenomics
The Current State of Pharmacoeconomics and Reimbursement for Pharmacogenomics
Key points
Introduction
Guidelines for testing
Health coverage in the United States
Billing and coding for pharmacogenetic testing
Reimbursement for testing services
Medicare coverage
Private health coverage for testing
Barriers to pharmacogenetic testing
Summary
Clinics care points
Disclosure
Long-read Sequencing for Germline Pharmacogenomic Testing
Key points
Introduction
Clinical pharmacogenomics
Resources for pharmacogenomic testing and implementation
Molecular genetic testing technologies: genotyping and short-read sequencing
Molecular genetic testing technologies: long-read sequencing
Pharmacogenomic long-read sequencing
Summary and future directions
Disclosure
Funding
Practical Approaches to Pharmacogenomics in Patients Using Vitamins/Supplements and Medical Marijuana
Key points
Dietary supplements
Vitamins
Cannabis
Summary
Clinics care points
Informatics
Computer-Based Simulation of DNA Short-Read Next-Generation Sequencing: A Review of Software from a Clinical Perspective
Key points
Introduction
Software for de novo simulation of DNA short-read next-generation sequencing data
ART
ArtificialFastqGenerator
CapSim
Enhanced Artificial Genome Engine
General Error Model-Based Simulator
NExt-generation sequencing Analysis Toolkit
Pair-End Reads Simulator
VarIant SimulatOR
Wessim/weighted-Wessim
Software that primarily simulate genomic variation
HeteroGenesis
Pysim-SV
RSVsim
Varsim
Perspectives on simulated genomic data in the clinical laboratory setting
Future directions for development
Clinics care points
Solid Tumors
Minimal Residual Disease Testing in Solid Tumors
Key points
Introduction
Solid tumor minimal residual disease testing through liquid biopsy
Sensitivity of solid tumor minimal residual disease testing
Clinical utility of minimal residual disease testing in solid tumors
Current limitation/future directions
Summary
Clinics care points
Disclosure
Mutational Signatures in Solid Tumors
Key points
Introduction
Types of mutations
Laboratory techniques to detect mutational signatures
Mutational signatures currently identified
Endogenous causes of mutational signatures
Discussion
Clinical application of mutational signatures
Summary
Clinics care points
Disclosure
Multi-Cancer Early Detection: Blood-Based Screening, Multiomics, Machine Learning, and New Clinical Pathways
Key points
Introduction
Defining multi-cancer early detection
Multi-cancer early detection analytes
Multiomics cancer screening
Multi-cancer early detection data analysis
Assessing multi-cancer early detection test performance
Clinical considerations for multi-cancer early detection testing
What could the future look like? Promise and peril
Disclosure
Hot Topics in Molecular Pathology
Rapid Whole Genome Sequencing in Critically Ill Newborns
Key points
Introduction
General content
Discussion
Summary/Conclusions
Clinics care points
Molecular Diagnosis of Emerging Pathogens: Policy and Practical Considerations for Laboratorians
Key points
Introduction
The Emergency Use Authorization process for beginners
COVID-19—a case study in meeting EUA compliance
Mpox—considerations for rapid implementation of novel pathogen testing
Summary
Clinics care points
Disclosure

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.

Affiliations and expertise

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

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