Advances in Molecular Pathology, 2021

1st Edition, Volume 4-1 - October 13, 2021
Imprint: Elsevier
Editor: Gregory J. Tsongalis
Language: English
Hardback ISBN:
9 7 8 - 0 - 3 2 3 - 8 1 3 3 5 - 8
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 8 1 3 3 6 - 5

Advances in Molecular Pathology is an annual review publication that covers the current practices and latest developments in the field of Molecular Pathology. Each issue is divided… Read more

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Advances in Molecular Pathology is an annual review publication that covers the current practices and latest developments in the field of Molecular Pathology. Each issue is divided into sections for comprehensive coverage of all subspecialty areas within molecular pathology, including, Genetics, Hematopathology, Infectious Disease, Pharmacogenomics, Informatics, Solid Tumors, and special topics on COVID-19. The Editor-in-Chief of the publication is Dr. Gregory Tsongalis, a leading expert in the field. Topics covered this year include but are not limited to: Phenotype Association and Variant Pathogenicity Prediction Tools in Genomic Analysis; The application of noninvasive prenatal screening to detect copy number variations; Next generation cytogenomics using optical mapping; Review of molecular in APL; NGS for MRD in acute leukemia; Review of emerging technologies as they pertain to infectious disease testing; Germline genetic variants that predict drug response; Nutrigenomics; PGx of hypertension; Genomic data for blood typing, specifically both through NGS and arrays; Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis; and Cell-free nucleic acids in cancer: Current approaches, challenges, and future directions.

Cover image
Title page
Table of Contents
Copyright
Editorial Board
Contributors
Preface
Genetics
Current Tools, Databases, and Resources for Phenotype and Variant Analysis of Clinical Exome Sequencing
Key points
Introduction
Phenotype association tools and databases
Variant pathogenicity: evidence codes, tools, and databases
Genomic analysis: current and future avenues to consider
Summary
Clinics care points
Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA
Key points
Introduction
Factors affecting noninvasive prenatal testing screening subchromosomal copy number variation
Challenges
Summary
Applications of Optical Genome Mapping in Next-Generation Cytogenetics and Genomics
Key points
Introduction
Significance
From massively parallel sequencing to next-generation karyo-mapping
Cytogenomic applications of optical mapping in constitutional disease
Cytogenomic applications using optical mapping in acquired disease
Resolving intractable regions of the human genome: repeat expansions disorders
Bioinformatics workflow in optical genome mapping
Present relevance and future avenues of optical mapping in medical genetics
Summary
Hematopathology
Diagnosis of Variant Translocations in Acute Promyelocytic Leukemia
Key points
Introduction
Clinical features
Microscopy
Immunophenotype and special stains
Genetic profile
Variant translocations
Molecular prognostic markers
Treatment
Prognosis
Summary
Next-Generation Sequencing for Measurable Residual Disease Assessment in Acute Leukemia
Key points
Introduction
Next generation sequencing-based measurable residual disease assessment: performance characteristics and comparison with other assessment methodologies
Disease-specific applications of next generation sequencing-based measurable residual disease assessment
Additional methodologies and considerations
Summary
Clinics care points
Molecular Profile of BCR-ABL1 Negative Myeloproliferative Neoplasms and Its Impact on Prognosis and Management
Key points
Introduction
Driver mutations in myeloproliferative neoplasms
Additional mutations in myeloproliferative neoplasms
Clinical applications of next-generation sequencing in myeloproliferative neoplasms
Summary
Disclosure
Infectious Disease
Engineering Consideration for Emerging Essential Nucleic Acid Tests for Point-of-Care Diagnostics
Key points
Introduction
Significance
Three stages of nucleic acid test
Discussion and summary
Summary and future directions
Acknowledgements
Emerging Molecular Diagnostic Methods for Prosthetic Joint Infections
Key points
Introduction
Discussion
Summary
Clinics care points
Pharmacogenomics
The Role of the Human Gutome on Chronic Disease: A Review of the Microbiome and Nutrigenomics
Key points
Introduction
Significance
Discussion and future perspectives
Summary
The Importance of Use of Genetics to Guide Hypertension Therapy: Using β-Blockade as an Example
Key points
Introduction
Summary
Clinics care points
Author contributions
Informatics
Blood Group Genotyping
Key points
Introduction
Significance
Present relevance and future avenues to consider or to investigate
Summary
Definitions
Clinic care points
Artificial Intelligence in Anatomic Pathology
Key points
Introduction
Slides at scale
Introduction to machine learning
Deep learning
Training and validating model
Emerging technologies, applications, and challenges
Summary
Acknowledgements
Clinics care points
Solid Tumors
Operationalizing Genomic Medicine: Laboratory Practice Considerations Beyond the Assay
Key points
Introduction
Summary
Disclosure
Cell-free Nucleic Acids in Cancer: Current Approaches, Challenges, and Future Directions
Key points
Preanalytical requirements
Technical approaches
Clinical applications
Summary
Clinics care points
Disclosure
Tumor Mutational Burden Calculation and Microsatellite Instability Detection in Clinical Next-Generation Sequencing Assays
Key points
Checkpoint blockade therapy, tumor mutational burden, and microsatellite instability
Tumor mutational burden algorithms
Microsatellite instability detection
Validation of microsatellite instability determination and tumor mutational burden calculation
Clinics care points
COVID-19
A PENNdemic Year in Review
Key points
Introduction
The first phase: navigating the emergency
The second phase: building a testing strategy
The third phase: expansion
The fourth phase: looking forward
Summary
Review of SARS-CoV-2 Antigen and Antibody Testing in Diagnosis and Community Surveillance
Key points
Introduction
Antibody testing
Antibody response
COVID-19 vaccines
SARS-CoV-2 antigen testing
Summary
Clinics care points
The Genomic Landscape of Severe Acute Respiratory Syndrome Coronavirus 2: Surveillance of Variants of Concern
Key points
Variants of concern in resource-limited settings
Seroprevalence and efficacy of vaccines
The role of genomic surveillance for monitoring a pandemic

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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Advances in Molecular Pathology, 2021

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Gregory J. Tsongalis

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