Practical Oncologic Molecular Pathology: Frequently Asked Questions

Description

This book is a review and high-yield reference on the clinical molecular diagnostics of malignant neoplasms. It aims to address the practical questions frequently encountered in the molecular oncology practice, as well as key points and pitfalls in the clinical interpretation of molecular tests in guiding precision cancer management. The text uses a Q&A format and case presentations, with emphasis on understanding the molecular test methods, diagnosis, classification, risk assessment and clinical correlation. Starting with an update on the molecular biology of cancer, the book focuses on the topics related to molecular diagnostics and genetics-based precision oncology. Separate chapters are dedicated to discussion of the bioinformatics for the analysis of genetic/genomic data generated from molecular assays, and quality control (QC)/quality assurance (QA) programs in the clinical laboratories; both are critical in producing high quality results for clinical care of cancer patients. These are followed by organ system-based reviews and discussions on the molecular genetic abnormalities and related tests covering diverse types of common to rare malignant neoplasms. This book also provides up-to-date knowledge related to malignant neoplasms, discusses the established as well as evolving requirements for pathologic diagnosis of these malignancies. It also discusses the cost effective utilization of molecular tests in clinical oncology. Written by experts in the field, Practical Oncologic Molecular Pathology serves as a valuable reference for practicing pathologists, fellows, residents and other health care professionals. Preface Contents Contributors Part I: Molecular Methods and Data Analysis in Clinical Molecular Diagnostic Laboratories 1: The Molecular Pathobiology of Malignant Process and Molecular Diagnostic Testing for Cancer List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objectives Case History Initial Work-up Histologic Findings Molecular Genetic Study Final Diagnosis Discussion Case 2 Learning Objectives Case History Molecular Genetic Studies Final Diagnosis Clinical Follow-Up Discussion Case 3 Learning Objectives Case History Laboratory Findings Molecular Genetic Studies Final Diagnosis Discussion Case 4 Learning Objective Case History Molecular Genetic Studies Final Diagnosis Discussion Case 5 Learning Objectives Case History Molecular Genetic Studies Final Diagnosis Discussion References 2: Molecular Diagnostic Methods List of Frequently Asked Questions Frequently Asked Questions Case Examples Case #1 Learning Objectives Case History Final Diagnosis Discussion Case #2 Learning Objectives Case History Laboratory Work-up Histologic Findings Molecular Genetic Studies Final Diagnosis Discussion NGS Sequencing Results Case #3 Learning Objectives Case History Final Diagnosis Discussion Case #4 Learning Objectives Case History Final Diagnosis Discussion References 3: Bioinformatics Analysis in Molecular Pathology List of Frequently Asked Questions Frequently Asked Questions Cases Case 1: HGVS Nomenclature and Rules Discussion for Case 1 Case 2: Read Depth and Molecular Bar Coding Discussion for Case 2 Case 3: FASTQ Format and Mate-Pairs Discussion for Case 3 Case 4: Variant Filtering Discussion for Case 4 Case 5: Protected Health Information and Cloud Services Discussion for Case 5 References 4: Quality Assurance and Quality Control in Molecular Diagnostic Laboratories List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Case 2 Learning Objective Case History Case 3 Learning Objective Case History References Part II: Molecular Pathology of Solid and Soft Tissue Tumors 5: Breast and Gynecologic Tumors List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Case History Histologic Finding Differential Diagnosis Ancillary Studies Final Diagnosis Discussion Case 2 History HER2 Testing Final HER2 Interpretation Discussion Case 3 History Gross Findings Histologic Findings Differential Diagnosis Ancillary Studies Final Diagnosis Discussion Case 4 History Histologic Findings MMR Studies Genetic Testing Follow-up Discussion References 6: Tumors of the Central Nervous System List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Discussion Case 2 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Discussion Case 3 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Discussion Case 4 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Discussion Case 5 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Discussion Case 6 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Discussion References 7: Lung Cancer List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objectives Case History Pathological Diagnosis Molecular Genetic Study Clinical Follow-Up Discussion Case 2 Learning Objective Case History Pathological Diagnosis Molecular Genetic Studies Clinical Follow-Up Discussion Case 3 Learning Objectives Case History Pathologic Diagnosis Molecular Genetic Studies Discussion Case 4 Learning Objectives Case History Pathological Diagnosis Molecular Genetic Studies Discussion Case 5 Learning Objectives Case History Pathologic Diagnosis FISH Analysis Discussion Case 6 Learning Objective Case History Pathologic Diagnosis Molecular Genetic Studies Discussion References 8: Gastrointestinal, Hepatobiliary, and Pancreatic Tumors List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Surgical Pathology Findings Molecular Genetic Findings Final Diagnosis/Summary Follow-Up Discussion Case 2 Learning Objective Case History Surgical Pathology Findings Molecular Genetic Findings Final Diagnosis/Summary Follow-Up Discussion Case 3 Learning Objective Case History Surgical Pathology Findings Molecular Genetic Findings Final Diagnosis/Summary Follow-Up Discussion References 9: Skin Tumors List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Histologic Findings Genetic Study Final Diagnosis Follow-Up Discussion Case 2 Learning Objective Case History Histologic Findings Genetic Study Final Diagnosis Follow-Up Discussion Case 3 Learning Objective Case History Histologic Findings Genetic Study Additional Clinical History Final Diagnosis Follow-Up Discussion Case 4 Learning Objective Case History Histologic Findings Genetic Study Final Diagnosis Follow-Up Discussion References 10: Soft Tissue Tumors List of Frequently Asked Questions Frequently Asked Questions Case 1 Case History Histologic Features Choice of Molecular Testing Molecular Study Final Diagnosis Case Discussion Case 2 Case History Histologic Features Molecular Study Final Diagnosis Case Discussion Case 3 Case History Histologic Features Molecular Study Final Diagnosis Case Discussion Case 4 Case History Histologic Features FISH Results Final Diagnosis Case Discussion Case 5 Case History Histologic Features Molecular Study Final Diagnosis Case Discussion Case 6 Case History Histologic Features FISH Results Final Diagnosis Case Discussion Case 7 Case History Histologic Features Molecular Study Final Diagnosis Case Discussion Case 8 Case History Histologic Features Molecular Study Final Diagnosis Case Discussion Case 9 Case History Histologic Features Molecular Study Reflective FISH Results Final Diagnosis Case Discussion Case 10 Case History Histologic Features Molecular Study Final Diagnosis Case Discussion References 11: Genitourinary Neoplasms List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Histologic Findings Molecular Genetic Study Final Diagnosis Follow-Up Discussion Case 2 Learning Objective Case History Molecular Genetic Study Histologic Findings Final Diagnosis Follow-Up Discussion Case 3 Learning Objective Case History Histologic Findings Molecular Genetic Study Final Diagnosis Follow-Up Discussion References 12: Hereditary Cancer Syndromes and Inherited Cancer Risks List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objectives Case History Genetic Study Final Diagnosis Follow-Up Discussion Case 2 Learning Objective Case History Genetic Study Final Diagnosis Follow-Up Discussion Case 3 Learning Objective Case History Genetic Study Final Diagnosis Follow-Up Discussion Case 4 Learning Objective Case History Genetic Study Final Diagnosis Follow-Up Discussion Case 5 Learning Objective Case History Genetic Study Final Diagnosis Follow-Up Discussion Case 6 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Follow-Up Discussion Case 7 Learning Objective Case History Histologic Features Genetic Study Final Diagnosis Follow-Up Discussion References Part III: Molecular Hematopathology 13: Acute Myeloid Leukemia List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objectives Case History and Laboratory Findings Laboratory Findings Pathology Molecular Genetic Tests Final Diagnosis Follow-Up Discussion Case 2 Learning Objectives Case History Laboratory Findings Flow Cytometry Histologic Features Preliminary Diagnosis Cytogenetic and Molecular Tests Final Diagnosis Discussion Case 3 Learning Objective Case History Cytogenetic Studies Molecular Genetic Studies Final Diagnosis Discussion Case 4 Learning Objective Case History Molecular Genetic Studies Final Diagnosis Treatment and Clinical Follow-Up Discussion Case 5 Learning Objective Case History Genetic and Molecular Studies Final Diagnosis Treatment and Clinical Follow-Up Discussion References 14: Myeloproliferative Neoplasms, Myelodysplastic/Myeloproliferative Neoplasms, and Myelodysplastic Syndromes List of Frequently Asked Questions Frequently Asked Questions Case Presentation Case 1 Learning Objectives Case History Bone Marrow, Biopsy, and Aspirate Differential Diagnosis Ancillary Studies Final Diagnosis Take Home Messages Case 2 Learning Objectives Case History Bone Marrow, Biopsy and Aspirate Differential Diagnosis Ancillary Studies Final Diagnosis Take Home Messages Case 3 Learning Objectives Case History Bone Marrow, Biopsy, and Aspirate (BM-184793) Differential Diagnosis Ancillary Studies Final Diagnosis Take Home Messages Case 4 Learning Objectives Case History Bone Marrow, Biopsy, and Aspirate Differential Diagnosis Ancillary Studies Final Diagnosis Take Home Messages Case 5 Learning Objectives Case History Bone Marrow, Biopsy, and Aspirate Differential Diagnosis Ancillary Studies Final Diagnosis Take Home Messages Case 6 Learning Objectives Case History Bone Marrow, Biopsy, and Aspirate Differential Diagnosis Ancillary Studies Final Diagnosis Take Home Messages References 15: Precursor Lymphoid Neoplasms List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Laboratory Findings Genetic Study Final Diagnosis Discussion Case 2 (Courtesy of Dr. Peter Papenhausen at LabCorp) Learning Objective Case History Laboratory Findings Genetic Study Final Diagnosis Discussion Case 3 Learning Objective Case History Genetic Study Final Diagnosis Follow-Up Discussion Case 4 Learning Objective Case History Laboratory Findings Genetic Study Final Diagnosis Follow-Up Discussion References 16: Mature B-Cell Neoplasms List of Frequently Asked Questions Frequently Asked Questions Cases Presentation Case 1 Learning Objectives Case History Initial Workup Histologic Findings Molecular Genetic Study Final Diagnosis Follow-Up Discussion Case 2 Learning Objectives Case History Histologic Findings Molecular Genetic Study Final Diagnosis Follow-Up Discussion Case 3 Learning Objectives Case History Initial Workup Histologic Findings Molecular Genetic Study Final Diagnosis Follow-Up Discussion References 17: Plasma Cell Neoplasms List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective(s) Case History Laboratory and Morphology Findings Imaging Studies Genetic Study Final Diagnosis Discussion Case 2 Learning Objectives Case History Laboratory and Morphology Findings Imaging Studies Genetic Studies Final Diagnosis Follow-Up Discussion Case 3 Learning Objective(s) Case History Laboratory and Morphologic Findings Imaging Studies Genetic Studies Final Diagnosis Follow-Up Discussion Case 4 Learning Objectives Case History Laboratory and Morphology Findings Genetic Studies Final Diagnosis Follow-Up Discussion Case 5 Learning Objectives Case History Laboratory and Morphology Findings Genetic Studies Final Diagnosis Follow-Up Discussion References 18: Mature T- and NK-Cell Neoplasms List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Histologic Features Laboratory Findings Molecular Genetic Studies Final Diagnosis Follow-Up Discussion Case 2 Case History Histologic Features Laboratory Findings Molecular Genetic Study Final Diagnosis Follow-Up Discussion Case 3 Learning Objective Case History Histologic Features Laboratory Findings Molecular Genetic Studies Final Diagnosis Follow-Up Discussion Case 4 Case History Histologic Features Laboratory Findings Molecular Genetic Studies Final Diagnosis Follow-Up Discussion Case 5 Case History Histologic Features Laboratory Findings Molecular Genetic Studies Final Diagnosis Discussion References 19: Histiocytic and Dendritic Cell Neoplasms List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case #1 Learning Objectives Case History Morphologic and Immunophenotypic Features Molecular Studies Diagnosis Discussion Case #2 Learning Objectives Case History Morphologic and Immunophenotypic Features Molecular and Genetic Studies Diagnosis Discussion Case #3 Learning Objectives Case History Clinical Imaging Studies Morphologic and Immunophenotypic Features Molecular and Genetic Studies Diagnosis Discussion Case #4 Learning Objectives Case History Morphologic and Immunophenotypic Features Diagnosis Discussion Case #5 Learning Objectives Case History Morphologic and Immunophenotypic Features Final Diagnosis Discussion Case #6 Learning Objectives Case History Morphologic and Immunophenotypic Features Diagnosis Discussion Case #7 Learning Objectives Case History Morphologic and Immunophenotypic Features Molecular and Genetic Studies Diagnosis Discussion References 20: Bone Marrow Engraftment Analysis List of Frequently Asked Questions Frequently Asked Questions Case Presentations Case 1 Learning Objective Case History Laboratory Findings Final Diagnosis Follow-Up Discussion Case 2 Learning Objective Case History Laboratory Testing Discussion Case 3 Learning Objective Case History Laboratory Findings Genetic Study Final Diagnosis Discussion References Index