Molecular Surgical Pathology

Since the first edition of this book in 2012, the field of molecular pathology has expanded exponentially. The advent of complete cancer genome sequencing, new diagnostic molecular tests, and biomarkers for targeted therapy and immunotherapy have demonstrated the importance of molecular tools both in patient care and in the practice of pathology. Furthermore, the development of many new molecular technologies has revolutionized the practice of modern pathology. The rapid growth of this field has led to an expansion of knowledge of molecular processes and many more clinical applications in our daily practice of surgical pathology. Thus, this updated second edition of Molecular Surgical Pathology aims to serve as the best available “quick reference” for pathologists, oncologists, geneticists, primary care physicians, and other medical professionals with an interest in this specialty. Molecular Surgical Pathology 2nd Edition focuses on the practical utility of molecular techniques and on molecular biomarkers for the practicing surgical pathologist. The emphasis is on the impact of molecular pathology for tumor classification, diagnosis and differential diagnosis, as well as its implications for patient management and personalized care. This concise overview of molecular surgical pathology and molecular classification of tumors of different organ sites will help not only practicing physicians, but also those in training, including residents and fellows in various disciplines. Preface Contents Contributors 1: Molecular Techniques/Molecular Diagnostics for Surgical Pathologists: An Overview Introduction Roles for Molecular Surgical Pathology Background Information for Molecular Genomics Background on Genome Organization DNA Sequence Variation Background for RNA Analysis Overview of Molecular Methods Sample Preparation Sample Types Sample Adequacy Fixatives DNA/RNA Extraction Basic Steps Preparation of DNA from Formalin Fixed Paraffin Embedded Tissue DNA Methylation RNA Extraction Quality Assessment of DNA and RNA Cytogenetics Background Information for Cytogenetics Classes of Pathogenic Cytogenetic Variation Cytogenetic Methods Karyotyping Fluorescent In Situ Hybridization Microarrays Molecular Diagnostics Basic Methods DNA/RNA Electrophoresis The Art of Detection Target Amplification Versus Signal Amplification Methods: PCR Principles of PCR Real-Time PCR PCR Contamination Real-Time PCR Formats SNV Detection by PCR Methods: Digital Droplet PCR (ddPCR) Methods: Rolling Circle Amplification (RCA) Methods: Hybridization Chain Reaction (HCR) Methods: Branched DNA (bDNA) Methods: Whole-Genome Amplification (WGA) Sequencing General Remarks Methods: Sequencing/Sanger Sequencing Second-Generation Sequencing Second Generation Sequencing Platforms Outline of a Representative Illumina Protocol Outline of a Representative Thermo-Fisher (Ion Torrent) Protocol Third-Generation Sequencing PacBio Oxford Nanoporetech Other Applications of NGS Bioinformatics Single-Cell ‘Omics’ General Remarks Single-Cell Protocols Spatial ‘Omics: Not Quite the Final Frontier General Remarks In Situ Hybridization (ISH) Single Molecule FISH (smFISH) Representative Method: SeqFISH+ Representative Method: MERFISH In Situ Sequencing In Situ Capture–Ex Situ Sequencing (Generic) Representative Implementation: GeoMx Digital Space Profiler Representative Implementation: Seq-Scope Illumina Representative Implementation: HDST Representative Implementation: Visium (10× Genomics) In Situ Genomic (DNA) Sequencing Extended by Ex Situ Sequencing Analysis Achievements of Spatial Genomics Future Directions/Predictions Further Reading 2: Bioinformatics, Digital Pathology, and Computational Pathology for Surgical Pathologists Introduction Bioinformatics, a Distinct Field in Pathology and Where Are We Now Pathology Bioinformaticians and Their Role Specialized Training in Bioinformatics Definitions and Terminologies Related to Bioinformatics and Computational Pathology Annotation Artificial Intelligence (AI) Black Box/Glass Box Cloud Computing Computational Pathology (CPATH) Convolutional Neural Network (CNN) Deep Learning Data Augmentation Digital Pathology (DP) Gold Standard Ground Truth Image Analysis Machine Learning (ML) Metadata Supervised Machine Learning Unsupervised Machine Learning Whole-Slide Image (WSI) Differences Between Traditional Image Analysis and Computational Pathology Digital Pathology, Machine Learning, and Computational Pathology Training Algorithm Case Selection Whole-Slide Imaging Traditional Image Analysis Enhanced by Machine Learning Pathologist-Centered Medical System Global Pathology Service Model Examples of Bioinformatics and AI-Driven Pathology Workflow Prostate Cancer Colorectal Cancer Breast Cancer Cancer Cytopathology Challenges and Limitations Infrastructure Considerations Processor Speed and Sources Network Limitations Acquiring Training Data Data Variability Public Sources Crowdsourcing Active Learning Quality Control and Reliability of the Algorithm Understanding Algorithms Ethics Cyber-Security Future Directions Conclusions Further Reading 3: Molecular Cytopathology Introduction Cytology Sample Collection Cytology Sample Preparation Types of Molecular Alterations Assays to Detect Different Molecular Alterations Assay Validation and Molecular Testing Workflows Clinical Settings for Molecular Cytopathology Further Reading 4: Next-Generation Immunohistochemistry in the Workup of Neoplasm of Uncertain Lineage and CUP Introduction: Immunohistochemistry Complements a Morphology and Epidemiology-Based Approach to Tumor Diagnosis Immunohistochemistry Basics IHC Protocol IHC Optimization/Validation IHC Readout IHC Common Pitfalls Next-Generation Immunohistochemistry Cancer Epidemiology Clinical Aspects of Cancer (Typically Carcinoma) of Unknown Primary Broad Tumor Classes and Associated Screening Markers Broad-Spectrum Epithelial Markers S-100 Versus SOX10 Noncanonical Expression of Screening Markers Immunohistochemical Approach to Small Round Blue Cell Tumor Immunohistochemical Approach to Carcinoma Typing Coordinate Expression of CK7/CK20 Immunohistochemical Approach to “Garden Variety Adenocarcinoma” Presenting in the Liver Immunohistochemical Approach to Primary Versus Metastatic Ovarian Tumor with Mucinous Features Immunohistochemical Approach to Tumors Presenting at Other Sites Immunohistochemical Approach to Distinction of Squamous and Urothelial Carcinoma Immunohistochemical Approach to Neuroendocrine Tumor Site of Origin Assignment Immunohistochemical Approach to Neuroendocrine Carcinoma Site of Origin Assignment Immunohistochemical Approach to the Distinction of NET G3 from NEC Immunohistochemical Approach to Undifferentiated/Dedifferentiated Carcinoma Immunohistochemical Approach to High-Grade Neoplasms Negative for Screening Markers Immunohistochemistry for Hereditary Cancer Predisposition Syndromes Further Reading 5: Molecular Pathology of Colorectal Tumors Introduction Epidemiology Etiology Prognosis and Treatment Screening Guidelines Pathogenesis and Molecular Classifications of Colorectal Cancer Colorectal Carcinogenesis Molecular Classifications of Colorectal Cancer DNA-Based Genomic Classification by the Cancer Genome Atlas (TCGA) RNA-Based Transcriptomic Profiling by Colorectal Cancer Subtyping Consortium Practical Molecular Diagnostics of Colorectal Cancer Universal Screening Algorithm MMR Immunohistochemistry Interpretation and Pitfalls Specimen Selection for CRC Molecular Testing Established Predictive Biomarkers RAS (KRAS and NRAS) for EGFR Antibody Immunotherapy Selection BRAF Mutation Microsatellite Instability for Therapy Selection Emerging and Partially Established Biomarkers Cancer Immunotherapy Other Biomarkers with Targeted Therapy Implications Hereditary Cancer Syndromes Lynch Syndrome Definition Pathologic Features Genetic Features Lynch Syndrome Variants and Related Syndromes Familial Adenomatous Polyposis and Variants Definition Clinical Features Pathologic Features Genetic Features FAP Variants Mut Y Homolog-Associated Polyposis Syndrome Definition Pathologic Features Genetics Features Serrated Polyposis Syndrome Definition Clinical Features Pathologic Features Genetic Features Peutz–Jeghers Polyposis Syndrome Definition Clinical Features Pathologic Features Genetic Features Juvenile Polyposis Syndrome Definition Clinical Features Pathologic Features Genetics Cowden Syndrome Definition Clinical Features Pathologic Features Genetics Features Other Polyposis Syndromes That Can Include Multiple Adenomas Hereditary Mixed Polyposis Syndrome Definition Genetic Features NTHL1-Associated Polyposis Definition Polymerase Proofreading-Associated Polyposis Definition Pathologic Features AXIN2-Associated Polyposis Syndrome Definition Current Challenges and Emerging Trends Further Reading 6: Molecular Pathology of Gastroesophageal Tumors Introduction Clinical and Molecular Features of Esophageal Neoplasms Esophageal Squamous Cell Carcinoma Esophageal Adenocarcinoma Esophageal Undifferentiated Carcinoma Other Esophageal Neoplasms Clinical and Molecular Features of Gastric Neoplasms Precursor Polyps Gastric Adenocarcinoma Gastric Neuroendocrine Carcinoma Other Gastric Neoplasms Genetic Predisposition Syndromes Molecular Diagnostics for Gastroesophageal Cancers Further Reading 7: Molecular Pathology of Pancreatic Tumors Introduction to Normal Pancreas Neoplasms with Ductal Differentiation Pancreatic Ductal Adenocarcinoma Clinical Features Pathologic Features Genetic Features Variants of Ductal Adenocarcinoma Adenosquamous Carcinoma Colloid Carcinoma Hepatoid Carcinoma Medullary Carcinoma Signet Ring Cell Carcinoma Undifferentiated Carcinoma Undifferentiated Carcinoma with Osteoclast-Like Giant Cells Intraductal Papillary Neoplasms Clinical Features Pathologic Features Genetic Features Intraductal Oncocytic Papillary Neoplasm Intraductal Tubulopapillary Neoplasm Mucinous Cystic Neoplasm Clinical Features Pathologic Features Genetic Features Serous Cystadenoma Clinical Features Pathologic Features Genetic Features Neoplasms with Neuroendocrine Differentiation Well-Differentiated Pancreatic Neuroendocrine Tumors Clinical Features Pathologic Features Genetic Features Neuroendocrine Carcinoma Clinical Features Pathologic Features Genetic Features Neoplasms with Ambiguous Direction of Differentiation Solid Pseudopapillary Neoplasm Clinical Features Pathologic Features Genetic Features Neoplasms with Acinar Differentiation Acinar Cell Carcinoma Clinical Features Pathologic Features Genetic Features Pancreatoblastoma Clinical Features Pathologic Features Genetic Features Hereditary/Genetic Syndromes Mutations in the Fanconi Anemia/BRCA Pathway Ataxia-Telangiectasia Mutated Familial Atypical Multiple Mole Melanoma Syndrome Peutz–Jeghers Syndrome Hereditary Pancreatitis Hereditary Nonpolyposis Colorectal Cancer Familial Adenomatous Polyposis von Hippel–Lindau Syndrome Other Hereditary/Genetic Syndromes Summary of Molecular Pathology of Pancreatic Cancer Further Reading 8: Molecular Pathology of Liver Tumors Introduction Hepatocellular Adenoma Definition Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Hepatocellular Carcinoma Definition Clinical Features Pathologic Features Diagnosis and Differential Diagnosis Genetic Features Prognosis and Predictive Factors Intrahepatic Cholangiocarcinoma Definition Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Combined Hepatocellular-Cholangiocarcinoma Definition Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Hepatoblastoma Definition Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Hepatic Neuroendocrine Neoplasms Definition Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Malignant Vascular Neoplasms Definitions Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Hepatic Angiomyolipoma Definitions Clinical Features Pathologic Features Differential Diagnosis Genetic Features Prognosis and Predictive Factors Summary of Molecular Pathology of Liver Tumors Further Reading 9: Molecular Pathology of Lung Tumors Introduction Clinical Features Molecular Genetic Pathology Epidermal Growth Factor Receptor (EGFR) Molecular Diagnostics KRAS Proto-Oncogene, GTPase (KRAS) Molecular Diagnostics B-Raf Proto-Oncogene, Serine/Threonine Kinase (BRAF) Molecular Diagnostics ALK Receptor Tyrosine Kinase (ALK) Molecular Diagnostics ROS Proto-Oncogene 1, Receptor Tyrosine Kinase (ROS1) Molecular Diagnostics Ret Proto-Oncogene (RET) Molecular Diagnostics MET Proto-Oncogene, Receptor Tyrosine Kinase (MET) Molecular Diagnostics Neurotrophic Receptor Tyrosine Kinases 1/2/3 (NTRK1/2/3) Molecular Diagnostics Other Alterations in Lung Adenocarcinoma Less Common Oncogenic Mutations with Emerging Clinical Significance Less Common Gene Fusions and Amplifications Other Tumor Suppressor Gene Mutations Molecular Pathology Related to NSCLC Immunotherapy Considerations of Molecular Tests for NSCLC Management Important Molecular Alterations in Other Lung Carcinomas Squamous Cell Carcinoma (SCC) Small Cell Lung Carcinoma (SCLC) Genetically Defined Thoracic Tumor Entities NUT Carcinoma Molecular Diagnostics Thoracic SMARCA4-Deficient Undifferentiated Tumor (SMARCA4-UT) Molecular Diagnostics Important Molecular Alterations in Mesothelioma Further Reading 10: Molecular Pathology of Breast Tumors Introduction Normal Characteristics of the Female Human Breast Gross, Microscopic, and Molecular Anatomy Breast Development Traditional Pathological Classification and Biomarkers in Routine Clinical Practice Estrogen Receptor and Progesterone Receptor Progesterone Receptor Ki67 and ER+ Breast Cancer Human Epidermal Growth Factor Receptor 2 Gene HER2-low TNBC Immunohistochemistry Guidelines for Hormone Receptor and HER2 Testing in Breast Cancer ASCO-CAP Guidelines for HER2 Assessment ASCO-CAP Guidelines for Hormone Receptor Assessment Molecular Subtypes (Intrinsic Subtypes) Multigene Prognostic Indices in ER+/HER– Tumors Oncotype DX The Mammaprint Prosigna (PAM50) Assay Breast Cancer Index (BCI) Endopredict Concordance between Assays Familial and Hereditary Breast Cancer BRCA1 and BRCA2 Non-BRCA Hereditary Breast Cancer Familial Breast Cancer Next-Generation Sequencing Assays Molecular Breast Pathology to Advance Personalized Treatment of Cancer p53 Mutations PI3KCA Mutations ESR1 Mutations Hormonally Directed Therapeutics Recent Developments in the Breast Cancer Landscape that Revolutionize the Treatment Strategies CDK4/6 Inhibitors in Breast Cancer- Co-Targeting CDk4/6 with Endocrine Therapy Landscape of HER2-low Metastatic Breast Cancer and Antibody Drug Conjugates (ADCs) for HER2+ Disease The Immune Landscape of Breast Cancer and Immune Checkpoint Inhibitors Clinical Utility of Trop-2 in Breast Cancer Summary and Conclusions Further Reading 11: Molecular Pathology of Ovarian Tumors Introduction Classification of Ovarian Epithelial Neoplasms Type I Tumors Type II Tumors Molecular Pathways and Alterations by Tumor Type Type I Ovarian Tumors Low-Grade Serous Tumors Introduction Genetic Pathways: Functions, Role in Pathogenesis, and Frequency of Abnormalities Clinical Implications Summary Endometrioid and Clear Cell Carcinomas Introduction Genetic Pathways: Functions, Role in Pathogenesis, and Frequency of Abnormalities Clinical Implications Summary Mucinous Tumors Introduction Genetic Pathways: Functions, Role in Pathogenesis, and Frequency of Abnormalities Clinical Implications Summary Brenner Tumors Type II Ovarian Tumors High-Grade Serous Carcinoma and Carcinosarcoma Introduction Genetic Pathways: Functions, Role in Pathogenesis, and Frequency of Abnormalities Clinical Implications Summary Undifferentiated/Dedifferentiated Carcinoma Molecular Abnormalities Not Associated with Specific Histology Molecular Abnormalities Associated with Rarer/Nonepithelial Ovarian Cancers Hereditary/Familial Ovarian Cancers Conclusions Further Reading 12: Molecular Pathology of Endometrial Tumors Introduction WHO Classification of Endometrial Carcinoma (WHO 2020) Histological Grade Reproducibility of Histological Typing Molecular Features of Endometrioid–Endometrial Carcinoma Microsatellite Instability/Mismatch Repair Deficiency Phosphatase and Tensin Homolog (PTEN) PIK3CA and PIK3R1 RAS–MAPK Pathway Beta-Catenin ARID1A Molecular Features of Serous Carcinoma TP53 Other Alterations Molecular Features of Clear Cell Carcinoma Molecular Features of Mixed Endometrioid–Nonendometrioid Adenocarcinomas Molecular Features of Endometrioid Carcinomas with Ambiguous Features Molecular Features of Undifferentiated Carcinoma and Dedifferentiated Carcinoma Molecular Features of Carcinosarcoma (Malignant Mixed Müllerian Tumors) Molecular Features of Mesonephric-Like Carcinomas Molecular Aspects of Staging Intratumor Heterogeneity cDNA Array Results TCGA-Based Molecular Classification Current Targeted Therapies Potential-Targeted Therapies Approaches Summary Further Reading 13: Molecular Pathology of Kidney Tumors Introduction Genetic Renal Neoplasia Syndromes von Hippel–Lindau Disease Molecular Pathogenesis Clinical and Pathologic Manifestations Hereditary Papillary Renal Carcinoma Molecular Pathogenesis Hereditary Leiomyomatosis and Renal Cell Carcinoma Molecular Pathogenesis Clinical and Pathologic Manifestations Tuberous Sclerosis Molecular Pathogenesis Clinical and Pathologic Manifestations Birt–Hogg–Dubé Syndrome Molecular Pathogenesis Clinical and Pathological Manifestations Succinate Dehydrogenase Germline Mutations Molecular Pathogenesis Clinical and Pathologic Manifestations Constitutional Chromosome 3 Translocation BAP1 Mutations and Familial Kidney Cancer Clinical and Pathologic Manifestations Cowden Syndrome (PTEN Hamartoma Tumor Syndrome) Malignant Neoplasms Clear Cell Renal Cell Carcinoma Light Microscopy Molecular Characteristics Multifocality Molecular Differential Diagnosis Papillary Renal Cell Carcinoma Light Microscopy Molecular Characteristics Multifocality Molecular Differential Diagnosis Hereditary Leiomyomatosis RCC Syndrome–Associated RCC Chromophobe Renal Cell Carcinoma Light Microscopy Molecular Characteristics Molecular Differential Diagnosis Collecting Duct Carcinoma Light Microscopy Molecular Characteristics Molecular Differential Diagnosis Renal Medullary Carcinoma Light Microscopy Molecular Characteristics MiT Family Translocation Carcinoma TFE3-Rearranged/Xp11.2 Translocation Renal Cell Carcinoma Light Microscopy Molecular Characteristics Molecular Differential Diagnosis TFEB-Rearranged/T(6;11) Renal Cell Carcinoma Light Microscopy Molecular Characteristics TFEB-Amplified Renal Cell Carcinoma Molecular Differential Diagnosis SDH-Deficient Renal Carcinoma Mucinous Tubular and Spindle Cell Carcinoma Molecular Characteristics Tubulocystic Renal Cell Carcinoma Molecular Characteristics Acquired Cystic Disease-Associated Renal Cell Carcinoma Light Microscopy Molecular Characteristics Thyroid-Like Follicular Renal Cell Carcinoma Light Microscopy Molecular Characteristics Molecular Differential Diagnoses ALK Rearrangement-Associated Renal Cell Carcinoma Light Microscopy Molecular Characteristics Renal Cell Carcinoma with Fibromyomatous Stroma Light Microscopy Molecular Characteristics Eosinophilic Solid and Cystic Renal Cell Carcinoma Light Microscopy Molecular Characteristics Unclassified Renal Cell Carcinoma Sarcomatoid Renal Cell Carcinoma Molecular Characteristics Other Tumors Eosinophilic Vacuolated Tumor Light Microscopy Molecular Characteristics Epithelioid Angiomyolipoma and Other Renal PEComas Molecular Characteristics Adult Nephroblastoma (Wilms Tumor) Neuroendocrine Tumors/Carcinomas Molecular Characteristics Primitive Neuroectodermal Tumor/Ewing Family of Tumors Urothelial Carcinoma Molecular Characteristics Molecular Differential Diagnosis Unknown/Low Malignant Potential Neoplasms Multilocular Cystic Renal Neoplasm, Low Malignant Potential Clear Cell Papillary Renal Cell Tumor Molecular Characteristics Molecular Differential Diagnosis Papillary Renal Neoplasm with Reverse Polarity Light Microscopy Molecular Characteristics Low-Grade Oncocytic Tumor Light Microscopy Molecular Characteristics Atrophic Kidney-Like Lesion Light Microscopy Benign Neoplasms Angiomyolipoma Oncocytoma Molecular Differential Diagnosis Papillary Adenoma Cystic Nephroma Adult Cystic Nephroma Pediatric Cystic Nephroma Mixed Epithelial and Stromal Tumor Juxtaglomerular Cell Tumor Metanephric Adenoma Molecular Characteristics Molecular Differential Diagnosis Renomedullary Interstitial Cell Tumor (Medullary Fibroma) Pediatric Neoplasms General Molecular Characteristics Nephroblastoma (Wilms Tumor) Molecular Characteristics Clear Cell Sarcoma Molecular Characteristics Rhabdoid Tumor Molecular Characteristics Congenital Mesoblastic Nephroma Molecular Characteristics Metanephric Tumors Molecular Characteristics Neuroblastoma Molecular Characteristics Renal Cell Carcinoma Associated with Neuroblastoma Light Microscopy Molecular Characteristics Pediatric Cystic Nephroma Molecular Characteristics Further Reading 14: Molecular Pathology of Prostate Cancer Introduction Biology of Prostatic Epithelium Epidemiology and Etiology of Prostate Cancer Clinical Features Histopathology of Prostate Cancer Precursor Lesions Intraductal Carcinoma (IDC-P) Acinar Adenocarcinoma Ductal Adenocarcinomas Rare Subtypes Neuroendocrine Carcinoma (NEPC) Other Histological Variants/Patterns of Differentiation Grading of Adenocarcinoma Artificial Intelligence in Prostate Cancer Histopathology Molecular Features of Prostate Cancer Germline Alterations Somatic Genomic Alterations in Prostate Cancer ETS Gene Fusions Other Apparently Mutually Exclusive (with ETS Alterations) and Truncal Somatic Mutations Other Genetic Alterations in Prostate Cancer Epigenetic Alterations in Prostate Cancer Tumor Microenvironment in Prostate Cancer Prognostic Utility of Somatic Tissue-based Genetic Testing Suggested Readings 15: Molecular Pathology of Urinary Bladder Tumors Introduction Oncogenic Pathways in Urothelial Carcinoma of the Urinary Bladder Prognostic Biomarkers in Bladder Cancer General Background Chromosomal Numerical Alterations–Early Culprit of Genetic Instability in Bladder Cancer Receptor Tyrosine Kinase Alterations p53, Cell Cycle Regulators, and Proliferation Activity Index Epigenetic Alterations Intrinsic Molecular Genomic Subtypes of Urothelial Carcinoma Bladder Cancer TCGA 2014 Bladder Cancer TCGA 2017 Molecular Markers for Early Detection of Urothelial Carcinoma UroVysion BTA-Stat NMP22 ImmunoCyt UroSEEK Circulating Tumor Cells Other Markers Molecular Grading and Staging of Bladder Cancer Molecular Grading Molecular Staging Molecular Detection of Lymph Node Metastasis Targeted Therapy and Predictive Markers in Bladder Cancer Immunotherapy in Bladder Cancer Summary Suggested Reading 16: Molecular Pathology of Testicular Cancer Introduction Germ Cell Tumors General Classification Type I (Pediatric) Germ Cell Tumor Type II (Adult) Germ Cell Tumors Type III Germ Cell Tumors (Spermatocytic Tumor) Selected Sex Cord-Stromal Tumors Leydig Cell Tumors Sertoli Cell Tumors Granulosa Cell Tumors Summary Suggested Reading 17: Molecular Pathology of Melanoma and Nonmelanoma Skin Tumors Introduction Ultraviolet Radiation and Skin Cancer Melanoma Overview Pathogenesis Diagnosis Classification Melanomas Arising in Sun-Exposed Skin Pathway I: Low-Cumulative Solar Damage (Low-CSD)/SSM Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway II: High-CSD Melanoma/LMM Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway III: Desmoplastic Melanoma (DM) Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Melanomas Arising at Sun-Shielded Sites or Without Known Etiological Associations with UVR Exposure Pathway IV: Malignant Spitz Tumor (Spitz Melanoma; SM) Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway V: Acral Melanoma Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway VI: Mucosal Melanoma (MM) Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway VII: Melanoma Arising in a Congenital Nevus Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway VIII: Melanoma Arising in a Blue Nevus Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Pathway IX: Uveal Melanoma Epidemiology Clinical Features Histopathology Precursor Lesions Molecular Features Nodular Melanoma Pediatric Melanoma Immunotherapy and Targeted Therapy Nonmelanoma Skin Cancer Basal Cell Carcinoma Clinical Features Genetics and Pathogenesis Histopathology Molecular Therapies and Drug Resistance Mechanisms Squamous Cell Carcinoma Overview Pathogenesis Squamous Cell Carcinoma Precursors Squamous Cell Carcinoma In Situ (Bowen disease) Invasive Squamous Cell Carcinoma Molecular Features Immunotherapy for SCC Merkel Cell Carcinoma Overview Pathogenesis Clinical Features Histopathology Molecular Features Immunotherapy Dermatofibrosarcoma Protuberans Overview Pathogenesis Clinical Features Histopathology Molecular Features Therapy Cutaneous Adnexal Neoplasms Trichoblastoma Overview Clinical features Histopathology Molecular Features Cylindroma and Spiradenoma Overview Clinical Features Histopathology Molecular Features Pilomatricoma Overview Clinical Features Histopathology Molecular Features Pilomatrical Carcinoma Sebaceous Neoplasms Overview Clinical Features Histopathology Molecular Features Genetic/Hereditary Syndromes Familial Melanoma Xeroderma Pigmentosum Carney Complex BAP-1 Tumor Predisposition Syndrome (BAP1-TPDS) Muir Torre Syndrome Brooke–Spiegler Syndrome Nevoid Basal Cell Carcinoma Syndrome (Gorlin Syndrome) Suggested Reading Ultraviolet Light and Skin Cancer Melanoma Nonmelanoma Skin Cancer Merkel Cell Carcinoma Dermatofibrosarcoma Protuberans Cutaneous Adnexal Neoplasms Genetic/Hereditary Syndromes 18: Molecular Pathology of Head and Neck Tumors Introduction Conventional Squamous Cell Carcinoma Squamous Cell Carcinoma of the Oral Cavity Squamous Cell Carcinoma of the Hypopharynx, Larynx, Trachea, and Parapharyngeal Space Precursors to Conventional Squamous Cell Carcinoma Oral Cavity Dysplasia Laryngeal Dysplasia Laryngeal Squamous Papilloma Human Papillomavirus-Associated Squamous Cell Carcinoma of the Oropharynx Immunotherapy for Head and Neck Cancer Additional Oral Cavity Tumors Ectomesenchymal Chondromyxoid Tumor GLI1-Altered Mesenchymal Neoplasms Nasal Cavity, Paranasal Sinus, and Skull Base Tumors Sinonasal Papilloma Inverted Type Oncocytic Type Exophytic Type Types of Carcinoma Squamous Cell Carcinoma Keratinizing Squamous Cell Carcinoma Nonkeratinizing Squamous Cell Carcinoma Intestinal-Type Adenocarcinoma Nonintestinal-Type Adenocarcinoma Neuroendocrine Carcinoma Lymphoepithelial Carcinoma NUT Carcinoma SWI/SNF-Deficient Malignancies SMARCB1 (INI-1)-Deficient Sinonasal Carcinoma SMARCA4 (BRG1)-Deficient Sinonasal Carcinoma IDH-Mutant Sinonasal Carcinoma Human Papillomavirus-Associated Multiphenotypic Sinonasal Carcinoma Mesenchymal Tumors Nasal Chondromesenchymal Hamartoma Sinonasal Glomangiopericytoma Biphenotypic Sinonasal Sarcoma Spindle Cell/Sclerosing Rhabdomyosarcoma Emerging Molecularly-Defined Entities DEK::AFF2 Fusion-Associated Carcinoma Adamantinoma-Like Ewing Sarcoma Hematolymphoid Tumors Extranodal NK/T-Cell Lymphoma, Nasal Type Neuroectodermal Tumors Olfactory Neuroblastoma Nasopharyngeal Tumors Nasopharyngeal Angiofibroma Nasopharyngeal Carcinoma Nonkeratinizing Squamous Cell Carcinoma Keratinizing Squamous Cell Carcinoma Odontogenic Tumors Ameloblastoma Ameloblastic Carcinoma Odontogenic and Non-Odontogenic Developmental Cysts Odontogenic Keratocyst Calcifying Odontogenic Cyst Giant Cell Lesions Central Giant Cell Lesion Peripheral Giant Cell Lesions Ear External Auditory Canal Squamous Cell Carcinoma Middle and Inner Ear Tumors Endolymphatic Sac Tumor Paraganglioma Suggested Reading 19: Molecular Pathology of Salivary Gland Tumors Introduction Practical Tips for Utilizing Molecular Techniques in Salivary Gland Tumors Fine-Needle Aspiration Tissue Preparation of Biopsies and Resection Specimens Tissue Selection for Testing Malignant Neoplasms Acinic Cell Carcinoma Light Microscopy NR4A3 Rearrangement Utility of NR4A3 Rearrangement in the Diagnosis of AciCC Other Genetic Changes in AciCC Adenoid Cystic Carcinoma Light Microscopy MYB Alterations Utility of MYB Alteration in the Diagnosis of AdCC Other Genetic Alterations Described in AdCC Epithelial Myoepithelial Carcinoma Light Microscopy HRAS Mutations Utility of Detecting HRAS Mutations in the Diagnosis of EMC Other Genetic Changes Observed in EMC Hyalinizing Clear Cell Carcinoma Light Microscopy EWSR1 Rearrangement Utility of Detecting EWSR1 Gene Rearrangement Other Genetic Changes in HCCC Intraductal Carcinoma Light Microscopy RET Rearrangement Utility of RET Rearrangement in the Diagnosis of Intraductal Carcinoma Mucoepidermoid carcinoma Light Microscopy MAML2 Rearrangement Utility of MAML2 Rearrangement in Diagnosis of MEC Microsecretory Adenocarcinoma Light Microscopy SS18 Rearrangement Utility of SS18 in the Diagnosis of MSA Other Genetic Changes in MSA Myoepithelial Carcinoma Light Microscopy PLAG1 and HMGA2 Genetic Changes EWSR1 Rearrangement Utility of Detecting PLAG1 or EWSR1 Rearrangement Polymorphous Adenocarcinoma Light Microscopy PRKD Gene Alterations Utility of Detecting PRKD Gene Alterations in PAC Salivary Duct Carcinoma Light Microscopy Androgen Receptor Human Epidermal Growth Factor Receptor 2 (HER2) Utility of Detecting AR and HER2 in SDC Other Genetic Alterations in SDC Sclerosing Microcystic Adenocarcinoma Light Microscopy CDK11B Mutations Utility of Detecting CDK11B Mutations Secretory Carcinoma Light Microscopy ETV6 Rearrangement Utility of Detecting ETV6 or NTRK Rearrangement in SC Other Genetic Changes in SC Pleomorphic Adenoma Light Microscopy PLAG1 or HMGA2 Rearrangement Utility of Detecting PLAG1 or HMGA2 Rearrangement in PA Carcinoma Ex-Pleomorphic Adenoma Light Microscopy PLAG1 or HMGA2 Rearrangement Utility of Detecting PLAG1 or HMGA2 Rearrangement in CXPA Other Genetic Changes in CXPA Basal Cell Adenoma Light Microscopy CTNNB1 and CYLD1 Mutations Detection of CTNNB1 and CYLD1 Mutations Basal Cell Adenocarcinoma Suggested Reading Introduction Acinic Cell Carcinoma Adenoid Cystic Carcinoma Epithelial Myoepithelial Hyalinizing Clear Cell Carcinoma Intraductal Carcinoma Mucoepidermoid Carcinoma Microsecretory Adenocarcinoma Myoepithelial Carcinoma Polymorphous Adenocarcinoma Salivary Duct Carcinoma Sclerosing Microcystic Adenocarcinoma Secretory Carcinoma Pleomorphic Adenoma and Carcinoma Ex Pleomorphic Adenoma Basal Cell Adenoma and Adenocarcinoma 20: Molecular Pathology of the Heart and Cardiovascular System Selected Primary Tumors of the Heart and Cardiovascular System Introduction Benign Tumors Myxoma Papillary Fibroelastoma Rhabdomyoma Fibroma Lipomatous Hypertrophy of th