Diagnostic Pathology: Molecular Oncology

SECTION 1: INTRODUCTION

4 Structure of Chromosomes and Nucleic Acids
Jeremy C. Wallentine, MD
8 DNA Replication, Transcription, and Translation
Jeremy C. Wallentine, MD
12 Gene Mutations
Jeremy C. Wallentine, MD

SECTION 2: COMMON TECHNIQUES FOR ANALYSIS OF ALTERATIONS IN CHROMOSOMES AND DNA

18 Cytogenetics and FISH
Mohammad A. Vasef, MD and David R. Czuchlewski, MD
22 Chromosomal Microarray
Mohammad A. Vasef, MD and Sibel Kantarci, PhD
26 Amplification Methods
Devon Chabot-Richards, MD
30 DNA High-Resolution Melting Curve Analysis
Amer Mahmoud, MD, FCAP
32 Sequencing Technologies
Eric Y. Loo, MD and Mohammad A. Vasef, MD
36 High-Throughput Methods in Molecular Pathology
Rama Gullapalli, MD, PhD
38 DNA Methylation Analysis
Devon Chabot-Richards, MD
SECTION 3: MOLECULAR GENETIC TESTS IN HEMATOPOIETIC TUMORS
42 BCR::ABL1 Fusion
Eric Y. Loo, MD and Mohammad A. Vasef, MD
46 PML::RARA Fusion
Devon Chabot-Richards, MD
48 Reverse Transcription PCR for Myeloid Leukemia Transcripts
Kristin Hunt Karner, MD
50 FLT3, NPM1, and CEBPA Mutations
Devon Chabot-Richards, MD
54 JAK2 Mutations and Rearrangements
Mohammad A. Vasef, MD
56 MPL Mutations
Eric Y. Loo, MD and David R. Czuchlewski, MD
58 Calreticulin (CALR) Mutations
Eric Y. Loo, MD and Mohammad A. Vasef, MD
60 CSF3R Mutations
Amer Mahmoud, MD, FCAP
62 SETBP1 Mutations
Amer Mahmoud, MD, FCAP
64 KIT Mutations
Eric Y. Loo, MD and Mohammad A. Vasef, MD
68 IDH1 and IDH2 Mutations
Eric Y. Loo, MD and David R. Czuchlewski, MD
70 Other Mutations and Gene Panel Testing in Myeloid Neoplasms
Mohammad A. Vasef, MD and David R. Czuchlewski, MD
72 Immunoglobulin Heavy (IGH) Chain Gene Rearrangements
Mohammad A. Vasef, MD and Anna P. Matynia, MD
76 T-Cell Receptor Gamma (TRG) and Delta (TRD) Chain Rearrangements
Mohammad A. Vasef, MD and Anna P. Matynia, MD
80 T-Cell Receptor Beta (TRB) Chain Gene Rearrangements
Mohammad A. Vasef, MD and Anna P. Matynia, MD
84 Southern Blot Analysis of Antigen Receptor Genes
Mohammad A. Vasef, MD
86 EBV-Associated Human Neoplasms
Mohammad A. Vasef, MD
94 MYD88 Mutation
Giovanni Insuasti-Beltran, MD
96 NOTCH1 Mutation
Giovanni Insuasti-Beltran, MD
98 EZH2 Mutation
Amer Mahmoud, MD, FCAP

SECTION 4: MOLECULAR GENETIC TESTS IN SOLID TUMORS, BONE AND SOFT TISSUE TUMORS, AND CNS TUMORS

104 ALK Rearrangements and Mutations
Guanghua Wang, MD
106 ROS1 Rearrangements
Mohammad A. Vasef, MD and David R. Czuchlewski, MD
108 RET Rearrangements
Eric Y. Loo, MD and David R. Czuchlewski, MD
110 FISH for MET Amplifications
Devon Chabot-Richards, MD
114 FISH for ERBB2 (HER2) Amplifications
M. Carmen Frias Kletecka, MD and Kristin Hunt Karner, MD
116 KRAS Mutations
Guanghua Wang, MD
118 BRAF Mutations
Yongjie Zhou, MD, PhD and Guanghua Wang, MD
120 EGFR Mutations
Guanghua Wang, MD
122 Targeted Hotspot Gene Panel Using Massively
Parallel Sequencing (Next-Generation Sequencing)
Mohammad A. Vasef, MD and David R. Czuchlewski, MD
124 Targeted Hotspot Gene Panel Table
Mohammad A. Vasef, MD and David R. Czuchlewski, MD
130 MGMT Promoter Gene Methylation Assay
Devon Chabot-Richards, MD

SECTION 5: MOLECULAR PATHOLOGY OF MYELOID NEOPLASMS

134 Molecular Work-Up of Myeloid Neoplasms
Mohammad A. Vasef, MD and David R. Czuchlewski, MD
MYELOPROLIFERATIVE NEOPLASMS
136 Chronic Myeloid Leukemia, BCR::ABL1-Positive
Mohammad A. Vasef, MD, Kaaren K. Reichard, MD, and David R. Czuchlewski, MD
144 Chronic Neutrophilic Leukemia
Devon Chabot-Richards, MD and David R. Czuchlewski, MD
148 Polycythemia Vera
Mohammad A. Vasef, MD and M. Carmen Frias Kletecka, MD
152 Primary Myelofibrosis
Devon Chabot-Richards, MD, Kaaren K. Reichard, MD, and Daniel Babu, MD
156 Essential Thrombocythemia
Giovanni Insuasti-Beltran, MD
160 Chronic Eosinophilic Leukemia, NOS
Devon Chabot-Richards, MD, Kaaren K. Reichard, MD, and Daniel Babu, MD
162 Myeloproliferative Neoplasm, Unclassifiable
Devon Chabot-Richards, MD, Kaaren K. Reichard, MD, and Daniel Babu, MD

MASTOCYTOSIS
166 Mastocytosis
Mohammad A. Vasef, MD

MYELOID/LYMPHOID NEOPLASMS WITH EOSINOPHILIA AND GENE REARRANGEMENT
174 Myeloid/Lymphoid Neoplasms With Eosinophilia and Tyrosine Kinase Gene Fusions
Devon Chabot-Richards, MD and David R. Czuchlewski, MD

PREMALIGNANT CLONAL HEMATOPOIESIS AND CYTOPENIAS
178 VEXAS Syndrome
Mohammad A. Vasef, MD and Michael M. Franklin, DO
182 Clonal Hematopoiesis and Premalignant Clonal Cytopenia
Mohammad A. Vasef, MD

MYELODYSPLASTIC SYNDROME (MDS)
184 Overview and Classification of Myelodysplastic Syndrome
Devon Chabot-Richards, MD, David R. Czuchlewski, MD, and Carla S. Wilson, MD, PhD
188 Myelodysplastic Syndrome With Mutated SF3B1
Mohammad A. Vasef, MD and Carla S. Wilson, MD, PhD
192 Myelodysplastic Syndrome, NOS
Kristin Hunt Karner, MD
200 Myelodysplastic Syndrome With del(5q)
Giovanni Insuasti-Beltran, MD
204 Myelodysplastic Syndrome With TP53 Multihit Mutations
Kristin Hunt Karner, MD
206 Myelodysplastic Syndrome/Acute Myeloid Leukemia
Kristin Hunt Karner, MD
208 Pediatric Myelodysplastic Syndrome and Refractory Cytopenia of Childhood
Devon Chabot-Richards, MD and Carla S. Wilson, MD, PhD

MYELODYSPLASTIC/MYELOPROLIFERATIVE NEOPLASMS
214 Overview of Myelodysplastic/Myeloproliferative Neoplasms
Devon Chabot-Richards, MD
216 Chronic Myelomonocytic Leukemia
Kristin Hunt Karner, MD
220 Atypical Chronic Myeloid Leukemia
Devon Chabot-Richards, MD
224 Juvenile Myelomonocytic Leukemia
Devon Chabot-Richards, MD and Qian-Yun Zhang, MD, PhD
228 Myelodysplastic/Myeloproliferative Neoplasm, NOS
Devon Chabot-Richards, MD and Kathryn Foucar, MD

ACUTE MYELOID LEUKEMIA
232 Overview of Acute Myeloid Leukemia
Mohammad A. Vasef, MD and Kaaren K. Reichard, MD
240 Acute Myeloid Leukemia With t(8;21)/RUNX1::RUNX1T1
Devon Chabot-Richards, MD, Kaaren K. Reichard, MD, and David R. Czuchlewski, MD
244 Acute Myeloid Leukemia With inv(16) or t(16;16)/CBFB::MYH11
Devon Chabot-Richards, MD, Kaaren K. Reichard, MD, and David R. Czuchlewski, MD
248 Acute Promyelocytic Leukemia With t(15;17)/PML::RARA
Mohammad A. Vasef, MD
254 Acute Myeloid Leukemia With t(9;11)/MLLT3::KMT2A
Devon Chabot-Richards, MD, Kaaren K. Reichard, MD, and David R. Czuchlewski, MD
258 Acute Myeloid Leukemia With t(6:9)/DEK::NUP214
Eric Y. Loo, MD and David R. Czuchlewski, MD
260 Acute Myeloid Leukemia With inv(3) or t(3;3)/GATA2; MECOM
Eric Y. Loo, MD and David R. Czuchlewski, MD
262 Acute Myeloid Leukemia (Megakaryoblastic) With t(1;22)/RBM15::MRTFA
Eric Y. Loo, MD and David R. Czuchlewski, MD
264 Acute Myeloid Leukemia With Myelodysplasia-Related Gene Mutations or Cytogenetic Abnormalities
Kathryn Foucar, MD and Mohammad A. Vasef, MD
270 Acute Myeloid Leukemia, NOS
Kristin Hunt Karner, MD
276 Myeloid Sarcoma
Devon Chabot-Richards, MD
280 Myeloid Proliferations Associated With Down Syndrome
Eric Y. Loo, MD and David R. Czuchlewski, MD

BLASTIC PLASMACYTOID DENDRITIC CELL NEOPLASM
284 Blastic Plasmacytoid Dendritic Cell Neoplasm
Mohammad A. Vasef, MD

SECTION 6: MOLECULAR PATHOLOGY OF LYMPHOID NEOPLASMS

292 Overview of Lymphoid Neoplasms
Nadine Aguilera, MD
296 Molecular Work-Up of Lymphoid Neoplasms
Mohammad A. Vasef, MD and David R. Czuchlewski, MD

DETERMINATION OF CLONALITY IN B-, T-, AND NK-CELL NEOPLASMS
298 Lymphoma-Associated Chromosomal Translocations
Kristin Hunt Karner, MD

PRECURSOR LYMPHOID NEOPLASMS
302 B-Lymphoblastic Leukemia/Lymphoma With Recurrent Genetic Abnormalities
Kristin Hunt Karner, MD
306 B-Lymphoblastic Leukemia/Lymphoma, BCR::ABL1-Like (Ph-Like ALL)
Joanna L. Conant, MD and Mohammad A. Vasef, MD
310 T-Lymphoblastic Leukemia/Lymphoma
Mohammad A. Vasef, MD

MATURE B-CELL NEOPLASMS
316 Small Lymphocytic Lymphoma/Chronic Lymphocytic Leukemia
Devon Chabot-Richards, MD
322 B-Cell Prolymphocytic Leukemia
Aaron Auerbach, MD, MPH
326 Splenic Marginal Zone Lymphoma
Aaron Auerbach, MD, MPH and Roberto N. Miranda, MD
332 Hairy Cell Leukemia
Mohammad A. Vasef, MD
336 Splenic B-Cell Lymphoma/Leukemia, Unclassifiable
Nadine Aguilera, MD
344 Lymphoplasmacytic Lymphoma
Aaron Auerbach, MD, MPH
350 Monoclonal Gammopathy of Undetermined Significance
Nadine Aguilera, MD
354 Multiple Myeloma (Plasma Cell Myeloma)
Nadine Aguilera, MD and Carla S. Wilson, MD, PhD
362 Follicular Lymphoma
Aaron Auerbach, MD, MPH, C. Cameron Yin, MD, PhD, and John Schmieg, MD, PhD
370 Mantle Cell Lymphoma
Aaron Auerbach, MD, MPH
376 Diffuse Large B-Cell Lymphoma
Nadine Aguilera, MD
386 Burkitt Lymphoma
Aaron Auerbach, MD, MPH and Carlos Bueso-Ramos, MD, PhD

MATURE T- AND NK-CELL NEOPLASMS
394 T-Cell Prolymphocytic Leukemia
Nadine Aguilera, MD
398 Chronic Lymphoproliferative Disorder of NK Cells
Nadine Aguilera, MD
402 Aggressive NK-Cell Leukemia
Nadine Aguilera, MD
406 Extranodal NK-/T-Cell Lymphoma
Aaron Auerbach, MD, MPH and L. Jeffrey Medeiros, MD
410 Adult T-Cell Leukemia/Lymphoma
Nadine Aguilera, MD
416 Intestinal T-Cell Lymphoma
Aaron Auerbach, MD, MPH and Sa A. Wang, MD
424 Hepatosplenic T-Cell Lymphoma
Aaron Auerbach, MD, MPH and Roberto N. Miranda, MD
428 Subcutaneous Panniculitis-Like T-Cell Lymphoma
Aaron Auerbach, MD, MPH
432 Mycosis Fungoides/Sézary Syndrome
Aaron Auerbach, MD, MPH and Sa A. Wang, MD
438 Primary Cutaneous CD30-Positive T-Cell
Lymphoproliferative Disorders
Aaron Auerbach, MD, MPH
442 Peripheral T-Cell Lymphoma, NOS
Aaron Auerbach, MD, MPH
448 Nodal Follicular Helper T-Cell Lymphoma
Aaron Auerbach, MD, MPH
456 Anaplastic Large Cell Lymphoma, ALK-Negative
Mohammad A. Vasef, MD
462 Anaplastic Large Cell Lymphoma, ALK-Positive
Mohammad A. Vasef, MD

SECTION 7: MOLECULAR PATHOLOGY OF DENDRITIC CELL AND HISTIOCYTIC NEOPLASMS

470 Histiocytic Sarcoma
Nadine Aguilera, MD
478 Langerhans Cell Histiocytosis
Guanghua Wang, MD
484 Interdigitating Dendritic Cell Sarcoma
Aaron Auerbach, MD, MPH and Sa A. Wang, MD
488 Follicular Dendritic Cell Sarcoma
Aaron Auerbach, MD, MPH

SECTION 8: MOLECULAR PATHOLOGY OF SOLID TUMORS

HEAD AND NECK, INCLUDING SINONASAL TUMORS AND SALIVARY GLANDS
494 HPV-Associated Head and Neck Carcinomas
Thèrése Bocklage, MD
500 Head and Neck Mucosal Squamous Cell Carcinoma, Non-HPV Related
Thèrése Bocklage, MD
506 Important Alterations in Non-HPV-Related Head and Neck Squamous Cell Carcinoma
Thèrése Bocklage, MD
508 Translocation-Specific Salivary Gland Tumors
Thèrése Bocklage, MD
518 Translocation-Specific Salivary Gland Tumors (Continued)
Thèrése Bocklage, MD
526 Nasopharyngeal EBV-Related Squamous Cell Carcinoma
Thèrése Bocklage, MD
530 Other Head and Neck Tumors
Thèrése Bocklage, MD

THYROID
538 Papillary Thyroid Carcinoma
Giovanni Insuasti-Beltran, MD
542 Follicular Thyroid Carcinoma
Giovanni Insuasti-Beltran, MD
546 Poorly Differentiated Thyroid Carcinoma
Von Samedi, MD, PhD
550 Anaplastic Thyroid Carcinoma
Von Samedi, MD, PhD
554 Medullary Thyroid Carcinoma
Giovanni Insuasti-Beltran, MD

LUNG
560 Adenocarcinoma, Lung
Jeremy C. Wallentine, MD
568 Squamous Cell Carcinoma, Lung
Jeremy C. Wallentine, MD
572 Small Cell Neuroendocrine Carcinoma
M. Carmen Frias Kletecka, MD and Samuel Reynolds, MD
576 Mesothelioma
Mohammad A. Vasef, MD and Khalil Sheibani, MD, FCAP

LUMINAL GASTROINTESTINAL TRACT
580 Gastric Adenocarcinoma
M. Carmen Frias Kletecka, MD and Joshua Anspach Hanson, MD
584 Colorectal Adenocarcinoma and Precancerous Lesions
M. Carmen Frias Kletecka, MD and Joshua Anspach Hanson, MD
590 Gastrointestinal Stromal Tumor
M. Carmen Frias Kletecka, MD and Joshua Anspach Hanson, MD

LIVER
598 HNF1A-Inactivated Hepatocellular Adenoma
Giovanni Insuasti-Beltran, MD and Joshua Anspach Hanson, MD
602 ß-Catenin-Activated Hepatocellular Adenoma
Giovanni Insuasti-Beltran, MD and Joshua Anspach Hanson, MD
606 Inflammatory Hepatocellular Adenoma
Giovanni Insuasti-Beltran, MD and Joshua Anspach Hanson, MD
610 Hepatocellular Carcinoma
Rama Gullapalli, MD, PhD

PANCREATICOBILIARY
614 Pancreatic Ductal Adenocarcinoma
Von Samedi, MD, PhD
618 Pancreatic Mucinous Cystic Neoplasm
Von Samedi, MD, PhD
620 Pancreatic Intraductal Papillary Mucinous Neoplasm
Von Samedi, MD, PhD
622 Cholangiocarcinoma
Rama Gullapalli, MD, PhD

TESTIS
624 Testicular Germ Cell Tumors
Edgar Fischer, MD, PhD

KIDNEY
630 Clear Cell Renal Cell Carcinoma
Edgar Fischer, MD, PhD
634 Chromophobe Renal Cell Carcinoma
Edgar Fischer, MD, PhD
636 Papillary Renal Cell Carcinoma
Edgar Fischer, MD, PhD
638 TFE3-Rearranged and TFEB-Altered Renal Cell Carcinomas
Edgar Fischer, MD, PhD
642 Wilms Tumor
Marc Barry, MD
648 Clear Cell Sarcoma of Kidney
Marc Barry, MD
650 Oncocytoma
Marc Barry, MD
652 Rhabdoid Tumor of Kidney
Marc Barry, MD

BLADDER
654 Urothelial Carcinoma
Marc Barry, MD

ADRENAL
660 Pheochromocytoma/Paraganglioma
M. Carmen Frias Kletecka, MD and Samuel Reynolds, MD
666 Adrenal Cortical Carcinoma
M. Carmen Frias Kletecka, MD and Samuel Reynolds, MD
672 Neuroblastoma
Giovanni Insuasti-Beltran, MD, Thèrése Bocklage, MD, and Samuel Reynolds, MD
680 Adrenal Cortical Adenoma
M. Carmen Frias Kletecka, MD and Samuel Reynolds, MD

PROSTATE
684 Prostatic Adenocarcinoma, Acinar Type and High-Grade Prostatic Intraepithelial Neoplasia
Edgar Fischer, MD, PhD

BREAST
688 ADH and DCIS (Dysplastic, Premalignant)
David G. Hicks, MD
694 Ductal Carcinomas
David G. Hicks, MD
700 Lobular Carcinoma
David G. Hicks, MD
706 Invasive Ductal Carcinoma of No Special Type With Medullary Features
Rania Bakkar, MD
710 Metaplastic Breast Carcinoma
Rania Bakkar, MD
716 Phyllodes Tumors
Rania Bakkar, MD
720 Basal-Like and Triple-Negative Breast Carcinomas
David G. Hicks, MD and Susan C. Lester, MD, PhD

CERVIX/VULVA/VAGINA
730 Preneoplastic Conditions, Cervix/Vulva/Vagina
Nancy Joste, MD
734 Squamous Cell Carcinoma, Cervix/Vulva/Vagina
Nancy Joste, MD
738 Adenocarcinoma, Cervix/Vulva/Vagina
Nancy Joste, MD

UTERUS
742 Endometrial Intraepithelial Neoplasia
Lesley Lomo, MD
744 Uterine Endometrioid Carcinoma
Lesley Lomo, MD
748 Uterine Serous Carcinoma
Lesley Lomo, MD
750 Clear Cell Carcinoma, Uterus
Lesley Lomo, MD
754 Uterine Sarcomas
Thèrése Bocklage, MD

OVARIES/FALLOPIAN TUBE
762 Serous Tumors of Ovary and Fallopian Tube
Rania Bakkar, MD
768 Other Surface Epithelial Tumors of Ovary
Rania Bakkar, MD
774 Sex Cord-Stromal Tumors of Ovary
Rania Bakkar, MD
780 Germ Cell Tumor, Ovary
Rania Bakkar, MD and Aaron Auerbach, MD, MPH

SKIN
784 Premalignant Conditions, Skin
David Cassarino, MD, PhD
788 Melanoma
David Cassarino, MD, PhD
792 Squamous Cell Carcinoma, Skin
David Cassarino, MD, PhD
796 Basal Cell Carcinoma, Skin
David Cassarino, MD, PhD
800 Sebaceous Tumors
David Cassarino, MD, PhD
802 Dermatofibroma and Dermatofibrosarcoma Protuberans
David Cassarino, MD, PhD

BONE
804 Overview of Molecular Pathology of Bone and Soft Tissue Tumors
Thèrése Bocklage, MD
810 Osteosarcomas
Thèrése Bocklage, MD
818 Ewing Sarcoma
Thèrése Bocklage, MD
824 Other Small Round Blue Cell Sarcomas
Thèrése Bocklage, MD
832 Giant Cell Tumor of Bone
Thèrése Bocklage, MD
838 Intermediate and Malignant Cartilaginous Tumors of Bone
Thèrése Bocklage, MD

SOFT TISSUE
848 Intermediate and Malignant Myofibroblastic/Fibroblastic Tumors
Thèrése Bocklage, MD
858 Liposarcomas
Thèrése Bocklage, MD
868 Muscle Sarcomas
Thèrése Bocklage, MD
878 Intermediate and Malignant Vascular Tumors
Thèrése Bocklage, MD
886 Malignant Peripheral Nerve Sheath Tumor
Thèrése Bocklage, MD and David R. Lucas, MD
892 Representative Genetic Findings in Bone and Soft Tissue Tumors
Thèrése Bocklage, MD

SARCOMAS OF UNCERTAIN DIFFERENTIATION
898 Rare Sarcomas of Uncertain Differentiation With Specific Molecular Alterations
Thèrése Bocklage, MD
908 Rare Sarcomas of Uncertain Differentiation With Specific Molecular Alterations (Continued)
Thèrése Bocklage, MD

CNS
916 Glioblastoma, IDH Wildtype
Elisabeth Rushing, MD and Mohammad A. Vasef, MD
920 Astrocytoma, IDH-Mutant
Elisabeth Rushing, MD and Mohammad A. Vasef, MD
924 Pilocytic Astrocytoma
Aaron Auerbach, MD, MPH, Karen SantaCruz, MD, and Elisabeth Rushing, MD
928 Oligodendroglioma, IDH Mutant, and 1p/19q Codeleted
Aaron Auerbach, MD, MPH, Karen SantaCruz, MD, and Elisabeth Rushing, MD
932 Ependymal Tumors
Mohammad A. Vasef, MD and Fausto J. Rodríguez, MD
938 Medulloblastoma
Mohammad A. Vasef, MD and Fausto J. Rodríguez, MD
944 Choroid Plexus Tumors
Mohammad A. Vasef, MD and Fausto J. Rodríguez, MD
948 Meningioma
Mohammad A. Vasef, MD and Karen SantaCruz, MD
952 Retinoblastoma
Mohammad A. Vasef, MD and Fausto J. Rodríguez, MD

SECTION 9: QUALITY ASSURANCE AND REGULATORY ISSUES

958 Federal Agencies and Regulation of Laboratories
Amer Mahmoud, MD, FCAP
960 FDA Regulations
Yongjie Zhou, MD, PhD
966 Proficiency Testing and Accreditation
Amer Mahmoud, MD, FCAP