Chapter 3. Molecular Diagnosis of Tumors

Summary

This chapter contains sections titled:

• Introduction

  • Molecular Diagnosis of Tumors at the Genomic Level

• Nucleic Acids and Techniques

  • Working with DNA

    • DNA Extraction

    • Storage, Quantification and Determination of Quality of Genomic DNA

  • Working with RNA

    • RNA Extraction

  • Polymerase Chain Reaction

    • Standard Polymerase Chain Reaction

    • Multiplex PCR

    • Real-Time PCR

  • Reverse Transcriptase Polymerase Chain Reaction

    • One-Step RT-PCR

    • Two-Step RT-PCR

    • Notes for Performing RT-PCR

  • Quality Control for DNA and RNA Extraction and Amplification

  • Electrophoresis and Detection of Mutations

    • Polyacrylamide Gel

    • Agarose Gel

    • Principle of Denaturing Gel Analysis

  • Detection of Mutations by Electrophoresis

    • Single-Strand Conformational Polymorphism

    • Heteroduplex Analysis

  • In Situ Hybridization

    • ISH Technique

• Diagnosis of Tumors, Micrometastases and Circulating Tumor Cells by Molecular Detection of Specific Chromosomal Translocations

  • Introduction

  • Molecular Diagnosis of Solid Tumors

    • Molecular Detection of Synovial Sarcoma

    • Molecular Detection of Ewing's Sarcoma and Primitive Neuroectodermal Tumor

    • Molecular Detection of Desmoplastic Small Round Cell Tumor

    • Molecular Detection of Clear Cell Sarcoma (Malignant Melanoma of Soft Tissue)

    • Molecular Detection of Alveolar Rhabdomyosarcoma

    • Molecular Detection of Myxoid Liposarcoma

    • Molecular Detection of Extraskeletal Myxoid Chondrosarcoma

    • Molecular Detection of Dermatofibrosarcoma Protuberans and Giant Cell Fibroblastoma

    • Molecular Detection of Inflammatory Myofibroblastic Tumor

    • Molecular Detection of Alveolar Soft Part Sarcoma

    • Molecular Detection of Congenital Fibrosarcoma and Mesoblastic Nephroma

    • Molecular Detection of Endometrial Stromal Tumors

    • Molecular Detection of Papillary and Follicular Thyroid Carcinoma

  • Molecular Diagnosis of Hematopoietic and Lymphoid Neoplasia

    • Molecular Detection of Follicular Lymphoma

    • Molecular Detection of Mantle Cell Lymphoma

    • Molecular Detection of Anaplastic Large Cell Lymphoma

    • Molecular Detection of Chronic Myeloid Leukemia

    • Molecular Detection of Acute Lymphoblastic Leukemia

    • Molecular Detection of Acute Myeloid Leukemia

• Diagnosis of Lymphoma and Residual Tumor Cells by Molecular Detection of Gene Rearrangements

  • Introduction

  • Detection of Immunoglobulin Heavy Chain (IgH) Gene Rearrangement in B-Cell Lymphoma

  • Detection of T-Cell Receptor Gene Rearrangement in T-Cell Neoplasia

• Diagnosis of Tumors, Micrometastases, Isolated and Circulating Tumor Cells by Molecular Detection of Tissue-Specific Gene Expression

  • Introduction

  • Detection of Micrometastases and Circulating Tumor Cells of Prostatic Carcinoma by Amplification of Prostate-Specific Antigen, Prostate-Specific Membrane Antigen and PTI-1 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Follicular and Papillary Thyroid Carcinoma by Amplification of Thyroglobulin, Thyroid Peroxidase and TTF-1 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Hepatocellular Carcinoma by Amplification of Alpha-Fetoprotein and Albumin mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Malignant Melanoma by Amplification of mRNA of Melanoma-Associated Antigens: Tyrosinase, P97, MUC-18, HMB45, Melan-A, MAGE and GAGE Family Members

  • Detection of Micrometastases and Circulating Tumor Cells of Adenocarcinomas by Amplification of Carcinoembryonic Antigen mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Neuroblastoma by Amplification of Tyrosine Hydroxylase and PGP 9.5 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Tumors with Neuroendocrine Differentiation, PNET and Small Cell Carcinoma of the Lung by Amplification of Neuroendocrine-Specific Markers mRNA: Chromogranin A, Neuron-Specific Enolase, Choline Acetyltransferase, Secretogranin II and Somatostatin Receptor Type 2

  • Molecular Diagnosis of Rhabdomyosarcoma and Detection of Micrometastases and Circulating Tumor Cells by Amplification of Muscle-Specific Markers mRNA: Myo D1, Myogenin, Myoglobin and Fetal Acetylcholine Receptor

  • Detection of Micrometastases and Circulating Tumor Cells of Squamous Cell Carcinoma by Amplification of Squamous Cell Carcinoma Antigen mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Adenocarcinoma by Amplification of MUC-1 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Colorectal Adenocarcinoma by Amplification of Guanylyl Cyclase C and CDX-2 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Breast Carcinoma by Amplification of Mammaglobin mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Transitional Cell Carcinoma by Amplification of Uroplakins mRNA

• Diagnosis of Tumors, Micrometastases, Isolated and Circulating Tumor Cells by Molecular Detection of Tissue-Specific Cytokeratins

  • Introduction

  • Detection of Micrometastases and Circulating Tumor Cells of Malignant Epithelial Neoplasia by the Amplification of Cytokeratin 8 and Cytokeratin 18 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Malignant Epithelial Neoplasia by the Amplification of Cytokeratin 19 mRNA

  • Detection of Micrometastases and Circulating Tumor Cells of Malignant Epithelial Neoplasia by the Amplification of Cytokeratin 20 mRNA

• Molecular Detection of Tumor-Associated Viruses

  • Introduction

    • DNA Viruses

    • RNA Viruses

  • Detection of Human Papillomavirus

  • Detection of Human Herpesviruses: Epstein–Barr Virus and Human Herpesvirus 8

    • Epstein–Barr Virus

    • Human Herpesvirus-8