Molecular Diagnostics Fundamentals Methods and Clinical Applications 3rd edition by Lela Buckingham ISBN 0803699565 9780803699564

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ISBN 10: 0803699565
ISBN 13: 9780803699564
Author: Lela Buckingham

Meet the challenges of this rapidly expanding field
Molecular diagnostics continues to grow in importance in the clinical laboratory. This respected text will prepare your students with a grounding in the fundamental principles of molecular biology. current methods, and their clinical applications.

With a focus on the application of molecular concepts to diagnostic purposes, the text explains and illustrate the use and interpretation of molecular-based assays in patient care. Now with an expanded discussion of nucleic acid sequencing, with added emphasis on next generation sequencing (NGS), and updated coverage of proteomics and mass spectrometry applications, your students will have the most current information available today.

Molecular Diagnostics Fundamentals Methods and Clinical Applications 3rd Table of contents:

Section I: Fundamentals of Molecular Biology: An Overview

1. Nucleic Acids and Proteins

   • DNA

     • DNA Structure

     • Nucleotides

     • Nucleic Acid

     • DNA Replication

       • Polymerases

   • Enzymes that Metabolize DNA

     • Restriction Enzymes

     • DNA Ligase

     • Other DNA Metabolizing Enzymes

   • Recombination in Sexually Reproducing Organisms

   • Recombination in Asexual Reproduction

     • Conjugation

     • Transduction

     • Transformation

   • Plasmids

2. RNA

   • Transcription

     • Transcription Initiation

     • Transcription Elongation

     • Transcription Termination

   • Types/Structures of RNA

     • Ribosomal RNA

     • Messenger RNA

     • Small Nuclear RNA

     • Transfer RNA

     • Other RNAs

   • RNA Polymerases

   • Other RNA-Metabolizing Enzymes

     • Ribonucleases

     • RNA Helicases

3. Proteins and the Genetic Code

   • Amino Acids

   • Genes

   • The Genetic Code

   • Translation

     • Amino Acid Charging

     • Protein Synthesis

Section II: Gene Expression and Epigenetics

1. Transcription

   • Transcription Initiation

   • Transcription Elongation

   • Transcription Termination

2. Regulation of Transcription

   • Regulation of Messenger RNA Synthesis at Initiation

   • Post-Transcriptional Regulation

   • Post-Translational Regulation

3. Epigenetics

   • Histone Modification

   • Nucleic Acid Methylation

   • Classification of Epigenetic Factors

4. Noncoding RNAs

   • MicroRNAs

   • Small Interfering RNAs

   • Other Small RNAs

   • Long Noncoding RNAs

Section III: Common Techniques in Molecular Biology

1. Nucleic Acid Extraction Methods

   • Isolation of DNA

     • Preparing the Sample

     • DNA Isolation Chemistries

   • Isolation of RNA

     • Total RNA

     • Specimen Collection

     • RNA Isolation Chemistries

2. Measurement of Nucleic Acid Quality and Quantity

   • Electrophoresis

   • Spectrophotometry

   • Fluorometry

   • Microfluidics

Section IV: Resolution and Detection of Nucleic Acids

1. Electrophoresis of Nucleic Acids

   • Gel Systems

     • Agarose Gels

     • Polyacrylamide Gels

   • Capillary Electrophoresis

   • Buffer Systems

     • Buffer Additives

   • Electrophoresis Equipment

     • Gel Loading

2. Detection Systems

   • Fluorescent Dyes

   • Silver Stain

Section V: Analysis and Characterization of Nucleic Acids and Proteins

1. Restriction Enzyme Mapping of DNA

2. CRISPR Enzyme Systems

3. Hybridization Technologies

   • Southern Blots

   • Probe Hybridization

   • Northern Blots

   • Western Blots

4. Probes

   • DNA Probes

   • RNA Probes

   • Other Nucleic Acid Probe Types

   • Protein Probes

   • Probe Labeling

   • Nucleic Acid Probe Design

5. Hybridization Conditions, Stringency

6. Detection Systems

7. Interpretation of Results

8. Array-Based Hybridization

   • Dot/Slot Blots

   • Genomic Array Technology

9. Solution Hybridization

Section VI: Nucleic Acid Amplification

1. Target Amplification

   • Polymerase Chain Reaction

   • Transcription-Based Amplification Systems

   • Genomic Amplification Methods

2. Probe Amplification

   • Ligase Chain Reaction

   • Strand Displacement Amplification

   • Qβ Replicase

3. Signal Amplification

   • Branched DNA Amplification

   • Hybrid Capture Assays

   • Cleavage-Based Amplification

   • Cycling Probe

Section VII: Chromosomal Structure and Chromosomal Mutations

1. Chromosomal Structure and Analysis

   • Chromosomal Compaction and Histones

   • Chromosome Morphology

   • Visualizing Chromosomes

2. Detection of Genome and Chromosomal Mutations

   • Karyotyping

   • Fluorescence In Situ Hybridization

   • Comparative Genome Hybridization (CGH)

Section VIII: Gene Mutations

1. Types of Gene Mutations

2. Detection of Gene Mutations

   • Biochemical Methods

   • Nucleic Acid Analyses

3. Gene Variant Nomenclature

4. Gene Names

Section IX: DNA Sequencing

1. Direct Sequencing

   • Manual Sequencing

   • Automated Fluorescent Sequencing

2. Pyrosequencing

3. Bisulfite DNA Sequencing

4. RNA Sequencing

5. Next-Generation Sequencing

   • Gene Panels

   • NGS Library Preparation

     • Targeted Libraries

   • Sequencing Platforms

   • Sequence Quality

   • Filtering and Annotation

6. Bioinformatics

   • The Human Genome Project

   • Variant Associations With Phenotype

Section X: Techniques in the Clinical Laboratory

1. DNA Polymorphisms and Human Identification

   • Types of Polymorphisms

     • RFLP Typing

     • Genetic Mapping With RFLPs

     • RFLP and Parentage Testing

   • Human Identification Using RFLPs

   • STR Typing by PCR

     • STR Analysis

     • Y-STR

     • Linkage Analysis

     • Bone Marrow Engraftment Testing Using DNA Polymorphisms

   • PSTR Testing

   • Post-Transplant Engraftment Testing

   • Quality Assurance for Surgical Sections Using STR

   • Single-Nucleotide Polymorphisms

   • The Human Haplotype Mapping (HapMap) Project

   • Mitochondrial DNA Polymorphisms

   • Other Identification Methods

     • Protein-Based Identification

     • Epigenetic Profiles

2. Detection and Identification of Microorganisms

   • Specimen Collection

   • Sample Preparation

   • Quality Assurance

     • Controls

     • Quality Control

   • Selection of Sequence Targets for Detection of Microorganisms

   • Molecular Detection of Microorganisms

     • Bacteria

     • Viruses

     • Mycology

     • Parasites

   • Antimicrobial Agents

     • Resistance to Antimicrobial Agents

     • Molecular Detection of Resistance

   • Molecular Epidemiology

     • Molecular Strain Typing Methods for Epidemiological Studies

     • Comparison of Typing Methods

3. Molecular Detection of Inherited Diseases

   • The Molecular Basis of Inherited Diseases

   • Chromosomal Abnormalities

   • Patterns of Inheritance in Single-Gene Disorders

   • Molecular Basis of Single-Gene Disorders

     • Lysosomal Storage Diseases

     • Factor V Leiden

     • Prothrombin

     • Methylenetetrahydrofolate Reductase

     • Hemochromatosis

     • Cystic Fibrosis

     • Cytochrome P-450

   • Single-Gene Disorders with Nonclassical Patterns of Inheritance

     • Mutations in Mitochondrial Genes

     • Nucleotide-Repeat Expansion Disorders

     • Genomic Imprinting

     • Multifactorial Inheritance

   • Limitations of Molecular Testing

4. Molecular Oncology

   • Classification of Neoplasms

   • Molecular Basis of Cancer

   • Analytical Targets of Molecular Testing

     • Gene and Chromosomal Mutations in Solid Tumors

       • Human Epidermal Growth Factor Receptor 2, HER2/neu/erb-b2 1 (17q21.1)

       • Epidermal Growth Factor Receptor, EGFR (7p12)

       • Kirsten Rat Sarcoma Viral Oncogene Homolog, K-ras (12p12)

       • Neuroblastoma ras, N-ras (1p13)

       • Harvey Rat Sarcoma Viral Oncogene Homolog, H-ras (11p15)

       • Ewing Sarcoma, EWS (22q12)

       • Synovial Sarcoma Translocation, Chromosome 18—Synovial Sarcoma Breakpoint 1 and 2, SYT-SSX1, SYT-SSX2 t(X;18) (p11.2;q11.2)

       • Paired Box-Forkhead in Rhabdomyosarcoma, PAX3-FKHR, PAX7-FKHR, t(1;13), t(2;13)

       • Tumor Protein 53, TP53 (17p13)

       • Ataxia Telangiectasia Mutated Gene, ATM (11q22)

       • Breast Cancer 1 Gene, BRCA1 (17q21), and Breast Cancer 2 Gene, BRCA2 (13q12)

       • Von Hippel–Lindau Gene, VHL (3p26)

       • V-myc Avian Myelocytomatosis Viral-Related Oncogene, Neuroblastoma-Derived, MYCN or n-myc (2p24)

       • V-Ros Avian UR2 Sarcoma Virus Oncogene Homolog 1 (ROS1) Proto-Oncogene (6q22.1)

       • Rearranged During Transfection (RET) Proto-Oncogene (10q11)

       • Anaplastic Lymphoma Receptor Tyrosine Kinase (ALK) Proto-Oncogene, 2p23.1

       • V-Kit Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog, KIT, c-KIT (4q12)

     • Other Molecular Abnormalities

       • Microsatellite Instability

       • Loss of Heterozygosity

       • Liquid Biopsy

   • Molecular Analysis of Leukemia and Lymphoma

     • Gene Rearrangements

     • Mutations in Hematological Malignancies

     • Mutation Spectra

5. DNA-Based Tissue Typing

   • The MHC Locus

   • HLA Polymorphisms

   • HLA Nomenclature

   • Molecular Analysis of the MHC

     • Serological Analysis

     • DNA-Based Typing

     • Combining Typing Results

     • HLA Test Discrepancies

   • Coordination of HLA Test Methods

   • Additional Recognition Factors

     • Minor Histocompatibility Antigens

     • Nonconventional MHC Antigens

     • Killer Cell Immunoglobulin-Like Receptors

   • MHC Disease Association

6. Quality Assurance and Quality Control in the Molecular Laboratory

   • Specimen Handling

     • Collection Tubes for Molecular Testing

     • Precautions

     • Holding and Storage Requirements

   • Test Performance

     • Next-Generation Sequencing

     • Calibrators and Method Calibration

   • Controls

     • Quality Control

   • Instrument Maintenance

     • Instrument Calibration

   • Reagents

     • Reagent Categories

     • Chemical Safety

     • Reagent Storage

     • Reagent Labeling

   • Proficiency Testing

   • Documentation of Test Results

     • Gene Nomenclature

     • Gene Sequencing Results

   • Reporting Results

Appendices

• Appendix A: Study Question Answers

• Appendix B: Answers to Case Studies

• Glossary

• Index

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Tags: Lela Buckingham, Molecular Diagnostics, Fundamentals Methods, Clinical Applications