Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications 3rd Edition by Lela Buckingham, ISBN-13: 978-0803668294

Description

Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications 3rd Edition by Lela Buckingham, ISBN-13: 978-0803668294

[PDF eBook eTextbook]

• Publisher: ‎ F.A. Davis Company; Third edition (February 22, 2019)
• Language: ‎ English
• ‎576 pages
• ISBN-10: ‎ 0803668295
• ISBN-13: ‎ 978-0803668294

The only book you need to become certified.

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.

Table of Contents:

Cover

Title Page

Copyright Page

Dedication

Preface

Reviewers

Acknowledgments

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

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

PROTEINS AND THE GENETIC CODE

Amino Acids

Genes

The Genetic Code

TRANSLATION

Amino Acid Charging

Protein Synthesis

2 Gene Expression and Epigenetics

TRANSCRIPTION

Transcription Initiation

Transcription Elongation

Transcription Termination

REGULATION OF TRANSCRIPTION

Regulation of Messenger RNA Synthesis at Initiation

Post-Transcriptional Regulation

Post-Translational Regulation

EPIGENETICS

Histone Modification

Nucleic Acid Methylation

CLASSIFICATION OF EPIGENETIC FACTORS

NONCODING RNAs

MicroRNAs

Small Interfering RNAs

Other Small RNAs

Long Noncoding RNAs

Section II: Common Techniques in Molecular Biology

3 Nucleic Acid Extraction Methods

ISOLATION OF DNA

Preparing the Sample

DNA Isolation Chemistries

ISOLATION OF RNA

Total RNA

Specimen Collection

RNA Isolation Chemistries

MEASUREMENT OF NUCLEIC ACID QUALITY AND QUANTITY

Electrophoresis

Spectrophotometry

Fluorometry

Microfluidics

4 Resolution and Detection of Nucleic Acids

ELECTROPHORESIS OF NUCLEIC ACIDS

GEL SYSTEMS

Agarose Gels

Polyacrylamide Gels

CAPILLARY ELECTROPHORESIS

BUFFER SYSTEMS

Buffer Additives

ELECTROPHORESIS EQUIPMENT

Gel Loading

DETECTION SYSTEMS

Fluorescent Dyes

Silver Stain

5 Analysis and Characterization of Nucleic Acids and Proteins

RESTRICTION ENZYME MAPPING OF DNA

CRISPR ENZYME SYSTEMS

HYBRIDIZATION TECHNOLOGIES

Southern Blots

PROBE HYBRIDIZATION

Northern Blots

Western Blots

PROBES

DNA Probes

RNA Probes

Other Nucleic Acid Probe Types

Protein Probes

Probe Labeling

Nucleic Acid Probe Design

HYBRIDIZATION CONDITIONS, STRINGENCY

DETECTION SYSTEMS

INTERPRETATION OF RESULTS

ARRAY-BASED HYBRIDIZATION

Dot/Slot Blots

Genomic Array Technology

SOLUTION HYBRIDIZATION

6 Nucleic Acid Amplification

TARGET AMPLIFICATION

Polymerase Chain Reaction

Transcription-Based Amplification Systems

Genomic Amplification Methods

PROBE AMPLIFICATION

Ligase Chain Reaction

Strand Displacement Amplification

Qβ Replicase

SIGNAL AMPLIFICATION

Branched DNA Amplification

Hybrid Capture Assays

Cleavage-Based Amplification

Cycling Probe

7 Chromosomal Structure and Chromosomal Mutations

CHROMOSOMAL STRUCTURE AND ANALYSIS

Chromosomal Compaction and Histones

Chromosome Morphology

Visualizing Chromosomes

DETECTION OF GENOME AND CHROMOSOMAL MUTATIONS

Karyotyping

Fluorescence In Situ Hybridization

COMPARATIVE GENOME HYBRIDIZATION (CGH)

8 Gene Mutations

TYPES OF GENE MUTATIONS

DETECTION OF GENE MUTATIONS

Biochemical Methods

Nucleic Acid Analyses

GENE VARIANT NOMENCLATURE

GENE NAMES

9 DNA Sequencing

DIRECT SEQUENCING

Manual Sequencing

Automated Fluorescent Sequencing

PYROSEQUENCING

BISULFITE DNA SEQUENCING

RNA SEQUENCING

NEXT-GENERATION SEQUENCING

Gene Panels

NGS Library Preparation

Targeted Libraries

Sequencing Platforms

Sequence Quality

Filtering and Annotation

BIOINFORMATICS

THE HUMAN GENOME PROJECT

Variant Associations With Phenotype

Section III: Techniques in the Clinical Laboratory

10 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

11 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

12 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

13 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); and 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) and 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

14 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

SUMMARY OF LABORATORY TESTING

15 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

QUALITY ASSURANCE

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

Appendix A Study Question Answers

Appendix B Answers to Case Studies

Glossary

Index

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