Nucleic Acids As Molecular Diagnostics

By integrating technology, supporting infrastructure and efficient application, the all-in-one guide presents molecular diagnostics as an essential component of modern, personalized clinical practice. It considers all important aspects, from the hardware and software needed, to recent improvements in blood- and non-blood-based biomarker tests. Chapters on ethical challenges and a look at current trends and the latest innovations are also included.
Bridging the gap between industry and academia, this is a highly useful resource for practitioners as well as for developers of modern, DNA- and RNA-based molecular diagnostics.

Andreas Keller studied Computational Biology at Saarland University in Saarbrucken (Germany), completing his PhD in 2009. He joined Febit Biomed GmbH in 2008 where he directed the biomarker discovery effort. In 2011, he joined the healthcare division of Siemens AG in Erlangen as director diagnostic innovation. In 2013 he became professor for Clinical Computational Biology at Saarland University. Dr. Keller has published more than 80 peer-reviewed manuscripts and field more than 30 patents in the area of biomarker discovery and molecular diagnostics.

Eckart Meese is Professor of Human Genetics and Molecular Biology at Saarland University Medical School in Homburg (Germany), where he directs the Institute of Human Genetics. He obtained his PhD in biology in 1987 and did postdoc work at the Arizona Cancer Center in Tucson (USA). He then joined the University of Michigan Medical Center as Assistant Professor, before joining Saarland University in 1992. His scientific focus is on miRNA and autoantibody profiling for the diagnosis of cancer and other diseases.

Preface

NEXT-GENERATION SEQUENCING FOR CLINICAL DIAGNOSTICS OF CARDIOMYOPATHIES
Introduction
Cardiomyopathies and Why Genetic Testing is Needed
NGS
NGS for Cardiomyopathies
Sample Preparation
Bioinformatics Analysis Pipeline
Interpretation of Results and Translation into Clinical Practice

MICRORNAs AS NOVEL BIOMARKERS IN CARDIOVASCULAR MEDICINE
Introduction
miRNAs are Associated with Cardiovascular Risk Factors
miRNAs in Coronary Artery Disease
miRNAs in Cardiac Ischemia and Necrosis
miRNAs as Biomarkers of Heart Failure
Future Challenges

MICRORNAs IN PRIMARY BRAIN TUMORS: FUNCTIONAL IMPACT AND POTENTIAL USE FOR DIAGNOSTIC PURPOSES
Background
Gliomas
Meningiomas
Pituitary Adenomas
Medulloblastomas
Other Brain Tumors
Summary and Outlook

GENETIC AND EPIGENETIC ALTERATIONS IN SPORADIC COLORECTAL CANCER: CLINICAL IMPLICATIONS
Introduction
Microsatellite Instability
Driver Somatic Mutations in CRC
Epigenetic Instability in CRC
Hypomethylation
CpG Island Methylator Phenotype
Concluding Remarks

NUCLEIC ACID-BASED MARKERS IN UROLOGIC MALIGNANCIES
Introduction
Bladder Cancer
Prostate Cancer
Renal Cell Carcinoma
Summary

FROM THE GENETIC MAKE-UP TO THE MOLECULAR SIGNATURE OF NON-CODING RNA IN BREAST CANCER
Introduction
Molecular Breast Cancer Detection
Molecular Breast Cancer Subtypes and Prognostic/Predictive Molecular Biomarkers

NUCLEIC ACID-BASED DIAGNOSTICS IN GYNECOLOGICAL MALIGNANCIES
Introduction
Cervix, Vulva, and Vaginal Carcinoma
Endometrial Carcinoma (Carcinoma Corpus Uteri)
Ovarian Carcinoma
Breast Cancer
Conclusion

NUCLEIC ACIDS AS MOLECULAR DIAGNOSTICS IN HEMATOPOIETIC MALIGNANCIES -
IMPLICATIONS IN DIAGNOSIS, PROGNOSIS, AND THERAPEUTIC MANAGEMENT
Introduction
Methodological Approaches
Cytogenetic Analysis to Molecular Diagnostics
Minimal Residual Disease
Chronic Myeloid Leukemia
Acute Myeloid Leukemia
Acute Lymphocytic Leukemia
Chronic Lymphocytic Leukemia
Outlook and Perspectives

TECHNIQUES OF NUCLEIC ACID-BASED DIAGNOSIS IN THE MANAGEMENT OF BACTERIAL AND VIRAL INFECTIOUS DISEASES
Importance of Nucleic Acid-Based Molecular Assays in Clinical Microbiology
Nucleic Acid Amplification Techniques
Post-Amplification Analyses
General Overview and Concluding Remarks

MICRORNAs IN HUMAN MICROBIAL INFECTIONS AND DISEASE OUTCOMES
Introduction
General Aspects of miRNAs in Infectious Diseases
miRNAs as Biomarkers and Therapeutic Agents in Tuberculosis and Hepatitis C Infections
miRNA-Targeting Therapeutics
Concluding Remarks

TOWARDS THE IDENTIFICATION OF CONDITION-SPECIFIC MICROBIAL POPULATIONS FROM HUMAN METAGENOMIC DATA
Introduction
Nucleic Acid-Based Methods in Diagnostic Microbiology
Need for Comprehensive Microbiome Characterization in Medical Diagnostics
Challenges for Metagenomics-Based Diagnostics: Read Lengths, Sequencing Library Sizes, and Microbial Community Composition
Deconvolution of Population-Level Genomic Complements from Metagenomic Data
Need for Comparative Metagenomic Data Analysis Tools
Future Perspectives in Microbiome-Enabled Diagnostics

GENOME, EXOME, AND GENE PANEL SEQUENCING IN A CLINICAL SETTING
Introduction
Genetic Diagnostics from a Laboratory Perspective -
From Sanger to NGS
NGS Diagnostics in a Clinical Setting -
Comparison Between Genome, Exome, and Panel Diagnostics
Conclusion and Outlook

ANALYSIS OF NUCLEIC ACIDS IN SINGLE CELLS
Introduction
Isolating Single Cells
Looking at the DNA of a Single Cancer Cell
Molecular DNA Analysis in Single Cells
Approaches to Analyze RNA of a Single Cell
Expression Analysis in Single Cells and its Biological Relevance in Cancer
Thoughts on Bioinformatics Approaches
Future Impact of Single-Cell Analysis in Clinical Diagnosis

DETECTING DYSREGULATED PROCESSES AND PATHWAYS
Introduction
Measuring and Normalizing Expression Profiles
Biological Networks
Measuring the Degree of Deregulation of Individual Genes
Over-Representation Analysis and Gene Set Enrichment Analysis
Detecting Deregulated Networks and Pathways
miRNA Expression Data
Differential Network Analysis
Conclusion

COMPANION DIAGNOSTICS AND BEYOND -
AN ESSENTIAL ELEMENT IN THE PUZZLE OF TRANSFORMING HEALTHCARE
Introduction
The Healthcare Environment
What is Companion Diagnostics?
What are the Drivers for Companion Diagnostics?
Companion Diagnostics Market
Partnerships and Business Models for Companion Diagnostics
Regulatory Environment for Compantion Diagnostics Tests
Outlook -
Beyond Companion Diagnostics Towards Holistic Solutions

ETHICAL, LEGAL, AND PSYCHOSOCIAL ASPECTS OF MOLECULAR GENETIC DIAGNOSIS
General Peculiarities of Genetic Diagnoses
Informed Consent and Genetic Counseling
Medical Secrecy and Data Protection
Predictive Diagnosis
Prenatal Diagnosis
Multiparameter Testing

Index