Nucleic Acids as 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 CARDIOMYOPATHIESIntroductionCardiomyopathies and Why Genetic Testing is NeededNGSNGS for CardiomyopathiesSample PreparationBioinformatics Analysis PipelineInterpretation of Results and Translation into Clinical Practice MICRORNAs AS NOVEL BIOMARKERS IN CARDIOVASCULAR MEDICINEIntroductionmiRNAs are Associated with Cardiovascular Risk FactorsmiRNAs in Coronary Artery DiseasemiRNAs in Cardiac Ischemia and NecrosismiRNAs as Biomarkers of Heart FailureFuture Challenges MICRORNAs IN PRIMARY BRAIN TUMORS: FUNCTIONAL IMPACT AND POTENTIAL USE FOR DIAGNOSTIC PURPOSESBackgroundGliomasMeningiomasPituitary AdenomasMedulloblastomasOther Brain TumorsSummary and Outlook GENETIC AND EPIGENETIC ALTERATIONS IN SPORADIC COLORECTAL CANCER: CLINICAL IMPLICATIONSIntroductionMicrosatellite InstabilityDriver Somatic Mutations in CRCEpigenetic Instability in CRCHypomethylationCpG Island Methylator PhenotypeConcluding Remarks NUCLEIC ACID-BASED MARKERS IN UROLOGIC MALIGNANCIESIntroductionBladder CancerProstate CancerRenal Cell CarcinomaSummary FROM THE GENETIC MAKE-UP TO THE MOLECULAR SIGNATURE OF NON-CODING RNA IN BREAST CANCERIntroductionMolecular Breast Cancer DetectionMolecular Breast Cancer Subtypes and Prognostic/Predictive Molecular Biomarkers NUCLEIC ACID-BASED DIAGNOSTICS IN GYNECOLOGICAL MALIGNANCIESIntroductionCervix, Vulva, and Vaginal CarcinomaEndometrial Carcinoma (Carcinoma Corpus Uteri)Ovarian CarcinomaBreast CancerConclusion NUCLEIC ACIDS AS MOLECULAR DIAGNOSTICS IN HEMATOPOIETIC MALIGNANCIES -IMPLICATIONS IN DIAGNOSIS, PROGNOSIS, AND THERAPEUTIC MANAGEMENTIntroductionMethodological ApproachesCytogenetic Analysis to Molecular DiagnosticsMinimal Residual DiseaseChronic Myeloid LeukemiaAcute Myeloid LeukemiaAcute Lymphocytic LeukemiaChronic Lymphocytic LeukemiaOutlook and Perspectives TECHNIQUES OF NUCLEIC ACID-BASED DIAGNOSIS IN THE MANAGEMENT OF BACTERIAL AND VIRAL INFECTIOUS DISEASESImportance of Nucleic Acid-Based Molecular Assays in Clinical MicrobiologyNucleic Acid Amplification TechniquesPost-Amplification AnalysesGeneral Overview and Concluding Remarks MICRORNAs IN HUMAN MICROBIAL INFECTIONS AND DISEASE OUTCOMESIntroductionGeneral Aspects of miRNAs in Infectious DiseasesmiRNAs as Biomarkers and Therapeutic Agents in Tuberculosis and Hepatitis C InfectionsmiRNA-Targeting TherapeuticsConcluding Remarks TOWARDS THE IDENTIFICATION OF CONDITION-SPECIFIC MICROBIAL POPULATIONS FROM HUMAN METAGENOMIC DATAIntroductionNucleic Acid-Based Methods in Diagnostic MicrobiologyNeed for Comprehensive Microbiome Characterization in Medical DiagnosticsChallenges for Metagenomics-Based Diagnostics: Read Lengths, Sequencing Library Sizes, and Microbial Community CompositionDeconvolution of Population-Level Genomic Complements from Metagenomic DataNeed for Comparative Metagenomic Data Analysis ToolsFuture Perspectives in Microbiome-Enabled Diagnostics GENOME, EXOME, AND GENE PANEL SEQUENCING IN A CLINICAL SETTINGIntroductionGenetic Diagnostics from a Laboratory Perspective -From Sanger to NGSNGS Diagnostics in a Clinical Setting -Comparison Between Genome, Exome, and Panel DiagnosticsConclusion and Outlook ANALYSIS OF NUCLEIC ACIDS IN SINGLE CELLSIntroductionIsolating Single CellsLooking at the DNA of a Single Cancer CellMolecular DNA Analysis in Single CellsApproaches to Analyze RNA of a Single CellExpression Analysis in Single Cells and its Biological Relevance in CancerThoughts on Bioinformatics ApproachesFuture Impact of Single-Cell Analysis in Clinical Diagnosis DETECTING DYSREGULATED PROCESSES AND PATHWAYSIntroductionMeasuring and Normalizing Expression ProfilesBiological NetworksMeasuring the Degree of Deregulation of Individual GenesOver-Representation Analysis and Gene Set Enrichment AnalysisDetecting Deregulated Networks and PathwaysmiRNA Expression DataDifferential Network AnalysisConclusion COMPANION DIAGNOSTICS AND BEYOND -AN ESSENTIAL ELEMENT IN THE PUZZLE OF TRANSFORMING HEALTHCAREIntroductionThe Healthcare EnvironmentWhat is Companion Diagnostics?What are the Drivers for Companion Diagnostics?Companion Diagnostics MarketPartnerships and Business Models for Companion DiagnosticsRegulatory Environment for Compantion Diagnostics TestsOutlook -Beyond Companion Diagnostics Towards Holistic Solutions ETHICAL, LEGAL, AND PSYCHOSOCIAL ASPECTS OF MOLECULAR GENETIC DIAGNOSISGeneral Peculiarities of Genetic DiagnosesInformed Consent and Genetic CounselingMedical Secrecy and Data ProtectionPredictive DiagnosisPrenatal DiagnosisMultiparameter Testing Index