Cover image for Nucleic Acids As Molecular Diagnostics.
Nucleic Acids As Molecular Diagnostics.
Title:
Nucleic Acids As Molecular Diagnostics.
Author:
Keller, Andreas.
ISBN:
9783527672233
Personal Author:
Edition:
1st ed.
Physical Description:
1 online resource (393 pages)
Contents:
Nucleic Acids as Molecular Diagnostics -- Contents -- List of Contributors -- Preface -- 1 Next-Generation Sequencing for Clinical Diagnostics of Cardiomyopathies -- 1.1 Introduction -- 1.2 Cardiomyopathies and Why Genetic Testing is Needed -- 1.3 NGS -- 1.4 NGS for Cardiomyopathies -- 1.5 Sample Preparation -- 1.6 Bioinformatics Analysis Pipeline -- 1.7 Interpretation of Results and Translation into Clinical Practice -- References -- 2 MicroRNAs as Novel Biomarkers in Cardiovascular Medicine -- 2.1 Introduction -- 2.2 miRNAs are Associated with Cardiovascular Risk Factors -- 2.3 miRNAs in Coronary Artery Disease -- 2.4 miRNAs in Cardiac Ischemia and Necrosis -- 2.5 miRNAs as Biomarkers of Heart Failure -- 2.6 Future Challenges -- Acknowledgments -- References -- 3 MicroRNAs in Primary Brain Tumors: Functional Impact and Potential Use for Diagnostic Purposes -- 3.1 Background -- 3.2 Gliomas -- 3.2.1 miRNA as Biomarkers in Glioma Tissue -- 3.2.2 Circulating miRNA as Biomarkers -- 3.3 Meningiomas -- 3.4 Pituitary Adenomas -- 3.5 Medulloblastomas -- 3.6 Other Brain Tumors -- 3.6.1 Schwannomas -- 3.6.2 PCNSLs -- 3.7 Summary and Outlook -- References -- 4 Genetic and Epigenetic Alterations in Sporadic Colorectal Cancer: Clinical Implications -- 4.1 Introduction -- 4.2 Chromosomal Instability -- 4.3 Microsatellite Instability -- 4.4 Driver Somatic Mutations in CRC -- 4.4.1 APC -- 4.4.2 TP53 -- 4.4.3 KRAS -- 4.4.4 BRAF -- 4.4.5 PIK3CA -- 4.4.6 Other Mutations -- 4.5 Epigenetic Instability in CRC -- 4.6 Hypomethylation -- 4.7 CpG Island Methylator Phenotype -- 4.8 Concluding Remarks -- References -- 5 Nucleic Acid-Based Markers in Urologic Malignancies -- 5.1 Introduction -- 5.2 Bladder Cancer -- 5.2.1 Hereditary Factors for Bladder Cancer -- 5.2.2 Single Nucleotide Polymorphisms -- 5.2.3 RNA Alterations in Bladder Cancer -- 5.2.3.1 FGFR3 Pathway.

5.2.3.2 p53 Pathway -- 5.2.3.3 Urine-Based Markers -- 5.2.3.4 Serum-Based Markers -- 5.2.4 Sporadic Factors for Bladder Cancer -- 5.2.5 Genetic Changes in Non-Invasive Papillary Urothelial Carcinoma -- 5.2.5.1 FGFR 3 -- 5.2.5.2 Changes in the Phosphatidylinositol 3-Kinase Pathway -- 5.2.6 Genetic Changes in Muscle-Invasive Urothelial Carcinoma -- 5.2.6.1 TP53, RB, and Cell Cycle Control Genes -- 5.2.6.2 Other Genomic Alterations -- 5.2.7 Genetic Alterations with Unrecognized Associations to Tumor Stage and Grade -- 5.2.7.1 Alterations of Chromosome 9 -- 5.2.7.2 RAS Gene Mutations -- 5.3 Prostate Cancer -- 5.3.1 Hereditary Factors for Prostate Cancer -- 5.3.2 Sporadic Factors for Prostate Cancer -- 5.3.2.1 PSA and Other Protein Markers -- 5.3.2.2 Nucleic Acid Biomarkers -- 5.3.3 Prostate Cancer: Summary -- 5.4 Renal Cell Carcinoma -- 5.4.1 Hereditary Factors for RCC -- 5.4.2 Sporadic Factors for RCC -- 5.4.2.1 The Old -- 5.4.2.2 The New -- 5.5 Summary -- References -- 6 From the Genetic Make-Up to the Molecular Signature of Non-Coding RNA in Breast Cancer -- 6.1 Introduction -- 6.2 Molecular Breast Cancer Detection -- 6.2.1 Circulating Free DNA -- 6.2.2 Long Intergenic Non-Coding RNA -- 6.2.2.1 HOTAIR -- 6.2.2.2 H19 -- 6.2.2.3 GAS5 -- 6.2.2.4 LSINCT5 -- 6.2.2.5 LOC554202 -- 6.2.2.6 SRA1 -- 6.2.2.7 XIST -- 6.2.3 Natural Antisense Transcripts -- 6.2.3.1 HIF-1a-AS -- 6.2.3.2 H19 and H19-AS (91H) -- 6.2.3.3 SLC22A18-AS -- 6.2.3.4 RPS6KA2-AS -- 6.2.3.5 ZFAS1 -- 6.2.4 miRNAs -- 6.2.4.1 Tissue-Based miRNA Profiling in Breast Cancer -- 6.2.4.2 Circulating miRNAs -- 6.3 Molecular Breast Cancer Subtypes and Prognostic/Predictive Molecular Biomarkers -- References -- 7 Nucleic Acid-Based Diagnostics in Gynecological Malignancies -- 7.1 Introduction -- 7.2 Cervix, Vulva, and Vaginal Carcinoma -- 7.2.1 Background -- 7.2.2 Routine Diagnostics for HPV Infection.

7.2.2.1 Digene Hybrid Capture 2 High-Risk HPV DNA Test (Qiagen) -- 7.2.2.2 Cervista HPV HR (Holologics) -- 7.2.2.3 cobas 4800 System (Roche) -- 7.2.2.4 APTIMA HPV (Gen-Probe) -- 7.2.2.5 Abbot RealTime High Risk HPV Assay (Abbot) -- 7.2.2.6 PapilloCheck Genotyping Assay (Greiner BioOne) -- 7.2.2.7 INNO-LiPA HPVG enotyping Extra (Innogenetics) -- 7.2.2.8 Linear Array (Roche) -- 7.2.2.9 Recommendations for Clinical Use -- 7.2.3 Outlook - DNA Methylation Patterns -- 7.3 Endometrial Carcinoma (Carcinoma Corpus Uteri) -- 7.3.1 Background -- 7.3.2 Routine Diagnostics - Microsatellite Instability -- 7.3.3 Emerging Diagnostics - miRNA Markers -- 7.4 Ovarian Carcinoma -- 7.4.1 Background -- 7.4.2 Routine Diagnostics -- 7.4.3 Emerging Diagnostics/Perspective - miRNA Profiling -- 7.5 Breast Cancer -- 7.5.1 Background -- 7.5.2 Routine Diagnostics -- 7.5.2.1 HER2 Diagnostics -- 7.5.2.2 Gene Expression Profiling -- 7.5.2.3 Hereditary Breast Cancer/BRCA Diagnostics -- 7.5.3 Emerging Diagnostics/Perspectives -- 7.6 Conclusion -- References -- 8 Nucleic Acids as Molecular Diagnostics in Hematopoietic Malignancies - Implications in Diagnosis, Prognosis, and Therapeutic Management -- 8.1 Introduction -- 8.2 Methodological Approaches -- 8.3 Cytogenetic Analysis to Molecular Diagnostics -- 8.4 Minimal Residual Disease -- 8.5 Chronic Myeloid Leukemia -- 8.6 Acute Myeloid Leukemia -- 8.7 Acute Lymphocytic Leukemia -- 8.8 Chronic Lymphocytic Leukemia -- 8.9 Outlook and Perspectives -- References -- 9 Techniques of Nucleic Acid-Based Diagnosis in the Management of Bacterial and Viral Infectious Diseases -- 9.1 Importance of Nucleic Acid-Based Molecular Assays in Clinical Microbiology -- 9.2 Nucleic Acid Amplification Techniques -- 9.2.1 Target Amplification Techniques -- 9.2.1.1 PCR-Based Techniques -- 9.2.1.2 Transcription-Based Amplification Methods.

9.2.2 Signal Amplification Techniques -- 9.3 Post-Amplification Analyses -- 9.3.1 Sequencing and Pyrosequencing -- 9.3.2 Reverse Hybridization -- 9.3.3 High-Throughput Nucleic Acid-Based Analyses -- 9.3.3.1 DNA Microarrays -- 9.3.3.2 Mass Spectrometry -- 9.3.3.3 NGS -- 9.4 General Overview and Concluding Remarks -- Acknowledgments -- References -- 10 MicroRNAs in Human Microbial Infections and Disease Outcomes -- 10.1 Introduction -- 10.2 General Aspects of miRNAs in Infectious Diseases -- 10.2.1 miRNAs in Bacterial Infections -- 10.2.2 miRNAs in Viral Infections -- 10.2.2.1 Cellular miRNAs Control Viral Infections -- 10.2.2.2 Viruses Use miRNAs for Their Own Benefit -- 10.3 miRNAs as Biomarkers and Therapeutic Agents in Tuberculosis and Hepatitis C Infections -- 10.3.1 Tuberculosis: A Major Bacterial Pathogen -- 10.3.1.1 Tuberculosis Diagnosis and the Need for Immunological Biomarkers -- 10.3.1.2 miRNAs Regulation in Response to M. tuberculosis -- 10.3.1.3 Future Perspectives -- 10.3.2 Chronic Hepatitis C: A Major Viral Disease -- 10.3.2.1 Liver Fibrosis Progression and Treatment Outcome -- 10.3.2.2 miRNAs Involved in Liver Fibrogenesis -- 10.3.2.3 Prediction of Treatment Outcome in Chronic HCV-1 Infected Patients -- 10.3.2.4 Future Perspectives -- 10.4 miRNA-Targeting Therapeutics -- 10.5 Concluding Remarks -- Acknowledgments -- References -- 11 Towards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data -- 11.1 Introduction -- 11.2 Nucleic Acid-Based Methods in Diagnostic Microbiology -- 11.2.1 Limitations of Culture-Dependent Approaches -- 11.2.2 Culture-Independent Characterization of Microbial Communities -- 11.2.3 Metagenomics -- 11.2.4 Fecal Samples as Proxies to Evaluate Human Microbiome-Related Health Status -- 11.3 Need for Comprehensive Microbiome Characterization in Medical Diagnostics.

11.4 Challenges for Metagenomics-Based Diagnostics: Read Lengths, Sequencing Library Sizes, and Microbial Community Composition -- 11.5 Deconvolution of Population-Level Genomic Complements from Metagenomic Data -- 11.5.1 Reference-Dependent Metagenomic Data Analysis -- 11.5.1.1 Alignment-Based Approaches -- 11.5.1.2 Sequence Composition-Based Approaches -- 11.5.2 Reference-Independent Metagenomic Data Analysis -- 11.6 Need for Comparative Metagenomic Data Analysis Tools -- 11.6.1 Reference-Based Comparative Tools -- 11.6.2 Reference-Independent Identification of Condition-Specific Microbial Populations from Human Metagenomic Data -- 11.7 Future Perspectives in Microbiome-Enabled Diagnostics -- Acknowledgments -- References -- 12 Genome, Exome, and Gene Panel Sequencing in a Clinical Setting -- 12.1 Introduction -- 12.1.1 Genetic Inheritance and Sequencing -- 12.1.2 Genetic Testing by DNA Sequencing -- 12.2 Genetic Diagnostics from a Laboratory Perspective - From Sanger to NGS -- 12.2.1 Sanger Sequencing -- 12.2.2 NGS -- 12.2.3 Practical Workflow: From a Patient's DNA to NGS Sequencing Analysis -- 12.2.3.1 Preparation of gDNA -- 12.2.3.2 Quality Control -- 12.2.3.3 Library Preparation and Evaluation -- 12.2.3.4 Enrichment -- 12.2.3.5 Quality Control -- 12.2.3.6 Sequencing -- 12.3 NGS Diagnostics in a Clinical Setting - Comparison Between Genome, Exome, and Panel Diagnostics -- 12.3.1 Overview -- 12.3.2 Clinical Application of WGS -- 12.3.3 Clinical Application of WES -- 12.3.4 Clinical Application of Diagnostic Panels -- 12.4 Conclusion and Outlook -- References -- 13 Analysis of Nucleic Acids in Single Cells -- 13.1 Introduction -- 13.2 Isolating Single Cells -- 13.3 Looking at the DNA of a Single Cancer Cell -- 13.4 Molecular DNA Analysis in Single Cells -- 13.5 Approaches to Analyze RNA of a Single Cell.

13.6 Expression Analysis in Single Cells and its Biological Relevance in Cancer.
Abstract:
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.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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