Circulating Nucleic Acids in Early Diagnosis, Prognosis and Treatment Monitoring : An Introduction.

Intro -- What This Book Series Is About… -- Current Healthcare: What Is Behind the Issue? -- Advanced Healthcare Tailored to the Person: What Is Beyond the Issue? -- Why Integrative Medical Approach by PPPM as the Medicine of the Future? -- Preface -- Abbreviations -- Contents -- Contributors -- About the Editor -- Part I: Background -- A Brief History and the Present and Future Status of CNAPS -- 1 Introduction -- 2 The Occurrence of Circulating DNA -- 3 The ``Silent´´ Period 1948-1977 -- 4 Applications in the Early Studies of CNAPS -- 4.1 Implied Costs for Such Tests -- 5 Ethical and Other Implications of CNAPS Applications -- References -- The Biology of CNAPS -- 1 Introduction -- 2 cfNucleic Acids and Nuclease Content -- 3 Nucleic Acid Sources -- 3.1 cfDNA -- Leukocytes -- Bacteria and Viruses -- Necrosis -- Apoptosis -- Exosomes -- Virtosomes -- Transposons and Retrotransposons -- Mitochondrial DNA Release -- Parasite DNA Release -- 3.2 RNA -- Leukocytes -- Bacteria and Viruses -- Necrosis and Apoptosis -- Exosomes -- Virtosomes -- Mitochondria -- Parasite RNA Release -- 4 Mechanisms of Exit from and Entry into Cells by cfDNA and cfRNA -- 4.1 Mechanisms for the Exit of cfDNA and cfRNA from Cells -- 4.2 Mechanisms for the Entry of cfDNA and cfRNA into Cells -- Cytoplasmatic Entry -- cfCNA Entry into the Nucleus -- 4.3 Conclusions -- 5 Mitochondrial Release and Uptake of cfNAs -- 6 cfNAs Can Enter and Express in Other Cells -- 6.1 cfDNA -- Immune Response -- Effects on Cell Division -- cfDNA Effects in Irradiated Cells - By-Stander Effect -- cfDNA Effects on Myocardiocyte Contraction Rates -- Tumor Induction -- Gene Replacement Therapy -- 6.2 cfRNA -- 7 Can cfNAs Influence the F1 Generation? -- References -- Part II: Methodology -- Pre-analytical Requirements for Analyzing Nucleic Acids from Blood -- 1 Introduction -- 2 Optimal Blood Sampling.

2.1 Serum or Plasma? -- State of the Art -- Our Observations -- 2.2 Optimal Blood Collection Tube for Plasma Preparation -- 2.3 Blood Drawing Conditions -- 2.4 Storage Conditions of Blood Samples -- 2.5 cfDNA Concentration -- State of the Art -- Our Observations -- 2.6 cfDNA Fragmentation -- 2.7 Influence of Storage Conditions on Cell-Free DNATM Blood Collection Tube-Drawn Blood Samples -- 2.8 Comparison Between K3EDTA and Cell-Free DNATM Blood Collection Tubes -- 2.9 Optimal Plasma Preparation -- State of the Art -- Our Observations -- 3 Pre-analytical Treatment of Plasma Samples Before Nucleic Acid Extraction -- 3.1 Influence of Storage Conditions -- cfDNA Concentration - State of the Art -- cfDNA Concentration - Our Observations -- 3.2 cfDNA Fragmentation -- 3.3 Influence of Freeze-Thaw Cycles -- cfDNA Concentration -- cfDNA Fragmentation -- 4 Pre-analytical Treatment of cfDNA Extracts Between Nucleic Acid Extraction and cfDNA Analysis -- 5 Long-Term Storage of Plasma Samples and cfDNA Extracts -- 5.1 State of the Art -- 5.2 Our Observations -- 6 Optimal Pre-analytical Treatment of Sera Samples -- 6.1 From Blood Drawing to Serum Preparation -- 6.2 From Serum Preparation to the Analytical Process -- 6.3 Long Term Storage of Sera Samples -- 7 Preanalytical Treatment for cfRNA Analysis -- 7.1 From Blood Drawing to Plasma or Serum Preparation -- Plasma Preparation from K3EDTA Blood Shipped Samples -- Plasma Preparation from cfRNA BCTs Blood Shipped Samples -- Serum Preparation from K3EDTA Blood Shipped Samples -- 8 Conclusions -- References -- Circulating DNA and miRNA Isolation -- 1 Circulating cfDNA Isolation -- 1.1 cfDNA Extraction Methods -- Non-commercially Available Methods -- Commercially Available Methods -- 1.2 Specificity of Extracted cfDNA -- 1.3 Studies on the Extraction Methods for cfDNA Extraction.

1.4 Criteria for Selecting an Optimal Extraction Procedure -- 1.5 Direct Analysis of cfDNA Without an Extraction Procedure -- 2 miRNA Isolation -- 2.1 miRNA Stability in Blood and Plasma/Serum Samples -- 2.2 Sample Collection: Plasma vs. Serum -- 2.3 miRNA Extraction Methods -- 2.4 Quality Control of the Extracted miRNAs -- References -- Detection of Genetic Alterations by Nucleic Acid Analysis: Use of PCR and Mass Spectroscopy-Based Methods -- 1 PCR-Based Methods -- 1.1 First PCR Application in CNAPS -- 1.2 Importance of a Good Knowledge of Structure and Size of cfNAs Prior to PCR Analysis -- 1.3 Methods Based on an Increased Sensitivity for the Detection of Genetic Alterations with CNAPS -- 1.4 Other Approaches -- 1.5 General Guidelines Applicable to All PCR Applications for CNAPS Analysis -- DNA Preparation -- Anti-contaminations Procedures -- Choice of the Target Size -- Thermal Cycling -- Normalization -- Melt Curve Analysis -- 1.6 Conclusion -- 2 Mass Spectrometry-Based Methods -- 2.1 Mass Spectrometry in Nucleic Acids Sequencing -- 2.2 SNP Genotyping Using Mass Spectrometry -- 2.3 Application of Mass Spectrometry to the Studies of Circulating Cell-Free Nucleic Acids -- 2.4 Conclusion -- References -- Genomic Approaches to the Analysis of Cell Free Nucleic Acids -- 1 Introduction of High Throughput Sequencing -- 2 Overview of the High Throughput Analysis Methods for cfNAs -- 3 Sample Preparation for High Throughput Analysis of cfNAs -- 4 High Throughput Sequencing and Analysis -- 4.1 Whole Genome Sequencing -- 4.2 Exome Sequencing -- 4.3 Targeted Amplicon Sequencing -- 5 Characterization of cfNAs Using High Throughput Sequencing -- 6 The Counting Principle -- 6.1 Detection of Copy Number Variation (CNV) -- 6.2 Detection of Point Mutation -- 7 Applications for Human Biology and Diagnostics -- 8 Profiling of cfRNA -- 8.1 Profiling of cfmRNA.

8.2 Profiling of Cell-Free Small RNA -- 9 Perspective -- References -- Part III: Applications -- CNAPS and General Medicine -- 1 Introduction -- 2 Multiple Sclerosis -- 3 Cardiovascular Disease -- 4 Stroke -- 5 Sepsis -- 6 Hemodialysis -- 7 Liver and Kidney Diseases -- 8 Pancreatitis -- 9 Transplantation -- 10 Trauma -- 11 Implications of cfNAs in Aging -- 12 Clinical Relevance of cfNAs in General Medicine -- References -- Fetal CNAPS - DNA/RNA -- 1 Introduction -- 2 Characteristics of Fetal Circulating Nucleic Acids -- 2.1 Circulating cffDNA -- 2.2 Circulating cffRNA -- 3 Fetal Epigenetic Markers -- 4 Detection of Paternally Inherited Traits -- 4.1 Fetal Sex Determination -- 4.2 Fetal Rhesus D Genotyping -- 5 Detection of Fetal Aneuploidy -- 5.1 Enrichment of Fetal Nucleic Acid -- Physical Enrichment of cffNAs -- Molecular Enrichment of cffNAs -- Fetal Epigenetic Markers -- cffRNA Markers -- 5.2 Determining the Fetal Chromosome Dosage of Enriched cffNAs -- Allelic Ratio Analysis -- Epigentic-Genetic Chromosome Dosage Method -- Single-Molecule Counting Approach -- Whole Genome Approach -- Detecting Trisomy 18 and Trisomy 13 with MPS -- Sex Chromosomal Aneuploidy -- Chromosome-Selective Approach -- SNP-Based Approach -- 6 Clinical Implementation -- 7 Mosaicism -- 8 Aneuploidy Detection for Twin Pregnancies -- 9 Abnormal NIPT Results -- 10 Detection of Subchromosomal Aberrations -- 11 Detection of Single-Gene Disorders -- 12 Decoding the Fetal Genome -- 13 Conclusion -- 13.1 The Present -- 13.2 The Future -- References -- Circulating Nucleic Acids and Diabetes Mellitus -- 1 Introduction -- 1.1 Pathogenesis of Diabetes and miRNA -- 1.2 Circulating Nucleic Acids as Biomarkers -- 2 Identification of the at Risk Population -- 2.1 Type 1 DM -- 2.2 Type 2 DM -- 2.3 Diagnosis of DM -- 2.4 Gestational DM (GDM) -- 3 Diabetic Complications.

3.1 Diabetic Retinopathy -- MicroRNA and Diabetic Retinopathy -- 4 Diabetic Nephropathy -- 4.1 Diabetic Neuropathy -- 4.2 Macrovascular Complications -- Concluding Remarks -- References -- Extracellular Nucleic Acids and Cancer -- 1 Introduction -- 2 General Remarks -- 3 DNA Quantification/DNA Integrity -- 3.1 Synopsis -- 4 Number Crunching with dPCR and BEAMing -- 4.1 Synopsis -- 5 Mutation Analysis -- 5.1 Synopsis -- 6 miRNA -- 6.1 cfmiRNA Quantification for Prognosis, Diagnosis, Follow-Up and Treatment Monitoring -- 6.2 Why Is cfmiRNA Quantification Not Yet a Clinically Useful Tool? -- 6.3 Synopsis -- 7 cfNAs in Stool and Urine (See also Sect. 4) -- 7.1 Synopsis -- 8 Microsatellite Alterations -- 8.1 Synopsis -- 9 Epigenetic Modifications -- 9.1 Synopsis -- 10 Inflammation and Cancer -- 11 Functional and Biological Aspects -- 12 Technical Issues and Study Design -- 12.1 Choice of Material -- 12.2 Pre-analytic Variables -- 12.3 Technical/Biological Pitfalls -- Blood Preparations and RNAs -- Isolation Methods -- Real-Time Quantification -- Choice of Appropriate Controls -- 13 Early Tumor Detection -- 14 Literature Search -- 15 Summary -- References -- Other Body Fluids as Non-invasive Sources of Cell-Free DNA/RNA -- 1 Introduction -- 2 Amniotic Fluid (AF) -- 2.1 cffDNA in AF -- Aneuploidy -- Fetal Sex -- 2.2 cffRNA in AF -- Human Fetal Development -- Aneuploidies -- Twin-to-Twin Transfusion Syndrome (TTTS) -- 3 Saliva -- 3.1 Saliva cfRNA -- Premature-Born Infants -- Cancer -- 4 Urine -- 4.1 Urine cfNAs (See also Sect. 7) -- Bladder Tumors -- Prostate Cancer -- Colorectal Cancer (CRC) -- Transplant Rejection Markers -- Diabetic Nephropathy (DN) (see also Chapter ``Circulating Nucleic Acids and Diabetes Mellitus´´) -- Lupus Nephritis (LN) -- 5 Cerebrospinal Fluid (CSF) -- 5.1 Aneurysmal Subarachnoid Hemorrhage.

5.2 Primary Central Nervous System Lymphoma (PCNSL).

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.