http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
Next generation sequencing based clinical molecular diagnosis of human genetic disorders
Next Generation Sequencing technology has been applied to clinical diagnoses in the past three to five years using various approaches, including target gene panels and whole exomes. The purpose of this book is to summarize the experiences, the results, advantages and disadvantages, along with future development in the area of NGS-based molecular diagnosis. This up-to-date volume will not only provide the readers working with Next Generation Sequencing the basics on how to apply the technology to molecular diagnosis, but will present the results and experience of practical application.
Preface; Contents; Overview of the Clinical Utility of Next Generation Sequencing in Molecular Diagnoses of Human Genetic Disorders; 1 Introduction; 2 Traditional Step-Wise Molecular Diagnostic Approaches Are No longer Adequate; 3 Next Generation Sequencing; 4 Target Sequence Enrichment and NGS Platforms; 5 Clinical Validation; 6 Panel Design; 7 Examples of Clinical Application; 7.1 The Advantage of NGS-Based Analysis of Large Genes; 7.2 Pathway Driven Panel Analysis; 8 Caveats of Capture-Based NGS; 9 Allele Dropout: Pitfalls of Amplicon-Based Analysis.
10 Factors Affecting Diagnostic Yields of NGS-Based Panels11 Conclusion; References; Detection of Copy Number Variations (CNVs) Based on the Coverage Depth from the Next Generation Sequencing Data; 1 Introduction; 2 Strategies for NGS Based CNV Detection; 2.1 Paired-End Mapping Method; 2.2 Split-Read; 2.3 Depth of Coverage Based; 2.4 Assembly Based; 3 Procedures to Detect CNVs Based on Depth of Coverage; 3.1 Reference Samples; 3.2 DOC Based CNV Detection Using Exon as Sliding Window; 3.3 Normalization of the Depth of Sequence Read to the Total Amount of DNA Loaded to Sequencing Machine.
3.4 Generation of Reference File3.5 Normalization of DOC of the Testing Sample (Second Normalization); 3.6 Detection and Visualization of CNVs; 4 Confirmation of CNV; 5 Sensitivity and Specificity; 6 Challenges and Issues; 7 Future; References; Next Generation Sequencing (NGS) Based Panel Analysis of Metabolic Pathways; 1 Introduction; 2 NGS Based Panel Analysis: General Approach; 2.1 Design of NGS-Based Panels; 2.2 Enrichment of Target Genes; 2.3 Massively Parallel Sequencing: Clinical Validation; 2.4 Low Coverage and Homologous Regions.
2.5 Variant Calls: Single Nucleotide Variants (SNVs) and CNVs3 Examples of Panels; 3.1 Overview of Panels; 3.2 Brief Description of Some Clinically Validated Panels; 3.2.1 Maple Syrup Urine Disease (MSUD); 3.2.2 Urea Cycle Disorders (UCD); 3.2.3 The Cobalamin Pathway; 3.2.4 Glycogen Storage Diseases (GSDs) and Other Similar Metabolic Pathways; 3.2.5 Maturity-Onset Diabetes of the Young (MODY); 3.2.6 Hyperinsulinism and Hypoglycemia; 4 Points for Consideration; 4.1 Single Gene Versus Panel Analysis, Panel Overlap; 4.2 Panel Size and Capture Library Size; 4.3 Advantages of Panels over WES.
5 ConclusionReferences; The Next Generation Sequencing Based Molecular Diagnosis of Visual Diseases; 1 Introduction; 2 The Clinical Utility of Molecular Testing for Eye Diseases; 3 Methodology; 4 Retinal Dystrophies; 4.1 Diagnostic Rates; 4.2 Inheritance Models; 4.3 Pathogenic Variants; 5 Retinoblastoma; 6 Congenital Cataracts; 7 Glaucoma; 8 Challenges; References; Application of Next-Generation Sequencing to Hearing Loss; 1 Introduction; 2 Syndromes that Include Hearing Loss; 3 Nonsyndromic Hearing Loss; 4 Significance of Early Hearing Loss Recognition and Genetic Testing.
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Includes bibliographical references at the end of each chapters and index.