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Clinical Genomics.

Author: Shashikant Kulkarni
Publisher: Elsevier Science, 2014.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also  Read more...
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Genre/Form: Electronic books
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Shashikant Kulkarni
ISBN: 132230534X 9781322305349 9780124047488 0124047483
OCLC Number: 896647265
Description: 1 online resource
Contents: Front Cover --
Clinical Genomics --
Copyright Page --
Dedication --
Contents --
List of Contributors --
Foreword --
Preface --
Acknowledgments --
I. Methods --
1 Overview of Technical Aspects and Chemistries of Next-Generation Sequencing --
Clinical Molecular Testing: Finer and Finer Resolution --
Sanger Sequencing --
Chemistry of Sanger Sequencing, Electrophoresis, Detection --
Applications in Clinical Genomics --
Technical Constraints --
Read Length and Input Requirements --
Pooled Input DNA Puts a Limit on Sensitivity --
Cyclic Array Sequencing --
Illumina Sequencing --
Library Prep and Sequencing Chemistry --
Choice of Platforms --
Phasing --
SOLiD Sequencing --
Ion Torrent Sequencing --
AmpliSeq Library Preparation --
Roche 454 Genome Sequencers --
Third-Generation Sequencing Platforms --
References --
2 Clinical Genome Sequencing --
Introduction --
Next-Generation Sequencing --
Sequencing in the Clinical Laboratory --
Applications and Test Information --
Challenges of Defining a Test Offering That Is Specific to Each Case --
Laboratory Process, Data Generation, and Quality Control --
Preanalytical and Quality Laboratory Processes --
Analytical --
Bioinformatics --
Validation --
Proficiency Testing --
Interpretation and Reporting --
Conclusion --
References --
3 Targeted Hybrid Capture Methods --
Introduction --
Basic Principles of Hybrid Capture-Based NGS --
Specimen Requirements and DNA Preparation --
Determining the Target ROI --
Designing Capture Baits --
General Overview of Library Preparation --
Coverage and Uniformity --
Specificity and Sensitivity --
Obstacles of Target Capture --
Library Complexity --
Hybrid Capture-Based Target Enrichment Strategies --
Solid-Phase Hybrid Capture --
Solution-Based Hybrid Capture --
Molecular Inversion Probes --
Comparison of Targeted Hybrid Capture Enrichment Strategies. Amplification-Based Enrichment Versus Capture-Based Enrichment --
Clinical Applications of Target Capture Enrichment --
Exome Capture --
Selected Gene Panels --
Disease-Associated Exome Testing --
Variant Detection --
Practical and Operational Considerations --
Workflow and TAT --
Conclusions --
References --
4 Amplification-Based Methods --
Introduction --
Principles of Amplification-Based Targeted NGS --
Sequencing Workflow --
Samples Requirements --
Nucleic Acids Preparation --
Primer Design for Multiplex PCR --
Library Preparation and Amplification --
Other Amplification-Based Target Enrichment Approaches --
Comparison of Amplification- and Capture-Based Methods --
Clinical Applications --
Conclusion --
References --
5 Emerging DNA Sequencing Technologies --
Introduction --
Third-Generation Sequencing Approaches --
Single-Molecule Real-Time (SMRT) DNA Sequencing --
Heliscope Genetic Analysis System --
Fourth-Generation Sequencing --
Nanopore Sequencing --
Selected Novel Technologies --
In Situ DNA Sequencing --
Transmission Electron Microscopy --
Electronic Sequencing --
Summary --
References --
6 RNA-Sequencing and Methylome Analysis --
Introduction --
Approaches to Analysis of RNA --
Microarray Analysis of Differential Gene Expression --
Next-Generation Methods of RNA-Seq --
Workflow --
Typical RNA-Seq Protocol --
Bioinformatic Analyses of Sequence Generated from RNA-Seq Experiment --
Initial Processing of Raw Reads: Quality Assessment --
Read Mapping Strategies --
De Novo Read Assembly --
Read Alignment --
Alignment to Reference Genome --
RNA-Seq Variant Calling and Filtering --
Expression Estimation: Summarization, Normalization, and Differential Expression --
Differential Expression --
Fusion Detection --
Depth of Coverage Issues --
Utility of RNA-Seq to Characterize Alternative Splicing Events. Utility of RNA-Seq for Genomic Structural Variant Detection --
RNA-Seq: Challenges, Pitfalls, and Opportunities in Clinical Applications --
Methylome Sequencing --
Conclusions --
References --
List of Acronyms and Abbreviations --
II. Bioinformatics --
7 Base Calling, Read Mapping, and Coverage Analysis --
Introduction --
Library Preparation and Amplification --
Base Calling --
Read Mapping --
Platform-Specific Base Calling Methods --
Illumina: Platform and Run Metrics --
Density --
Intensity by Cycle --
QScore Distribution --
QScore Heatmap --
IVC Plot --
%Phasing/Prephasing --
PhiX-Based Quality Metrics --
Torrent: Platform and Run Metrics --
Loading or ISP Density --
Live ISPs --
Library and Test ISPs --
Key Signal --
Clonal --
Usable Sequence --
Test Fragment Metrics --
Illumina: Base Calling --
Template Generation --
Base Calling --
Quality Scoring --
Torrent: Base Calling --
Key Processes --
Postprocessing --
Intrinsic and Platform-Specific Sources of Error --
Read Mapping --
Reference Genome --
NGS Alignment Tools --
MAQ --
Bowtie --
BWA --
Novoalign --
MOSAIK --
Isaac --
TMAP --
Sequence Read and Alignment Formats --
Sequence Alignment Factors --
Alignment Processing --
Coverage Analysis: Metrics for Assessing Genotype Quality --
Performance and Diagnostic Metrics --
Total Read Number --
Percent of Mapped Reads --
Percent of Read Pairs Aligned --
Percent of Reads in the Exome or Target Region --
Library Fragment Length --
Depth of Coverage --
Percent of Unique Reads --
Target Coverage Grap --
Summary --
References --
8 Single Nucleotide Variant Detection Using Next Generation Sequencing --
Introduction --
Sources of SNVs --
Endogenous Sources of Damage Leading to SNVs --
Reactive Oxygen Species --
Spontaneous Chemical Reactions --
Metal Ions --
Errors in DNA Replication --
Exogenous Sources of Damage Leading to SNVs --
Chemical Mutagens. Radiation --
Consequences of SNVs --
SNVs in Coding Regions --
Synonymous SNVs --
Missense SNVs --
Nonsense SNVs --
Consequences of SNVs on RNA Processing --
Altered RNA Splicing --
SNVs in Regulatory Regions --
Technical Issues --
Platform --
Target Size --
Target Enrichment Approach --
Library Complexity --
Depth of Sequencing --
Anticipated Sample Purity --
Sample Type --
Bioinformatic Approaches for SNV Calling --
Parameters Used for SNV Detection --
High Sensitivity Tools --
Tumor/Normal Analyses --
Implications for Clinical NGS --
Orthogonal Validation --
Interpretation of SNVs --
Online Resources and Databases --
Prediction Tools for Missense Variants --
Prediction Tools for Possible Splice Effects --
Kindred Testing --
Paired Tumor-Normal Testing --
Reporting --
Summary --
References --
9 Insertions and Deletions (Indels) --
Overview of Insertion/Deletion Events (Indels) --
Introduction --
Indel Definition and Relationship to Other Classes of Mutations --
Testing for Indels in Constitutional and Somatic Disease --
Sources, Frequency, and Consequences of Indels --
Mechanisms of Indel Generation --
Slipped Strand Mispairing (Polymerase Slippage) --
Secondary Structure Formation --
Imperfect Double-Strand DNA Break Repair --
Defective Mismatch Repair --
Unequal Meiotic Recombination --
Frequency of Indels in Human Genomes --
Functional Consequences --
Decreased Transcription --
Abnormal Protein Aggregation --
Microsatellite Instability/Rapid Repeat Expansion --
Altered Splicing --
Frameshift --
In-Frame, Decreased Protein Activity --
In-Frame, Increased Protein Activity --
Synonymous, Missense, and Nonsense --
Predicting Functional Effects of Novel Indels --
Technical Issues That Impact Indel Detection by NGS --
Sequencing Platform Chemistry --
Sequence Read Type and Alignment --
Library Preparation Technique --
Depth of Coverage --
Assay Design. Specimen Issues That Impact Indel Detection by NGS --
Specimen Cellularity and Heterogeneity --
Library Complexity --
Bioinformatics Approaches to NGS Indel Detection --
General Bioinformatics Approaches to Indel Detection and Annotation --
Local Realignment --
Left Alignment --
Probabilistic Modeling Using Mapped Reads --
Split-Read Analysis --
Sensitivity and Specificity Issues --
Indel Length --
Indel Annotation --
Definition of Indel "Truth" --
Reference Standards --
Summary --
References --
10 Translocation Detection Using Next-Generation Sequencing --
Introduction to Translocations --
Discovery of Translocations in Human Disease --
Mechanisms of Translocation Formation --
Translocations in Human Disease --
Translocations in Hematologic Malignancies --
Translocations in Leukemias --
Translocations in Lymphomas --
Translocations in Solid Tumors --
Sarcomas --
Carcinomas --
Translocations in Inherited Disorders --
Developmental Delay --
Recurrent Miscarriages --
Hereditary Cancer Syndromes --
Translocation Detection --
Conventional Methods --
Translocation Detection by Whole Genome DNA Sequencing --
Translocation Detection by Targeted DNA Sequencing --
Translocation Detection by RNA-Seq --
Informatic Approaches to Translocation Detection --
Discordant Paired-End and Split Read-Based Analysis --
Detection of Translocations and Inversions --
RNA-Seq-Based Analysis --
Translocation Detection in Clinical Practice --
Laboratory Issues --
Online Resources --
Summary and Conclusion --
References --
11 Copy Number Variant Detection Using Next-Generation Sequencing --
Overview of Copy Number Variation and Detection via Clinical Next-Generation Sequencing --
Introduction --
CNV Definition and Relationship to Other Classes of Structural Variation --
Clinical CNV Screening and Potential for NGS-Based Discovery.

Abstract:

Provides an overview of the various next-generation sequencing (NGS) technologies that are used in clinical diagnostic laboratories. This book focuses on the challenges of diagnostic interpretation  Read more...

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