Tools

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001 1649446;

005 20170427123028.0;

008 140911s2015 ne a b 001 0 eng ;

019 a| 822894417a| 822895551;

020 a| 9780124047488 (hbk);

020 a| 0124047483 (hbk);

035 a| (Sirsi) a4621814;

035 9| 101649446;

041 09 a| eng;

042 a| nlmcopyc;

044 9| Netherlands;

060 00 a| 2015 A-138;

060 10 a| QU 460;

130 0 a| Clinical genomics (Kulkarni)?| UNAUTHORIZED;

245 10 a| Clinical genomics /c| edited by Shashikant Kulkarni, John Pfeifer.;

264 1 a| Amsterdam :b| Elsevier/Academic Press,c| [2015];

300 a| online resource;

336 a| textb| txt2| rdacontent;

337 a| unmediatedb| n2| rdamedia;

338 a| volumeb| nc2| rdacarrier;

504 a| Includes bibliographical references and index.;

505 0 a| Machine generated contents note: I.Methods -- 1.Overview of Technical Aspects and Chemistries of Next-Generation Sequencing / Ian S. Hagemann -- Clinical Molecular Testing: Finer and Finer Resolution -- Sanger Sequencing -- Cyclic Array Sequencing -- Illumina Sequencing -- SOLiD Sequencing -- Ion Torrent Sequencing -- Roche 454 Genome Sequencers -- Third-Generation Sequencing Platforms -- References -- 2.Clinical Genome Sequencing / Erica Ramos -- Introduction -- Applications and Test Information -- Laboratory Process, Data Generation, and Quality Control -- Conclusion -- References -- 3.Targeted Hybrid Capture Methods / Elizabeth C. Chastain -- Introduction -- Basic Principles of Hybrid Capture-Based NGS -- Hybrid Capture-Based Target Enrichment Strategies -- Clinical Applications of Target Capture Enrichment -- Variant Detection -- Practical and Operational Considerations -- Conclusions -- References -- 4.Amplification-Based Methods / Yuri E. Nikiforov -- Introduction --;

505 0 a| Contents note continued: Principles of Amplification-Based Targeted NGS -- 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 / John Pfeifer -- Introduction -- Third-Generation Sequencing Approaches -- Fourth-Generation Sequencing -- Selected Novel Technologies -- Summary -- References -- 6.RNA-Sequencing and Methylome Analysis / Shashikant Kulkarni -- Introduction -- Approaches to Analysis of RNA -- Workflow -- 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 --;

505 0 a| Contents note continued: II.Bioinformatics -- 7.Base Calling, Read Mapping, and Coverage Analysis / Paul Cliften -- Introduction -- Platform-Specific Base Calling Methods -- Read Mapping -- Coverage Analysis: Metrics for Assessing Genotype Quality -- Summary -- References -- 8.Single Nucleotide Variant Detection Using Next Generation Sequencing / John Pfeifer -- Introduction -- Sources of SNVs -- Consequences of SNVs -- Technical Issues -- Bioinformatic Approaches for SNV Calling -- Interpretation of SNVs -- Reporting -- Summary -- References -- 9.Insertions and Deletions (Indels) / Jennifer K. Sehn -- Overview of Insertion/Deletion Events (Indels) -- Sources, Frequency, and Consequences of Indels -- Technical Issues That Impact Indel Detection by NGS -- Specimen Issues That Impact Indel Detection by NGS -- Bioinformatics Approaches to NGS Indel Detection -- Summary -- References -- 10.Translocation Detection Using Next-Generation Sequencing / Eric Duncavage --;

505 0 a| Contents note continued: Introduction to Translocations -- Translocations in Human Disease -- Translocation Detection -- Informatic Approaches to Translocation Detection -- Translocation Detection in Clinical Practice -- Summary and Conclusion -- References -- 11.Copy Number Variant Detection Using Next-Generation Sequencing / Colin Pritchard -- Overview of Copy Number Variation and Detection via Clinical Next-Generation Sequencing -- Sources, Frequency, and Functional Consequences of Copy Number Variation in Humans -- CNV Detection in Clinical NGS Applications -- Conceptual Approaches to NGS CNV Detection -- Detection in the Clinic: Linking Application, Technical Approach, and Detection Methods -- Reference Standards -- Orthogonal CNV Validation -- Summary and Conclusion -- References -- Glossary -- List of Acronyms and Abbreviations -- III.Interpretation -- 12.Reference Databases for Disease Associations / Donna R. Maglott -- Introduction --;

505 0 a| Contents note continued: Identification and Validation of Human Variation -- Identification of Common Variation -- Interpretation of Common Variation -- Defining Diseases and Phenotypes -- Representation of Variation Data in Public Databases -- Data Access and Interpretation -- Determination of Variant Pathogenicity -- Global Data Sharing -- Conclusion -- References -- List of Acronyms and Abbreviations -- 13.Reporting of Clinical Genomics Test Results / Elaine Lyon -- Introduction -- Components of the Written NGS Report -- Beyond the Written Report: Other NGS Reporting Issues to Consider -- Conclusion -- References -- List of Acronyms and Abbreviations -- 14.Reporting Software / Rakesh Nagarajan -- Introduction -- Clinical Genomic Test Order Entry -- Laboratory Information Management Systems (LIMS) Tracking -- Analytics: From Reads to Variant Calls -- Analytics: Variant Annotation and Classification -- Variant Interpretation -- Final Report Transmission to the EMR --;

505 0 a| Contents note continued: Leveraging Standards in Clinical Genomics Software Systems -- Regulatory Compliance -- Support Personnel -- Conclusion -- References -- List of Acronyms and Abbreviations -- 15.Constitutional Diseases: Amplification-Based Next-Generation Sequencing / Madhuri R. Hegde -- Introduction -- Multigene Panel Validation -- Clinical Workflow -- Conclusion -- References -- List of Acronyms and Abbreviations -- 16.Targeted Hybrid Capture for Inherited Disease Panels / Birgit Funke -- Introduction -- Target Selection Using Hybridization-Based Capture -- Design and Implementation of Targeted Hybridization-Based Capture Panels -- Targeted Hybrid Capture: Selecting a Panel for Constitutional Diseases -- Applications in Clinical Practice: Lessons Learned -- References -- 17.Constitutional Disorders: Whole Exome and Whole Genome Sequencing / Benjamin D. Solomon -- Introduction -- Genomic Sequencing --;

505 0 a| Contents note continued: Analyzing Individual and Multiple Data Sets for Causal Mutation Discovery -- Conclusion and Future Directions -- Acknowledgment -- References -- Glossary -- 18.Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing / Marilyn M. Li -- Introduction -- NGS Technologies -- Amplification-Based NGS Technologies -- Advantages and Disadvantages of Amplification-Based NGS -- Clinical Application of Amplification-Based NGS in Cancer -- Data Analysis -- Interpretation and Reporting -- Challenges and Perspectives -- References -- 19.Targeted Hybrid Capture for Somatic Mutation Detection in the Clinic / Hussam Al-Kateb -- Introduction -- Clinical Utility of Somatic Mutation Detection in Cancer -- Description of Hybridization-Based Methodology -- Utility of Targeted Hybrid Capture -- NGS in a Clinical Laboratory Setting -- Conclusion -- References -- 20.Somatic Diseases (Cancer): Whole Exome and Whole Genome Sequencing / Jennifer K. Sehn --;

505 0 a| Contents note continued: Introduction to Exome and Genome Sequencing in Cancer -- Interpretative Considerations in Exome and Genome Cancer Sequencing -- Analytic Considerations for Exome and Genome Sequencing in Cancer -- Summary -- References -- IV.Regulation, Reimbursement, And Legal Issues -- 21.Assay Validation / Ira M. Lubin -- Introduction -- NGS Workflow -- The Regulatory and Professional Framework for Assuring Quality -- Assay Validation -- Accuracy -- Precision -- Analytical Sensitivity and Analytical Specificity -- Reportable and Reference Ranges -- Quality Control -- Reference Materials -- Conclusion -- Acknowledgment -- References -- List of Acronyms and Abbreviations -- 22.Regulatory Considerations Related to Clinical Next Generation Sequencing / John Pfeifer -- Introduction -- Regulatory Standards -- FDA Oversight of Clinical NGS -- Total Quality Management: QC -- Total Quality Management: QA -- Conclusion -- References --;

505 0 a| Contents note continued: 23.Genomic Reference Materials for Clinical Applications / Marc Salit -- Introduction -- Genome in a Bottle Consortium -- Reference Data -- Other Reference Materials for Genome-Scale Measurements -- Conclusion -- References -- 24.Ethical Challenges to Next-Generation Sequencing / Stephanie Solomon -- Introduction -- Challenging Existing Frameworks -- Notifying of Results -- Privacy and Confidentiality -- Informed Consent -- Conclusion -- References -- Glossary -- List of Acronyms and Abbreviations -- 25.Legal Issues / Roger D. Klein -- Introduction -- Patent Overview -- History of Gene Patents -- Arguments for and Against Gene Patents -- Important Legal Cases -- Implication of Recent Court Decisions for Genetic Testing -- Genetic Information Nondiscrimination Act -- References -- 26.Billing and Reimbursement / John Pfeifer -- Introduction -- Insurance Payers -- Reimbursement Processes -- Test Design Factors That Impact Reimbursement --;

505 0 a| Contents note continued: Patient Protection and Affordable Care Act -- Cost Structure -- Summary -- References.;

538 a| Mode of Access: World Wide Web;

650 12 a| Genomics.=| ^A936706;

650 22 a| Clinical Medicine.=| ^A918945;

655 4 a| Electronic books.;

700 1 a| Kulkarni, Shashikant,e| editor.=| ^A1322436;

700 1 a| Pfeifer, John D.,e| editor.=| ^A945560;

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Clinical genomics / edited by Shashikant Kulkarni, John Pfeifer.

Other author	Kulkarni, Shashikant, editor.
Other author	Pfeifer, John D., editor.
Format	Book
Publication	Amsterdam : Elsevier/Academic Press, [2015]
Description	online resource
Supplemental Content	Connect to this resource online
Subjects	Genomics. Clinical Medicine.

Uniform title	Clinical genomics (Kulkarni)
Contents	Machine generated contents note: I.Methods -- 1.Overview of Technical Aspects and Chemistries of Next-Generation Sequencing / Ian S. Hagemann -- Clinical Molecular Testing: Finer and Finer Resolution -- Sanger Sequencing -- Cyclic Array Sequencing -- Illumina Sequencing -- SOLiD Sequencing -- Ion Torrent Sequencing -- Roche 454 Genome Sequencers -- Third-Generation Sequencing Platforms -- References -- 2.Clinical Genome Sequencing / Erica Ramos -- Introduction -- Applications and Test Information -- Laboratory Process, Data Generation, and Quality Control -- Conclusion -- References -- 3.Targeted Hybrid Capture Methods / Elizabeth C. Chastain -- Introduction -- Basic Principles of Hybrid Capture-Based NGS -- Hybrid Capture-Based Target Enrichment Strategies -- Clinical Applications of Target Capture Enrichment -- Variant Detection -- Practical and Operational Considerations -- Conclusions -- References -- 4.Amplification-Based Methods / Yuri E. Nikiforov -- Introduction --
Contents	Contents note continued: Principles of Amplification-Based Targeted NGS -- 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 / John Pfeifer -- Introduction -- Third-Generation Sequencing Approaches -- Fourth-Generation Sequencing -- Selected Novel Technologies -- Summary -- References -- 6.RNA-Sequencing and Methylome Analysis / Shashikant Kulkarni -- Introduction -- Approaches to Analysis of RNA -- Workflow -- 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 --
Contents	Contents note continued: II.Bioinformatics -- 7.Base Calling, Read Mapping, and Coverage Analysis / Paul Cliften -- Introduction -- Platform-Specific Base Calling Methods -- Read Mapping -- Coverage Analysis: Metrics for Assessing Genotype Quality -- Summary -- References -- 8.Single Nucleotide Variant Detection Using Next Generation Sequencing / John Pfeifer -- Introduction -- Sources of SNVs -- Consequences of SNVs -- Technical Issues -- Bioinformatic Approaches for SNV Calling -- Interpretation of SNVs -- Reporting -- Summary -- References -- 9.Insertions and Deletions (Indels) / Jennifer K. Sehn -- Overview of Insertion/Deletion Events (Indels) -- Sources, Frequency, and Consequences of Indels -- Technical Issues That Impact Indel Detection by NGS -- Specimen Issues That Impact Indel Detection by NGS -- Bioinformatics Approaches to NGS Indel Detection -- Summary -- References -- 10.Translocation Detection Using Next-Generation Sequencing / Eric Duncavage --
Contents	Contents note continued: Introduction to Translocations -- Translocations in Human Disease -- Translocation Detection -- Informatic Approaches to Translocation Detection -- Translocation Detection in Clinical Practice -- Summary and Conclusion -- References -- 11.Copy Number Variant Detection Using Next-Generation Sequencing / Colin Pritchard -- Overview of Copy Number Variation and Detection via Clinical Next-Generation Sequencing -- Sources, Frequency, and Functional Consequences of Copy Number Variation in Humans -- CNV Detection in Clinical NGS Applications -- Conceptual Approaches to NGS CNV Detection -- Detection in the Clinic: Linking Application, Technical Approach, and Detection Methods -- Reference Standards -- Orthogonal CNV Validation -- Summary and Conclusion -- References -- Glossary -- List of Acronyms and Abbreviations -- III.Interpretation -- 12.Reference Databases for Disease Associations / Donna R. Maglott -- Introduction --
Contents	Contents note continued: Identification and Validation of Human Variation -- Identification of Common Variation -- Interpretation of Common Variation -- Defining Diseases and Phenotypes -- Representation of Variation Data in Public Databases -- Data Access and Interpretation -- Determination of Variant Pathogenicity -- Global Data Sharing -- Conclusion -- References -- List of Acronyms and Abbreviations -- 13.Reporting of Clinical Genomics Test Results / Elaine Lyon -- Introduction -- Components of the Written NGS Report -- Beyond the Written Report: Other NGS Reporting Issues to Consider -- Conclusion -- References -- List of Acronyms and Abbreviations -- 14.Reporting Software / Rakesh Nagarajan -- Introduction -- Clinical Genomic Test Order Entry -- Laboratory Information Management Systems (LIMS) Tracking -- Analytics: From Reads to Variant Calls -- Analytics: Variant Annotation and Classification -- Variant Interpretation -- Final Report Transmission to the EMR --
Contents	Contents note continued: Leveraging Standards in Clinical Genomics Software Systems -- Regulatory Compliance -- Support Personnel -- Conclusion -- References -- List of Acronyms and Abbreviations -- 15.Constitutional Diseases: Amplification-Based Next-Generation Sequencing / Madhuri R. Hegde -- Introduction -- Multigene Panel Validation -- Clinical Workflow -- Conclusion -- References -- List of Acronyms and Abbreviations -- 16.Targeted Hybrid Capture for Inherited Disease Panels / Birgit Funke -- Introduction -- Target Selection Using Hybridization-Based Capture -- Design and Implementation of Targeted Hybridization-Based Capture Panels -- Targeted Hybrid Capture: Selecting a Panel for Constitutional Diseases -- Applications in Clinical Practice: Lessons Learned -- References -- 17.Constitutional Disorders: Whole Exome and Whole Genome Sequencing / Benjamin D. Solomon -- Introduction -- Genomic Sequencing --
Contents	Contents note continued: Analyzing Individual and Multiple Data Sets for Causal Mutation Discovery -- Conclusion and Future Directions -- Acknowledgment -- References -- Glossary -- 18.Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing / Marilyn M. Li -- Introduction -- NGS Technologies -- Amplification-Based NGS Technologies -- Advantages and Disadvantages of Amplification-Based NGS -- Clinical Application of Amplification-Based NGS in Cancer -- Data Analysis -- Interpretation and Reporting -- Challenges and Perspectives -- References -- 19.Targeted Hybrid Capture for Somatic Mutation Detection in the Clinic / Hussam Al-Kateb -- Introduction -- Clinical Utility of Somatic Mutation Detection in Cancer -- Description of Hybridization-Based Methodology -- Utility of Targeted Hybrid Capture -- NGS in a Clinical Laboratory Setting -- Conclusion -- References -- 20.Somatic Diseases (Cancer): Whole Exome and Whole Genome Sequencing / Jennifer K. Sehn --
Contents	Contents note continued: Introduction to Exome and Genome Sequencing in Cancer -- Interpretative Considerations in Exome and Genome Cancer Sequencing -- Analytic Considerations for Exome and Genome Sequencing in Cancer -- Summary -- References -- IV.Regulation, Reimbursement, And Legal Issues -- 21.Assay Validation / Ira M. Lubin -- Introduction -- NGS Workflow -- The Regulatory and Professional Framework for Assuring Quality -- Assay Validation -- Accuracy -- Precision -- Analytical Sensitivity and Analytical Specificity -- Reportable and Reference Ranges -- Quality Control -- Reference Materials -- Conclusion -- Acknowledgment -- References -- List of Acronyms and Abbreviations -- 22.Regulatory Considerations Related to Clinical Next Generation Sequencing / John Pfeifer -- Introduction -- Regulatory Standards -- FDA Oversight of Clinical NGS -- Total Quality Management: QC -- Total Quality Management: QA -- Conclusion -- References --
Contents	Contents note continued: 23.Genomic Reference Materials for Clinical Applications / Marc Salit -- Introduction -- Genome in a Bottle Consortium -- Reference Data -- Other Reference Materials for Genome-Scale Measurements -- Conclusion -- References -- 24.Ethical Challenges to Next-Generation Sequencing / Stephanie Solomon -- Introduction -- Challenging Existing Frameworks -- Notifying of Results -- Privacy and Confidentiality -- Informed Consent -- Conclusion -- References -- Glossary -- List of Acronyms and Abbreviations -- 25.Legal Issues / Roger D. Klein -- Introduction -- Patent Overview -- History of Gene Patents -- Arguments for and Against Gene Patents -- Important Legal Cases -- Implication of Recent Court Decisions for Genetic Testing -- Genetic Information Nondiscrimination Act -- References -- 26.Billing and Reimbursement / John Pfeifer -- Introduction -- Insurance Payers -- Reimbursement Processes -- Test Design Factors That Impact Reimbursement --
Contents	Contents note continued: Patient Protection and Affordable Care Act -- Cost Structure -- Summary -- References.
Bibliography note	Includes bibliographical references and index.
Technical details	Mode of Access: World Wide Web
Genre/form	Electronic books.
ISBN	9780124047488 (hbk)
ISBN	0124047483 (hbk)

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