http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
Clinical applications for next-generation sequencing
Machine generated contents note: NGS Versus Traditional (Sanger Sequencing) / Ratal Ploski -- Coverage / Ratal Ploski -- NGS Library Preparation / Ratal Ploski -- Sequence Assembly: De Novo Sequencing vs Resequencing / Ratal Ploski -- Paired-End and Mate-Pair Libraries and Long Fragment Read Technology / Ratal Ploski -- NGS Platforms / Ratal Ploski -- Illumina / Ratal Ploski -- Semiconductor-based platforms / Ratal Ploski -- Sequencing by the Oligo Ligation Detection (SOLiD) Platform / Ratal Ploski -- Pyrosequencing on Roche/454 platforms / Ratal Ploski -- Complete genomics analysis (CGATM) platform / Ratal Ploski -- Single-Molecule Sequencing / Ratal Ploski -- Targeted Resequencing/Enrichment Strategies / Ratal Ploski -- Whole Exome Sequencing and Whole Genome Sequencing / Ratal Ploski -- Limitations of NGS in Clinical Medicine / Ratal Ploski -- Conclusion / Ratal Ploski -- References / Ratal Ploski
Note continued: Software Tools / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Input Sequence Preprocessing / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Mapping / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Processing and Interpreting Mapping / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Insertions and Deletions Realignment / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Base Quality Recalibration / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Variant Calling / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Major Approaches to the Variant Calling / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Variant Calling Format / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski
Note continued: Variant Annotation / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Software and Hardware Issues / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Computational Architecture / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Storage Architecture / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- References / Piotr Stawinski / Ravi Sachidanandam / Izabela Chojnicka / Rafal Ploski -- Introduction / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- Structural Variants in the Human Genome / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- Structural Variation and Human Disease / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra
Note continued: Analysis of Structural Variation by Legacy Technologies / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- Structural Variation and Next Generation Sequencing / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- Methods for Estimation of Copy Number Variation from NGS Data / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- Structural Variation, NGS, Cancer, and the Clinic / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- NGS-Based Structural Variation Detection Software / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra
Note continued: Future Directions / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- Acknowledgments / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- References / Dariusz Plewczynski / Slawomir Gruca / Przemyslaw Szalaj / Krystian Gulik / Silviene Fabiana de Oliveira / Ankit Malhotra -- NGS in Cancer Research / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- NGS in Clinical Settings / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Familial Genetic Testing / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Molecular Disease Classification / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Pharmacogenomics / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Testing in "Last-Resort" Patients / Eliza Glodkowska-Mrowka / Tomasz Stoklosa
Note continued: Circulating Cell-Free Tumor DNA and Circulating Tumor Cells / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Treatment Monitoring / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Biomarkers in Clinical Decision-Making / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Current Obstacles Preventing NGS from Wide Application in Clinical Settings / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Targeted versus Genome-Wide Approach / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Future of Oncogenomics / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Pros and Cons of Traditional versus NGS Sequencing Approach / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Challenges in Clinical Oncogenomics / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- References / Eliza Glodkowska-Mrowka / Tomasz Stoklosa -- Introduction / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Childhood and Adult Acute Lymphoblastic Leukemias / Iwona Malinowska / Eliza Glodkowska-Mrowka
Note continued: T-Cell Acute Lymphoblastic Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- BCR[--]ABL1-like Acute Lymphoblastic Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Hypodiploid Acute Lymphoblastic Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Relapsed Acute Lymphoblastic Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Acute Myeloid Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Genetic Concept of Acute Myeloid Leukemia Pathogenesis / Iwona Malinowska / Eliza Glodkowska-Mrowka -- BRAF Mutation in Hairy Cell Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- CSF3R Mutation in Chronic Neutrophilic Leukemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- NGS in Chronic Lymphocytic Lymphoma / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Non-Hodgkin Lymphomas / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Inherited Bone Marrow Failure Syndromes / Iwona Malinowska / Eliza Glodkowska-Mrowka
Note continued: Fanconi Anemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Dyskeratosis Congenita / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Thrombocytopenia Absent Radius Syndrome / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Diamond[--]Blackfan Anemia / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Commercial NGS-Based Assays for Clinical Use in Hematology Practice / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Implementation of NGS-Based Techniques in Clinical Practice in Hematology / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Conclusion / Iwona Malinowska / Eliza Glodkowska-Mrowka -- References / Iwona Malinowska / Eliza Glodkowska-Mrowka -- Introduction / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Genetic Testing in Neurology and Psychiatry / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk
Note continued: Epilepsy / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Ataxia / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Hereditary Spastic Paraplegias / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Movement Disorders / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Neuromuscular Disorders / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Neurodegenerative Diseases with Dementia / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Neuropsychiatric Disorders / Anna Kostera-Pruszczyk / Krzysztof Szczaluba / Krystyna Szymatiska / Tomasz Wolanczyk -- Intellectual Disability / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk
Note continued: Autism / Anna Kostera-Pruszczyk / Krzysztof Szczaluba / Krystyna Szymatiska / Tomasz Wolanczyk -- Intellectual Disability and Autism[--]A Practical Approach / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Genetic Testing in Autism and ID[--]A Proposal / Krystyna Szymatiska / Krzysztof Szczaluba / Tomasz Wolanczyk / Anna Kostera-Pruszczyk -- Autism Databases / Krystyna Szymatiska / Anna Kostera-Pruszczyk / Krzysztof Szczaluba / Tomasz Wolanczyk -- Major Psychiatric Disorders / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- References / Krystyna Szymatiska / Krzysztof Szczaluba / Anna Kostera-Pruszczyk / Tomasz Wolanczyk -- Dysmorphology[--]Past and Present / Robert Smigiel / Urszula Demkow -- Diagnostic Process in Dysmorphology / Robert Smigiel / Urszula Demkow -- Genetic Testing in Dysmorphology / Robert Smigiel / Urszula Demkow
Note continued: NGS Testing in Dysmorphology and Rare Multiple Congenital Defects Syndromes / Robert Smigiel / Urszula Demkow -- Dilemmas / Robert Smigiel / Urszula Demkow -- Reverse Dysmorphology / Robert Smigiel / Urszula Demkow -- NGS and Screening of Rare Disorders in Newborns / Robert Smigiel / Urszula Demkow -- Conclusions / Robert Smigiel / Urszula Demkow -- List of Abbreviations / Robert Smigiel / Urszula Demkow -- References / Robert Smigiel / Urszula Demkow -- Introduction / Monika Oldak -- NGS Tests for Vision and Hearing Disorders / Monika Oldak -- Compatibility of Standard Enrichment Panels with Genetic Vision and Hearing Disorders / Monika Oldak -- Utility of NGS Testing for Diagnostic Purposes of Vision and Hearing Disorders / Monika Oldak -- Cumulative Mutation Load / Monika Oldak -- Digenic and Oligogenic Inheritance / Monika Oldak -- De Novo Mutations / Monika Oldak -- Copy Number Variations / Monika Oldak
Note continued: Novel Genes and "Erroneous" Disease Genes / Monika Oldak -- Conclusions / Monika Oldak -- Abbreviations / Monika Oldak -- Acknowledgments / Monika Oldak -- References / Monika Oldak -- Introduction / Ozgur Cogulu -- Conventional Prenatal Diagnostics and Methods / Ozgur Cogulu -- Use of Fetal Biological Material in the Maternal Circulation for Prenatal Diagnosis / Ozgur Cogulu -- Fetal DNA in Prenatal Diagnosis / Ozgur Cogulu -- Properties of Cell-Free Fetal DNA / Ozgur Cogulu -- Applications of Noninvasive Prenatal Tests / Ozgur Cogulu -- NGS in the Determination of Genomic Disorders by Using cffDNA in Maternal Plasma / Ozgur Cogulu -- Single-Nucleotide Polymorphism Sequencing of Cell-Free Fetal DNA / Ozgur Cogulu -- Limitations and Challenges of NGS-Based Noninvasive Prenatal Testing / Ozgur Cogulu -- Clinical Implementation of Noninvasive Prenatal Testing for Aneuploidies / Ozgur Cogulu -- Conclusion / Ozgur Cogulu -- References / Ozgur Cogulu
Note continued: Introduction / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- General Information on Multigene Panels / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Cardiomyopathies / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Hypertrophic Cardiomyopathy / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Dilated Cardiomyopathy / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Arrhythmogenic Right Ventricular Cardiomyopathy / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Restrictive Cardiomyopathy / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Left-Ventricular Noncompaction / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Arrhythmias / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Long QT Syndrome / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Brugada Syndrome / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska
Note continued: Catecholaminergic Polymorphic Ventricular Tachycardia / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Cardiac Conduction Disease / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Short QT Syndrome / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Atrial Fibrillation / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Thoracic Aortic Aneurysms and Dissections / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Congenital Heart Disease / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Familial Hypercholesterolemia / Rafal Ploski / Zofia T. Bilinska / Joanna Poninska -- Conclusions / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- List of Acronyms and Abbreviations / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Acknowledgments / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- References / Joanna Poninska / Rafal Ploski / Zofia T. Bilinska -- Introduction / Urszula Demkow
Note continued: Cancer Therapy / Urszula Demkow -- Clinical Trials in Oncology / Urszula Demkow -- Ethical Issues in Oncopharmacogenomics / Urszula Demkow -- Multicenter Collaborations in Oncopharmacogenomics / Urszula Demkow -- NGS in Noncancer Pharmacogenomics / Urszula Demkow -- Cytochrome P450 / Urszula Demkow -- Non-P450 Drug-Metabolizing Enzymes / Urszula Demkow -- Drug Transporters / Urszula Demkow -- Clinical Applications of Pharmacogenomics / Urszula Demkow -- Anticoagulants / Urszula Demkow -- Psychiatry / Urszula Demkow -- Analgesics / Urszula Demkow -- Transplantology / Urszula Demkow -- Anti-Human Immunodeficiency Virus Drugs / Urszula Demkow -- Multigene Pharmacogenetic Tests Assessing Pharmacokinetics and Pharmacodynamics Response / Urszula Demkow -- Quality Requirements for NGS-Based Pharmacogenomic Tests / Urszula Demkow -- Guidelines for Clinical Application of Pharmacogenomics / Urszula Demkow
Note continued: NGS in Pharmacogenomics[--]Other Possible Applications / Urszula Demkow -- Limitations of NGS in Pharmacogenomics / Urszula Demkow -- Conclusions / Urszula Demkow -- References / Urszula Demkow -- Introduction / Asude Durmaz / Burak Durmaz -- Genetic Counseling / Asude Durmaz / Burak Durmaz -- Genetic Counseling in the NGS Era / Asude Durmaz / Burak Durmaz -- Pretest Genetic Counseling / Asude Durmaz / Burak Durmaz -- Informed Consent Form / Asude Durmaz / Burak Durmaz -- Return of Results / Asude Durmaz / Burak Durmaz -- Future Perspectives / Asude Durmaz / Burak Durmaz -- List of Acronyms and Abbreviations / Asude Durmaz / Burak Durmaz -- References / Asude Durmaz / Burak Durmaz -- Overview / Urszula Demkow -- The Overall Genetic Testing Strategy in Undiagnosed Diseases[--]Looking for the Needle in a Haystack / Urszula Demkow -- The Analysis of NGS Testing Results for Rare Diseases / Urszula Demkow -- Pathogenicity / Urszula Demkow
Note continued: Good Laboratory Practice in Genetic Testing for Undiagnosed Diseases / Urszula Demkow -- Test Validation / Urszula Demkow -- The Importance of Genetic Diagnosis in Rare Diseases / Urszula Demkow -- Conclusions / Urszula Demkow -- References / Urszula Demkow -- United States / Jacub Owoc -- Great Britain / Jacub Owoc -- Holland / Jacub Owoc -- Germany / Jacub Owoc -- Conclusions / Jacub Owoc -- References / Jacub Owoc -- Sequencing Platforms / Michal Okoniewski / Rafal Ploski / Urszula Demkow / Marek Wiewiorka -- Nanopore Sequencing / Michal Okoniewski / Marek Wiewiorka / Rafal Ploski / Urszula Demkow -- Emerging Commercial Solutions / Rafal Ploski / Michal Okoniewski / Marek Wiewiorka / Urszula Demkow -- Future Directions of Clinical Genomics Data Processing / Marek Wiewiorka / Rafal Ploski / Michal Okoniewski / Urszula Demkow -- Data Size Estimates and Current Processing Limitations / Michal Okoniewski / Rafal Ploski / Marek Wiewiorka / Urszula Demkow
Note continued: Data Processing Models / Marek Wiewiorka / Rafal Ploski / Michal Okoniewski / Urszula Demkow -- Hadoop Ecosystem Tools That Can Be Used in Genomic Medicine / Michal Okoniewski / Rafal Ploski / Marek Wiewiorka / Urszula Demkow -- Data Security and Biobanking / Michal Okoniewski / Rafal Ploski / Urszula Demkow / Marek Wiewiorka -- Currently Developing Scenarios and Cases / Michal Okoniewski / Marek Wiewiorka / Rafal Ploski / Urszula Demkow -- Expected Challenges and Limitations of Future Data Processing Tools and Models / Michal Okoniewski / Rafal Ploski / Marek Wiewiorka / Urszula Demkow -- Education of Physicians and Medical Researchers in the Understanding and Use of Genomic Data Processing / Marek Wiewiorka / Rafal Ploski / Michal Okoniewski / Urszula Demkow -- Electronic Health Records / Marek Wiewiorka / Rafal Ploski / Michal Okoniewski / Urszula Demkow
Note continued: Conclusion[--]Vision of Near-Future Medical Genomics Information Systems / Michal Okoniewski / Rafal Ploski / Marek Wiewiorka / Urszula Demkow -- References / Michal Okoniewski / Rafal Ploski / Marek Wiewiorka / Urszula Demkow -- Introduction / John D. Lantos -- Differences between WGS and Genetic Testing in Other Contexts / John D. Lantos -- Newborn Metabolic Screening / John D. Lantos -- Carrier Testing in Carefully Selected High-Risk Populations / John D. Lantos -- Genetic Testing of Stored Samples in Biorepositories / John D. Lantos -- The Specific Ethical Issues of Whole-Genome Sequencing for Clinical Diagnosis / John D. Lantos -- Thinking about Harms and Benefits / John D. Lantos -- Conclusions / John D. Lantos -- Unpredictable Consequences of the Next Generation / Urszula Demkow / Andrzej Kochanski -- Sequencing-Related Technological Revolution in Medical Genetics / Urszula Demkow / Andrzej Kochanski
Note continued: Problem 1: The Right Not to Know / Urszula Demkow / Andrzej Kochanski -- Problem 2: Incidental/Unsolicited Findings / Andrzej Kochanski / Urszula Demkow -- Problem 3: Genetic Determinism and Discrimination / Andrzej Kochanski / Urszula Demkow -- Problem 4: Genetically-Based Selection of Human Embryos and Assisted Reproductive Technology / Urszula Demkow / Andrzej Kochanski -- Problem 5: NGS and Social Issues / Urszula Demkow / Andrzej Kochanski -- Conclusions / Urszula Demkow / Andrzej Kochanski -- References / Andrzej Kochanski / Urszula Demkow.
Includes bibliographical references and index.