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El. knyga: Computational Exome and Genome Analysis

(Charite Universitatsmedizin Berlin, Germany), , (Freie Universitat Berlin, Germany)
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Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.

Recenzijos

"This book represents a timely contribution to the burgeoning field of exome and genome sequencing data analysis. It covers all pertinent topics ranging from raw data quality control to medical interpretation of genetic mutations, with detailed command line examples as well as in-depth explanations on every step of analysis. Highly recommended to any researchers, scientists, clinicians or students who are interested to learn practical skills on genome analysis."

-Kai Wang, Department of Biomedical Informatics, Columbia University

"This book provides a very comprehensive overview of all the fundamentals that are needed to work as a bioinformatician in the field of exome and genome analysis. All of the important processing steps are illustrated with practical examples and code. In addition, the casual writing style makes this book an easy read."

-Christian Gilissen, Department of Human Genetics, Radbound Univeristy Medical Center

"This book is an excellent example of a hybrid between a textbook and an up-to-date research reference on the latest bioinformatics tools available in this eld. Its rigorous and thorough approach makes it a reliable starting point for bioinformaticians and biologists. By including details on methodological aspects of some of the algorithms used for various components of the data analysis and coupling these with fully-commented examples and exercises, this book presents itself as a must-have for novices and experts alike. Given the fast pace of the field, no book can be exhaustive, however, the wide variety of tools presented here recommend it to a wide audience, both as expertise and focused research interests."

-Irina Ioana Mohorianu, Zentralblatt MATH "This book represents a timely contribution to the burgeoning field of exome and genome sequencing data analysis. It covers all pertinent topics ranging from raw data quality control to medical interpretation of genetic mutations, with detailed command line examples as well as in-depth explanations on every step of analysis. Highly recommended to any researchers, scientists, clinicians or students who are interested to learn practical skills on genome analysis."

-Kai Wang, Department of Biomedical Informatics, Columbia University

"This book provides a very comprehensive overview of all the fundamentals that are needed to work as a bioinformatician in the field of exome and genome analysis. All of the important processing steps are illustrated with practical examples and code. In addition, the casual writing style makes this book an easy read."

-Christian Gilissen, Department of Human Genetics, Radbound Univeristy Medical Center

"This book is an excellent example of a hybrid between a textbook and an up-to-date research reference on the latest bioinformatics tools available in this eld. Its rigorous and thorough approach makes it a reliable starting point for bioinformaticians and biologists. By including details on methodological aspects of some of the algorithms used for various components of the data analysis and coupling these with fully-commented examples and exercises, this book presents itself as a must-have for novices and experts alike. Given the fast pace of the field, no book can be exhaustive, however, the wide variety of tools presented here recommend it to a wide audience, both as expertise and focused research interests."

-Irina Ioana Mohorianu, Zentralblatt MATH

Preface xv
Contributors xxi
Part I Introduction
Chapter 1 Introduction
3(8)
Chapter 2 NGS Technology
11(10)
Chapter 3 Illumina Technology
21(26)
Chapter 4 Data
47(10)
Part II Raw Data Processing
Chapter 5 FASTQ
57(10)
Chapter 6 Q/C: Raw Data
67(14)
Chapter 7 Q/C: Trimming
81(14)
Part III Alignment
Chapter 8 Alignment
95(16)
Chapter 9 SAM/BAM
111(18)
Chapter 10 Postprocessing the Alignment
129(20)
Chapter 11 Alignment Data: Quality Control
149(14)
Part IV Variant Calling
Chapter 12 Variant Calling & Quality-Based Filtering
163(20)
Chapter 13 VCF
183(20)
Chapter 14 Jannovar
203(6)
Chapter 15 Variant Annotation
209(20)
Chapter 16 Variant Calling QC
229(4)
Chapter 17 Integrative Genomics Viewer
233(14)
Chapter 18 De Novo Variants
247(12)
Chapter 19 Structural Variation
259(38)
Part V Variant Filtering
Chapter 20 Pedigree Analysis
297(18)
Chapter 21 Intersection and RVAS Analysis
315(6)
Chapter 22 Variant Frequency
321(8)
Chapter 23 Variant Pathogenicity
329(20)
Part VI Prioritization
Chapter 24 Prioritization
349(6)
Chapter 25 Random Walk
355(12)
Chapter 26 Phenotype Analysis
367(20)
Chapter 27 Exomiser
387(20)
Chapter 28 Medical Interpretation
407(12)
Part VII Cancer
Chapter 29 A (Very) Short Introduction to Cancer
419(10)
Chapter 30 Somatic Variants
429(38)
Chapter 31 Tumor Evolution and Sample Purity
467(10)
Chapter 32 Driver Mutations and Mutational Signatures
477(22)
Appendix A Hints and Answers 499(4)
References 503(44)
Index 547
Peter Robinson is Professor for Medical Genomics at the Charité Universitätsmedizin Berlin, and professor for Bioinformatics at the Free University of Berlin. He studied Mathematics and Computer Science at Columbia University as well as Medicine at the University of Pennsylvania. Peter has led a bioinformatics research group since 2004. He has led the development of the Human Phenotype Ontology, which is used internationally to describe the clinical manifestations of patients with genetic disorders and to empower exome and genome analysis. His group has published algorithms for exome, genome, ChIP-seq and NGS T Cell Receptor profiling. Rosario M. Piro is an Assistant Professor of Bioinformatics at Freie Universität Berlin and Charité-Universitätsmedizin Berlin, Germany. His research is mainly focused on computational neuropathology, including cancer genetics/genomics of brain tumors as well as network analysis and disease gene prediction for neurological disorders; and computational oncology in general, including the development and evolution of cancers in other organs or tissues. His expertise in next-generation sequencing data analysis techniques is complemented by a past research experience in the field of data-intensive distributed computing.



Marten Jäger is a graduate student in Peter Robinsons group and has developed pipelines for exome and genome sequencing data. Martens work has involved the development of algorithms for variant annotation, exome prioritization, RNA-seq, and integrative genomics analysis.