Keywords:
Sequence Analysis, DNA.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (282 pages)
Edition:
1st ed.
ISBN:
9783527625147
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=482085
DDC:
572.8633
Language:
English
Note:
Intro -- Next-Generation Genome Sequencing -- Contents -- Preface -- List of Contributors -- Part One Sanger DNA Sequencing -- 1 Sanger DNA Sequencing -- 1.1 The Basics of Sanger Sequencing -- 1.2 Into the Human Genome Project (HGP) and Beyond -- 1.3 Limitations and Future Opportunities -- 1.4 Bioinformatics Holds the Key -- 1.5 Where to Next? -- References -- Part Two Next-Generation Sequencing: Toward Personalized Medicine -- 2 Illumina Genome Analyzer II System -- 2.1 Library Preparation -- 2.2 Cluster Creation -- 2.3 Sequencing -- 2.4 Paired End Reads -- 2.5 Data Analysis -- 2.6 Applications -- 2.6.1 Genome Sequencing Applications -- 2.6.2 Epigenomics -- 2.6.3 Transcriptome Analysis -- 2.6.4 Protein-Nucleic Acid Interactions -- 2.6.5 Multiplexing -- 2.7 Conclusions -- References -- 3 Applied Biosystems SOLiD™ System: Ligation-Based Sequencing -- 3.1 Introduction -- 3.2 Overview of the SOLiD™ System -- 3.2.1 The SOLiD Platform -- 3.2.1.1 Library Generation -- 3.2.1.2 Emulsion PCR -- 3.2.1.3 Bead Purification -- 3.2.1.4 Bead Deposition -- 3.2.1.5 Sequencing by Ligation -- 3.2.1.6 Color Space and Base Calling -- 3.3 SOLiD™ System Applications -- 3.3.1 Large-Scale Resequencing -- 3.3.2 De novo Sequencing -- 3.3.3 Tag-Based Gene Expression -- 3.3.4 Whole Transcriptome Analysis -- 3.3.5 Whole Genome Resequencing -- 3.3.6 Whole Genome Methylation Analysis -- 3.3.7 Chromatin Immunoprecipitation -- 3.3.8 MicroRNA Discovery -- 3.3.9 Other Tag-Based Applications -- 3.4 Conclusions -- References -- 4 The Next-Generation Genome Sequencing: 454/Roche GS FLX -- 4.1 Introduction -- 4.2 Technology Overview -- 4.3 Software and Bioinformatics -- 4.3.1 Whole Genome Assembly -- 4.3.2 Resequencing and Mutation Detection -- 4.3.3 Ultradeep Sequencing -- 4.4 Research Applications -- References -- 5 Polony Sequencing: History, Technology, and Applications.
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5.1 Introduction -- 5.2 History of Polony Sequencing -- 5.2.1 Introduction to Polonies -- 5.2.2 Evolution of Polonies -- 5.2.3 Current Applications of the Original Polonies Method -- 5.3 Polony Sequencing -- 5.3.1 Constructing a Sequencing Library -- 5.3.2 Loading the Library onto Beads Using BEAMing -- 5.3.3 Immobilizing the Beads in the Sequencing Flow Cell -- 5.3.4 Sequencing -- 5.3.5 Data Analysis -- 5.4 Applications -- 5.4.1 Human Genome Sequencing -- 5.4.1.1 Requirements of an Ultrahigh-Throughput Sequencing Technology -- 5.4.2 Challenges of Sequencing the Human Genome with Short Reads -- 5.4.2.1 Chromosome Sequencing -- 5.4.2.2 Exon Sequencing -- 5.4.2.3 Impact on Medicine -- 5.4.3 Transcript Profiling -- 5.4.3.1 Polony SAGE -- 5.4.3.2 Transcript Characterization with Polony SAGE -- 5.4.3.3 Digital Karyotyping -- 5.5 Conclusions -- References -- Part Three The Bottleneck: Sequence Data Analysis -- 6 Next-Generation Sequence Data Analysis -- 6.1 Why Next-Generation Sequence Analysis is Different? -- 6.2 Strategies for Sequence Searching -- 6.3 What is a "Hit," and Why it Matters for NGS? -- 6.3.1 Word Hit -- 6.3.2 Segment Hit -- 6.3.3 SeqID Hit or Gene Hit -- 6.3.4 Region Hit -- 6.3.5 Mapped Hit -- 6.3.6 Synteny Hit -- 6.4 Scoring: Why it is Different for NGS? -- 6.5 Strategies for NGS Sequence Analysis -- 6.6 Subsequent Data Analysis -- References -- 7 DNASTAR's Next-Generation Software -- 7.1 Personalized Genomics and Personalized Medicine -- 7.2 Next-Generation DNA Sequencing as the Means to Personalized Genomics -- 7.3 Strengths of Various Platforms -- 7.4 The Computational Challenge -- 7.5 DNASTAR's Next-Generation Software Solution -- 7.6 Conclusions -- References -- Part Four Emerging Sequencing Technologies -- 8 Real-Time DNA Sequencing -- 8.1 Whole Genome Analysis -- 8.2 Personalized Medicine and Pharmacogenomics.
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8.3 Biodefense, Forensics, DNA Testing, and Basic Research -- 8.4 Simple and Elegant: Real-Time DNA Sequencing -- References -- 9 Direct Sequencing by TEM of Z-Substituted DNA Molecules -- 9.1 Introduction -- 9.2 Logic of Approach -- 9.3 Identification of Optimal Modified Nucleotides for TEM Visual Resolution of DNA Sequences Independent of Polymerization -- 9.4 TEM Substrates and Visualization -- 9.5 Incorporation of Z-Tagged Nucleotides by Polymerases -- 9.6 Current and New Sequencing Technology -- 9.7 Accuracy -- 9.8 Advantages of ZSG's Proposed DNA Sequencing Technology -- 9.9 Advantages of Significantly Longer Read Lengths -- 9.9.1 De novo Genome Sequencing -- 9.9.2 Transcriptome Analysis -- 9.9.3 Haplotype Analysis -- References -- 10 A Single DNA Molecule Barcoding Method with Applications in DNA Mapping and Molecular Haplotyping -- 10.1 Introduction -- 10.2 Critical Techniques in the Single DNA Molecule Barcoding Method -- 10.3 Single DNA Molecule Mapping -- 10.3.1 Sequence Motif Maps of Lambda DNA -- 10.3.2 Identification of Several Viral Genomes -- 10.4 Molecular Haplotyping -- 10.4.1 Localization of Polymorphic Alleles Tagged by Single Fluorescent Dye Molecules Along DNA Backbones -- 10.4.2 Direct Haplotype Determination of a Human DNA Sample -- 10.5 Discussion -- References -- 11 Optical Sequencing: Acquisition from Mapped Single-Molecule Templates -- 11.1 Introduction -- 11.2 The Optical Sequencing Cycle -- 11.2.1 Optical Sequencing Microscope and Reaction Chamber Setup -- 11.2.1.1 Microscope Setup -- 11.2.1.2 Optical Sequencing Reaction Chamber Setup -- 11.2.2 Surface Preparation -- 11.2.3 Genomic DNA Mounting/Overlay -- 11.2.4 Nicking Large Double-Stranded Template DNA Molecules -- 11.2.4.1 Nicking Mounted DNA Template Molecules -- 11.2.4.2 Gapping Nick Sites -- 11.2.5 Optical Sequencing Reactions -- 11.2.5.1 Basic Process.
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11.2.5.2 Choices of DNA Polymerases -- 11.2.5.3 Polymerase-Mediated Incorporations of Multiple Fluorochrome-Labeled Nucleotides -- 11.2.5.4 Washes to Remove Unincorporated Labeled Free Nucleotides and Reduce Background -- 11.2.6 Imaging Fluorescent Nucleotide Additions and Counting Incorporated Fluorochromes -- 11.2.7 Photobleaching -- 11.2.8 Demonstration of Optical Sequencing Cycles -- 11.3 Future of Optical Sequencing -- References -- 12 Microchip-Based Sanger Sequencing of DNA -- 12.1 Integrated Microfluidic Devices for Genomic Analysis -- 12.2 Improved Polymer Networks for Sanger Sequencing on Microfluidic Devices -- 12.2.1 Poly(N,N-dimethylacrylamide) Networks for DNA Sequencing -- 12.2.2 Hydrophobically Modified Polyacrylamides for DNA Sequencing -- 12.3 Conclusions -- References -- Part Five Next-Generation Sequencing: Truly Integrated Genome Analysis -- 13 Multiplex Sequencing of Paired End Ditags for Transcriptome and Genome Analysis -- 13.1 Introduction -- 13.2 The Development of Paired End Ditag Analysis -- 13.3 GIS-PET for Transcriptome Analysis -- 13.4 ChIP-PET for Whole Genome Mapping of Transcription Factor Binding Sites and Epigenetic Modifications -- 13.5 ChIA-PET for Whole Genome Identification of Long-Range Interactions -- 13.6 Perspective -- References -- 14 Paleogenomics Using the 454 Sequencing Platform -- 14.1 Introduction -- 14.2 The DNA Degradation Challenge -- 14.3 The Effects of DNA Degradation on Paleogenomics -- 14.4 Degradation and Sequencing Accuracy -- 14.5 Sample Contamination -- 14.6 Solutions to DNA Damage -- 14.7 Solutions to Contamination -- 14.8 What Groundwork Remains, and What Does the Future Hold? -- References -- 15 ChIP-seq: Mapping of Protein-DNA Interactions -- 15.1 Introduction -- 15.2 History -- 15.3 ChIP-seq Method -- 15.4 Sanger Dideoxy-Based Tag Sequencing -- 15.5 Hybridization-Based Tag Sequencing.
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15.6 Application of Sequencing by Synthesis -- 15.7 Medical Applications of ChIP-seq -- 15.8 Challenges -- 15.9 Future Uses of ChIP-seq -- References -- 16 MicroRNA Discovery and Expression Profiling using Next-Generation Sequencing -- 16.1 Background on miRNAs -- 16.2 miRNA Identification -- 16.3 Experimental Approach -- 16.3.1 Sample Collection -- 16.3.2 Library Construction -- 16.3.3 Massively Parallel Sequencing -- 16.3.4 Bioinformatic Analysis -- 16.3.4.1 MicroRNA Discovery -- 16.3.4.2 miRNA Expression Profiling -- 16.4 Validation -- 16.5 Outlook -- References -- 17 DeepSAGE: Tag-Based Transcriptome Analysis Beyond Microarrays -- 17.1 Introduction -- 17.2 DeepSAGE -- 17.3 Data Analysis -- 17.4 Comparing Tag-Based Transcriptome Profiles -- 17.5 Future Perspectives -- References -- 18 The New Genomics and Personal Genome Information: Ethical Issues -- 18.1 The New Genomics and Personal Genome Information: Ethical Issues -- 18.2 The New Genomics: What Makes it Special? -- 18.3 Innovation in Ethics: Why do We Need it? -- 18.4 A Proviso: Global Genomics and Local Ethics -- 18.5 Medical Ethics and Hippocratic Confidentiality -- 18.6 Principles of Biomedical Ethics -- 18.7 Clinical Research and Informed Consent -- 18.8 Large-Scale Research Ethics: New Concepts -- 18.9 Personal Genomes -- 18.9.1 What is a Personal Genome and What is New About It? -- 18.9.2 But, Can Making Promises that Cannot be Substantiated be Ever Morally Justifiable? -- 18.10 The Personal Genome Project: Consenting to Disclosure -- References -- Index.
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