Next-generation genome sequencing: towards personalized medicine
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| Other Authors: | |
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| Format: | Book |
| Language: | English |
| Published: |
[Weinheim]
Wiley-Blackwell
2008
Weinheim Wiley-VCH-Verl. |
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XX, 260 S. Ill., graph. Darst. 24 cm |
| ISBN: | 9783527320905 |
Staff View
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| 245 | 1 | 0 | |a Next-generation genome sequencing |b towards personalized medicine |c ed. by Michal Janitz |
| 264 | 1 | |a [Weinheim] |b Wiley-Blackwell |c 2008 | |
| 264 | 1 | |a Weinheim |b Wiley-VCH-Verl. | |
| 300 | |a XX, 260 S. |b Ill., graph. Darst. |c 24 cm | ||
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| 500 | |a Literaturangaben | ||
| 650 | 4 | |a Chromosome Mapping | |
| 650 | 4 | |a Genomics |x methods | |
| 650 | 4 | |a Human gene mapping | |
| 650 | 4 | |a Medical genetics | |
| 650 | 4 | |a Nucleotide sequence | |
| 650 | 4 | |a Sequence Analysis, DNA | |
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Record in the Search Index
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|---|---|
| adam_text |
PART ONE 1.1 1.2 1.3 1.4 1.5 PART TWO 2 2,1 2,2 2,3 2.4 2,5 2,6 2.6.1
2.6.2 2.6.3 2.6.4 2.6.5 IV CONTENTS PREFACE XII I LIST OF CONTRIBUTORS
XVII SANGER DNA SEQUENCING SANGER DNA SEQUENCING 3 ARTEM E. MEN, PETER
WILSON, KIRBY SIEMERING, AND SUSAN FORREST THE BASICS OF SANGER
SEQUENCING 3 INTO THE HUMAN GENOME PROJECT (HGP) AND BEYOND 6
LIMITATIONS AND FUTURE OPPORTUNITIES 7 BIOINFORMATICS HOLDS THE KEY 8
WHERE TO NEXT? 9 REFERENCES 10 NEXT-GENERATION SEQUENCING: TOWARD
PERSONALIZED MEDICINE 13 ILLUMINA GENOME ANALYZER II SYSTEM 15 ABIZAR
LAKDAWALLA AND HARPER VANSTEENHOUSE LIBRARY PREPARATION 15 CLUSTER
CREATION 17 SEQUENCING 19 PAIRED END READS 19 DATA ANALYSIS 20
APPLICATIONS 21 GENOME SEQUENCING APPLICATIONS 23 EPIGENOMICS 23
TRANSCRIPTOME ANALYSIS 23 PROTEIN-NUCLEIC ACID INTERACTIONS 26
MULTIPLEXING 26 NEXT-GENERATION GENOME SEQUENCING: TOWARDS PERSONALIZED
MEDICINE. EDITED BY MICHAL LANITZ COPYRIGHT 2008 WI LEY-VCH VERLAG GMBH
& CO. KGAA. WEINHEIM ISBN: 978-3-527-32090-5 VI I CONTENTS 2.7* 3 3.1*
3.2* 3.2.1* 3.2.1.1* 3.2.1.2* 3.2.1.3* 3.2.1.4* 3.2.1.5* 3.2.1.6* 3.3*
3.3.1* 3.3.2* 3.3.3* 3.3.4* 3.3.5* 3.3.6* 3.3.7* 3.3.8* 3.3.9* 3.4* 4
4.1* 4.2* 4.3* 4.3.1* 4.3.2* 4.3.3* 4.4* 5 5.1* 5.2* 5.2.1* 5.2.2*
5.2.3* CONCLUSIONS 26* REFERENCES 27* APPLIED BIOSYSTEMS SOLID* SYSTEM:
LIGATION-BASED SEQUENCING 29 VICKI PANDEY, ROBERT C. NUTTER, AND ELLEN
PREDIGER LNTRODUCTION 29 OVERVIEW OF THE SOLID * SYSTEM 29 THE SOLID
PLATFORM 30 LIBRARY GENERATION 30 EMULSION PCR 3 ] BEAD PURIFICATION 3 ]
BEAD DEPOSITION 33 SEQUENCING BY LIGATION 33 COLOR SPACE AND BASE
CALLING 35 SO LID * SYSTEM APPLICATIONS 35 LARGE-SCALE RESEQUENCING 35
DE NOVO SEQUENCING 35 TAG- BASED GENE EXPRESSION 36 WHOLE TRANSCRIPTOME
ANALYSIS 37 WHOLE GENOME RESEQUENCING 38 WHOLE GENOME METHYLATION
ANALYSIS 38 CHROMATIN LMMUNOPRECIPITATION 39 MICRORNA DISCOVERY 39 OTHER
TAG-BASED APPLICATIONS 40 CONCLUSIONS 40 REFERENCES 41 THE
NEXT-GENERATION GENOME SEQUENCING: 454/ROCHE GS FLX 43 LEI DU AND
MICHAEL EGHOLM INTRODUCTION 43 TECHNOLOGY OVERVIEW 44 SOFTWARE AND
BIOINFORMATICS 47 WHOLE GENOME ASSEMBLY 47 RESEQUENCING AND MUTATION
DETECTION 47 ULTRADEEP SEQUENCING 47 RESEARCH APPLICATIONS 49 REFERENCES
51 POLONY SEQUENCING: HISTORY, TECHNOLOGY, AND APPLICATIONS 57 JEREMY S.
EDWARDS LNTRODUCTION 57 HISTORY OF POLONY SEQUENCING 57 LNTRODUCTION TO
POLONIES 58 EVOLUTION OF POLONIES 59 CURRENT APPLICATIONS OF THE
ORIGINAL POLONIES METHOD 6] REFERENCES 87 5.3* POLONY SEQUENCING 62
5.3.1* CONSTRUCTING A SEQUENCING LIBRARY 63* 5.3.2* LOADING THE LIBRARY
ONTO BEADS USING BEAMING 64* 5.3.3 5.3.4* SEQUENCING 66* 5.3.5* DATA
ANALYSIS 68* 5.4* APPLICATIONS 69 5.4.1* HUMAN GENOME SEQUENCING 69
5.4.1.1 REQUIREMENTS OF AN ULTRAHIGH-THROUGHPUT SEQUENCING 5.4.2*
CHALLENGES OF SEQUENCING THE HUMAN GENOME WITH SHORT READS 70 5.4.2.1*
CHROMOSOME SEQUENCING 72 5.4.2.2* EXON SEQUENCING 72 5.4.2.3* IMPACT ON
MEDICINE 72 5.4.3* TRANSCRIPT PROFILING 73 5.4.3.1* POLONY SAGE 73
5.4.3.2* TRANSCRIPT CHARACTERIZATION WITH POLONY SAG E 73 5.4.3.3*
DIGITAL KARYOTYPING 75 5.5* CONCLUSIONS 75* PART THREE THE BOTTLENECK:
SEQUENCE DATA ANALYSIS 77* 6* NEXT-GENERATION SEQUENCE DATA ANALYSIS 79
6.1* WHY NEXT-GENERATION SEQUENCE ANALYSIS IS DIFFERENT? 79 6.2* 6.3*
WHAT IS A "HIT," AND WHY IT MATTERS FOR NGS? 82 6.3.1* WORD HIT 82
6.3.2* SEGMENT HIT 82 6.3.3* SEQID HIT OR GENE HIT 82 6.3.4* REGION HIT
82 6.3.5* MAPPED HIT 83 6.3.6* SYNTENY HIT 83 6.4* SCORING: WHY IT IS
DIFFERENT FOR NGS? 83 6.5* STRATEGIES FOR NGS SEQUENCE ANALYSIS 84 6.6*
SUBSEQUENT DATA ANALYSIS 86 7* DNASTAR'S NEXT-GENERATION SOFTWARE 89
7.1* PERSONALIZED GENOMICS AND PERSONALIZED MEDICINE 89 7.2*
NEXT-GENERATION DNA SEQUENCING AS THE MEANS TO PERSONALIZED 89 GENOMICS
CONTENTS I VII* IMMOBILIZING THE BEADS IN THE SEQUENCING FLOW CELL 65*
TECHNOLOGY 69* REFERENCES 76* LEONARD N. BLOKSBERG STRATEGIES FOR
SEQUENCE SEARCHING 80* TIM DURFEE AND THOMAS E. SCHWEI VIII I CONTENTS
7.3* STRENGTHS OF VARIOUS PLATFORMS 90 7.4* THE COMPUTATIONAL CHALLENGE
90 7.5* DNASTAR'S NEXT-GENERATION SOFTWARE SOLUTION 91 7.6* CONCLUSIONS
94* REFERENCES 94* PART FOUR* EMERGING SEQUENCING TECHNOLOGIES 95 8*
REAL-TIME DNA SEQUENCING 97 SUSAN H. HARDIN 8.1* WHOLE GENOME ANALYSIS
97 8.2* PERSONALIZED MEDICINE AND PHARMACOGENOMICS 97 8.3* BIODEFENSE,
FORENSICS, DNA TESTING, AND BASIC RESEARCH 98 8.4* SIMPLE AND ELEGANT:
REAL-TIME DNA SEQUENCING 98* REFERENCES 101* 9* DIRECT SEQUENCING BY TEM
OF Z-SUBSTITUTED DNA MOLECULES 103 WILLIAM 1 ' THOMAS AND WILLIAM GLOVER
9.1* INTRODUCTION 103 9.2* LOGIC OF APPROACH 104 9.3* IDENTIFICATION OF
OPTIMAL MODIFIED NUCLEOTIDES FOR TEM VISUAL RESOLUTION OF DNA SEQUENCES
LNDEPENDENT OF POLYMERIZATION 106 9.4* TEM SUBSTRATES AND VISUALIZATION
107 9.5* LNCORPORATION OF Z-TAGGED NUCLEOTIDES BY POLYMERASES 108 9.6*
CURRENT AND NEW SEQUENCING TECHNOLOGY 109 9.7* ACCURACY 111 9.8*
ADVANTAGES OFZSE'S PROPOSED DNA SEQUENCING TECHNOLOGY 111 9.9*
ADVANTAGES OF SIGNIFICANTLY LONGER READ LENGTHS 112 9.9.1* DE NOVO
GENOME SEQUENCING 112 9.9.2* TRANSCRIPTOME ANALYSIS 113 9.9.3* HAPLOTYPE
ANALYSIS 114* REFERENCES 115* 10* A SINGLE DNA MOLECULE BARCODING METHOD
WITH APPLICATIONS IN DNA MAPPING AND MOLECULAR HAPLOTYPING 117 MING XIAO
AND PUI- YAN KWOK 10.1* INTRODUCTION 117 10.2* CRITICAL TECHNIQUES IN
THE SINGLE DNA MOLECULE BARCODING METHOD 118 10.3* SINGLE DNA MOLECULE
MAPPING 120 10.3.1* SEQUENCE MOTIF MAPS OF LAMBDA DNA 121 10.3.2*
IDENTIFICATION OF SEVERAL VIRAL GENOMES 123 10.4 10.4.1 10.4.2 10.5 11*
11.1 11.2 11.2.1 11.2.1.1 11.2.1.2 11.2.2 11.2.3 11.2.4 11.2.4.1
11.2.4.2 11.2.5 11.2.5.1 11.2.5.2 11.2.5.3 11.2.5.4 11.2.6 11.2.7 11.2.8
11.3 12* 12.1 12.2 12.2.1 12.2.2 12.3 CONTENTS IIX MOLECULAR HAPLOTYPING
124* LOCALIZATION OF POLYMORPHIC ALLELES TAGGED BY SINGLE FLUORESCENT
DYE* MOLECULES ALONG DNA BACKBONES 125* DIRECT HAPLOTYPE DETERMINATION
OF A HUMAN DNA SAMPLE 127* DISCUSSION 129* REFERENCES 13 1* OPTICAL
SEQUENCING: ACQUISITION FROM MAPPED SINGLE-MOLECULE* TEMPLATES 133*
SHIGUO ZHOU, LOUISE PAPE, AND DAL)ID C. SCHWARTZ INTRODUCTION 133* THE
OPTICAL SEQUENCING CYCLE 135* OPTICAL SEQUENCING MICROSCOPE AND REACTION
CHAMBER SETUP 13 7* MICROSCOPE SETUP 13 7* OPTICAL SEQUENCING REACTION
CHAMBER SETUP 13 7* SURFACE PREPARATION 13 7* GENOMIC DNA
MOUNTING/OVERLAY 139* NICKING LARGE DOUBLE-STRANDED TEMPLATE DNA
MOLECULES 139* NICKING MOUNTED DNA TEMPLATE MOLECULES 139* GAPPING NICK
SITES 139* OPTICAL SEQUENCING REACTIONS 140* BASIC PROCESS 140* CHOICES
OF DNA POLYMERASES 140* POLYMERASE-MEDIATED INCORPORATIONS OF MULTIPLE
FLUOROCHROME-LABELED* NUCLEOTIDES 140* WASHES TO REMOVE UNINCORPORATED
LABELED FREE NUCLEOTIDES AND* REDUCE BACKGROUND 141* IMAGING FLUORESCENT
NUCLEOTIDE ADDITIONS AND COUNTING INCORPORATED* FLUOROCHROMES 141*
PHOTOBLEACHING 147* DEMONSTRATION OF OPTICAL SEQUENCING CYCLES 147*
FUTURE OF OPTICAL SEQUENCING 148* REFERENCES 149* MICROCHIP-BASED SANGER
SEQUENCING OF DNA 153* RYAN E. FORSTER, CHRISTOPHER P. FREDLAKE, AND
ANNELISE E. BARRON INTEGRATED MICROF1UIDIC DEVICES FOR GENOMIC ANALYSIS
154* IMPROVED POLYMER NETWORKS FOR SANGER SEQUENCING ON* MICROF1UIDIC
DEVICES 156* POLY(N,N-DIMETHYLACRYLAMIDE) NETWORKS FOR DNA* SEQUENCING
156* HYDROPHOBICALLY MODIFIED POLYACRYLAMIDES FOR DNA SEQUENCING 159*
CONCLUSIONS 160* REFERENCES 160* X I CONTENTS PART FIVE* NEXT-GENERATION
SEQUENCING: TRULY INTEGRATED GENOME ANALYSIS 165 13* MULTIPLEX
SEQUENCING OF PAIRED END DITAGS FOR TRANSCRIPTOME* AND GENOME ANALYSIS
167* CHIA-LIN WEI AND YIJUN RUAN 13.1* INTRODUCTION 167 13.2* THE
DEVELOPMENT OF PAIRED END DITAG ANALYSIS 168 13.3* GIS-PET FOR
TRANSCRIPTOME ANALYSIS 170 13.4* CHIP- PET FOR WHOLE GENOME MAPPING OF
TRANSCRIPTION FACTOR BINDING SITES AND EPIGENETIC MODIFICATIONS 173
13.5* CHIA-PET FOR WHOLE GENOME IDENTIFICATION OF LONG-RANGE*
INTERACTIONS 175* 13.6* PERSPECTIVE 179* REFERENCES 180* 14*
PALEOGENOMICS USING THE 454 SEQUENCING PLATFORM 183 M. THOMAS P. GILBERT
14.1* INTRODUCTION 183 14.2* THE DNA DEGRADATION CHALLENGE 184 14.3* THE
EFFECTS OF DNA DEGRADATION ON PALEOGENOMICS 785 14.4* DEGRADATION AND
SEQUENCING ACCURACY 185 14.5* SAMPLE CONTAMINATION 189 14.6* SOLUTIONS
TO DNA DAMAGE 191 14.7* SOLUTIONS TO CONTAMINATION 792 14.8* WHAT
GROUNDWORK REMAINS, AND WHAT DOES THE FUHLRE HOLD? 195 REFERENCES 196
15* CHIP-SEQ: MAPPING OF PROTEIN-DNA INTERACTIONS 201 ANTHONY PETER
FEJES AND STEVEN J. M. JONES 15.1* INTRODUCTION 201 15.2* HISTORY 202
15.3* CHIP-SEQ METHOD 202 15.4* SANGER DIDEOXY-BASED TAG SEQUENCING 203
15.5* HYBRIDIZATION-BASED TAG SEQUENCING 205 15.6* APPLICATION OF
SEQUENCING BY SYNTHESIS 206 15.7* MEDICAL APPLICATIONS OF CHIP-SEQ 209
15.8* CHALLENGES 209 15.9* FUTURE USES OF CHIP-SEQ 217* REFERENCES 213*
16* MICRORNA DISCOVERY AND EXPRESSION PROFILING USING* NEXT-GENERATION
SEQUENCING 217* EUGENE BEREZIKOV AND EDWIN CUPPEN 16.1* BACKGROUND ON
MIRNAS 217 16.2* MIRNA IDENTIFICATION 218 16.3 16.3.1 16.3.2 16.3.3
16.3.4 16.3.4.1 16.3.4.2 16.4 16.5 17 17.1 17.2 17.3 17.4 17.5 18 18.1
18.2 18.3 18.4 18.5 18.6 18.7 18.8 18.9 18.9.1 18.9.2 18.10 CONTENTS I
XI EXPERIMENTAL APPROACH 219 SAMPLE COLLECTION 219 LIBRARY CONSTRUCTION
221 MASSIVELY PARALLEL SEQUENCING 222 BIOINFORMATIC ANALYSIS 223
MICRORNA DISCOVERY 223 MIRNA EXPRESSION PROFILING 225 VALIDATION 225
OUTLOOK 226 REFERENCES 226 DEEPSAGE: TAG-BASED TRANSCRIPTOME ANALYSIS
BEYOND MICROARRAYS 229 KARE L. NIELSEN, ANNABETH H. PETERSEN, AND JEPPE
EMMERSEN INTRODUCTION 229 DEEPSAG E 231 DATA ANALYSIS 235 COMPARING TAG-
BASED TRANSCRIPTOME PROFILES 235 FUTURE PERSPECTIVES 238 REFERENCES 23 9
THE NEW GENOMICS AND PERSONAL GENOME INFORMATION: ETHICAL ISSUES 245
JEANTINE E. LUNSHOF THE NEW GENOMICS AND PERSONAL GENOME LNFORMATION:
ETHICAL LSSUES 245 THE NEW GENOMICS: WHAT MAKES IT SPECIAL? 245
INNOVATION IN ETHICS: WHY DO WE NEED IT? 246 A PROVISO: GLOBAL GENOMICS
AND LOCAL ETHICS 247 MEDICAL ETHICS AND HIPPOCRATIC CONFIDENTIALITY 247
PRINCIPLES OF BIOMEDICAL ETHICS 248 CLINICAL RESEARCH AND INFORMED
CONSENT 248 LARGE-SCALE RESEARCH ETHICS: NEW CONCEPTS 249 PERSONAL
GENOMES 250 WHAT IS A PERSONAL GENOME AND WHAT IS NEW ABOUT IT? 250 BUT,
CAN MAKING PROMISES THAT CANNOT BE SUBSTANTIATED BE EVER MORALLY
JUSTIFIABLE? 251 THE PERSONAL GENOME PROJECT: CONSENTING TO DISCLOSURE
251 REFERENCES 252 INDEX 255 |
| any_adam_object | 1 |
| author2 | Janitz, Michal |
| author2_role | edt |
| author2_variant | m j mj |
| author_GND | (DE-588)136355838 |
| author_facet | Janitz, Michal |
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| callnumber-search | QH445.2 |
| callnumber-sort | QH 3445.2 |
| callnumber-subject | QH - Natural History and Biology |
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| classification_tum | BIO 180f CHE 893f |
| ctrlnum | (OCoLC)230188668 (DE-599)DNB988249464 |
| dewey-full | 611.018 572.8633 |
| dewey-hundreds | 600 - Technology (Applied sciences) 500 - Natural sciences and mathematics |
| dewey-ones | 611 - Human anatomy, cytology, histology 572 - Biochemistry |
| dewey-raw | 611.018 572.8633 |
| dewey-search | 611.018 572.8633 |
| dewey-sort | 3611.018 |
| dewey-tens | 610 - Medicine and health 570 - Biology |
| discipline | Biologie Chemie Medizin |
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| indexdate | 2024-07-20T09:58:07Z |
| institution | BVB |
| isbn | 9783527320905 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017011839 |
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| physical | XX, 260 S. Ill., graph. Darst. 24 cm |
| publishDate | 2008 |
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| publisher | Wiley-Blackwell Wiley-VCH-Verl. |
| record_format | marc |
| spelling | Next-generation genome sequencing towards personalized medicine ed. by Michal Janitz [Weinheim] Wiley-Blackwell 2008 Weinheim Wiley-VCH-Verl. XX, 260 S. Ill., graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Literaturangaben Chromosome Mapping Genomics methods Human gene mapping Medical genetics Nucleotide sequence Sequence Analysis, DNA Gentherapie (DE-588)4296957-8 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Genanalyse (DE-588)4200230-8 s Gentherapie (DE-588)4296957-8 s DE-604 Janitz, Michal (DE-588)136355838 edt text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3089621&prov=M&dok_var=1&dok_ext=htm Inhaltstext OEBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017011839&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Next-generation genome sequencing towards personalized medicine Chromosome Mapping Genomics methods Human gene mapping Medical genetics Nucleotide sequence Sequence Analysis, DNA Gentherapie (DE-588)4296957-8 gnd Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4296957-8 (DE-588)4200230-8 (DE-588)4143413-4 |
| title | Next-generation genome sequencing towards personalized medicine |
| title_auth | Next-generation genome sequencing towards personalized medicine |
| title_exact_search | Next-generation genome sequencing towards personalized medicine |
| title_full | Next-generation genome sequencing towards personalized medicine ed. by Michal Janitz |
| title_fullStr | Next-generation genome sequencing towards personalized medicine ed. by Michal Janitz |
| title_full_unstemmed | Next-generation genome sequencing towards personalized medicine ed. by Michal Janitz |
| title_short | Next-generation genome sequencing |
| title_sort | next generation genome sequencing towards personalized medicine |
| title_sub | towards personalized medicine |
| topic | Chromosome Mapping Genomics methods Human gene mapping Medical genetics Nucleotide sequence Sequence Analysis, DNA Gentherapie (DE-588)4296957-8 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Chromosome Mapping Genomics methods Human gene mapping Medical genetics Nucleotide sequence Sequence Analysis, DNA Gentherapie Genanalyse Aufsatzsammlung |
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| work_keys_str_mv | AT janitzmichal nextgenerationgenomesequencingtowardspersonalizedmedicine |