Cancer diagnostics with DNA microarrays
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| Format: | Elektronisch E-Book |
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| Sprache: | English |
| Veröffentlicht: |
Hoboken, NJ
Wiley
2006
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| Online-Zugang: | DE-861 DE-355 Volltext Volltext Inhaltsverzeichnis |
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| 650 | 4 | |a DNA microarrays |x Diagnostic use | |
| 650 | 4 | |a Cancer |x Diagnosis | |
| 650 | 4 | |a Neoplasms |x diagnosis | |
| 650 | 4 | |a Oligonucleotide Array Sequence Analysis |x methods | |
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Datensatz im Suchindex
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| adam_text | Contents
Preface xv
Acknowledgments xvii
1. Introduction to DNA Microarray Technology 1
1.1 Hybridization / 1
1.2 The Technology Behind DNA Microarrays / 3
1.2.1 Affymetrix GeneChip Technology / 4
1.2.2 Spotted Arrays / 6
1.2.3 Digital Micromirror Arrays / 8
1.2.4 InkJet Arrays / 8
1.2.5 Bead Arrays / 9
1.2.6 Electronic Microarrays / 9
1.2.7 Serial Analysis of Gene Expression (SAGE) / 10
1.3 Parallel Sequencing on Microbead Arrays / II
1.3.1 Emerging Technologies / 12
1.4 Summary / 13
Further Reading / 14
2. Image Analysis 16
2.1 Gridding / 16
2.2 Segmentation / 17
2.3 Intensity Extraction / 17
2.4 Background Correction / 17
Viii CONTENTS
2.5 Software / 19
2.5.1 Free Software for Array Image Analysis / 19
2.5.2 Commercial Software for Array Image Analysis / 19
2.6 Summary / 20
3. Basic Data Analysis 22
3.1 Normalization / 22
3.1.1 One or More Genes Assumed Expressed at Constant Rate / 23
3.1.2 Sum of Genes Is Assumed Constant / 24
3.1.3 Subset of Genes Is Assumed Constant / 24
3.1.4 Majority of Genes Assumed Constant / 24
3.1.5 Logit Normalization / 24
3.1.6 Spike Controls / 25
3.2 Dye Bias, Spatial Bias, Print Tip Bias / 25
3.3 Expression Indices / 26
3.3.1 Average Difference / 26
3.3.2 Signal / 26
3.3.3 Model Based Expression Index / 26
3.3.4 Robust Multiarray Average / 27
3.3.5 Position Dependent Nearest Neighbor Model / 27
3.3.6 Logit t / 27
3.4 Detection of Outliers / 28
3.5 Fold Change / 28
3.6 Significance / 29
3.6.1 Multiple Conditions / 30
3.6.2 Nonparametric Tests / 30
3.6.3 Correction for Multiple Testing / 30
3.6.4 Example I: f Test and ANOVA / 31
3.6.5 Example II: Number of Replicates / 32
3.7 Mixed Cell Populations / 33
3.8 Summary / 34
Further Reading / 34
4. Visualization by Reduction of Dimensionality 37
4.1 Principal Component Analysis / 37
4.2 Supervised Principal Component Analysis / 39
4.3 Independent Component Analysis / 39
4.4 Example I: PCA on Small Data Matrix / 39
4.5 Example II: PCA on Real Data / 41
4.6 Summary / 42
Further Reading / 42
5. Cluster Analysis 44
5.1 Hierarchical Clustering / 44
CONTENTS IX
5.2 A Means Clustering / 46
5.3 Self Organizing Maps / 46
5.4 Distance Measures / 47
5.4.1 Example: Comparison of Distance Measures / 49
5.5 Time Series Analysis / 51
5.6 Gene Normalization / 51
5.7 Visualization of Clusters / 52
5.8 Summary / 52
Further Reading / 52
6. Molecular Classifiers for Cancer 54
6.1 Supervised versus Unsupervised Analysis / 54
6.2 Feature Selection / 55
6.3 Validation / 55
6.4 Classification Schemes / 56
6.4.1 Nearest Neighbor / 56
6.4.2 Nearest Centroid / 57
6.4.3 Neural Networks / 57
6.4.4 Support Vector Machine / 58
6.5 Performance Evaluation / 58
6.6 Example I: Classification of SRBCT Cancer Subtypes / 59
6.7 A Network Approach to Molecular Classification / 59
6.7.1 Construction of HG U95Av2 Chip Based Gene Network / 61
6.7.2 Construction of HG U133A Chip Based Gene Network / 61
6.7.3 Example: Lung Cancer Classification with Mapped
Subnetwork / 61
6.7.4 Example: Brain Cancer Classification with Mapped
Subnetwork / 62
6.7.5 Example: Breast Cancer Classification with Mapped
Subnetwork / 62
6.7.6 Example: Leukemia Classification with Mapped Subnetwork / 62
6.8 Summary / 63
Further Reading / 64
7. Survival Analysis 66
7.1 Kaplan Meier Approach / 66
7.2 Cox Proportional Hazards Model / 67
7.3 Software / 68
Further Reading / 68
8. Meta Analysis 69
8.1 Gene Matching / 69
8.2 Combining Measurements / 70
8.2.1 Intensity / 70
X CONTENTS
8.2.2 Effect Size / 70
8.2.3 P Values / 70
8.2.4 Selected Features / 70
8.2.5 Vote Counting / 70
8.3 Meta Classification / 71
8.4 Summary / 71
Further Reading / 71
9. The Design of Probes for Arrays 73
9.1 Gene Finding / 73
9.2 Selection of Regions Within Genes / 74
9.3 Selection of Primers for PCR / 74
9.3.1 Example: Finding PCR Primers for Gene AF105374 / 74
9.4 Selection of Unique Oligomer Probes / 75
9.5 Remapping of Probes / 76
Further Reading / 76
10. Software Issues and Data Formats 78
10.1 Standardization Efforts / 79
10.2 Databases / 79
10.3 Standard File Format / 79
10.4 Software for Clustering / 80
10.5 Software for Statistical Analysis / 80
10.5.1 Example: Statistical Analysis with R / 80
10.5.2 The affy Package of Bioconductor / 83
10.5.3 Survival Analysis / 85
10.5.4 Commercial Statistics Packages / 85
10.6 Summary / 85
Further Reading / 85
11. Breast Cancer 87
11.1 Introduction / 87
11.1.1 Anatomy of the Breast / 87
11.1.2 Breast Tumors / 87
11.2 Current Diagnosis / 88
11.2.1 Staging / 88
11.2.2 Histopathological Grading / 89
11.2.3 Clinical Markers / 89
11.3 Current Therapy / 90
11.3.1 Surgery / 90
11.3.2 Chemotherapy / 90
11.3.3 Hormone Therapy / 90
11.3.4 Monoclonal Antibody Therapy / 90
CONTENTS XI
11.4 Microarray Studies of Breast Cancer / 90
11.4.1 The Stanford Group / 90
11.4.2 The Netherlands Cancer Institute Group / 91
11.4.3 The Duke University Group / 92
11.4.4 The Lund Group / 92
11.4.5 The Karolinska Group / 93
11.4.6 The Tokyo Group / 93
11.4.7 The Veridex Group / 93
11.4.8 The National Cancer Institute Group / 93
11.5 Meta Classification of Breast Cancer / 93
11.6 Summary / 95
Further Reading / 95
12. Leukemia 97
12.1 Current Diagnosis / 98
12.2 Current Therapy / 98
12.3 Microarray Studies of Leukemia / 99
12.3.1 The Boston Group / 99
12.3.2 The Austria Group / 99
12.3.3 The Utah Group / 99
12.3.4 The Memphis Group / 100
12.3.5 The Japan Group / 100
12.3.6 The Munich Group / 100
12.3.7 The Stanford Group / 101
12.3.8 The Copenhagen Group / 101
12.3.9 The Netherlands Group / 101
12.4 Summary / 101
Further Reading / 101
13. Lymphoma 104
13.1 Microarray Studies of Lymphoma / 105
13.1.1 The Stanford Group / 105
13.1.2 The Boston Group / 105
13.1.3 The NIH Group / 105
13.1.4 The NCI Group / 106
13.2 Meta Classification of Lymphoma / 106
13.2.1 Matching of Components / 107
13.2.2 Blind Test Set / 109
13.3 Summary / 112
Further Reading / 112
14. Lung Cancer 114
14.1 Microarray Studies of Lung Cancer / 114
14.1.1 The Harvard/Whitehead Group / 114
XH CONTENTS
14.1.2 The Minnesota Group / 116
14.1.3 The Vanderbilt Group / 116
14.1.4 The Tokyo Group / 116
14.1.5 The Michigan Group / 116
14.1.6 The Mayo Clinic / 116
14.1.7 The Toronto Group / 117
14.1.8 The NIH Group / 117
14.1.9 The Stanford Group / 117
14.1.10 The Israel Group / 117
14.2 Meta Classification of Lung Cancer / 117
14.3 Summary / 122
Further Reading / 122
15. Bladder Cancer 123
15.1 Microarray Studies of Bladder Cancer / 124
15.1.1 The Aarhus Group / 124
15.1.2 The New York Group / 125
15.1.3 The Dusseldorf Group / 125
15.2 Summary / 125
Further Reading / 125
16. Colon Cancer 127
16.1 Microarray Studies of Colon Cancer / 127
16.1.1 The Princeton Group / 127
16.1.2 The Maryland Group / 128
16.1.3 The Aarhus Group / 128
16.1.4 The Marseilles Group / 128
16.1.5 The San Diego Group / 128
16.1.6 The Helsinki Group / 129
16.2 Summary / 129
Further Reading / 129
17. Ovarian Cancer 130
17.1 Microarray Studies of Ovarian Cancer / 130
17.1.1 Duke University Medical Center / 130
17.1.2 The Stanford Group / 131
17.1.3 The London Group / 131
17.1.4 The UCLA Group / 131
17.1.5 The NIH Group / 131
17.1.6 The Novartis Group / 132
17.2 Summary / 132
Further Reading / 132
CONTENTS Xlii
18. Prostate Cancer 134
18.1 Microarray Studies of Prostate Cancer / 134
18.1.1 University of Michigan Medical School / 134
18.1.2 Memorial Sloan Kettering Cancer Center / 134
18.1.3 The NIH Group / 135
18.1.4 The Harvard Group / 135
18.1.5 The Australian Group / 135
18.1.6 The Stanford Group / 136
18.2 Summary / 136
Further Reading / 136
19. Melanoma 138
19.1 Microarray Studies of Melanoma / 138
19.1.1 Memorial Sloan Kettering Cancer Center / 138
19.1.2 The NIH Group / 138
19.2 Summary / 139
Further Reading / 139
20. Brain Tumors 142
20.1 Microarray Studies of Brain Tumors / 144
20.1.1 Harvard Medical School / 144
20.1.2 M. D. Anderson Cancer Center / 144
20.1.3 UCLA School of Medicine / 144
20.1.4 The Lausanne Group / 144
20.1.5 Deutsches Krebsforschungszentrum / 144
20.1.6 Children s Hospital, Boston / 145
20.2 Summary / 145
Further Reading / 145
21. Organ or Tissue Specific Classification 147
Further Reading / 148
22. Sample Collection and Stability 149
22.1 Tissue Samples / 149
22.1.1 Stability of Tissue After Surgical Removal / 149
22.1.2 Stability of Sample in Storage / 150
22.1.3 Paraffin Embedded Tissue Samples / 150
22.2 Blood Samples / 150
22.3 Sample Heterogeneity / 151
XIV CONTENTS
22.4 Summary / 151
Further Reading / 151
References 152
Index 183
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| id | DE-604.BV022402228 |
| illustrated | Not Illustrated |
| indexdate | 2024-12-23T20:01:48Z |
| institution | BVB |
| isbn | 0470041102 0471784079 9780470041109 9780471784074 |
| language | English |
| lccn | 2006046423 |
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| record_format | marc |
| spellingShingle | Cancer diagnostics with DNA microarrays DNA microarrays Diagnostic use Cancer Diagnosis Neoplasms diagnosis Oligonucleotide Array Sequence Analysis methods Data Interpretation, Statistical DNS-Chip (DE-588)4721796-0 gnd Krebs Medizin (DE-588)4073781-0 gnd Diagnostik (DE-588)4113303-1 gnd |
| subject_GND | (DE-588)4721796-0 (DE-588)4073781-0 (DE-588)4113303-1 |
| title | Cancer diagnostics with DNA microarrays |
| title_auth | Cancer diagnostics with DNA microarrays |
| title_exact_search | Cancer diagnostics with DNA microarrays |
| title_full | Cancer diagnostics with DNA microarrays Steen Knudsen |
| title_fullStr | Cancer diagnostics with DNA microarrays Steen Knudsen |
| title_full_unstemmed | Cancer diagnostics with DNA microarrays Steen Knudsen |
| title_short | Cancer diagnostics with DNA microarrays |
| title_sort | cancer diagnostics with dna microarrays |
| topic | DNA microarrays Diagnostic use Cancer Diagnosis Neoplasms diagnosis Oligonucleotide Array Sequence Analysis methods Data Interpretation, Statistical DNS-Chip (DE-588)4721796-0 gnd Krebs Medizin (DE-588)4073781-0 gnd Diagnostik (DE-588)4113303-1 gnd |
| topic_facet | DNA microarrays Diagnostic use Cancer Diagnosis Neoplasms diagnosis Oligonucleotide Array Sequence Analysis methods Data Interpretation, Statistical DNS-Chip Krebs Medizin Diagnostik |
| url | https://onlinelibrary.wiley.com/doi/book/10.1002/0470041102 http://www3.interscience.wiley.com/cgi-bin/bookhome/112219205 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015610849&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT knudsensteen cancerdiagnosticswithdnamicroarrays |