Microarray Innovations: Technology and Experimentation (Drug Discovery Series)

MICROARRAY INNOVATIONS: TECHNOLOGY AND EXPERIMENTATION......Page 4
Contents......Page 6
Preface......Page 8
Acknowledgments......Page 10
Editor......Page 12
Contributors......Page 14
CHAPTER 5: HOW TO EVALUATE A MICROARRAY SCANNER......Page 18
CHAPTER 9: DATA NORMALIZATION SELECTION......Page 19
CHAPTER 13: DNA METHYLATION ARRAYS: METHODS AND ANALYSIS......Page 20
CHAPTER 17: DEVELOPMENT OF AN INTEGRATED MOLECULAR DIAGNOSTIC TEST TO IDENTIFY RESPIRATORY VIRUSES......Page 21
CHAPTER 19: OPTIMIZATION OF PROTEIN ARRAY FABRICATION FOR ESTABLISHING HIGH-THROUGHPUT ULTRA-SENSITIVE MICROARRAY ASSAYS FOR CANCER RESEARCH......Page 22
1.1 INTRODUCTION......Page 24
1.2 DNA HYBRIDIZATIONS IN MICROARRAY TECHNOLOGY: SEQUENCE-SPECIFIC BINDING......Page 26
1.3 CREATING A DNA MICROARRAY......Page 27
1.4 SAMPLE PREPARATION FOR DNA MICROARRAY HYBRIDIZATION......Page 28
1.6 DNA MICROARRAY SCANNING......Page 31
REFERENCES......Page 32
2.1 INTRODUCTION......Page 34
2.2.2 CDNA MICROARRAYS......Page 35
2.3.1 QUALITY ASSESSMENT......Page 36
2.3.2 PREPROCESSING......Page 37
2.3.3 DIFFERENTIAL EXPRESSION......Page 39
2.3.4 CLUSTER ANALYSIS......Page 40
2.3.5 FUNCTIONAL ANALYSIS AND INTERPRETATION......Page 43
REFERENCES......Page 45
3.1 INTRODUCTION......Page 48
3.2.3 CONDUCT THE EXPERIMENT......Page 49
3.2.6.1 Gene Expression Profile Comparisons......Page 50
3.3 PRINCIPLES OF EXPERIMENTAL DESIGN......Page 51
3.3.4.1 Completely Randomized Design......Page 52
3.4 SAMPLE SIZE AND POWER CONSIDERATIONS......Page 53
REFERENCES......Page 54
4.1 WHY LABORATORY AUTOMATION?......Page 56
4.2.1 CONTACT PRINTING......Page 57
4.2.2 NONCONTACT PRINTING......Page 58
4.2.3 SPOT MORPHOLOGY AND PLACEMENT ISSUES......Page 59
4.4.1 TYPES OF OPTICS AND SENSORS......Page 60
4.4.4 AUTOMATION OF MICROARRAY IMAGE ANALYSIS......Page 61
4.5.1 MATERIAL HANDLING LABORATORY AUTOMATION......Page 62
REFERENCES......Page 63
5.1 INTRODUCTION......Page 64
5.2.1 INTRA-SYSTEM EVALUATION......Page 65
5.2.1.2 Scanner Uniformity......Page 66
5.2.1.3 Scanner Alignment and Focus......Page 67
5.2.1.4 Dynamic Range......Page 68
5.2.1.6 PMT Responses......Page 69
5.2.1.7 Channel Cross-Talk......Page 70
5.2.2 INTER-SYSTEM CALIBRATION......Page 71
STORAGE......Page 72
DESCRIPTION......Page 73
SPECIFICATION......Page 74
REFERENCES......Page 75
6.1 INTRODUCTION......Page 76
6.2 SLIDE PROPERTIES......Page 77
6.3 CHEMICAL COATINGS......Page 78
6.4 OPTICAL AND ANALYTICAL COATINGS......Page 80
6.5 PRACTICAL CONSIDERATIONS FOR CHOOSING THE RIGHT SUBSTRATE......Page 83
6.6 HIGH SAMPLE THROUGHPUT MICROARRAY SOLUTIONS......Page 85
6.7 SUMMARY......Page 88
REFERENCES......Page 89
7.1 INTRODUCTION......Page 94
7.2 HYBRIDIZATION SYSTEMS COMPATIBLE WITH STANDARD MICROARRAYS......Page 95
7.3 COMMERCIALLY AVAILABLE SYSTEMS......Page 96
7.4 NEXT GENERATION MICROFLUIDICS DESIGNS......Page 98
7.5.1 INTRODUCTION TO HYBRIDIZATION PROCESSES......Page 99
7.5.2 EFFECTS OF VELOCITY, MODE OF CONVECTION, AND CHANNEL DEPTH......Page 100
7.5.3 EFFECTS OF CONVECTION AND CONCENTRATION......Page 101
7.5.4 COMPARISON OF SDH WITH DIFFUSION UNDER COVERSLIP AND AUTOMATED HYBRIDIZATION......Page 102
7.5.5 SUMMARY AND DISCUSSION......Page 103
7.6 CONCLUSIONS......Page 104
7.7 MATERIALS AND METHODS......Page 105
REFERENCES......Page 107
8.1 INTRODUCTION......Page 110
8.2.1 ASSAY DESIGN......Page 111
8.2.2 MEASURING HYBRIDIZATION STOICHIOMETRY OF A REFERENCE RNA SAMPLE......Page 112
8.3 DISCUSSION......Page 115
8.4.2 CONSTRUCTION OF THE SUA......Page 116
8.4.5 HYBRIDIZATION, SCANNING, AND IMAGE ANALYSIS......Page 117
8.4.7 CALCULATION OF ARRAY FEATURES......Page 118
REFERENCES......Page 119
9.1 INTRODUCTION......Page 120
9.2 MICROARRAY EXPRESSION PLATFORMS......Page 121
9.3 EXPRESSION PLATFORM TYPES......Page 122
9.4 SEVERAL ALTERNATIVE GLASS-SUBSTRATE EXPRESSION TECHNOLOGIES......Page 124
9.5 RNA DEGRADATION NORMALIZATION......Page 125
9.6 NORMALIZATION METHODS: HISTORY......Page 126
9.7.3 DCHIP......Page 127
9.7.7 OTHERS......Page 128
9.9 CROSS-PLATFORM COMPARISONS: EXPERIMENTAL DESIGN......Page 129
9.10 STATISTICAL MEASURE OF MICROARRAY VARIABILITY......Page 130
9.11 DISCUSSION......Page 131
REFERENCES......Page 137
10.1 INTRODUCTION......Page 142
10.3 HOW WE CHARACTERIZE MICROARRAYS: THE FOUR BASIC TESTS......Page 143
10.3.1 SPIKING EXPERIMENTS: LIMIT OF DETECTION, PRECISION, AND DYNAMIC RANGE......Page 144
10.3.5 CONCORDANCE OF RESULTS BETWEEN ORTHOGONAL TECHNOLOGIES......Page 145
10.5 CONCLUSION......Page 147
REFERENCES......Page 148
CONTENTS......Page 150
11.1 INTRODUCTION......Page 151
11.2.2 SIGNAL DETECTION......Page 152
11.2.4 FOLD-CHANGE CONCORDANCE WITH TAQMAN ASSAYS......Page 154
11.2.5 DIFFERENTIALLY EXPRESSED GENES......Page 158
11.2.6 REPRODUCIBILITY OF DIFFERENTIALLY EXPRESSED GENE LISTS......Page 159
11.3 DISCUSSION......Page 162
11.4.3.1 TaqMan Assays......Page 163
11.4.6 SIGNAL DETECTION ANALYSIS......Page 164
REFERENCES......Page 165
CONTENTS......Page 168
12.1 INTRODUCTION......Page 169
12.2.3.1.1 Probe Labeling, Hybridization, and Scanning......Page 171
12.2.3.2.2 Purification of cRNA......Page 173
12.2.3.4 cDNA......Page 174
12.2.3.7 Mergen......Page 175
12.3 DATA ANALYSIS: DATA ACQUISITION......Page 176
12.3.2 GENE MATCHING ACROSS DIFFERENT PLATFORMS......Page 177
12.3.3 EVALUATION OF INTRA- AND INTER-PLATFORM DATA CONSISTENCY......Page 178
12.4.1 ROCHE UNIVERSAL PROBELIBRARY......Page 179
12.5.1 MAGNITUDE OF THE RELATIVE MEASUREMENTS......Page 183
12.5.3 CONSISTENCY ACROSS PLATFORMS......Page 184
12.5.5 MAPPING OF PROBE SEQUENCES TO EXON POSITIONS......Page 185
12.5.6 QUANTITATIVE BIOLOGICAL VALIDATIONS......Page 188
12.6 DISCUSSION AND FUTURE WORK......Page 189
REFERENCES......Page 193
CONTENTS......Page 198
13.2 MAMMALIAN DNA METHYLATION......Page 199
13.2.1 MEASURING DNA METHYLATION......Page 201
13.3.1 WHAT SAMPLES TO HYBRIDIZE?......Page 202
13.3.2 OTHER EXPERIMENTAL DESIGN ISSUES......Page 203
13.4.2 METHYLATION-SENSITIVE/DEPENDENT DIGESTION WITH PCR ENRICHMENT......Page 205
13.4.3.1 Enrichment of Consecutive Methylated Sites......Page 207
13.4.5 METHYL ANTIBODY APPROACH......Page 209
13.4.6 DETECTING METHYLATED DNA BY METHYL-CPG BINDING DOMAIN PROTEINS AFFINITY PURIFICATION......Page 212
13.4.7 ARRAYS FOR BISULFITE-TREATED DNA......Page 213
13.5 ARRAY CHOICES......Page 214
13.6.1 NORMALIZATION ISSUES......Page 215
13.6.2 NORMALIZATION OPTIONS......Page 217
13.6.3 QUALITY ASSESSMENT OF DNA METHYLATION ARRAYS......Page 218
13.6.4.1 Calling Methylation within an Array......Page 219
13.7 ENZYME APPROACHES AND GENOMIC COPY NUMBER EFFECT......Page 221
13.8.1 BISULFITE SEQUENCING......Page 222
13.8.3 COMBINED BISULFITE RESTRICTION ANALYSIS......Page 223
13.9 CONCLUSIONS......Page 224
REFERENCES......Page 225
14.1 INTRODUCTION......Page 230
14.2.1 ELECTROPHORESIS ON THE MICROSCALE......Page 231
14.2.2 ELECTROCHEMISTRY ON THE WORKING ELECTRODE......Page 233
14.2.3 FUNCTIONAL HYDROGEL PERMEATION LAYERS......Page 235
14.2.4 HARDWARE......Page 237
14.3 OPEN PLATFORM ELECTRONIC MICROARRAYS......Page 239
14.4.1 ELECTRONIC CAPTURE LOADING......Page 240
14.5.1 TARGET DETECTION: CAP/SEPSIS ASSAY......Page 241
14.5.2 PHARMACOGENOMICS: RESEARCH ASSAY FOR DRD2 MUTANTS......Page 243
14.5.3 ON-CHIP AMPLIFICATION: AMPLIFICATION AND DETECTION OF STX......Page 244
14.6 SUMMARY......Page 245
REFERENCES......Page 246
15.1 INTRODUCTION......Page 248
15.2 USING MICROARRAYS TO COMPARE GENOMIC DNA SAMPLES......Page 249
15.2.2 DNA LABELING......Page 250
15.2.2.3 Purification and Assessing Labeling Efficiency......Page 251
15.3 USING MICROARRAYS FOR GLOBAL EXPRESSION PROFILING OF miRNAs......Page 254
15.3.1 PURIFICATION OF miRNAS......Page 255
15.3.3 MICROARRAY PROBE CONTENT......Page 256
15.3.4 AMPLIFICATION OF miRNAs IN SMALL SAMPLES......Page 259
15.4 VALIDATION OF MICROARRAY RESULTS......Page 261
ACKNOWLEDGMENTS......Page 262
REFERENCES......Page 263
CONTENTS......Page 266
16.1.1 OLIGONUCLEOTIDE MICROARRAYS FOR MUTATIONAL ANALYSIS......Page 267
16.1.2 PRINCIPLE OF CDH......Page 268
16.2.1 OLIGONUCLEOTIDE DESIGN, SYNTHESIS, AND QUALITY CONTROL......Page 270
16.2.1.1 Quality Control of Oligonucleotides by DHPLC (WAVE®)......Page 271
16.3.1 OLIGONUCLEOTIDE SPOTTING......Page 272
16.4.1.1 Single Sample Hybridization (Non-CDH)......Page 273
16.4.3.1 Single Sample Hybridization (Non-CDH)......Page 274
16.4.5.1 Non-CDH......Page 275
16.5.1 SLIDE PRETREATMENT......Page 276
16.5.4.1 Protocol 4.1: Pretreatment of Slides......Page 277
16.6.2 DETERMINATION OF MUTATIONS (M/W RATIO)......Page 278
16.6.3.1 M/W Ratio Determination......Page 279
REFERENCES......Page 280
17.1 INTRODUCTION......Page 282
17.1.3 CURRENT TESTS AVAILABLE......Page 283
17.2.2 COMPLETE DESCRIPTION......Page 284
17.3.1 REQUIREMENTS OF THE ASSAY......Page 285
17.3.4 SEQUENCES USED FOR DESIGN......Page 286
17.3.7 PRIMER DESIGN......Page 287
17.4.1 ABOUT VALIDATION......Page 288
17.4.3 MULTIPLEX PCR VALIDATION......Page 289
17.4.4 PRIMER EXTENSION VALIDATION......Page 290
REFERENCES......Page 291
18.1 INTRODUCTION......Page 294
18.2.1 DESIGNING THE MICROARRAY EXPERIMENT......Page 295
18.2.2 TISSUE PRESERVATION AND POSTMORTEM BRAIN......Page 297
18.2.3 SAMPLE COLLECTION......Page 298
18.2.5 RNA AMPLIFICATION......Page 300
18.2.6.2 Quantitative RT-PCR......Page 301
18.3 DATA ANALYSIS......Page 302
18.4 MICROARRAY-BASED STUDIES OF NEUROLOGICAL AND PSYCHIATRIC DISORDERS......Page 303
REFERENCES......Page 305
19.1 INTRODUCTION......Page 312
19.2 TECHNICAL CHALLENGES FOR OPTIMIZING ANTIBODY ASSAYS FOR ONCOLOGY DIAGNOSTIC APPLICATIONS......Page 313
19.3 ENSURING ACCURATE SPOTTING IN THE ARRAY FABRICATION PROCESS......Page 314
19.4 SPOTTING BUFFER OPTIMIZATION......Page 316
19.5 DISPENSE PARAMETER OPTIMIZATION......Page 318
19.6 APPLICATION OF SURFACE PLASMON RESONANCE TO MEASURE ANTIBODY-BINDING KINETICS......Page 319
19.7 IMPLEMENTING OPTIMIZED ARRAY FABRICATION FOR ULTRASENSITIVE PROTEIN ARRAY ASSAYS......Page 320
REFERENCES......Page 321
Color Insert......Page 323