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Date:6/12/2011

10 EPIGENOMICS WITHIN THE MOLECULAR BIOLOGY PARADIGM 53

DNA Methylation 53

FIGURE 11 EPIGENETIC CHANGES TO DNA AFFECT GENE EXPRESSION 54

Histones 54

FIGURE 12 HISTONE TAIL REGIONS MODIFIED BY HAT AND HDAC 55

DNA Methylation and Histone Analysis Workflow 56

FIGURE 13 UPSTREAM AND DOWNSTREAM STEPS IN EPIGENETIC ANALYSIS 57

DNA Methylation Microarrays 57

ChIP-on-Chip 58

TABLE 24 CHIP ASSAYS 59

TABLE 25 TECHNOLOGIES FOR MAPPING GENOMIC LOCATION OF CHROMATIN PROTEINS AND ENZYMES 60

TABLE 26 PLATFORMS FOR HIGH DENSITY OLIGONUCLEOTIDE EPIGENETICS ARRAYS 61

Cytogenetic Analysis 61

TABLE 27 COMPARISON OF CHROMOSOMAL CHANGE DETECTION TECHNOLOGIES 62

FIGURE 14 COMPETITIVE SPACE FOR CNV ANALYSIS 63

Cytogenetic Analysis (Continued) 64

TABLE 28 CGH MICROARRAY PROBE PLATFORMS 65

TABLE 29 CGH MICROARRAY TRENDS 66

Cytogenetic Analysis (Continued) 67

TABLE 30 FUTURE TECHNOLOGY NEEDS FOR CGH MICROARRAYS 68

miRNA Analysis 69

TABLE 31 WORKFLOW FOR AN MIRNA EXPERIMENT 70

TABLE 32 TECHNICAL CHALLENGES FOR MIRNAS 71

ARRAYS ON BEADS 72

TABLE 33 ARRAYS ON BEADS VERSUS PLANAR MICROARRAYS 72

CATALOG AND CUSTOM DNA MICROARRAYS 72

SUPPLY OF REAGENTS AND SAMPLE PREPARATION FOR MICROARRAYS 73

TOXICOGENOMICS 74

DNA SEQUENCING 75

FIGURE 15 COMPARISON OF SANGER WITH UHTS DNA SEQUENCING TECHNOLOGIES 76

TABLE 34 SMS TECHNOLOGY 77

TABLE 35 COMPARISON OF SELECTED DNA SEQUENCING PLATFORMS 78

FIGURE 16 COMPETITIVE SPACE FOR HIGH-THROUGHPUT GENOMIC ANALYSIS 79

TABLE 36 BIOCHIP CONTENT IN NHGRI GRANTEES FOR NEXT-GENERATION DNA SEQUENCING, 2005 80

TABLE 36 (CONTINUED) 81

TABLE 37 NEXT-GENERATION DNA SEQUENCING COMPANIES 82

RESEQUENCING APPROACHES IN
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SOURCE S OF COMPETITIVE ADVANTAGE IN DNA MICROARRAYS 265
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