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This is a Template course for Meta-data XML
1.Genotyping: principle, technology. application, and practice
2.¡§Genotype¡¨ vs ¡§Phenotype¡¨
3.slide 3
4.slide 4
5.slide 5
6.What is STRP?
7.Characteristics of STRP
8.Application of STRP
9.slide 9
10.Instrument
11.Pooling PCR Product
12.Instrument
13.Electrophoresis Analysis
14.Softwares
15.Size Calling
16.Allele Calling
17.Results of STRP genotyping
18.Genotyping Quality Control
19.slide 19
20.What is a SNP?
21.slide 21
22.slide 22
23.Features of Single Nucleotide Polymorphisms (SNPs)
24.Application of SNP
25.SNP genotyping
26.Genome-wide Linkage Analysis
27.Disease Gene Mapping
28.What is ¡§Haplotype¡¨?
29.International Haplotype Mapping (HapMap) Project
30.International Haplotype Mapping (HapMap) Project
31.slide 31
32.Cost and throughput consideration for genome-wide association study using SNP markers
28.What is ¡§Haplotype¡¨?
29.International Haplotype Mapping (HapMap) Project
30.International Haplotype Mapping (HapMap) Project
31.slide 31
32.Cost and throughput consideration for genome-wide association study using SNP markers
33.Factors in SNPs Technology Platforms Consideration
34.slide 34
33.Factors in SNPs Technology Platforms Consideration
34.slide 34
35.Target fragment amplification
36.slide 36
37.Allele discrimination based on DNA polymerases
38.Single-base extension
39.Allele-specific extension (ASE) and allele-specific PCR (AS-PCR)
40.Synchronized DNA synthesis - pyrosequencing
41.slide 41
42.Structure specific cleavage ¡V the Invader assay
43.slide 43
44.The 5¡¦ exonucleae activity ¡VTaqMan assay
45.slide 45
46.Allelic discrimination based on DNA ligases
47.slide 47
48.Allelic Discrimination based on Hybridization
49.slide 49
50.Mechanisms for product detection and identification
51.Fluorescent resonance energy transfer (FRET)
52.Strategies for FRET detection
53.FRET detection
54.FRET utilized SNP genotyping technologies
55.Identification of products by mass spectrometry
55.Identification of products by mass spectrometry
56.Microarray as supporter for genotyping
57.Fluorescent coded microbeads as supporters
58.Separation of products by electrophoresis
59.slide 59
60.slide 60
61.Cost structure of SNP genotyping
62.slide 62
63.MassARRAY Genotyping Platfrom  Utilizing MALDI-TOF Mass Spectrometer
64.slide 64
65.MassARRAY process
64.slide 64
65.MassARRAY process
66.slide 66
67.slide 67
68.Mass Spectrometry for Analysis and Scoring
69.MassEXTEND Reaction
70.Multiplex Analysis: 5-plex
69.MassEXTEND Reaction
70.Multiplex Analysis: 5-plex
71.slide 71
70.Multiplex Analysis: 5-plex
69.MassEXTEND Reaction
70.Multiplex Analysis: 5-plex
71.slide 71
72.slide 72
73.slide 73
72.slide 72
73.slide 73
74.slide 74
75.slide 75
76.Cost and Time for Case/Control Study: Conventional Technology
77.slide 77
78.slide 78
79.¡§Bead-Array¡¨ System Genotyping Platfrom
80.slide 80
81.slide 81
82.slide 82
83.slide 83
84.slide 84
83.slide 83
84.slide 84
83.slide 83
84.slide 84
85.slide 85
86.slide 86
87.slide 87
88.slide 88
89.slide 89
90.slide 90
91.slide 91
92.slide 92
93.Genome-wide Linkage Analysis
94.slide 94
95.slide 95
96.slide 96
97.slide 97
98.slide 98
99.slide 99
100.slide 100
101.slide 101
102.slide 102
103.slide 103
104.slide 104
105.slide 105
106.Affymetrix GeneChip SNP Genotyping Platform
107.Affymetrix Platform
108.slide 108
109.slide 109
110.slide 110
111.slide 111
112.slide 112
113.slide 113
114.slide 114
115.slide 115
116.slide 116
117.slide 117
118.slide 118
119.slide 119
120.slide 120
119.slide 119
120.slide 120
121.slide 121
122.slide 122
123.Affymetrix Platform
124.SNPlex Overview
125.SNPlex OLA/PCR Assay
126.slide 126
127.Detection
128.Universal Drag Chute
129.SNPlex 30-plex assay (48-plex capable)
130.Comparison between GeneChip and Bead-Array SNP genotyping
131.Could the high-density SNP panels be used in the case/control association studies?
132.slide 132
133.Incidence and Epidemiology of Stevens-Johnson Syndrome
134.slide 134
135.slide 135
136.Genome-wide scan approach with 100,000 SNP markers
137.Call Rate
138.Call Rates at NGC
139.Call Rate
140.Call Rate
141.Minor Allele Frequency
142.Allele 1 Frequency
143.Allele 1 Frequency
144.Allele 1 Frequency
145.Allele 1 Frequency
146.Allele 1 Frequency
147.Allele 1 Frequency
148.slide 148
149.Allele 1 Frequency
150.Allele 1 Frequency
151.Allele 1 Frequency
152.Heterozygosity
153.Test of HWE Proportion
154.Test of Allele Type Association
155.slide 155
156.Affymetrix Platform - Summary
157.Challenge of ultra-high throughput SNP genotyping