Chapter 2 - University of British Columbia

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Table 4.6. Summary of homozygous mutation analysis in cancer cell lines Gene # of Hz mutations # UPD # Gain # Loss # Neutral KRAS 33 10 18 4 1 BRAF 11 4 6 1 0 NRAS 5 1 3 1 0 PIK3CA 4 1 2 1 0 CTNNB1 3 2 0 1 0 HRAS 3 2 1 0 0 EGFR 2 1 1 0 0 NOTCH1 2 0 1 1 0 FGFR3 1 0 1 0 0 JAK2 1 0 1 0 0 ERBB2 1 1 0 0 0 RUNX1 1 1 0 0 0 Total 67 23 34 9 1 105
Table 4.7. RefSeq genes in focal regions of UPD Gene Symbol Chr Gene Symbol Chr DAB1 1 TNFAIP8 5 IL1R1 2 ZNF608 5 IL1RL2 2 E2F3 6 GPR39 2 ID4 6 EPC2 2 MBOAT1 6 KIF5C 2 B3GAT2 6 MBD5 2 C6orf191 6 OSBPL6 2 IMMP2L 7 RBM45 2 LRRN3 7 CUL3 2 GRM8 7 DOCK10 2 ODZ4 11 FAM124B 2 CASP4 11 FRG2C 3 DDI1 11 ZNF717 3 PDGFD 11 COL29A1 3 CADM1 11 COL6A6 3 HNT 11 LPHN3 4 OPCML 11 ANTXR2 4 ANO2 12 FGF5 4 KCNA5 12 PRDM8 4 NTF3 12 ADH5 4 AEBP2 12 EIF4E 4 PLEKHA5 12 METAP1 4 ALG10B 12 SLC7A11 4 CPNE8 12 ARRDC3 5 KIF21A 12 CHD1 5 TMEM132B 12 RGMB 5 FZD10 12 FBXL17 5 ZNF10 12 FER 5 ZNF140 12 PJA2 5 ZNF268 12 KCNN2 5 ATP10A 15 DMXL1 5 PLCB1 20 106
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DEVELOPMENT AND APPLICATION OF AN I
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Table of Contents Abstract ........
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3.3.2 Multi-dimensional analysis (M
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List of Tables Table 2.1. Features
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Figure 5.3. Overlay of chromosomal
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RB1 Retinoblastoma 1 RNA Ribonuclei
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Dedication To my family. xiii
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Chapter 5: Chari R, Thu KL, Wilson
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1.1 Lung cancer Lung cancer has the
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expression changes are reactive to
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number of different cancer types. M
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large number of tumors, that a give
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(B) By using an integrative approac
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platforms, with one of the latest s
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1.12.1 Development of tools for gen
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quantitative PCR experiments as wel
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1.13 References 1. Jemal A, Siegel
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33. Garber ME, Troyanskaya OG, Schl
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71. Shivapurkar N, Gazdar AF: DNA M
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Chapter 2: SIGMA 2 : A system for t
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Here, we present SIGMA 2 , a novel
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datasets. To utilize this, the user
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2.3.7 Analysis of data from multipl
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expression (Figure 2.8). ERBB2 has
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Figure 2.1 R -Segmentation -Statist
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Figure 2.3 numSamples
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Figure 2.5. Consensus calling and h
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Figure 2.6 HCC2218 HCC2218 HCC2218B
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Figure 2.8. Multi-dimensional persp
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Table 2.1. Features required for in
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2.6 References 1. Garnis C, Buys TP
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Chapter 3: An integrative multi-dim
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observed gene expression deregulati
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Raw gene expression profiles from a
Page 69 and 70: screening approach to gene amplific
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Page 75 and 76: PTEN expression [44]. Using this pa
Page 77 and 78: mechanisms at the DNA and RNA level
Page 79 and 80: In this study, three DNA dimensions
Page 81 and 82: Figure 3.2. Quantitative and qualit
Page 83 and 84: Figure 3.3 a Proportion of genes in
Page 85 and 86: 70 Figure 3.5 -log(pvalue) 5.0 4.0
Page 87 and 88: 72 Figure 3.7 Sample: HCC1008 Copy
Page 89 and 90: Figure 3.8 a b Proportion of random
Page 91 and 92: 16. Chari R, Lockwood WW, Coe BP, C
Page 93 and 94: 50. Giovane A, Pintzas A, Maira SM,
Page 95 and 96: 4.1 Introduction Genetic alteration
Page 97 and 98: 4.2.3 Determining frequent regions
Page 99 and 100: etween loss and UPD (Figure 4.3). S
Page 101 and 102: obtained, profiled and used as the
Page 103 and 104: Figure 4.1. Detection of UPD using
Page 105 and 106: Figure 4.2. Comparison of frequent
Page 107 and 108: Figure 4.3 Gain Loss 642 441 7 Figu
Page 109 and 110: 94 Figure 4.4 1 2 3 4 5 6 7 8 9 10
Page 111 and 112: Figure 4.6 a b c Percent of cases A
Page 113 and 114: Figure 4.7 a b 6p25.3 Log2 fold cha
Page 115 and 116: Chr BPStart BPEnd # of Chr BPStart
Page 117 and 118: Table 4.3. Overlap of oncogenes in
Page 119: Table 4.5. Cell lines and oncogene
Page 123 and 124: 4.6 References 1. Bell DW: Our chan
Page 125 and 126: 33. Garnis C, Coe BP, Lam SL, MacAu
Page 127 and 128: 5.1 Introduction In the past decade
Page 129 and 130: polymorphism (SNP) arrays with over
Page 131 and 132: substitutions) and UV exposure (C t
Page 133 and 134: developed antibodies and methylated
Page 135 and 136: Histone modification states. While
Page 137 and 138: metastasis [226]. High throughput a
Page 139 and 140: Implications on sample size require
Page 141 and 142: analyzed using the "minet" package
Page 143 and 144: expression. The next challenge is t
Page 145 and 146: Figure 5.2 # of copies Total copy n
Page 147 and 148: Figure 5.4. Integration of copy num
Page 149 and 150: Figure 5.5. Integration of copy num
Page 151 and 152: Figure 5.6 SHC1 GRB2 SOS2 RRAS ER R
Page 153 and 154: Figure 5.8 a Log2 Fold Change (T vs
Page 155 and 156: Figure 5.10 (a) (b) Figure 5.10. Au
Page 157 and 158: Table 5.2. List of genomic resource
Page 159 and 160: 5.5 References 1. Pinkel D, Segrave
Page 161 and 162: 37. Oliphant A, Barker DL, Stuelpna
Page 163 and 164: 75. Selzer RR, Richmond TA, Pofahl
Page 165 and 166: 111. Melcher R, Al-Taie O, Kudlich
Page 167 and 168: 145. Takai D, Yagi Y, Wakazono K, O
Page 169 and 170: 179. Kondo M, Suzuki H, Ueda R, Osa
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alterations in human prostate cance
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248. Xi L, Feber A, Gupta V, Wu M,
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281. Fernandez-Ranvier GG, Weng J,
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Chapter 6: Conclusions 162
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can identify nearly three times as
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was identified in a small set of sa
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will be done at the pathway level a
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previously described genetic and ep
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16. Zhang K, Li JB, Gao Y, Egli D,
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APPENDIX I: List of publications Th
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This publication is described in se
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This chapter details the technologi
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epigenetic alteration. This led to
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This manuscript describes the curre
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APPENDIX III: Sources of data Sampl
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APPENDIX V: Kaplan-Meier and Oncomi
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APPENDIX VI: Summary of Kaplan-Meie
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University of British Columbia - Br
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