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58. Mani RS, Tomlins SA, Callahan K, Ghosh A, Nyati MK, Varambally S, Palanisamy N, Chinnaiyan AM: Induced chromosomal proximity and gene fusions in prostate cancer. Science 2009, 326(5957):1230. 59. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R et al: Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310(5748):644-648. 60. Dang TP, Gazdar AF, Virmani AK, Sepetavec T, Hande KR, Minna JD, Roberts JR, Carbone DP: Chromosome 19 translocation, overexpression of Notch3, and human lung cancer. J Natl Cancer Inst 2000, 92(16):1355-1357. 61. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, Fujiwara S, Watanabe H, Kurashina K, Hatanaka H et al: Identification of the transforming EML4- ALK fusion gene in non-small-cell lung cancer. Nature 2007, 448(7153):561-566. 62. Knutsen T, Gobu V, Knaus R, Padilla-Nash H, Augustus M, Strausberg RL, Kirsch IR, Sirotkin K, Ried T: The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer 2005, 44(1):52-64. 63. Albertson DG, Collins C, McCormick F, Gray JW: Chromosome aberrations in solid tumors. Nat Genet 2003, 34(4):369-376. 64. Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL: Resolving the resolution of array CGH. Genomics 2007, 89(5):647-653. 65. Lockwood WW, Chari R, Chi B, Lam WL: Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 2006, 14(2):139-148. 66. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999, 23(1):41-46. 67. Almagro-Garcia J, Manske M, Carret C, Campino S, Auburn S, Macinnis BL, Maslen G, Pain A, Newbold CI, Kwiatkowski DP et al: SnoopCGH: software for visualizing comparative genomic hybridization data. Bioinformatics 2009, 25(20):2732-2733. 68. Chari R, Lockwood WW, Lam WL: Computational methods for the analysis of array comparative genomic hybridization. Cancer Inform 2007, 2:48-58. 69. Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL: SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics 2004, 5:13. 70. Chi B, deLeeuw RJ, Coe BP, Ng RT, MacAulay C, Lam WL: MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics 2008, 9:243. 71. Venkatraman ES, Olshen AB: A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007, 23(6):657-663. 72. Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR et al: High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004, 14(2):287-295. 73. Iacobucci I, Storlazzi CT, Cilloni D, Lonetti A, Ottaviani E, Soverini S, Astolfi A, Chiaretti S, Vitale A, Messa F et al: Identification and molecular characterization of recurrent genomic deletions on 7p12 in the IKZF1 gene in a large cohort of BCR-ABL1positive acute lymphoblastic leukemia patients: on behalf of Gruppo Italiano Malattie Ematologiche dell'Adulto Acute Leukemia Working Party (GIMEMA AL WP). Blood 2009, 114(10):2159-2167. 74. Niini T, Lopez-Guerrero JA, Ninomiya S, Guled M, Hattinger CM, Michelacci F, Bohling T, Llombart-Bosch A, Picci P, Serra M et al: Frequent deletion of CDKN2A and recurrent coamplification of KIT, PDGFRA, and KDR in fibrosarcoma of bone-An array comparative genomic hybridization study. Genes Chromosomes Cancer 2010, 49(2):132-143. 147
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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
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screening approach to gene amplific
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many regions of frequent LOH/AI do
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approach to examining the whole gen
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PTEN expression [44]. Using this pa
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mechanisms at the DNA and RNA level
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In this study, three DNA dimensions
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Figure 3.2. Quantitative and qualit
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Figure 3.3 a Proportion of genes in
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70 Figure 3.5 -log(pvalue) 5.0 4.0
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72 Figure 3.7 Sample: HCC1008 Copy
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Figure 3.8 a b Proportion of random
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16. Chari R, Lockwood WW, Coe BP, C
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50. Giovane A, Pintzas A, Maira SM,
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4.1 Introduction Genetic alteration
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4.2.3 Determining frequent regions
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etween loss and UPD (Figure 4.3). S
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obtained, profiled and used as the
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Figure 4.1. Detection of UPD using
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Figure 4.2. Comparison of frequent
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Figure 4.3 Gain Loss 642 441 7 Figu
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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 and 120: Table 4.5. Cell lines and oncogene
Page 121 and 122: Table 4.7. RefSeq genes in focal re
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: 37. Oliphant A, Barker DL, Stuelpna
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
Page 171 and 172: alterations in human prostate cance
Page 173 and 174: 248. Xi L, Feber A, Gupta V, Wu M,
Page 175 and 176: 281. Fernandez-Ranvier GG, Weng J,
Page 177 and 178: Chapter 6: Conclusions 162
Page 179 and 180: can identify nearly three times as
Page 181 and 182: was identified in a small set of sa
Page 183 and 184: will be done at the pathway level a
Page 185 and 186: previously described genetic and ep
Page 187 and 188: 16. Zhang K, Li JB, Gao Y, Egli D,
Page 189 and 190: APPENDIX I: List of publications Th
Page 191 and 192: This publication is described in se
Page 193 and 194: This chapter details the technologi
Page 195 and 196: epigenetic alteration. This led to
Page 197 and 198: This manuscript describes the curre
Page 199 and 200: APPENDIX III: Sources of data Sampl
Page 201 and 202: APPENDIX V: Kaplan-Meier and Oncomi
Page 203 and 204: APPENDIX VI: Summary of Kaplan-Meie
Page 205: University of British Columbia - Br
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