Chapter 2 - University of British Columbia

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List <strong>of</strong> Abbreviations Abbreviation Definition AC Adenocarcinoma ASCN Allele specific copy number BRAF v-raf murine sarcoma viral oncogene homolog B1 CDKN2A Cyclin-dependent kinase inhibitor 2A CGH Comparative Genomic Hybridization CNV Copy number variation DNA Deoxyribonucleic Acid EGFR Epidermal Growth Factor Receptor FISH Fluorescence in-situ hybridization GWAS Genome wide association studies KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene LOH Loss <strong>of</strong> Heterozygosity MASI Mutant allele specific imbalance MCD Multiple Concerted Disruption MDA Multi-Dimensional Analysis MUC1 Mucin 1 NSCLC Non-small cell lung cancer PCR Polymerase Chain Reaction qPCR Quantitative PCR x
RB1 Retinoblastoma 1 RNA Ribonucleic Acid RRM2 Ribonucleotide Reductase Subunit M2 SIGMA System for integrative genomic microarray analysis SIGMA2 System for integrative genomic multi-dimensional analysis SIRPA Signal Regulatory Protein Alpha SKY Spectral karyotyping SNP Single nucleotide polymorphism TUSC3 Tumor suppressor candidate 3 UPD Uniparental Disomy xi
Page 1 and 2: DEVELOPMENT AND APPLICATION OF AN I
Page 3 and 4: Table of Contents Abstract ........
Page 5 and 6: 3.3.2 Multi-dimensional analysis (M
Page 7 and 8: List of Tables Table 2.1. Features
Page 9: Figure 5.3. Overlay of chromosomal
Page 13 and 14: Dedication To my family. xiii
Page 15 and 16: Chapter 5: Chari R, Thu KL, Wilson
Page 17 and 18: 1.1 Lung cancer Lung cancer has the
Page 19 and 20: expression changes are reactive to
Page 21 and 22: number of different cancer types. M
Page 23 and 24: large number of tumors, that a give
Page 25 and 26: (B) By using an integrative approac
Page 27 and 28: platforms, with one of the latest s
Page 29 and 30: 1.12.1 Development of tools for gen
Page 31 and 32: quantitative PCR experiments as wel
Page 33 and 34: 1.13 References 1. Jemal A, Siegel
Page 35 and 36: 33. Garber ME, Troyanskaya OG, Schl
Page 37 and 38: 71. Shivapurkar N, Gazdar AF: DNA M
Page 39 and 40: Chapter 2: SIGMA 2 : A system for t
Page 41 and 42: Here, we present SIGMA 2 , a novel
Page 43 and 44: datasets. To utilize this, the user
Page 45 and 46: 2.3.7 Analysis of data from multipl
Page 47 and 48: expression (Figure 2.8). ERBB2 has
Page 49 and 50: Figure 2.1 R -Segmentation -Statist
Page 51 and 52: Figure 2.3 numSamples
Page 53 and 54: Figure 2.5. Consensus calling and h
Page 55 and 56: Figure 2.6 HCC2218 HCC2218 HCC2218B
Page 57 and 58: Figure 2.8. Multi-dimensional persp
Page 59 and 60: Table 2.1. Features required for in
Page 61 and 62:
2.6 References 1. Garnis C, Buys TP
Page 63 and 64:
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
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Figure 4.6 a b c Percent of cases A
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Figure 4.7 a b 6p25.3 Log2 fold cha
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Chr BPStart BPEnd # of Chr BPStart
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Table 4.3. Overlap of oncogenes in
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Table 4.5. Cell lines and oncogene
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Table 4.7. RefSeq genes in focal re
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4.6 References 1. Bell DW: Our chan
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33. Garnis C, Coe BP, Lam SL, MacAu
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5.1 Introduction In the past decade
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polymorphism (SNP) arrays with over
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substitutions) and UV exposure (C t
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developed antibodies and methylated
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Histone modification states. While
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metastasis [226]. High throughput a
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Implications on sample size require
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analyzed using the "minet" package
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expression. The next challenge is t
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Figure 5.2 # of copies Total copy n
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Figure 5.4. Integration of copy num
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Figure 5.5. Integration of copy num
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Figure 5.6 SHC1 GRB2 SOS2 RRAS ER R
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Figure 5.8 a Log2 Fold Change (T vs
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Figure 5.10 (a) (b) Figure 5.10. Au
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Table 5.2. List of genomic resource
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5.5 References 1. Pinkel D, Segrave
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37. Oliphant A, Barker DL, Stuelpna
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75. Selzer RR, Richmond TA, Pofahl
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111. Melcher R, Al-Taie O, Kudlich
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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
Page 205:
University of British Columbia - Br
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Chapter 2 - University of British Columbia

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