Chapter 2 - University of British Columbia
Chapter 2 - University of British Columbia
Chapter 2 - University of British Columbia
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Table <strong>of</strong> Contents<br />
Abstract ......................................................................................................................................... ii<br />
Table <strong>of</strong> Contents ......................................................................................................................... iii<br />
List <strong>of</strong> Tables ............................................................................................................................... vii<br />
List <strong>of</strong> Figures ............................................................................................................................. viii<br />
List <strong>of</strong> Abbreviations ...................................................................................................................... x<br />
Acknowledgements ..................................................................................................................... xii<br />
Dedication ................................................................................................................................... xiii<br />
Co-Authorship Statement ........................................................................................................... xiv<br />
<strong>Chapter</strong> 1: Introduction ................................................................................................................. 1<br />
1.1 Lung cancer ......................................................................................................................... 2<br />
1.2 Genomic pr<strong>of</strong>iling <strong>of</strong> lung cancer ......................................................................................... 3<br />
1.2.1 Gene expression analysis ............................................................................................. 3<br />
1.2.2 DNA copy number analysis .......................................................................................... 4<br />
1.2.3 Loss <strong>of</strong> heterozygosity (LOH) and allelic imbalance ..................................................... 5<br />
1.3 Somatic mutations in lung cancer ....................................................................................... 5<br />
1.4 Epigenetic alterations in lung cancer ................................................................................... 6<br />
1.4.1 DNA methylation ........................................................................................................... 6<br />
1.5 Current level <strong>of</strong> integrative analysis .................................................................................... 7<br />
1.6 Need for an integrative approach to study lung cancer ....................................................... 7<br />
1.7 Bioinformatic tools for genomic analysis ............................................................................. 8<br />
1.8 Thesis theme ....................................................................................................................... 9<br />
1.9 Objectives and hypothesis .................................................................................................. 9<br />
1.10 Specific aims and outline <strong>of</strong> thesis .................................................................................. 10<br />
1.11 Description <strong>of</strong> high throughput data in this thesis ............................................................ 13<br />
1.12 Other relevant contributions not included as chapters in this thesis ............................... 13<br />
1.12.1 Development <strong>of</strong> tools for genomic analysis .............................................................. 14<br />
1.12.2 Baseline gene expression in non-malignant lung tissue ........................................... 14<br />
1.12.3 Differential gene expression analysis in lung cancer ................................................ 15<br />
1.12.4 Integration <strong>of</strong> gene dosage and gene expression in lung cancer ............................. 16<br />
1.13 References ...................................................................................................................... 18<br />
iii