Chapter 2 - University of British Columbia

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APPENDIX VII: Copy of UBC Research Ethics Board certificate of approval 189
University of British Columbia - British Columbia Cancer Agency Research Ethics Board (UBC BCCA REB) UBC BCCA Research Ethics Board Fairmont Medical Building (6th Floor) 614 - 750 West Broadway Vancouver, BC V5Z 1H5 Tel: (604) 877-6284 Fax: (604) 708-2132 E-mail: reb@bccancer.bc.ca Website: http://www.bccancer.bc.ca > Research Ethics RISe: http://rise.ubc.ca Certificate of Expedited Approval: Annual Renewal PRINCIPAL INVESTIGATOR: INSTITUTION / DEPARTMENT: REB NUMBER: Wan Lam BCCA/BCCA/Cancer Genetics & Development (BCCA) H08-01392 INSTITUTION(S) WHERE RESEARCH WILL BE CARRIED OUT: Institution Site BC Cancer Agency Other locations where the research will be conducted: N/A Vancouver BCCA PRINCIPAL INVESTIGATOR FOR EACH ADDITIONAL PARTICIPATING BCCA CENTRE: Vancouver: Wan Lam Vancouver Island: N/A Fraser Valley: N/A Southern Interior: N/A Abbotsford Centre: N/A SPONSORING AGENCIES AND COORDINATING GROUPS: Canadian Institutes of Health Research (CIHR) PROJECT TITLE: Development of a multi-spectral platform for integrated analysis of clinical and research samples. APPROVAL DATE: EXPIRY DATE OF THIS APPROVAL: PAA#: H08-01392-A003 August 4, 2009 August 4, 2010 CERTIFICATION: 1. The membership of the UBC BCCA REB complies with the membership requirements for research ethics boards defined in Division 5 of the Food and Drug Regulations of Canada. 2. The UBC BCCA REB carries out its functions in a manner fully consistent with Good Clinical Practices. 3. The UBC BCCA REB has reviewed and approved the research project named on this Certificate of Approval including any associated consent form and taken the action noted above. This research project is to be conducted by the provincial investigator named above. This review and the associated minutes of the UBC BCCA REB have been documented electronically and in writing. The UBC BCCA Research Ethics Board has reviewed the documentation for the above named project. The research study as presented in documentation, was found to be acceptable on ethical grounds for research involving human subjects and was approved for renewal by the UBC BCCA REB. UBC BCCA Ethics Board Approval of the above has been verified by one of the following: Dr. George Browman, Chair Dr. Lynne Nakashima, Second Vice-Chair If you have any questions, please call: Bonnie Shields, Manager, BCCA Research Ethics Board: 604-877-6284 or e-mail: reb@bccancer.bc.ca Dr. George Browman, Chair: 604-877-6284 or e-mail: gbrowman@bccancer.bc.ca Dr. Lynne Nakashima, Second Vice-Chair: 604-707-5989 or e-mail: lnakas@bccancer.bc.ca https://rise.ubc.ca/rise/Doc/0/JKQ8088GG9RKN55VLAL9OHM869/fromString.html Page 1 of 1 15/04/2010
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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
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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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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
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: APPENDIX VI: Summary of Kaplan-Meie
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