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DNA copy number profiling of gastric cancer and its clinical implications

All rights reserved. No parts of this thesis may be reproduced, stored in a retrieval system, or transmitted in any form or means without the prior permission in writing from the author. Articles are reprinted with permission from the respective journals. Contents Chapter 1. Introduction 7 Chapter 2. DNA quality assessment and amplification for array CGH 35 Chapter 3. Across array comparative genomic hybridization: a strategy to reduce reference channel hybridizations 49 Chapter 4. NMD inhibition fails to identify tumor suppressor genes in microsatellite stable gastric cancer cell lines 69 Chapter 5. DNA copy number profiles of gastric cancer precursor lesions 85 Chapter 6. Mixed gastric carcinomas show similar chromosomal aberrations in both their diffuse and glandular components 101 Chapter 7. Young and elderly patients show different genomic profiles 117 Chapter 8. Gastric cancers of Western European and African patients show different patterns of genomic instability 129 Chapter 9. Losses of chromosome 5q and 14q mark a subset of gastric cancers with good clinical outcome 147 Chapter 10. High resolution analysis of DNA copy number aberrations of chromosomes 8, 13 and 20 in gastric cancers 163 Chapter 11. Gross genomic damage measured by DNA image cytometry independently predicts clinical outcome in gastric cancer 179 Chapter 12. MAL promoter hypermethylation as novel prognostic marker in gastric cancer 197 Chapter 13. Summary and general discussion 209 Chapter 14.