Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array

Experimental and Molecular Medicine

Volumn 41, Issue 7, 2009, Pages 462-470

  Jung, Seung Hyun ^a   Shin, Seung Hun ^a   Yim, Seon Hee ^a   Choi, Hye Sun ^a   Lee, Sug Hyung ^a   Chung, Yeun Jun ^a  

^a The Catholic University of Korea   (South Korea)

Author keywords

Cell line, tumor; Gene dosage; Gene expression profiling; Oligonucleotide array sequence analysis

Indexed keywords

RNA; TRANSCRIPTOME;

ARTICLE; CANCER GENETICS; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; MALIGNANT NEOPLASTIC DISEASE; POLYMERASE CHAIN REACTION;

EID: 68049104346     PISSN: 12263613     EISSN: 20926413     Source Type: Journal    
DOI: 10.3858/emm.2009.41.7.051     Document Type: Article

References (19)

1. Albertson DG, Pinkel D. Genomic microarrays in human genetic disease and cancer. Hum Mol Genet 2003;12:R145-52
2. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ, Kim M, Protopopov A, Chin L. High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 2004;64:4744-4748
3. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol 2004;57:644-646
4. Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006;10:529-541
5. Croce CM. Oncogenes and cancer. N Engl J Med 2008;358:502-511
6. Dehan E, Ben-Dor A, Liao W, Lipson D, Frimer H, Rienstein S, Simansky D, Krupsky M, Yaron P, Friedman E, Rechavi G, Perlman M, Aviram-Goldring A, Izraeli S, Bittner M, Yakhini Z, Kaminski N. Chromosomal aberrations and gene expression profiles in non-small cell lung cancer. Lung Cancer 2007;56:175-184
7. Han W, Han MR, Kang JJ, Bae JY, Lee JH, Bae YJ, Lee JE, Shin HJ, Hwang KT, Hwang SE, Kim SW, Noh DY. Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer. BMC Cancer 2006;6:92
8. Heidenblad M, Lindgren D, Veltman JA, Jonson T, Mahlamäki EH, Gorunova L, van Kessel AG, Schoenmakers EF, Höglund M. Microarray analyses reveal strong influence of DNA copy number alterations on the transcriptional patterns in pancreatic cancer: implications for the interpretation of genomic amplifications. Oncogene 2005;24:1794-1801
9. Jeong YB, Kim TM, Chung YJ. CGHscape: A software framework for the detection and visualization of copy number alterations. Genomics & Informatics 2008;6:126-129
10. Jones AM, Mitter R, Springall R, Graham T, Winter E, Gillett C, Hanby AM, Tomlinson IP, Sawyer EJ; Phyllodes Tumour Consortium. A comprehensive genetic profile of phyllodes tumours of the breast detects important mutations, intratumoral genetic heterogeneity and new genetic changes on recurrence. J Pathol 2008;214:533-544
11. Kim MY, Yim SH, Kwon MS, Kim TM, Shin SH, Kang HM, Lee C, Chung YJ. Recurrent genomic alterations with impact on survival in colorectal cancer identified by genome-wide array comparative genomic hybridization. Gastroenterology 2006;131:1913-1924
12. Kim TM, Yim SH, Shin SH, Xu HD, Jung YC, Park CK, Choi JY, Park WS, Kwon MS, Fiegler H, Carter NP, Rhyu MG, Chung YJ. Clinical implication of recurrent copy number alterations in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q. Int J Cancer 2008;123:2808-2815
13. Kim TM, Yim SH, Lee JS, Kwon MS, Ryu JW, Kang HM, Fiegler H, Carter NP, Chung YJ. Genome-wide screening of genomic alterations and their clinicopathologic implications in non-small cell lung cancers. Clin Cancer Res 2005;11:8235-8242
14. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001;25:402-408
15. Lynch M. Gene duplication and evolution. Science 2002;297:945-947
16. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998; 20:207-211
17. Vincent-Salomon A, Lucchesi C, Gruel N, Raynal V, Pierron G, Goudefroye R, Reyal F, Radvanyi F, Salmon R, Thiery JP, Sastre-Garau X, Sigal-Zafrani B, Fourquet A, Delattre O; breast cancer study group of the Institut Curie. Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breast. Clin Cancer Res 2008;14:1956-1965
18. Yim SH, Chung YJ. Current status and future clinical applications of Array based Comparative Genomic Hybridization. Genomics & Informatics 2004;2:113-120
19. Ylstra B, van den Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 2006;34:445-450