Oligonucleotide array comparative genomic hybridization refines the structure of 8p23.1, 17q12 and 20q13.2 amplifications in gastric carcinomas

Cytogenetic and Genome Research

Volumn 119, Issue 1-2, 2007, Pages 39-45

  Vauhkonen, H ^a,c   Vauhkonen, M ^b   Sipponen, P ^b   Knuutila, S ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^c UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICROSATELLITE DNA;

ARTICLE; CANCER CLASSIFICATION; CHROMOSOME 17Q; CHROMOSOME 20Q; CHROMOSOME 8P; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CYTOGENETICS; DNA MICROARRAY; HUMAN; HUMAN TISSUE; PRIORITY JOURNAL; STOMACH CARCINOMA;

AGED; AGED, 80 AND OVER; CHROMOSOMES, HUMAN, PAIR 17; CHROMOSOMES, HUMAN, PAIR 20; CHROMOSOMES, HUMAN, PAIR 8; GENE AMPLIFICATION; GENE DOSAGE; HUMANS; MIDDLE AGED; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; STOMACH NEOPLASMS;

EID: 37549046834     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000109617     Document Type: Article

References (38)

1. Albertson DG: Gene amplification in cancer. Trends Genet 22:447-455 (2006).
2. Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, et al: Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25:144-146 (2000).
3. Atiye J, Wolf M, Kaur S, Monni O, Bohling T, et al: Gene amplifications in osteosarcoma-CGH microarray analysis. Genes Chromosomes Cancer 42:158-163 (2005).
4. Belkhiri A, Zaika A, Pidkovka N, Knuutila S, Moskaluk C, et al: Darpp-32 : a novel antiapoptotic gene in upper gastrointestinal carcinomas . Cancer Res 65:6583-6592 (2005).
5. Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, et al: A National Cancer Institute workshop on microsatellite instability for cancer detection and familial predisposition; development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res 58:5248-5257 (1998).
6. Collins C, Rommens JM, Kowbel D, Godfrey T, Tanner M, et al: Positional cloning of ZNF217 and NABC1 : genes amplified at 20q13.2 and overexpressed in breast carcinoma. Proc Natl Acad Sci USA 95:8703-8708 (1998).
7. El-Rifai W, Smith MF Jr, Li G, Beckler A, Carl VS, et al: Gastric cancers overexpress DARPP-32 and a novel isoform, t-DARPP. Cancer Res 62:4061-4064 (2002).
8. Forozan F, Veldman R, Ammerman CA, Parsa NZ, Kallioniemi A, et al: Molecular cytogenetic analysis of 11 new breast cancer cell lines. Br J Cancer 81:1328-1334 (1999).
9. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, et al: Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6:96 (2006).
10. Garcia MJ, Pole JC, Chin SF, Teschendorff A, Naderi A, et al: A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 24:5235-5245 (2005).
11. Gorringe KL, Boussioutas A, Bowtell DD: Novel regions of chromosomal amplification at 6p21, 5p13, and 12q14 in gastric cancer identified by array comparative genomic hybridization. Genes Chromosomes Cancer 42:247-259 (2005).
12. Hughes SJ, Glover TW, Zhu XX, Kuick R, Thoraval D, et al: A novel amplicon at 8p22-23 results in overexpression of cathepsin B in esophageal adenocarcinoma. Proc Natl Acad Sci USA 95:12410-12415 (1998).
13. Joesting MS, Perrin S, Elenbaas B, Fawell SE, Rubin JS, et al: Identification of SFRP1 as a candidate mediator of stromal-to-epithelial signaling in prostate cancer. Cancer Res 65:10423-10430 (2005).
14. Jong K, Marchiori E, Meijer G, Vaart AV, Ylstra B: Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics 20:3636-3637 (2004).
15. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, et al: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818-821 (1992).
16. Kauraniemi P, Kuukasjarvi T, Sauter G, Kallioniemi A: Amplification of a 280-kilobase core region at the ERBB2 locus leads to activation of two hypothetical proteins in breast cancer. Am J Pathol 163:1979-1984 (2003).
17. Knuutila S, Autio K, Aalto Y: Online access to CGH data of DNA sequence copy number changes. Am J Pathol 157:689 (2000).
18. Kokkola A, Monni O, Puolakkainen P, Larramendy ML, Victorzon M, et al: 17q12-21 amplicon, a novel recurrent genetic change in intestinal type of gastric carcinoma: a comparative genomic hybridization study. Genes Chromosomes Cancer 20:38-43 (1997).
19. Laurén P: The two histological main types of gastric carcinoma: diffuse and so-called intestinal type carcinoma. An attempt at a histo-clinical classification. Acta Pathol Microbiol Scand 64:31-49 (1965).
20. Lengauer C, Kinzler KW, Vogelstein B: Genetic instability in human cancers. Nature 396:643-649 (1998).
21. Lin JC, Ho WH, Gurney A, Rosenthal A: The netrin-G1 ligand NGL-1 promotes the outgrowth of thalamocortical axons. Nat Neurosci 6:1270-1276 (2003).
22. Lin L, Aggarwal S, Glover TW, Orringer MB, Hanash S, et al: A minimal critical region of the 8p22-23 amplicon in esophageal adenocarcinomas defined using sequence tagged site-amplification mapping and quantitative polymerase chain reaction includes the GATA-4 gene. Cancer Res 60:1341-1347 (2000).
23. Maqani N, Belkhiri A, Moskaluk C, Knuutila S, Dar AA, et al: Molecular dissection of 17q12 amplicon in upper gastrointestinal adenocarcinomas. Mol Cancer Res 4:449-455 (2006).
24. Monni O, Barlund M, Mousses S, Kononen J, Sauter G, et al: Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci USA 98:5711-5716 (2001).
25. Oue N, Hamai Y, Mitani Y, Matsumura S, Oshimo Y, et al: Gene expression profile of gastric carcinoma: identification of genes and tags potentially involved in invasion, metastasis, and carcinogenesis by serial analysis of gene expression. Cancer Res 64:2397-2405 (2004).
26. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, et al: High resolution analysis of DNA copy number variation using comparative genomic hybridization. Nat Genet 20:207-211 (1998).
27. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, et al: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41-46 (1999).
28. Sakakura C, Mori T, Sakabe T, Ariyama Y, Shinomiya T, et al: Gains, losses, and amplifications of genomic materials in primary gastric cancers analyzed by comparative genomic hybridization. Genes Chromosomes Cancer 24:299-305 (1999).
29. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al: Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (2005).
30. Takada H, Imoto I, Tsuda H, Sonoda I, Ichikura T, et al: Screening of DNA copy-number aberrations in gastric cancer cell lines by array-based comparative genomic hybridization. Cancer Sci 96:100-110 (2005).
31. Tyybakinoja A, Saarinen-Pihkala U, Elonen E, Knuutila S: Amplified, lost, and fused genes in 11q23-25 amplicon in acute myeloid leukemia, an array-CGH study. Genes Chromosomes Cancer 45:257-264 (2006).
32. Vauhkonen M, Vauhkonen H, Sajantila A, Sipponen P: Differences in genomic instability between intestinal and diffuse type gastric cancer. Gastric Cancer 8:238-244 (2005).
33. Vauhkonen M, Vauhkonen H, Sipponen P: Molecular pathology of gastric cancer. Best Pract Res Clin Gastroenterol 20:651-674 (2006a).
34. Vauhkonen H, Vauhkonen M, Sajantila A, Sipponen P, Knuutila S: Characterizing genetically stable and unstable gastric cancers by microsatellites and array comparative genomic hybridization. Cancer Genet Cytogenet 170:133-139 (2006b).
35. Vauhkonen H, Vauhkonen M, Sajantila A, Sipponen P, Knuutila S: DNA copy number aberrations in intestinal-type gastric cancer revealed by array-based comparative genomic hybridization. Cancer Genet Cytogenet 167:150-154 (2006c).
36. Weiss MM, Snijders AM, Kuipers EJ, Ylstra B, Pinkel D, et al: Determination of amplicon boundaries at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization. J Pathol 200:320-326 (2003).
37. Weiss MM, Kuipers EJ, Postma C, Snijders AM, Pinkel D, et al: Genomic alterations in primary gastric adenocarcinomas correlate with clinicopathological characteristics and survival. Cell Oncol 26:307-317 (2004).
38. Willis S, Hutchins AM, Hammet F, Ciciulla J, Soo WK, et al: Detailed gene copy number and RNA expression analysis of the 17q12-23 region in primary breast cancers. Genes Chromosomes Cancer 36:382-392 (2003).