Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes

Cancer Research

Volumn 62, Issue 21, 2002, Pages 6218-6223

  Bourdon, Véronique ^a   Naef, Félix ^b   Rao, Pulivarthi H ^a   Reuter, Victor ^a   Mok, Samuel C ^c   Bosl, George J ^a   Koul, Sanjay ^d   Murty, Vundaralli V V S ^d   Kucherlapati, Raju S ^e   Chaganti, R S K ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d The New York Presbyterian Hospital   (United States)

^e LABORATORY FOR MOLECULAR MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; PROTEIN GCT1; PROTEIN GCT2; RNA; UNCLASSIFIED DRUG;

AMPLICON; ARTICLE; CANCER CELL CULTURE; CHROMOSOME 12P; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA HYBRIDIZATION; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENE SEQUENCE; GENETIC CODE; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; OVARY CANCER; PRIORITY JOURNAL; SEMINOMA; SEQUENCE ANALYSIS;

AGED; ALGORITHMS; BLOTTING, SOUTHERN; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 12; EXPRESSED SEQUENCE TAGS; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION; HUMANS; MALE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEMINOMA; TESTICULAR NEOPLASMS; TUMOR CELLS, CULTURED;

EID: 0036830029     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (27)

1. Schwab, M. Oncogene amplification in solid tumors. Semin. Cancer Biol., 9: 319-325, 1999.
2. Gray, J. W., and Collins, C. Genome changes and gene expression in human solid tumors. Carcinogenesis (Lond.), 21: 443-452, 2000.
3. Kallioniemi, A., Kallioniemi, O. P., Sudar, D., Rutovitz, D., Gray, J. W., Waldman, F., and Pinkel, D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science (Wash. DC), 258: 818-821, 1992.
4. Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, J., Benner, A., Dohner, H., Cremer, T., and Lichter, P. Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer, 20: 399-407, 1997.
5. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W. L., Chen, C., Zhai, Y., Dairkee, S. H., Ljung, B. M., Gray, J. W., and Albertson, D., G. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20: 207-211, 1998.
6. Albertson, D. G., Ylstra, B., Segraves, R., Collins, C., Dairkee, S. H., Kowbel, D., Kuo, W. L., Gray, J. W., and Pinkel, D. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat. Genet., 25: 144-146, 2000.
7. Hui, A. B., Lo, K. W., Yin, X. L., Poon, W. S., and Ng, H. K. Detection of multiple gene amplifications in glioblastoma multiforme using array-based comparative genomic hybridization. Lab. Investig., 81: 717-723, 2001.
8. Daigo, Y., Chin, S. F., Gorringe, K. L., Bobrow, L. G., Ponder, B. A., Pharoah, P. D., and Caldas, C. Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers: a new approach for the molecular analysis of paraffin-embedded cancer tissue. Am. J. Pathol., 158: 1623-1631, 2001.
9. Heiskanen, M. A., Bittner, M. L., Chen, Y., Khan, J., Adler, K. E., Trent, J. M., and Meltzer, P. S. Detection of gene amplification by genomic hybridization to cDNA microarrays. Cancer Res., 60: 799-802, 2000.
10. Pollack, J, R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., and Brown, P. O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23: 41-46, 1999.
11. Monni, O., Barlund, M., Mousses, S., Kononen, J., Sauter, G., Heiskanen, M., Paavola, P., Avela, K., Chen, Y., Bittner, M. L., and Kallioniemi, A. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc. Natl. Acad. Sci. USA, 98: 5711-5716, 2001.
12. Chaganti, R. S., and Houldsworth, J. Genetics and biology of adult human male germ cell tumors. Cancer Res., 60: 1475-1482, 2000.
13. Knuutila, S., Bjorkqvist, A. M., Autio, K., Tarkkanen, M., Wolf, M., Monni, O., Szymanska, J., Larramendy, M. L., Tapper, J., Pere, H., El-Rifai, W., Hemmer, S., Wasenius V. M., Vidgren, V., and Zhu, Y. DNA copy number amplifications in human neoplasms: Review of comparative genomic hybridization studies. Am. J. Pathol., 152: 1107-1123, 1998.
14. Suijkerbuijk, R. F., Sinke, R. J., Weghuis, D. E., Roque, L., Forus, A., Stellink, F., Siepman, A., van de Kaa, C., Soares, J., and Geurts van Kessel, A. Amplification of chromosome subregion 12p11.2-p12.1 in a metastasis of an i(12p)-negative seminoma: Relationship to tumor progression? Cancer Genet. Cytogenet., 78: 145-152, 1994.
15. Mostert, M. C., Verkerk, A. J., van de Pol, M., Heighway, J., Marynen, P., Rosenberg, C., van Kessel, A. G., van Echten, J., de Jong, B., Oosterhuis, J. W., and Looijenga, L. H. Identification of the critical region of 12p over-representation in testicular germ cell tumors of adolescents and adults. Oncogene, 16: 2617-2627, 1998.
16. Roelofs, H., Mostert, M. C., Pompe, K., Zafarana., G., van Oorschot, M., van Gurp, R. J., Gillis, A. J., Stoop, H., Beverloo, B., Oosterhuis, J. W., Bokemeyer, C., and Looijenga, L. H. Restricted 12p amplification and RAS mutation in human germ cell tumors of the adult testis. Am. J. Pathol., 157: 1155-1166, 2000.
17. Heidenreich, A., Srivastava, S., Moul, J. W., and Hofmann, R. Molecular genetic parameters in pathogenesis and prognosis of testicular germ cell tumors. Eur. Urol., 37: 121-135, 2000.
18. Rosenberg, C., Van Gurp, R. J., Geeler, E., Oosterhuis, J. W., and Looijenga, L. H. Overrepresentation of the short arm of chromosome 12 is related to invasive growth of human testicular seminomas and nonseminomas. Oncogene, 19: 5858-5862, 2000.
19. Schmidt, B. A., Rose, A., Steinhoff, C., Strohmeyer, T., Hartmann, M., and Ackermann, R. Up-regulation of cyclin-dependent kinase 4/cyclin D2 expression but down-regulation of cyclin-dependent kinase 2/cyclin E in testicular germ cell tumors. Cancer Res., 61: 4214-4221, 2001.
20. Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30: e15, 2002.
21. Rao, P. H., Murty, V. V., Louie, D. C., and Chaganti, R. S. Nonsyntenic amplification of MYC with CDK4 and MDM2 in a malignant mixed tumor of salivary gland. Cancer Genet. Cytogenet., 105: 160-163, 1998.
22. Cheung, V. G., Morley, M., Aguilar, F., Massimi, A., Kucherlapati, R., and Childs, G. Making and reading microarrays. Nat. Genet, 21: 15-19, 1999.
23. Rao, P. H., Houldsworth, J., Palanisamy, N., Murty, V. V., Reuter, V. E., Motzer, R. J., Bosl, G. J., and Chaganti, R. S. Chromosomal amplification is associated with cisplatin resistance of human male germ cell tumors. Cancer Res., 58: 4260-4263, 1998.
24. Schuler, G. D., Boguski, M. S., Stewart, E. A., Stein, L. D., Gyapay, G., Rice, K., White, R. E., Rodriguez-Tome, P., Aggarwal, A., Bajorek, E., Bentolila, S., Birren, B. B., Butler, A., Castle, A. B., Chiannilkulchai, N., Chu, A., Clee, C., Cowles, S., Day, P. J., Dibling, T., Drouot, N., Dunham, I., Duprat, S., East, C., Hudson, T. J., et al. A gene map of the human genome. Science (Wash. DC), 274: 540-546, 1996.
25. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R., and White, J. The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res., 29: 159-164, 2001.
26. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., Meyer, M. R., Slade, D., Lum, P. Y., Stepaniants, S. B., Shoemaker, D. D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M, and Friend, S. H. Functional discovery via a compendium of expression profiles. Cell, 102: 109-126, 2000.
27. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. Basic local alignment search tool. J. Mol. Biol., 215: 403-410, 1990.