An integrated study of aberrant gene copy number and gene expression in GIST and LMS

Technology in Cancer Research and Treatment

Volumn 9, Issue 2, 2010, Pages 171-177

  Yang, Da ^a   Ylipää, Antti ^a,b   Yang, Jilong ^a,c   Hunt, Kelly ^a   Pollock, Raphael ^a   Trent, Jonathan ^a   Yli Harja, Olli ^b   Shmulevich, Ilya ^d   Nykter, Matti ^b   Zhang, Wei ^a  

^a UNIVERSITY OF TEXAS   (United States)

^b TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^c TIANJIN MEDICAL UNIVERSITY   (China)

^d INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Array CGH; CNA; Gene expression; GIST; Leiomyosarcoma

Indexed keywords

BIOLOGICAL MARKER; MESSENGER RNA;

ARTICLE; CARCINOGENESIS; CHROMOSOME 14Q; CHROMOSOME 15Q; CHROMOSOME 1P; CHROMOSOME 22Q; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GASTROINTESTINAL STROMAL TUMOR; GENE DOSAGE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE MUTATION; GENE STRUCTURE; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; LEIOMYOSARCOMA; MULTIDIMENSIONAL SCALING; TUMOR GROWTH;

EID: 77952040509     PISSN: 15330346     EISSN: None     Source Type: Journal    
DOI: 10.1177/153303461000900206     Document Type: Article

References (29)

1. Chen, Y., Tzeng, C. C., Liou, C. P., Chang, M. Y., Li, C. F., Lin, C. N. Biological significance of chromosomal imbalance aberrations in gastrointestinal stromal tumors. J Biomed Sci 11, 65-71 (2004). (Pubitemid 38142354)
2. Wozniak, A., Sciot, R., Guillou, L., Pauwels, P., Wasag, B., Stul, M., Vermeesch, J. R., Vandenberghe, P., Limon, J., Debiec-Rychter, M. Array CGH analysis in primary gastrointestinal stromal tumors: cytogenetic profile correlates with anatomic site and tumor aggressiveness, irrespective of mutational status. Genes Chromosomes Cancer 46, 261-276 (2007). (Pubitemid 46155321)
3. Lasota, J., Wozniak, A., Kopczynski, J., Dansonka-Mieszkowska, A., Wasag, B., Mitsuhashi, T., Sarlomo-Rikala, M., Lee, J.R., Schneider-Stock, R., Stachura, J. et al. Loss of heterozygosity on chromosome 22q in gastrointestinal stromal tumors (GISTs): a study on 50 cases. Lab Invest 85, 237-247 (2005). (Pubitemid 40208927)
4. Chen, L. L., Trent, J. C., Wu, E. F., Fuller, G. N., Ramdas, L., Zhang, W., Raymond, A. K., Prieto, V. G., Oyedeji, C. O., Hunt, K. K. et al. A missense mutation in KIT kinase domain 1 correlates with imatinib resistance in gastrointestinal stromal tumors. Cancer Res 64, 5913-5919 (2004). (Pubitemid 39129383)
5. Kleinbaum, E. P., Lazar, A. J., Tamborini, E., McAuliffe, J. C., Sylvestre, P. B., Sunnenberg, T. D., Strong, L., Chen, L. L., Choi, H., Benjamin, R. S., et al. Clinical, histopathologic, molecular and therapeutic findings in a large kindred with gastrointestinal stromal tumor. Int J Cancer 122, 711-718 (2008). (Pubitemid 350308969)
6. Besmer, P., Murphy, J. E., George, P. C., Qiu, F. H., Bergold, P. J., Lederman, L., Snyder, H. W., Jr., Brodeur, D., Zuckerman, E. E., Hardy, W. D. A new acute transforming feline retrovirus and relationship of its oncogene v-kit with the protein kinase gene family. Nature 320, 415-421 (1986). (Pubitemid 16097805)
7. Jemal, A., Siegel, R., Ward, E., Hao, Y., Xu, J., Murray, T., Thun, M. J. Cancer statistics, 2008. CA Cancer J Clin 58, 71-96 (2008).
8. Mandahl, N., Fletcher, C. D., Dal Cin, P., De Wever, I., Mertens, F., Mitelman, F., Rosai, J., Rydholm, A., Sciot, R., Tallini, G. et al. Comparative cytogenetic study of spindle cell and pleomorphic leiomyosarcomas of soft tissues: a report from the CHAMP Study Group. Cancer Genet Cytogenet 116, 66-73 (2000).
9. Wang, R., Titley, J. C., Lu, Y. J., Summersgill, B. M., Bridge, J. A., Fisher, C., Shipley, J. Loss of 13q14-q21 and gain of 5p14-pter in the progression of leiomyosarcoma. Mod Pathol 16, 778-785 (2003). (Pubitemid 37011073)
10. Hu, J., Rao, U. N., Jasani, S., Khanna, V., Yaw, K., Surti, U. Loss of DNA copy number of 10q is associated with aggressive behavior of leiomyosarcomas: a comparative genomic hybridization study. Cancer Genet Cytogenet 161, 20-27 (2005). (Pubitemid 41096047)
11. Larramendy, M. L., Kaur, S., Svarvar, C., Bohling, T., Knuutila, S. Gene copy number profiling of soft-tissue leiomyosarcomas by array-comparative genomic hybridization. Cancer Genet Cytogenet 169, 94-101 (2006). (Pubitemid 44308364)
12. Joensuu, H. Gastrointestinal stromal tumor (GIST). Ann Oncol 17(Suppl 10), x280-6 (2006).
13. Meza-Zepeda, L. A., Kresse, S. H., Barragan-Polania, A. H., Bjerkehagen, B., Ohnstad, H. O., Namlos, H. M., Wang, J., Kristiansen, B. E., Myklebost, O. Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas. Cancer Res 66, 8984-8993 (2006). (Pubitemid 44521116)
14. Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004). (Pubitemid 41180205)
15. van de Wiel, M. A., Kim, K. I., Vosse, S. J., van Wieringen, W. N., Wilting, S. M., Ylstra, B. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23, 892-894 (2007).
16. Tusher, V. G., Tibshirani, R., Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98, 5116-5121 (2001). (Pubitemid 32397092)
17. Toedling, J., Schmeier, S., Heinig, M., Georgi, B., Roepcke, S. MACAT-microarray chromosome analysis tool. Bioinformatics 21, 2112-2113 (2005).
18. Benjamini, Y., Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B, 289-300 (1995).
19. Zhuang, Z., Lu, J., Lonser, R., Kovach, J. S. Enhancement of cancer chemotherapy by simultaneously altering cell cycle progression and DNA-damage defenses through global modification of the serine/threonine phospho-proteome. Cell Cycle 8, 3303-3306 (2009).
20. Turner, D. P., Findlay, V. J., Kirven, A. D., Moussa, O., Watson, D. K. Global gene expression analysis identifies PDEF transcriptional networks regulating cell migration during cancer progression. Mol Biol Cell 19, 3745-3757 (2008).
21. Khalil, I. G., Hill, C. Systems biology for cancer. Curr Opin Oncol 17, 44-48 (2005).
22. Pickeral, O. K., Li, J. Z., Barrow, I., Boguski, M. S., Makalowski, W., Zhang, J. Classical oncogenes and tumor suppressor genes: a comparative genomics perspective. Neoplasia 2, 280-286 (2000). (Pubitemid 30346084)
23. Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., Stratton, M. R. A census of human cancer genes. Nat Rev Cancer 4, 177-183 (2004).
24. Katoh, M., Katoh, M. Bioinformatics for cancer management in the post-genome era. Technol Cancer Res Treat 5, 169-175 (2006).
25. Yeoh, E. J., Ross, M. E., Shurtleff, S. A., Williams, W. K., Patel, D., Mahfouz, R., Behm, F. G., Raimondi, S. C., Relling, M. V., Patel, A. et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1, 133-143 (2002). (Pubitemid 41039160)
26. Fan, C., Oh, D. S., Wessels, L., Weigelt, B., Nuyten, D. S., Nobel, A. B., van't Veer, L. J., Perou, C. M. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 355, 560-569 (2006).
27. Price, N. D., Trent, J., El-Naggar, A. K., Cogdell, D., Taylor, E., Hunt, K. K., Pollock, R. E., Hood, L., Shmulevich, I., Zhang, W. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci USA 104, 3414-3419 (2007). (Pubitemid 46364173)
28. Liu, S., Bishop, W. R., Liu, M. Differential effects of cell cycle regulatory protein p21(WAF1/Cip1) on apoptosis and sensitivity to cancer chemotherapy. Drug Resist Updat 6, 183-195 (2003). (Pubitemid 37129918)
29. Ayollo, D. V., Zhitnyak, I. Y., Vasiliev, J. M., Gloushankova, N. A. Rearrangements of the actin cytoskeleton and e-cadherin-based adherens junctions caused by neoplasic transformation change cell-cell interactions. PLoS One 4, e8027 (2009).