DNA copy number analysis in gastrointestinal stromal tumors using gene expression microarrays

Cancer Informatics

Volumn 6, Issue , 2008, Pages 59-75

  Antonescu, Cristina R ^a   Wu, Kai ^b,c   Guoliang, Leon Xing ^b   Cao, Manqiu ^b,c   Turpaz, Yaron ^b,d   Leversha, Margaret A ^a   Hubbell, Earl ^b   Maki, Robert G ^a   Miyada, C Garrett ^b,e   Pillai, Raji ^b,f  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b Thermo Fisher Scientific   (United States)

^c INTEL CORPORATION   (United States)

^d Eli Lilly Singapore Pte Ltd   (Singapore)

^e NuGEN Technologies Inc   (United States)

^f Pathwork Diagnostics   (United States)

Author keywords

Array based comparative genomic hybridization; Copy number change; Gene expression; GIST; Sarcoma; Whole genome amplification

Indexed keywords

DNA; GENOMIC DNA;

ALGORITHM; ARTICLE; CELL LINE; CHROMOSOMAL LOCALIZATION; CHROMOSOME 1Q; CHROMOSOME ABERRATION; CHROMOSOME DELETION; CORRELATION ANALYSIS; DNA ISOLATION; DNA MICROARRAY; EXPRESSION MICROARRAY COPY NUMBER ANALYSIS; FLUORESCENCE IN SITU HYBRIDIZATION; GASTROINTESTINAL STROMAL TUMOR; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE MAPPING; GENE NUMBER; GENETIC ANALYSIS; HUMAN; HUMAN CELL; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA HYBRIDIZATION; GENE DELETION; GENE LOSS; GENE MUTATION; GENETIC GAIN; HUMAN TISSUE; MICROARRAY ANALYSIS; PEX11B GENE; RNA HYBRIDIZATION; TUMOR GENE;

EID: 49649101043     PISSN: 11769351     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/cin.s387     Document Type: Article

References (38)

1. Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutovitz, D., Gray, J.W., Waldman, F. et al. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science, 258(5083):818-21.
2. Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, J., Benner, A., Dohner, H. et al. 1997. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer, 20(4):399-407.
3. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D. et al. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20(2):207-11.
4. Pollack, J.R., Perou, C.M., Alizadeh, A.A., Eisen, M.B., Pergamenschikov, A., Williams, C.F. et al. 1999. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23(1):41-6.
5. Snijders, A.M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J. et al. 2001. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet., 29(3):263-4.
6. Barrett, M.T., Scheffer, A., Ben-Dor, A., Sampas, N., Lipson, D., Kincaid, R. et al. 2004. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. U.S.A., 101(51):17765-70.
7. Brennan, C., Zhang, Y., Leo, C., Feng, B., Cauwels, C., Aguirre, A.J. et al. 2004. High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res., 64(14):4744-8.
8. Bignell, G.R., Huang, J., Greshock, J., Watt, S., Butler, A., West, S. et al. 2004. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res., 14(2):287-95.
9. Huang, J., Wei, W., Zhang, J., Liu, G., Bignell, G.R., Stratton, M.R. et al. 2004. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genomics, 1(4):287-99.
10. Rauch, A., Ruschendorf, F., Huang, J., Trautmann, U., Becker, C., Thiel, C. et al. 2004. Molecular karyotyping using an SNP array for genomewide genotyping. J. Med. Genet., 41(12):916-22.
11. Zhao, X., Li, C., Paez, J.G., Chin, K., Janne, P.A., Chen, T.H. et al. 2004. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res., 64(9):3060-71.
12. Zhou, X., Mok, S.C., Chen, Z., Li, Y. and Wong, D.T. 2004. Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum. Genet., 115(4):327-30.
13. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J.P. et al. 1999. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286(5439):531-7.
14. Yeoh, E.J., Ross, M.E., Shurtleff, S.A., Williams, W.K., Patel, D., Mahfouz, R. et al. 2002. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell., 1(2):133-43.
15. Antonescu, C.R., Viale, A., Sarran, L., Tschernyavsky, S.J., Gonen, M., Segal, N.H. et al. 2004. Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site. Clin. Cancer Res., 10(10):3282-90.
16. Benetkiewicz, M., Wang, Y., Schaner, M., Wang, P., Mantripragada, K.K., Buckley, P.G. et al. 2005. High-resolution gene copy number and expression profiling of human chromosome 22 in ovarian carcinomas. Genes Chromosomes Cancer, 42(3):228-37.
17. Kasamatsu, A., Endo, Y., Uzawa, K., Nakashima, D., Koike, H., Hashitani, S. et al. 2005. Identification of candidate genes associated with salivary adenoid cystic carcinomas using combined comparative genomic hybridization and oligonucleotide microarray analyses. Int. J. Biochem. Cell. Biol., 37(9):1869-80.
18. Hyman, E., Kauraniemi, P., Hautaniemi, S., Wolf, M., Mousses, S., Rozenblum, E. et al. 2002. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res., 62(21):6240-5.
19. McArdle, L., McDermott, M., Purcell, R., Grehan, D., O'Meara, A., Breatnach, F. et al. 2004. Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis, 25(9):1599-609.
20. Nigro, J.M., Misra, A., Zhang, L., Smirnov, I., Colman, H., Griffin, C. et al. 2005. Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Res., 65(5):1678-86.
21. Platzer, P., Upender, M.B., Wilson, K., Willis, J., Lutterbaugh, J., Nosrati, A. et al. 2002. Silence of chromosomal amplifications in colon cancer. Cancer Res., 62(4):1134-8.
22. Pollack, J.R., Sorlie, T., Perou, C.M., Rees, C.A., Jeffrey, S.S., Lonning, P.E. et al. 2002. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc. Natl. Acad. Sci. U.S.A., 99(20):12963-8.
23. Miettinen, M., El-Rifai, W., L, H.L.S. and Lasota, J. 2002. Evaluation of malignancy and prognosis of gastrointestinal stromal tumors: a review. Hum. Pathol., 33(5):478-83.
24. Heinrich, M.C., Corless, C.L., Duensing, A. et al. 2003. PDGFRA activating mutations in gastrointestinal stromal tumors. Science, 299(5607):708-10.
25. Hirota, S., Isozaki, K., Moriyama, Y. et al. 1998. Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors. Science, 279(5350):577-80.
26. El-Rifai, W., Sarlomo-Rikala, M., Andersson, L.C., Knuutila, S. and Miettinen, M. 2000. DNA sequence copy number changes in gastrointestinal stromal tumors: tumor progression and prognostic significance. Cancer Res., 60(14):3899-903.
27. Knuutila, S., Armengol, G., Bjorkqvist, A.M., el-Rifai, W., Larramendy, M.L., Monni, O. et al. 1998. Comparative genomic hybridization study on pooled DNAs from tumors of one clinical-pathological entity. Cancer Genet. Cytogenet., 100(1):25-30.
28. Sarlomo-Rikala, M., Kovatich, A.J., Barusevicius, A. and Miettinen, M. 1998. CD117: a sensitive marker for gastrointestinal stromal tumors that is more specific than CD34. Mod. Pathol., 11(8):728-34.
29. Granitto, S.R., Kolachana, P., Antonescu, C.R., Johnson, R.C., DeMatteo, R.P. and Jhanwar, S.C. 2004. Genomic alterations in gastrointestinal stromal tumors as revealed by conventional and array-based comparative genomic hybridization. Cancer Genomics and Protemics, 1:105-116.
30. Affymetrix Technical Note 1: "Guide to Probe Logarithmic Intensity Error (PLIER.) Estimation". http://www.affymetrix.com/support/technical/ technotes/plier technote.pdf OR. www.affymetrix.com In.
31. Slater, H.R., Bailey, D.K., Ren, H., Cao, M., Bell, K., Nasioulas, S. et al. 2005. High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs. Am. J. Hum. Genet., 77(5):709-26.
32. Affymetrix Technical Note 2: "High-Resolution Chromosome Copy Number Analysis Using GeneChip® Mapping Arrays". http://www.affymetrix.com/ support/technical/technotes/chromosomecopy_numbertechnote.pdf OR. www.affymetrix.com In.
33. Waye JS, England SB, Willard HF. Genomic organization of alpha satellite DNA on human chromosome 7: evidence for two distinct alphoid domains on a single chromosome. Mol Cell Biol. 1987;7:349-56.
34. Waye JS, Durfy SJ, Pinkel D, Kenwrick S, Patterson M, Davies KE, Willard HF. Chromosome-specific alpha satellite DNA from human chromosome 1: hierarchical structure and genomic organization of a polymorphic domain spanning several hundred kilobase pairs of centromeric DNA. Genomics. 1987; 1:43-51.
35. Tukey, J.W. 1977. Some thoughts on clinical trials, especially problems of multiplicity. Science, 198(4318):679-84.
36. El-Rifai, W., Sarlomo-Rikala, M., Andersson, L.C., Miettinen, M. and Knuutila, S. High-resolution deletion mapping of chromosome 14 in stromal tumors of the gastrointestinal tract suggests two distinct tumor suppressor loci. Genes Chromosomes Cancer 2000; 27(4):387-91.
37. Auer, H., Newsom, D.L., Nowak, N.J., McHugh, K.M., Singh, S., Yu, C.Y. et al. 2007. Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays. BMC Genomics, 8:111.
38. Yamashita Y, Minoura K, Taya T, Fujiwara SI, Kurashina K, Watanabe H, Choi YL, Soda M, Hatanaka H, Enomoto M, Takada S, Mano H. Analysis of chromosome copy number in leukemic cells by different microarray platforms. Leukemia. 2007; 21:1333-7.