Identification of candidate tumor oncogenes by integrative molecular analysis of choroidal melanoma fine-needle aspiration biopsy specimens

Archives of Ophthalmology

Volumn 128, Issue 9, 2010, Pages 1170-1177

  McCannel, Tara A ^a,b,c   Burgess, Barry L ^a   Rao, Nagesh P ^a   Nelson, Stanley F ^a,c   Straatsma, Bradley R ^a,b,c  

^a JULES STEIN EYE INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASPIRATION BIOPSY; CHOROID MELANOMA; CHROMOSOME 3; CHROMOSOME 6P; CHROMOSOME LOSS; CYTOGENETICS; CYTOPATHOLOGY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE IDENTIFICATION; GENE MAPPING; HUMAN; HUMAN TISSUE; ONCOGENE; PRIORITY JOURNAL; RNA ANALYSIS; ADULT; AGED; CHOROID TUMOR; CHROMOSOME 6; CHROMOSOME ABERRATION; DNA MICROARRAY; FEMALE; GENE EXPRESSION PROFILING; GENETICS; MALE; MELANOMA; MIDDLE AGED; NEEDLE BIOPSY; PATHOLOGY;

DNA; ONCOPROTEIN;

ADULT; AGED; AGED, 80 AND OVER; BIOPSY, FINE-NEEDLE; CHOROID NEOPLASMS; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 3; CHROMOSOMES, HUMAN, PAIR 6; DNA, NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; MELANOMA; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENE PROTEINS;

EID: 77956986579     PISSN: 00039950     EISSN: 15383601     Source Type: Journal    
DOI: 10.1001/archophthalmol.2010.180     Document Type: Article

References (23)

1. Singh AD, Topham A. Survival rates with uveal melanoma in the United States: 1973-1997. Ophthalmology. 2003;110(5):962-965.
2. Kujala E, Mäkitie T, Kivelä T. Very long-term prognosis of patients with malignant uveal melanoma. Invest Ophthalmol Vis Sci. 2003;44(11):4651-4659.
3. Prescher G, Bornfeld N, Friedrichs W, Seeber S, Becher R. Cytogenetics of twelve cases of uveal melanoma and patterns of nonrandom anomalies and isochromosome formation. Cancer Genet Cytogenet. 1995;80(1):40-46.
4. Sisley K, Rennie IG, Parsons MA, et al. Abnormalities of chromosomes 3 and 8 in posterior uveal melanoma correlate with prognosis. Genes Chromosomes Cancer. 1997;19(1):22-28.
5. Tschentscher F, Hüsing J, Hölter T, et al. Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. Cancer Res. 2003;63(10):2578-2584.
6. Onken MD, Worley LA, Ehlers JP, Harbour JW. Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res. 2004;64(20):7205-7209.
7. van Gils W, Lodder EM, Mensink HW, et al. Gene expression profiling in uveal melanoma: two regions on 3p related to prognosis. Invest Ophthalmol Vis Sci. 2008;49(10):4254-4262.
8. Young TA, Burgess BL, Rao NP, Gorin MB, Straatsma BR. High-density genome array is superior to fluorescence in-situ hybridization analysis of monosomy 3 in choroidal melanoma fine needle aspiration biopsy. Mol Vis. 2007;13:2328-2333.
9. Beran TM, McCannel TA, Stanton AL, Straatsma BR, Burgess BL. Reactions to and desire for prognostic testing in choroidal melanoma patients. J Genet Couns. 2009;18(3):265-274.
10. Young TA, Rao NP, Glasgow BJ, Moral JN, Straatsma BR. Fluorescent in-situ hybridization for monosomy 3 via 30-gauge fine-needle aspiration biopsy of choroidal melanoma in vivo. Ophthalmology. 2007;114(1):142-146.
11. Young TA, Burgess BL, Rao NP, Glasgow BJ, Straatsma BR. Transscleral fine-needle aspiration biopsy of macular choroidal melanoma. Am J Ophthalmol. 2008;145(2):297-302.
12. Glasgow BJ, Foos RY. Methods in ocular cytology. In: Ocular Cytopathology. Boston, MA: Butterworth-Heinemann; 1993:1-6.
13. Day A, Carlson MRJ, Dong J, O'Connor BD, Nelson SF. Celsius: a community resource for Affymetrix microarray data. Genome Biol. 2007;8(6):R112. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394754/?tool=pubmed. Accessed June 15, 2010.
14. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A. 2001;98(1):31-36.
15. Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol. 2003;4(10):R70. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC328459/?tool=pubmed. Accessed June 16, 2010.
16. Worley LA, Onken MD, Person E, et al. Transcriptomic versus chromosomal prognostic markers and clinical outcome in uveal melanoma. Clin Cancer Res. 2007;13(5):1466-1471.
17. Hughes S, Damato BE, Giddings I, Hiscott PS, Humphreys J, Houlston RS. Microarray comparative genomic hybridization analysis of intraocular uveal melanomas identifies distinctive imbalances associated with loss of chromosome 3. Br J Cancer. 2005;93(10):1191-1196.
18. Ehlers JP, Worley L, Onken MD, Harbour JW. Integrative genomic analysis of aneuploidy in uveal melanoma. Clin Cancer Res. 2009;14(1):115-122.
19. Parrella P, Sidransky D, Merbs SL. Allelotype of posterior uveal melanoma: implications for a bifurcated tumor progression pathway. Cancer Res. 1999;59(13):3032-3037.
20. Höglund M, Gisselsson D, Hansen GB, et al. Dissecting karyotypic patterns in malignant melanomas: temporal clustering of losses and gains in melanoma karyotypic evolution. Int J Cancer. 2004;108(1):57-65.
21. Spanjaard RA, Whren KM, Graves C, Bhawan J. Tumor necrosis factor receptor superfamily member TROY is a novel melanoma biomarker and potential therapeutic target. Int J Cancer. 2007;120(6):1304-1310.
22. Abe Y, Kita Y, Niikura T. Mammalian Gup1, a homolog of Saccharomyces cerevisiae glycerol uptake/transporter 1, acts as a negative regulator for N-terminal palmitoylation of Sonic hedgehog. FEBS J. 2008;275(2):318-331.
23. Petrausch U, Martus P, Tönnies H, et al. Significance of gene expression analysis in uveal melanoma in comparison to standard risk factors for risk assessment of subsequent metastases. Eye (Lond). 2008;22(8):997-1007.