Genomic Identification of Significant Targets in Cancer (GISTIC) Analysis Resolves Regional Chromosomal Aberrations in 6q, 8p, 13q and16q of Primary Ciliochoroidal Melanomas Examined by GeneChip 250k Mapping Arrays

摘要

Purpose: : To determine the relationships between regional instabilities in chromosome copy number of ciliochoroidal melanomas and gene expression. Methods: : 58 primary ciliochoroidal melanomas were biopsied prior to plaque brachytherapy or immediately subsequent to enucleation. Nucleic acids were extracted and analyzed on Affymetrix GeneChip 250k NSPI Mapping Arrays and GeneChip U133 plus 2.0 Arrays. Mapping array data was processed through CNAT v4.01 for chromosome copy number and GISTIC for determination of regional chromosomal gain and loss information. Results: : 14 regions of deletion were found with focal regions on chromosomes 6q16.1, 8p21.3, 13q31.3 and 16q24.1 having the greatest significance. 6 regions of gain were identified with focal regions on 9p23 and 9q33.1 having the greatest significance. Conclusions: : High-resolution analysis of primary ciliochoroidal melanoma cytogenetic aberration patterns using GISTIC can be used to identify genes within focal regions of altered copy number.