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Genomic and Expression Analysis of the 12p11-p12 Amplicon Using EST Arrays Identifies Two Novel Amplified and Overexpressed Genes¹

Cell Biology Program [V. B., P. H. R., R. S. K. C.], Department of Medicine [G. J. B., R. S. K. C.], and Department of Pathology [V. R.], Memorial Sloan-Kettering Cancer Center, New York, New York 10021; Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021 [F. N.]; Laboratory of Gynecologic Oncology, Brigham and Women’s Hospital, Boston, Massachusetts 02115 [S. C. M.]; College of Physicians and Surgeons, Columbia University, New York, New York 10032 [S. K., V. V. V. S. M.]; and Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02155 [R. S. K.]

We performed parallel array comparative genomic hybridization and array expression analysis of the 12p11-p12 amplicon in human testicular seminomas and an ovarian carcinoma cell line using an expressed sequence tags (ESTs) array spotted with 8254 ESTs. The data were normalized using a robust statistical modeling and the significance inferred from the local SD. We identified two ESTs within the chromosomal amplicon that were amplified and overexpressed in 75–100% of analyzed tumors with the 12p11-p12 amplicon. These sequences, belonging to coding regions of two novel genes designated here as GCT1 and GCT2, were broadly expressed in a panel of human tissues, including testis and ovary. GCT1 and GCT2 were overexpressed in 92 and 71%, respectively, of a panel of seminomas tested. Combined array comparative genomic hybridization and array expression analysis is a valid approach for gene discovery in large chromosomal amplicons.