Oligonucleotide Array Analysis of the HER2 Amplicon in Breast Cancers
I Lytvak, SR Gunn, I Yeh. University of Texas Health Science Center at San Antonio, San Antonio, TX
Background: HER2 amplification is associated with poor prognosis, yet targeted therapy moderates the prognosis of some patients with amplified tumors. Prior studies have shown that breast cancers often have a complex pattern of genetic abnormalities, and that HER2 amplification is rarely the only gene that is amplified. Several other genes of interest co-localize with HER2 on chromosome 17, including StAR-related lipid transfer (STARD3), Growth Factor Receptor Bound Protein 7 (GRB7), Retinoic Acid Receptor Alpha (RARA), and DNA Topoisomerase II alpha (TOP2A). We undertook an analysis of the HER2 amplicon by oligonucleotide array in HER2 gene amplified tumors, with attention to these co-localized genes. The centromere of chromosome 17 was also analyzed, because commercially available FISH assays for HER2 typically include a probe to centromere 17 (CEP 17, D17Z1).
Design: Initial HER2 studies on breast cancers were performed by immunohistochemisty and FISH. Fourteen HER2 positive cancers were selected which had fresh frozen tissue available for assay by Agilent (Santa Clara, CA, USA) human genome CGH microarray 105A. Analysis was performed using Agilent (Santa Clara, CA, USA) genomic workbench 5.0 software. Loci evaluated included the centromere region (chr17:22,615,505-22,644,166), STARD3 (chr17:35,062,877-35,073,250), HER2 (chr17:35,109,780-35,138,441), GRB7 (chr17:35,149,746-35,157,064), RARA (chr17:35,751,868-35,767,420), and TOP2A (chr17:35,798,322-35,827,695). The gene copy number was noted as loss (-0.2 to <-0.7), normal (< 0.2 to >-0.2), gain (0.2 to < 0.5), or high copy gain (> 0.5).
Results: All 14 breast tumors exhibited high copy number gain by oligonucleotide array in the HER2 locus. In addition, all cases showed co-amplification of the STARD3 and GRB7 genes. In contrast, RARA and TOP2A showed co-amplification in only in 2 cases each and loss in 4 cases each. The centromere region of chromosome 17 showed a gain in copy number in 4 cases (including 1 high copy number gain), loss in 3 cases, and was normal in 7 cases.