Abstract P1-02-04: Array based resolution of HER2 amplification status in breast carcinomas displaying apparent chromosome 17 aneusomy

Abstract

Abstract Background: Molecular inversion probe (MIP) arrays offer high-quality copy number and genotype data with whole-genome coverage and high resolution of cancer related genes. The MIP array assay is specifically designed for use with Formalin Fixed Paraffin Embedded (FFPE) tissue due to its design which utilizes hybridization of short sequence inversion probes. In this study, we performed MIP array analysis on a cohort of breast carcinomas with putative chromosome 17 aneusomy identified by HER2/CEP17 dual probe FISH. We hypothesized that MIP array performed on cases with chromosome 17 aneusomy would allow HER2 amplification status resolution and provide additional clinically actionable data on genes with predictive and prognostic significance. Design: DNA was extracted from formalin fixed paraffin embedded tissue (Qiagen,Valencia, CA) from invasive breast carcinomas following macrodisection. Breast carcinomas utilized in this study segregated into three groups: 1) Aneusomic 2) Monosomic, and 3) Eusomic cases as determined by FISH utilizing a centromere 17 reference probe (PathVysion; Abbott Molecular). Matched patient normal lymph nodes were performed for a subset of cases from each group. MIP-array data was collected using the Affymetrix OncoScan™ array (Affymetrix, Santa Clara, CA). Analysis of array data was performed using Nexus software v6 (BioDiscovery, Inc., Hawthorne, CA). Result: Array-based detection of HER2 amplification in aneusomic breast carcinomas showed 100% concordance with single probe (HER2) FISH. However, based on genomic profiling, these cases showed great variability in regions of aneusomy along chromosome 17. In our aneusomic cohort, one region of chromosome 17 showed conserved eusomy status. This region was utilized for both array and FISH based ratio to resolve HER2 amplification status in 18 of 22 (82%) of cases. In addition to HER2 status resolution by MIP array, gains and losses in genes involved in modulating therapy were also identified, using this single assay. Conclusion: Use of MIP array-based genotyping as a single reflex assay in breast carcinomas with apparent chromosome 17 aneusomy resulted in HER2 amplification status resolution. In addition, use of this assay in our aneusomic cohort resulted in identification of a highly conserved region of chromosome 17 that is highly resistant to gains or losses in ploidy. The “D17S122” region was confirmed by FISH and use of a HER2/D17S122 ratio, allowed resolution of HER2 amplification status. In addition to HER2 status resolution and copy number data, MIP Array also provided comprehensive genomic coverage for analysis of non EGFR family genes potentially important for prognosis and therapy response prediction. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-02-04.