Utilization of Oligo-Array CGH To Determine HER2 Amplification Status, Amplicon Genomic Span, and Co-Amplification Signatures: Potential Complementary Role to HER2 FISH Testing
Bryce P Portier, Zhen Wang, Chris Lanigan, Galina Batiouchko, Erinn Downs-Kelly, Todd Richmond, Daniel Gerhardt, Kyle Munn, Willem Haagmans, Raymond Tubbs. Cleveland Clinic, Cleveland, OH; Roche NimbleGen, Inc., Madison, WI
Background: Utilization of array-based comparative genomic hybridization (aCGH) for determination of HER2 copy number is a relatively new tool for HER2 status determination. A clear advantage of aCGH over FISH testing has been reported in cases with aneusomy of chromosome 17. FISH testing, which relies on a ratio of HER2 to Centromere 17 (HER2/CEP17) can result in inaccurate HER2 determination in cases with apparent aneusomy attributable to gain at the alphacentromeric reference locus. In this study, we utilized aCGH to determine accurate amplicon size/genomic span, intra-HER2 gene amplification variability, and to compare aCGH/FISH assay concordance.
Design: DNA was extracted from formalin fixed paraffin embedded tissue (Qiagen,Valencia, CA) from invasive breast carcinomas following macrodisection. Samples utilized in this study segregated into three groups: 1) Aneusomy 2) Monosomy, and 3) Eusomic cases as determined by FISH utilizing a centromere 17 probe (PathVysion; Abbott Molecular). A custom 720k oligo-array CGH was utilized (Roche Nimblegen, Wisconsin) that tiled chromosome 17 (probe density varied from 100bp to 7,500bp; highest density in exons). Analysis of aCGH was performed using DEVA software suite (Roche-Nimblegen, Madison, WI).
Results: Detection of HER2 amplification by aCGH was visualized and quantified by HER2 Log value. Correlation between FISH HER2 score and aCGH Log HER2 value was strong (R2= 0.97). The amplicon size in the region surrounding HER2 was highly variable among cases and did not correlate with level of HER2 amplification identified by FISH. Furthermore, aCGH demonstrated intra-HER2 gene amplification variability in the majority of cases.
Conclusions: While aCGH HER2 results strongly correlated with FISH HER2 scores, variability within the HER2 gene was only identifiable by aCGH. This variable level of intra-HER2 gene amplification cannot be elucidated by FISH testing and could partially account for the variability in patient response to Trastuzumab therapy. aCGH detects the exact amplicon size/genomic span and enables generation of a molecular profile of all co-amplified or deleted genes on chromosome 17. Generation of this molecular signature could result in improved stratification and a more informative personalized medicine approach to selecting patients for Trastuzumab based therapy. Further testing in a larger, well characterized population with clinical outcome data is warranted.
Wednesday, March 21, 2012 9:30 AM
Poster Session V # 49, Wednesday Morning