Abstract 4274: High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix CytoScan HD chip

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging task. Here, we report that a modified method to analyze CNV in FFPE tissues using Affymetrix Cytoscan HD chips. Our analysis showed a 91% overlap in CNV detection between FFPE and the karyotype analysis on 8 cases of lymphoma samples. The CNV overlap between frozen and the matched FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The results suggest that the modified method using Affymetrix Cytoscan HD chip represents a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE methodology may hold promise for wide application of CNV analysis on clinical samples. Citation Format: Jian-Hua Luo, Amantha Michalopoulos, Ying Ding, Yan P. Yu. High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix CytoScan HD chip. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4274. doi:10.1158/1538-7445.AM2014-4274