Abstract P2-03-17: Assessing reproducibility of copy number arrays to assist breast cancer biomarker discovery
Authors: Yao Cindy Q , Crozier Cheryl , Quintayo Mary Anne , Bayani Jane , Spears Melanie , Livingstone Julie , Jung Esther , Fung Clement , Sabine Victoria , Boutros Paul C , Bartlett John MS 
Published: May 2015

Abstract
Introduction:
Large-scale interrogation of the genome has emerged as an attractive method for identifying useful characteristics of cancer biology; in particular, the study of copy number aberrations (CNA) has recently received tremendous attention. A number of different technologies have been developed to assess the copy-number landscape, allowing us to better understand the role of CNA in cancer cells. The OncoScan CNA platform (Affymetrix Inc.) has been particularly appealing for oncology due of its ability to work well with formalin-fixed, paraffin-embedded (FFPE) materials, which is the primary form for storage of clinical samples. In addition, its high resolution, rapid analysis time and ability to interrogate different genomic characteristics (CNA, loss of heterozygosity or mutation) make the OncoScan platform highly popular: it has been widely cited in the literature for use in biomarker discovery, clonal evolution and sub-clonal detection, as well as population-based analyses. While CNAs identified by the OncoScan platform have shown good concordance with fluorescence in-situ hybridization (FISH) results, to date, no studies have been conducted to thoroughly assess the reproducibility of the assay. In this study, we have assessed the reproducibility of the OncoScan platform using identical samples performed in replicates across multiple chip batches. Moreover, we have assessed the effect on reproducibility of DNA treatment, including elution in water or TE buffer, as well as in the use of varying amounts of DNA.
Methods:
Affymetrix OncoScan FFPE Express 3.0 SNP Arrays were performed using the optimal input DNA as recommended by the manufacturer as well as fewer input amounts for comparison. CNAs were called using BioDiscovery Nexus Copy Number™ software (http://www.biodiscovery.com/software/nexus-copy-number/) using the SNP-FASST2 algorithm with modified parameters (significance threshold of 1 x 10-9 and minimum number of probes per segment of 10).
Results:
Initial reproducibility analysis involving 12 samples repeated either 2, 4 or 6 times both within a single batch and across different batches has revealed that CNA calls were concordant between replicates for the majority of the genome (ranges between 81% to 100%), suggesting high precision of the assay. In addition, we are in the process of assessing and comparing mutation calls across replicates to gain a more in-depth understanding of the platform.
Conclusion:
This is the first study examining the reproducibility of OncoScan FFPE assays; initial results have suggested that the assay is precise and has the potential for robust biomarker discovery. Additional characterizations would be interesting for evaluating its use as a clinical tool in the long term.
Citation Format: Cindy Q Yao, Cheryl Crozier, Mary Anne Quintayo, Jane Bayani, Melanie Spears, Julie Livingstone, Esther Jung, Clement Fung, Victoria Sabine, Paul C Boutros, John MS Bartlett. Assessing reproducibility of copy number arrays to assist breast cancer biomarker discovery [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-17.