Abstract 626: Cross-site reproducibility and orthogonal validation of copy number and somatic mutation calls of OncoScan® FFPE Assay Kit in solid tumors
Authors: Foster Joseph M. , Oumie Assa , Togneri Fiona S. , Taylor Morag , Alyas Sofia , Wojtowicz Paula , Wood Henry , Tinkler-Hundal Emma , Southward Katie , McMullan Dominic , Quirke Phil , Keating Katherine E. , Griffiths Mike , Spink Karen G. , Brew Fiona , Fung Eric , Schmidt Jeanette 
Published: August 2015

Abstract
Objectives
Copy number (CN) and somatic mutation (SM) analysis in tumors is rapidly gaining importance in cancer management as a tool for differential diagnosis, determination of prognosis, and selection of therapeutic. Genome-wide copy number and LOH detection as well as a panel of frequently tested somatic mutations can be detected with OncoScan® FFPE Assay Kit. We report on a validation study of OncoScan FFPE Assay Kit CN and SM data by orthogonal technologies (FISH and NGS, respectively) to estimate the sensitivity and specificity parameters of the platform. In addition, we assessed the reproducibility of the platform across three different sites in the UK: Leeds Institute of Cancer and Pathology (LICP), West Midlands Regional Genetics Laboratory (WMRGL), and Almac Diagnostics (Almac).
Methods
Validation of CN data was performed on a cohort of cancer samples identified as Her2 positive/ambiguous by FISH. The panel of SMs available was validated by a custom targeted amplicon NGS panel on a diverse collection of samples derived from multiple cohorts across several tumor types sourced from both LICP and WMRGL. For the reproducibility study, 162 samples encompassing six different tumor types (breast, colorectal, lung, melanoma, prostate, and ovarian) were collected from LICP and WMRGL. DNA was extracted and plated in triplicate and distributed to the three testing sites: LICP, WMRGL, and Almac. Data from all sites was analyzed for reproducibility of genome-wide CN/LOH calls and SM calls.
Results
Cross-site comparisons of genome-wide CN and LOH profiles on 162 FFPE solid tumor samples showed greater than 95% average agreement between three sites (LICP, WMGRL, and Almac), while SM classification concordance between the sites averaged 97%. Initial orthogonal validation of Her2 amplification by FISH showed greater than 90% concordance, as did initial test samples used for validating OncoScan SM calls by a targeted amplicon NGS panel.
Conclusion
In this study we validated both CN and SM calls using OncoScan FFPE Assay Kit and demonstrated a high degree of agreement with orthogonal methods in all aspects. Reproducibility of whole-genome CN, LOH, and SM data using OncoScan FFPE Assay Kit has also been demonstrated for a range of FFPE samples, including highly degraded samples. This study is a step forward in evaluating the potential clinical utility of a platform combining genome-wide copy number and somatic mutation calls within the national health service of the UK.
Citation Format: Joseph M. Foster, Assa Oumie, Fiona S. Togneri, Morag Taylor, Sofia Alyas, Paula Wojtowicz, Henry Wood, Emma Tinkler-Hundal, Katie Southward, Dominic McMullan, Phil Quirke, Katherine E. Keating, Mike Griffiths, Karen G. Spink, Fiona Brew, Eric Fung, Jeanette Schmidt. Cross-site reproducibility and orthogonal validation of copy number and somatic mutation calls of OncoScan® FFPE Assay Kit in solid tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 626. doi:10.1158/1538-7445.AM2015-626