Abstract
BackgroundAdoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations.MethodsIn this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing).ResultsCross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%.ConclusionsReproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0079-z) contains supplementary material, which is available to authorized users.
Highlights
Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance
In order to evaluate the effect on copy number (CN) and loss of heterozygosity (LOH) results we calculated the genome-wide percentage CN Call agreement for the 56 samples affected by the plating issue on pairs of labs rather than all three sites
The low quantities of DNA available from Formalin fixed paraffin embedded (FFPE) together with the time and costs associated with employing multiple testing strategies highlight a need for multiplexing technologies that allow a broader view of the whole cancer genome from one test, ensuring that patients are diagnosed, stratified appropriately and that correct therapies are employed in clinically relevant timeframes
Summary
Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations. The genetic profiling of FFPE samples provides valuable clinical information for diagnosis, Foster et al BMC Medical Genomics (2015) 8:5 most assays are optimised to work with high quality and sufficient quantities of DNA isolated from fresh tissue. The OncoScan® FFPE Assay Kit (OncoScan® assay) has been optimised for whole genome copy number (CN), loss of heterozygosity (LOH) and somatic mutation (SM) detection from highly degraded FFPE samples. Based on molecular inversion Probe (MIP) [4] technology, this SNP assay provides whole genome coverage with increased resolution in approximately 900 cancer genes while currently detecting 74 clinically actionable SMs commonly found in 9 cancer genes. The OncoScan® assay has been adopted in a number of research and translational laboratories and its utility across a range of tumour types reported [5,6,7,8]
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