Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling.
In: BMC Medical Genomics, Jg. 8 (2015-02-01), Heft 1, S. 1-13
Online
academicJournal
Zugriff:
Background: 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. Methods: In 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). Results: Cross 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%. Conclusions: Reproducibility 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. [ABSTRACT FROM AUTHOR]
Titel: |
Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling.
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Autor/in / Beteiligte Person: | Foster, Joseph M. ; Oumie, Assa ; Togneri, Fiona S. ; Vasques, Fabiana Ramos ; Hau, Debra ; Taylor, Morag ; Tinkler-Hundal, Emma ; Southward, Katie ; Medlow, Paul ; McGreeghan-Crosby, Keith ; Halfpenny, Iris ; McMullan, Dominic J. ; Quirke, Phil ; Keating, Katherine E. ; Griffiths, Mike ; Spink, Karen G. ; Brew, Fiona |
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Zeitschrift: | BMC Medical Genomics, Jg. 8 (2015-02-01), Heft 1, S. 1-13 |
Veröffentlichung: | 2015 |
Medientyp: | academicJournal |
ISSN: | 1755-8794 (print) |
DOI: | 10.1186/s12920-015-0079-z |
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