Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling

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 som...

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Veröffentlicht in:BMC medical genomics 2015-02, Vol.8 (1), p.5-5, Article 5
Hauptverfasser: 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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container_issue 1
container_start_page 5
container_title BMC medical genomics
container_volume 8
creator 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
description 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. 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). 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%. 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.
doi_str_mv 10.1186/s12920-015-0079-z
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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. 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). 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%. 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><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25889064</pmid><doi>10.1186/s12920-015-0079-z</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record>
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source MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central Open Access; Springer Nature OA Free Journals; Springer Nature - Complete Springer Journals; PubMed Central
subjects Analysis
Biotechnology industry
Clinical Laboratory Techniques - standards
Comparative analysis
DNA Mutational Analysis
Female
Gene Expression Profiling - methods
Gene Expression Regulation, Neoplastic
Genome, Human
Health aspects
Humans
Innovations
Loss of Heterozygosity
Male
Mutation
Neoplasms - genetics
Neoplasms - metabolism
Oligonucleotide Array Sequence Analysis - methods
Paraffin Embedding
Quality Control
Reproducibility of Results
Sensitivity and Specificity
Sequence Analysis, DNA
Technical Advance
Tissue Fixation - methods
title Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling
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