Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Foster JM

PROVIDER: S-EPMC4342810 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Publications

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

Foster Joseph M JM Oumie Assa A Togneri Fiona S FS Vasques Fabiana Ramos FR Hau Debra D Taylor Morag M Tinkler-Hundal Emma E Southward Katie K Medlow Paul P McGreeghan-Crosby Keith K Halfpenny Iris I McMullan Dominic J DJ Quirke Phil P Keating Katherine E KE Griffiths Mike M Spink Karen G KG Brew Fiona F

BMC medical genomics 20150218

<h4>Background</h4>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.<h4>Methods</h4>In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three indepen ...[more]

PMID: 25889064

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Dataset Information

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

Background

Methods

Results

Conclusions

Publications

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

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