Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing

The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. We compared calls...

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Bibliographic Details
Published in:BMC medical genomics 2017-03, Vol.10 (1), p.17-17, Article 17
Main Authors: Wood, Henry M, Foster, Joseph M, Taylor, Morag, Tinkler-Hundal, Emma, Togneri, Fiona S, Wojtowicz, Paula, Oumie, Assa, Spink, Karen G, Brew, Fiona, Quirke, Philip
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatics
Carcinogenesis
Colorectal cancer
Comparative analysis
Deoxyribonucleic acid
DNA
DNA Mutational Analysis - methods
DNA sequencing
Gene expression
Gene frequency
Gene mutation
Genetic aspects
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Humans
Identification and classification
Laboratories
Mutation
Neoplasms - genetics
Oligonucleotide Array Sequence Analysis
Polymerase Chain Reaction
Precision medicine
Product development
Pseudogenes
Software
Studies
Tumors
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Summary:The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples. 392 fixed, clinical samples were sequenced, encompassing 641 PCR regions, 403 putative positive calls and 1528 putative negative calls. A small number of mutations could not be validated, either due to large indels or pseudogenes impairing parts of the NGS pipeline. For the remainder, if calls were filtered according to simple quality metrics, both sensitivity and specificity for the OncoScan platform were over 98%. This applied even to samples with poorer sample quality and lower variant allele frequency (5-10%) than product claims indicated. This benchmarking study will be useful to users and potential users of this platform, who wish to compare technologies or interpret their own results.
ISSN:1755-8794
1755-8794
DOI:10.1186/s12920-017-0254-5