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 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.
Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK. h.m.wood@leeds.ac.uk.
Henry M
HM
Wood
Affymetrix UK Ltd, High Wycombe, UK.
Joseph M
JM
Foster
Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK.
Morag
M
Taylor
Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK.
Emma
E
Tinkler-Hundal
West Midland Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
Fiona S
FS
Togneri
West Midland Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
Paula
P
Wojtowicz
Affymetrix UK Ltd, High Wycombe, UK.
Assa
A
Oumie
Affymetrix UK Ltd, High Wycombe, UK.
Karen G
KG
Spink
Affymetrix UK Ltd, High Wycombe, UK.
Fiona
F
Brew
Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK.
Philip
P
Quirke
D004252:DNA Mutational Analysis / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction
Benchmarking; Mutation calling; OncoScan array