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Published on: April 11, 2016
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Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation
Henry M Wood1, Joseph M Foster2, Morag Taylor3
1Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK. h.m.wood@leeds.ac.uk.
BMC Medical Genomics
|March 20, 2017
Summary
The Affymetrix OncoScan® Array platform offers accurate mutation calling in fixed pathology samples. This study confirms its high sensitivity and specificity for personalized medicine applications.
Area of Science:
- Oncology
- Genomics
- Pathology
Background:
- Accurate mutation calling in fixed pathology samples is crucial for personalized medicine.
- The Affymetrix OncoScan® Array platform aims to provide actionable mutation calls from archival material.
Purpose of the Study:
- To benchmark the sensitivity and specificity of the OncoScan platform.
- To compare OncoScan mutation calls against a custom PCR panel and next-generation sequencing (NGS).
Main Methods:
- 392 fixed clinical tumor samples were analyzed.
- Sequencing covered 641 PCR regions, with 403 putative positive and 1528 putative negative calls.
- OncoScan platform calls were compared to those from a custom PCR panel followed by NGS.
Main Results:
- OncoScan achieved over 98% sensitivity and specificity after applying quality filters.
- High performance was maintained even with lower sample quality and variant allele frequencies (5-10%).
- A small number of mutations were unvalidated due to large indels or pseudogenes affecting the NGS pipeline.
Conclusions:
- The OncoScan platform demonstrates high accuracy for mutation detection in fixed pathology samples.
- This benchmarking study provides valuable insights for users evaluating or interpreting OncoScan results.
- The platform supports the advancement of personalized medicine through reliable analysis of archival samples.
