Analytical Validation of AmpliChip p53 Research Test for Archival Human Ovarian FFPE Sections.

Matthew J Marton,D Michele Nikoloff,Aki Nakao,Jonathan Cheng,Andrew R Mcnamara,Sumitra Deb

doi:10.1371/journal.pone.0131497

Matthew J Marton, D Michele Nikoloff + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0131497

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Journal: PloS one	Publication Date: Jun 30, 2015
Citations: 2	License type: CC BY 4.0

Affiliation: MSD (United States), Materials Systems (United States)

Abstract

The p53 tumor suppressor gene (TP53) is reported to be mutated in nearly half of all tumors and plays a central role in genome integrity. Detection of mutations in p53 can be accomplished by many assays, including the AmpliChip p53 Research Test. The AmpliChip p53 Research Test has been successfully used to determine p53 status in hematologic malignancies and fresh frozen solid tissues but there are few reports of using the assay with formalin fixed, paraffin-embedded (FFPE) tissue. The objective of this study was to describe analytical performance characterization of the AmpliChip p53 Research Test to detect p53 mutations in genomic DNA isolated from archival FFPE human ovarian tumor tissues. Method correlation with sequencing showed 96% mutation-wise agreement and 99% chip-wise agreement. We furthermore observed 100% agreement (113/113) of the most prevalent TP53 mutations. Workflow reproducibility was 96.8% across 8 samples, with 2 operators, 2 reagent lots and 2 instruments. Section-to-section reproducibility was 100% for each sample across a 60 μm region of the FFPE block from ovarian tumors. These data indicate that the AmpliChip p53 Research Test is an accurate and reproducible method for detecting mutations in TP53 from archival FFPE human ovarian specimens.

Highlights

The p53 tumor suppressor gene (TP53) is one of the most studied genes in cancer, with more than 38,000 articles devoted to its study over the past 25 years [1,2,3]
Sanger sequencing is a gold standard for genotyping, it is not ideal for detecting somatic mutations that can be present in low abundance, from the shorter, degraded genomic DNA fragments that are typically obtained from FFPE tissue
The accurate and reproducible determination of TP53 mutation status of cancer specimens has become increasingly important to the interpretation of research results

Summary

Introduction

The p53 tumor suppressor gene (TP53) is one of the most studied genes in cancer, with more than 38,000 articles devoted to its study over the past 25 years [1,2,3]. The protein product of the TP53 gene is a transcription factor which is activated in response to a variety of cellular insults

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