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

PLoS One. 2015 Jun 30;10(6):e0131497. doi: 10.1371/journal.pone.0131497. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Base Sequence
  • DNA / genetics
  • Female
  • Formaldehyde / metabolism
  • Humans
  • Mutation / genetics
  • Oligonucleotide Array Sequence Analysis / methods*
  • Ovarian Neoplasms / genetics*
  • Paraffin Embedding*
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Tissue Fixation*
  • Tumor Suppressor Protein p53 / genetics*
  • Tumor Suppressor Protein p53 / metabolism

Substances

  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • Formaldehyde
  • DNA

Grants and funding

This work was funded by Merck & Co, Inc. MJM and JC are employees of Merck and were involved in study design, sample acquisition and data interpretation. ARM is a current employee of Roche Molecular Systems, Inc. DMN and AN were employees of Roche Molecular Systems, Inc. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.