title: Analytical Validation of AmpliChip p53 Research Test for Archival Human Ovarian FFPE Sections.
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.
authors.affiliation: Merck Research Laboratories, Molecular Biomarkers and Diagnostics, Rahway, New Jersey, United States of America.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Marton
authors.affiliation: Roche Molecular Systems, Inc., Pleasanton, California, United States of America.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: McNamara
authors.affiliation: Roche Molecular Systems, Inc., Pleasanton, California, United States of America.
authors.forename: D Michele
authors.initials: DM
authors.lastname: Nikoloff
authors.affiliation: Roche Molecular Systems, Inc., Pleasanton, California, United States of America.
authors.forename: Aki
authors.initials: A
authors.lastname: Nakao
authors.affiliation: Merck Research Laboratories, Clinical Oncology, North Wales, Pennsylvania, United States of America.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Cheng
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics; D005260:Female; D005557:Formaldehyde / Q000378:metabolism; D006801:Humans; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010051:Ovarian Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D016707:Tissue Fixation; D016159:Tumor Suppressor Protein p53 / Q000235:genetics* / Q000378:metabolism
chemical_list: C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D005557:Formaldehyde; D004247:DNA