Influence of pre-analytical factors on the success rates of smMIP and MLPA analyses in epithelial ovarian cancer

Mutation analyses are increasingly performed on tumor specimens to determine treatment eligibility and screen for genetic cancer predisposition. Sufficient tumor cell percentages and DNA concentrations are required to perform reliable mutation analyses, but even when these requirements are met, results do not always meet reliability standards. This study investigated potential factors associated with successful mutation analyses using single-molecule molecular inversion probe (smMIP)-based next generation sequencing (NGS) technology for the detection of BRCA1/2 pathogenic variants (PVs) in epithelial ovarian cancer. Data of a consecutive series of smMIP analyses performed between 2018 and 2022 in clinical practice were collected from hospital databases, including data of Multiplex Ligation-dependent Probe Amplification (MLPA) analyses if performed alongside the smMIP analysis. Data included analysis outcome (successful/not successful), storage time, histotype, FIGO stage, center of block preparation, material type, tumor cell percentage, and receival of chemotherapy. Successful analyses were defined as analyses providing test results deemed adequate for clinical decision-making, based on the judgement of a clinical scientist in molecular pathology. A minimum threshold of 100 × coverage for at least 97% of the regions of interest was applied. In total, 88.3% (401/454) of smMIP analyses and 78.4% (356/453) of MLPA analyses were successful. A time interval of ≤ 48 days between tumor specimen collection and analysis was significantly associated with successful smMIP and MLPA analyses (OR 2.05, 95% CI 1.07-3.93, p = 0.030; OR 1.88, 95% CI 1.19-2.98, p = 0.007; respectively). Based on these observations, we recommend performing the analyses directly after specimen collection to enhance efficiency and reduce costs.