Abstract 3640: Validation of qBiomarker as an accurate and efficient mutation detection method in a comprehensive analysis of patient-derived tumor xenografts

• Published in: Cancer research (Chicago, Ill.) Ill.), 2016-07, Vol.76 (14_Supplement), p.3640-3640
• Main Authors: Brait, Mariana, Izumchenko, Evgeny, Kagohara, Luciane, Long, Samuel, Wysocki, Piotr, Faherty, Brian, Fertig, Elana, Khor, Tin, Bruckheimer, Elizabeth, Baia, Gilson, Ciznadija, Daniel, Sloma, Ido, Ben-Zvi, Ido, Paz, Keren, Sidransky, David
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2016-3640

Screening of patients for cancer-driving mutations is now used for cancer prognosis, remission scoring and treatment selection. Although recently emerged targeted Next Generation Sequencing (NGS) - based approaches provide accurate results and offer promising diagnostic capabilities, there are still limitations which impede their adoption for large-scale population-based screening. There is a pressing clinical need for a well-validated, rapid, cost-effective and accurate mutation profiling system with optimal analytical performance in patient specimens. Given their speed, and cost-effectiveness, real-time, quantitative qPCR mutation detection techniques are well suited for the clinical environment. The novel qBiomarker somatic mutation PCR array has high sensitivity and shorter turnaround times compared to other methods. However a direct comparison to existing viable alternatives is required to assess its true potential and limitations. In this study, we extensively evaluated a panel of 117 patient-derived tumor xenografts (PDX) by the qBiomarker array and directly compared its efficacy with that of other routinely used methods for mutation detection, including Ion AmpliSeq sequencing, whole exome sequencing (WES), and ultra-sensitive droplet digital PCR (ddPCR) genotyping. Our comprehensive analysis demonstrates that qBiomarker's performance is on par with that of other routinely used but more complex, labor-intensive and expensive methods of cancer mutation detection, and provides a foundation for advancing the adoption of qBiomarker assay for cancer driving mutation profiling in clinical diagnostics. Furthermore, a large-scale direct comparison of different mutation detection approaches will lead to informed choice of screening methodologies, especially in lower budget conditions or timeframe limitations. Citation Format: Mariana Brait, Evgeny Izumchenko, Luciane Kagohara, Samuel Long, Piotr Wysocki, Brian Faherty, Elana Fertig, Tin Khor, Elizabeth Bruckheimer, Gilson Baia, Daniel Ciznadija, Ido Sloma, Ido Ben-Zvi, Keren Paz, David Sidransky. Validation of qBiomarker as an accurate and efficient mutation detection method in a comprehensive analysis of patient-derived tumor xenografts. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3640.