Abstract 4134: Development of MUT-MAP, a high-throughput multi-analyte mutation panel for cancer biomarkers discovery.

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC Molecular profiling plays an increasingly vital role in determining treatment options in oncology. These include expression profiling, mutation detection as well as copy number variation analysis (CNV). Hence there is an increasing need for a robust and high-throughput technology to detect oncogenic hotspot mutations - and copy number variation (CNV) in various kinds of cancer. Although there are commercial assays or kits available to detect genetic aberrations in a given oncogene, there is a need to simultaneously detect these hotspots in more than a few of these genes using very little DNA. Recent technological advances such as next-generation sequencing (NGS) platforms are the powerful tools to unravel the complex biological and genetic mechanisms in different human diseases. However, there are several challenges facing NGS platforms, such as high cost, and DNA input requirement, and difficult data analysis pipeline which require much longer data turnaround time that is not feasible in the clinical setting. We have developed a high-throughput microfluidic panel for detecting 120 somatic mutations across 11 genes of therapeutic interest using TaqMan or allele-specific PCR (AS-PCR) technologies. The 11-gene mutation panel is designed to detect hotspot mutations that have higher oncogenic potential. Additionally, we can detect (CNV) changes in a total of 18 genes. This mutation panel only requires as little as 2 ng of high quality (fresh frozen) or 100 ng of formalin-fixed, paraffin-embedded (FFPE) genomic DNA. A pre-amplification of 38 amplicons is carried out to enrich DNA carrying the targeted mutations, using custom-designed primer sets followed by detection of the mutations using TaqMan/AS-PCR assays carried out on a Biomark microfluidics system. Mutation, CNV calls including an automated data analysis process have been implemented to run 88 samples per day. We will present data showing validation of this platform using plasmids and archival samples, including correlation between amplified and unamplified samples on alternate mutation detection platforms that will demonstrate sensitivity and selectivity. The platform is being routinely used in our labs to analyze tissues from patients enrolled in clinical trials. Citation Format: Rachel Nga Wan Tam, Erica Schleifman, Ling-Yuh Huw, Rupal Desai, Rajesh Patel, Rajiv Raja. Development of MUT-MAP, a high-throughput multi-analyte mutation panel for cancer biomarkers discovery. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4134. doi:10.1158/1538-7445.AM2013-4134