High Density RT-PCR Arrays for Cancer Diagnosis and Prognosis

Pathrx, Inc., Newton MA

Investigators

Abstract

Significant progress has been made developing multi-analyte genomic signatures for the diagnosis and prognosis of cancer. However, current RT-PCR platforms require substantial high-grade RNA precluding the use of minimally invasive biopsy material as well as limiting the high-throughput needed to lower assay costs. To meet these challenges, two next-generation high-density RT -PCR platforms were evaluated during Phase I portion of the contact. The Life Technologies OpenArray/QuantStudio system was found to reduce RNA required for analysis of CRC FFPE tumor samples by 1/600th and increase the number of reactions run by 30-fold. Importantly, this instrument also maintained the sensitivity and reliability of conventional RT-PCR instruments. In Phase II , this new approach will be applied to develop a genomic signature for bladder cancer which for the first time combines measurement of gene expression, miRNA expression and mutation detection on a single high-density array capable of analyzing 16 patient samples in a single run. The overall prototype along with PathRX's proprietary RNA isolation and data analysis methods will be tested in several laboratories. The proposed work has the potential to significantly reduce the high costs and non-invasive use of cystoscopy to diagnose and manage bladder cancer, the 6th most common cancer and most expensive to treat in the US.