Expansion of Oncomine Cell-Free Research Panels to Enable Copy Number and Gene Fusion Detection from Liquid Biopsy Samples.

e24075 Background: With recent advances in next-generation sequencing technologies, it is now possible to detect somatic mutations with allele frequencies as low as 0.1% from circulating tumor DNA in blood samples. A natural extension to this achievement is adding the ability to simultaneously detect copy number variants and gene fusions. A panel such as this addresses a full repertoire of variant classes found to be linked with certain tumors and provides researchers additional tool sets to profile cancer samples dynamically. Methods: To achieve this, we have recently launched two new Oncomine cell-free assays to target all variant classes in lung and breast cancers. Control samples were used to test sensitivity and specificity of the assays. Results: In addition to maintaining the ability to detect somatic mutations at 0.1% limit of detection with > 80% sensitivity and > 98% specificity, we have reproducibly demonstrated detection of MET, ERBB2, FGFR1, and CCND1 gene amplifications at 1.4 fold difference with > 90% sensitivity and specificity. Input titration experiment demonstrated the robustness of CNV detection with as low as 1 ng cfDNA input. We also demonstrated the capability of detecting gene fusions simultaneously with DNA variants with no negative impact on sensitivity and specificity. Titration approach has demonstrated high sensitivity and specificity as fusion targets can be detected when as low as 10 copies are present in a sample. Conclusions: Overall, we have shown the ability to reproducibly and simultaneously detect copy number and gene fusion variants as well as somatic mutations at very low limits of detection in cell-free nucleic acid background derived from blood samples.