Background: Liquid biopsy approach has paved the way for selecting targeted therapies. When the tissue is absent, the advent of comprehensive Next Generation Sequencing (NGS) using CcfDNA has further allowed significant advances in precision oncology by pinpointing rare, novel, and actionable alterations in oncogenes, tumor suppressor genes, and cellular signaling pathways. Methods: Retrospective NGS-based genome profiling was performed on ccfDNA (circulating cell-free DNA) samples from 11 patients using OncoIndx proprietary gene panel that targets exonic regions of 600 cancer-related genes. Illumina-compatible libraries were prepared by the target hybridization method and sequenced on Nextseq 2000 platform in a pair-end fashion. Variant calling was performed using an in-house developed bioinformatics pipeline. The 11 cases comprised 5 gallbladder and 6 cholangiocarcinoma patients. Results: We uncovered several novel mutations such as MTORK1452N, ERBB2H878Y, JAK1A634T, SMAD3R287W, IDH1R132C, PRKNK161N and FGFR2Y105C. Although ERBB2H878Y and IDH1R132C are known in cholangiocarcinoma, this is the first report of gallbladder cancer. In addition to SMAD3 and PARKIN, alterations were also observed in tumor suppressor proteins APC, BARD1, BRCA1/2, and GATA2. High genomic instability as demonstrated by HRD and LOH correlated with FGFR2, PRKN, and IDH1 mutations. FAT domain mutations in mTOR such as MTORK1452N are known to be responsive to rapamycin. Similarly, ERBB2H878Y is known to respond to rapamycin as well as a TKI. The FGFR2Y105C activating mutation has previously been reported in one case of atypical Crouzon Syndrome but has never been reported in cancer. This could have potential implications for the use of FGFR2 targeting agents in cholangiocarcinoma. IDH1R132C mutation is known in ~11% of cholangiocarcinoma patients, however, this alteration has not been reported in gallbladder cancer. This observation has therapeutic implications for the use of IDH1 inhibitors in gallbladder cancer based on its promising data in cholangiocarcinoma. Conclusions: We report, for the first-time novel and actionable SNVs in key oncogenes and tumor suppressors related to critical signaling pathways in a population of gallbladder and cholangiocarcinoma patients. The data strongly underscores the importance of comprehensive NGS-based in-depth assessment in gaining clinically viable therapeutic insights for patients.