98. Utility and feasibility of Molecular Profiling of Circulating Tumor RNA (ctRNA) from FNA Supernatants

Aly Abdelkareem

Mohamed H. Maher

Currently, I’m a Sr. Research Assistant in the Genomic test development laboratory at The University of Texas, MD Anderson, Translational molecular pathology (TMP), my main focus is to develop new techniques for cancer genotyping in liquid biopsies, hematological malignancies, and solid tumors; partners with the Molecular Diagnostic Laboratory (MDL) at MD Anderson to assess, optimize and validate novel molecular diagnostic tests to facilitate transition into the CLIA environment. Before that, I Joined TMP as a Postdoctoral fellow for 2.5 years with a focus on studying the Impact of the genetic and epigenetic states in the development of Cholangiocarcinoma via cell lines and Experimental animals models

For Over 10 years, I have been fortunate a great multidisciplinary experience with great mentors, including my early clinical pharmacy practice, MSc study in Microbiology and Immunology, and a Ph.D. in Cancer Biology. This enriched my career goal to be fully committed to combating cancer via strong Clinical and translational research.

Besides academia and with more than 4 years of experience in Roche (Genentech), Egypt. Which raised my understanding of monoclonal Antibodies and TKI therapy in Colorectal, Lung, and Breast cancer and running clinical trials and drug pipelines in different disease areas via practice and highly specialized pieces of training I took in China, Turkey, Morocco, Tunis, and Dubai.


Mohamed H. Mahera, Dzifa Y. Duoseb, Gabrielle Carillob, Jessica Lanb, Ignacio I. Wistubab, Rajyalakshmi Luthrab, Sinchita Roy Chowdhurib

aThe University of Texas MD Anderson Cancer Center / Assiut University, SECI, Houston, TX, USA; bThe University of Texas MD Anderson Cancer Center, Houston, TX, USA

With the increasing use of targeted therapeutics in solid organ malignancies, DNA and RNA-based NGS assays are being used for comprehensive molecular diagnostics. Prior studies have shown that supernatant fluid derived from fine-needle aspiration (FNA) samples that are routinely discarded, provide substantial amounts of DNA and can be effectively used for DNA-based mutational analysis. In this study, we evaluated the feasibility of using ctRNA extracted from FNA supernatants for NGS-based fusion detection using three different extraction kits.

To evaluate the ctRNA extraction efficiency from FNA supernatants 17 specimens were processed with three different commercially available kits from Qiagen (cat # 217184), Norgen (cat # 57600), and ThermoFisher (cat# 36716). The RNA quantity (Qubit), quality (DV200), and purity (A260/280) were compared across the kits. The Norgen kit provided the most consistent overall performance with a median yield of 54.8 ng/ul, (range 119.3 and IQR 43.55) and a median DV200 of 31.68, (range 38.22 and IQR 13.8).

Eight of these samples were sequenced on the Oncomine Lung CfTNA panel (ThermoFisher). One sample demonstrated a MET exon 14 skipping mutation (MET-MET.M13-M15) covered by the Oncomine Lung cfTNA Research Assay. A second sample detected a KRAS G12C mutation but no fusions. And both samples had concurrent NGS analysis of the corresponding cytologic FNA tissue specimen that confirmed the findings. These results demonstrate a need for further studies investigating the ability to utilize otherwise-discarded supernatant fluid from cytology specimens to provide clinically relevant genomic information using both DNA and RNA-based assays.