Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS
A. Rose Brannon, Gowtham Jayakumaran, Monica Diosdado, Juber Patel, Anna Razumova, Yu Hu, Fanli Meng, Mohammad Mahfuzul Haque, Justyna Sadowska, Brian J. Murphy, Tessara Baldi, Ian Johnson, Ryan Ptashkin, Maysun Hasan, Preethi Srinivasan, Anoop Balakrishnan Rema, Ivelise Rijo, Aaron Agarunov, Helen Won, D. S. Perera, David N. Brown, Aliaksandra Samoila, Xiaohong Jing, Erika Gedvilaite, Julie L. Yang, Dennis Stephens, Jenna-Marie Dix, Nicole DeGroat, Khédoudja Nafa, Aijazuddin Syed, Alan Li, Emily S. Lebow, Anita S. Bowman, Donna C. Ferguson, Ying Liu, Douglas A. Mata, Rohit Sharma, Soo‐Ryum Yang, Tejus Bale, Jamal Benhamida, Jason C. Chang, Snjezana Doğan, Meera Hameed, Jaclyn F. Hechtman, Christine Moung, Dara S. Ross, Efsevia Vakiani, Chad Vanderbilt, JinJuan Yao, Pedram Razavi, Lillian M. Smyth, Sarat Chandarlapaty, Gopa Iyer, Wassim Abida, James J. Harding, Benjamin A. Krantz, Eileen M. O’Reilly, Helena A. Yu, Bob T. Li, Charles M. Rudin, Luis A. Díaz, David B. Solit, Maria E. Arcila, Marc Ladanyi, Brian Houck‐Loomis, Dana W.Y. Tsui, Michael F. Berger, Ahmet Zehir, Ryma Benayed
Abstract
Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.