Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay

• Published in: bioRxiv
• Main Authors: Angela Rose Brannon, Jayakumaran, Gowtham, Diosdado, Monica, Patel, Juber, Razumova, Anna, Hu, Yu, Meng, Fanli, Haque, Mohammad, Sadowska, Justyna, Murphy, Brian, Baldi, Tessera, Johnson, Ian, Ryan Ptashkin, Maysun Hasan, Srinivasan, Preethi, Anoop Balakrishnan Rema, Rijo, Ivelise, Agarunov, Aaron, Won, Helen, Perera, Dilmi, Brown, David N, Samolia, Aliaksandra, Jing, Xiaohong, Gedvilaite, Erika, Yang, Julie L, Stephens, Dennis P, Dix, Jenna-Marie, Degroat, Nicole, Nafa, Khedoudja, Aijazuddin Syed, Li, Alan, Lebow, Emily S, Bowman, Anita S, Ferguson, Donna C, Liu, Ying, Mata, Douglas A, Sharma, Rohit, Yang, Soo-Ryum, Bale, Tejus, Benhamida, Jamal K, Chang, Jason C, Dogan, Snjezana, Hameed, Meera R, Hechtman, Jaclyn F, Moung, Christine, Ross, Dara S, Vakiani, Efsevia, Vanderbilt, Chad M, Yao, Jinjuan, Razavi, Pedram, Smyth, Lillian M, Chandarlapaty, Sarat, Iyer, Gopa, Abida, Wassim, Harding, James J, Krantz, Benjamin, O'reilly, Eileen, Yu, Helena A, Li, Bob, Rudin, Charles, Diaz, Luis, Solit, David B, Arcila, Maria E, Ladanyi, Marc, Houck-Loomis, Brian, Tsui, Dana, Berger, Michael F, Zehir, Ahmet, Benayed, Ryma
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 29.06.2020; Cold Spring Harbor Laboratory
• Edition: 1.1
• Subjects: Biopsy; Biotechnology; Blood; Cancer; Clinical trials; Consultants; Copy number; Deoxyribonucleic acid; DNA; DNA fingerprinting; DNA sequencing; Epigenetics; Exons; Gene frequency; Genetic screening; Genomics; Introns; Liver cancer; Medical research; Mutation; Oncology; Patent applications; Patients; Research funding; Travel
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2020.06.27.175471

Circulating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 98% for a priori mutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance. Competing Interest Statement D.B.S. has served as a consultant for/received honoraria from Loxo Oncology, Lilly Oncology, Pfizer, QED Therapeutics, Vivideon Therapeutics and Illumina. M.E.A. received speaker fees from Raindance Technologies. M.L. has received advisory board compensation from Boehringer Ingelheim, AstraZeneca, Bristol-Myers Squibb, Takeda, and Bayer, and research support from LOXO Oncology and Helsinn Healthcare. A.R.B has stock ownership in Johnson & Johnson. S.R.Y has received consulting fees from Invitae. M.F.B. has received consulting fees from Roche and grant support from Illumina and Grail. M.F.B., D.T., P.S., J.B., B.H.L., M.H., and F.M. are co-inventors on a provisional patent application for systems and methods for detecting cancer via cfDNA screening. A.Z. received speaking fees from Illumina. B.H.L. receives royalties from BioLegend for development of products related to CITE-seq. J.H. has received research funding from Bayer, Eli Lilly, and Boehringer Ingelheim; and honoraria or consulting fees from Axiom Healthcare Stetegies, WebMD, Illumina, and Cor2Ed. K.N. has received honoraria from Biocartis. S.C. has received consulting fees from Sermonix, Paige.ai, Novartis, and Lilly. J.J.H. has received consulting fees from Bristol Myers Squibb, Exelexis, Eisai, Merck, ImVax, CytomX, and Eli Lilly and research support from Bristol Myers Squibb, the Wien Initiative in Liver Cancer Research, and the Society of MSKCC. H.Y. has consulted for AstraZeneca, Blueprint Medicine, Janssen Oncology and Daiichi. Her institution has received research funding for clinical trials from AstraZeneca, Daiichi, Pfizer, Novartis, Cullinan Oncology, Lilly. W.A. has received research funding from AstraZeneca, Zenith Epigenetics, Clovis Oncology, GlaxoSmithKline; and honoraria or consulting fees from CARET, Clovis Oncology, Janssen, MORE Health, ORIC Pharmaceuticals, Daiichi Sankyo. L.M.S. is an employee of Loxo Oncology at Lilly. LMS has consulted for Novartis, Pfizer, AstraZeneca and Roche Genentech; received research funding from AstraZeneca, Puma Biotechnology and Roche Genentech; travel or accommodations expenses from AstraZeneca, Pfizer, Puma Biotechnology and Roche Genentech; honoraria from Pfizer and AstraZeneca. D.T. has received research support from ThermoFisher Scientific, EPIC Sciences, speaking honoraria and travel support from Nanodigmbio, Cowen, BoA Merrill Lynch, D.T. and L.D. are co-inventors on a provisional patent application for systems and methods for distinguishing pathological mutations from clonal hematopoietic mutations in plasma cell-free DNA by fragment size analysis. R.B. has received a grant and travel credit from ArcherDx, honoraria for advisory board participation from Loxo oncology and speaking fees from Illumina.