Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay
Francesco Orlando, Alessandro Romanel, Blanca Trujillo, Michael Sigouros, Daniel Wetterskog, Orsetta Quaini, Gianmarco Leone, Jenny Xiang, Anna Wingate, Scott T. Tagawa, Anuradha Jayaram, Mark Linch, Charles Swanton, Mariam Jamal‐Hanjani, Chris Abbosh, Simone Zaccaria, Sonya Hessey, Kai‐Keen Shiu, John Bridgewater, Daniel Hochhauser, Martin Förster, Siow Ming Lee, Tanya Ahmad, Dionysis Papadatos-Pastos, Sam M. Janes, Peter Van Loo, Katey S.S. Enfield, Nicholas McGranahan, Ariana Huebner, Sergio A. Quezada, Stephan Beck, Peter J. Parker, Tariq Enver, Robert E. Hynds, Krijn K. Dijkstra, David R. Pearce, Mary Falzon, Ian Proctor, Ron Sinclair, Chi-wah Lok, Zoe Rhodes, David Moore, Teresa Marafioti, Miriam Mitchison, Peter Ellery, Monica Sivakumar, Mark Linch, Sebastian Brandner, Andrew Rowan, Crispin T. Hiley, Selvaraju Veeriah, Heather Shaw, G. Attard, Cristina Naceur‐Lombardelli, Antonia Toncheva, Paulina Prymas, Tom Watkins, C. Donovan Bailey, Carlos Martinez Ruiz, Kevin Litchfield, Maise Al-Bakir, Nnenna Kanu, Sophia Ward, Emilia L. Lim, James L. Reading, Benny Chain, Blanca Trujillo Alba, Tom Watkins, Melek Akay, Adrienne M. Flanagan, Dhruva Biswas, Oriol Pich, Michelle Dietzen, Clare Puttick, Emma Colliver, Alistair Magness, Mihaela Angelova, James R. Black, Olivia Lucas, William Hill, Wing-Kin Liu, Alexander M. Frankell, Neil Magno, Foteini Athanasopoulou, Gareth A. Wilson, Rachel Rosenthal, Roberto Salgado, Claudia Lee, Kristiana Grigoriadis, Othman Al‐Sawaf, Takahiro Karasaki, Abigail Bunkum, Imran Noorani, Sarah Benafif, Vittorio Barbè, Supreet Kaur Bola, Osvaldas Vainauskas, Anna Wingate, Daniel Wetterskog, Mahedi Hasan
Abstract
Abstract Sequencing of cell-free DNA (cfDNA) in cancer patients’ plasma offers a minimally-invasive solution to detect tumor cell genomic alterations to aid real-time clinical decision-making. The reliability of copy number detection decreases at lower cfDNA tumor fractions, limiting utility at earlier stages of the disease. To test a novel strategy for detection of allelic imbalance, we developed a prostate cancer bespoke assay, PCF_SELECT, that includes an innovative sequencing panel covering ∼25 000 high minor allele frequency SNPs and tailored analytical solutions to enable allele-informed evaluation. First, we assessed it on plasma samples from 50 advanced prostate cancer patients. We then confirmed improved detection of genomic alterations in samples with <10% tumor fractions when compared against an independent assay. Finally, we applied PCF_SELECT to serial plasma samples intensively collected from three patients previously characterized as harboring alterations involving DNA repair genes and consequently offered PARP inhibition. We identified more extensive pan-genome allelic imbalance than previously recognized in prostate cancer. We confirmed high sensitivity detection of BRCA2 allelic imbalance with decreasing tumor fractions resultant from treatment and identified complex ATM genomic states that may be incongruent with protein losses. Overall, we present a framework for sensitive detection of allele-specific copy number changes in cfDNA.