Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay
Authors: Orlando Francesco , Romanel Alessandro , Trujillo Blanca , Sigouros Michael , Wetterskog Daniel , Quaini Orsetta , Leone Gianmarco , Xiang Jenny Z , Wingate Anna , Tagawa Scott , Jayaram Anuradha , Linch Mark ,   PEACE Consortium, Swanton Charles , Jamal-Hanjani Mariam , Abbosh Chris , Zaccaria Simone , Hessey Sonya , Shiu Kai-Keen , Bridgewater John , Hochhauser Daniel , Forster Martin , Lee Siow-Ming , Ahmad Tanya , Papadatos-Pastos Dionysis , Janes Sam , Van Loo Peter , Enfield Katey , McGranahan Nicholas , Huebner Ariana , Quezada Sergio , Beck Stephan , Parker Peter , Enver Tariq , Hynds Robert E , Dijkstra Krijn , Pearce David R , Falzon Mary , Proctor Ian , Sinclair Ron , Lok Chi-wah , Rhodes Zoe , Moore David , Marafioti Teresa , Mitchison Miriam , Ellery Peter , Sivakumar Monica , Linch Mark , Brandner Sebastian , Rowan Andrew , Hiley Crispin , Veeriah Selvaraju , Shaw Heather , Attard Gert , Naceur-Lombardelli Cristina , Toncheva Antonia , Prymas Paulina , Watkins Tom , Bailey Chris , Martinez Ruiz Carlos , Litchfield Kevin , Al-Bakir Maise , Kanu Nnenna , Ward Sophie , Lim Emilia , Reading James , Chain Benny , Alba Blanca Trujillo , Watkins Tom , Akay Melek , Flanagan Adrienne , Biswas Dhruva , Pich Oriol , Dietzen Michelle , Puttick Clare , Colliver Emma , Magness Alistair , Angelova Mihaela , Black James , Lucas Olivia , Hill William , Liu Wing-Kin , Frankell Alexander , Magno Neil , Athanasopoulou Foteini , Wilson Gareth , Rosenthal Rachel , Salgado Roberto , Lee Claudia , Grigoriadis Kristiana , Al-Sawaf Othman , Karasaki Takahiro , Bunkum Abigail , Noorani Imran , Benafif Sarah , Barbe Vittorio , Bola Supreet , Vainauskas Osvaldas , Wingate Anna , Wetterskog Daniel , Hasan Mahedi , Lise Stefano , Leone GianMarco , Jayaram Anuradha , Alifrangis Constantine , McGovern Ursula , Thol Kerstin , Gamble Samuel , Ung Seng Kuong , Sahwangarrom Teerapon , Marin Claudia Peinador , Wong Sophia , Pawlik Piotr , Gishen Faye , Tookman Adrian , Stone Paddy , Stirling Caroline , Turajlic Samra , Larkin James , Pickering Lisa , Furness Andrew , Young Kate , Drake Will , Edmonds Kim , Hunter Nikki , Mangwende Mary , Pearce Karla , Grostate Lauren , Au Lewis , Spain Lavinia , Shepherd Scott , Yan Haixi , Shum Ben , Tippu Zayd , Hanley Brian , Spencer Charlotte , Emmerich Max , Gerard Camille , Schmitt Andreas Michael , Del Rosario Lyra , Carlyle Eleanor , Lewis Charlotte , Holt Lucy , Lucanas Analyn , O'Flaherty Molly , Hazell Steve , Mudhar Hardeep , Messiou Christina , Latifoltojar Arash , Fendler Annika , Byrne Fiona , Pallinkonda Husayn , Lobon Irene , Coulton Alex , Cattin Anne Laure , Deng Daqi , Feng Geoffrey Hugang , Rowan Andew , Yousaf Nadia , Popat Sanjay , Curtis Olivia , Milner-Watts Charlotte , Stamp Gordon , Toncheva Antonia , Nye Emma , Murra Aida , Korteweg Justine , Kelly Denise , Terry Lauren , Biano Jennifer , Peat Kema , Kelly Kayleigh , Hill Peter , Josephs Debra , Irshad Sheeba , Chandra Ashish , Spicer James , Mahadeva Ula , Green Anna , Stewart Ruby , Iredale Lara-Rose , Mackay Tina , Deakin Ben , Enting Debra , Rudman Sarah , Ghosh Sharmistha , Karapagniotou Lena , Pintus Elias , Tutt Andrew , Howlett Sarah , Michalarea Vasiliki , Brenton James , Caldas Carlos , Fitzgerald Rebecca , Jimenez-Linan Merche , Provenzano Elena , Cluroe Alison , Paterson Anna , Aitken Sarah , Allinson Kieren , Stewart Grant , McDermott Ultan , Beddowes Emma , Maughan Tim , Ansorge Olaf , Campbell Peter , Roxburgh Patricia , Fraser Sioban , Kidd Andrew , Blyth Kevin , Le Quesne John , Krebs Matthew , Blackhall Fiona , Summers Yvonne , Oliveira Pedro , Ortega-Franco Ana , Dive Caroline , Gomes Fabio , Carter Mat , Dransfield Jo , Thomas Anne , Fennell Dean , Shaw Jacqui , Naidu Babu , Baijal Shobhit , Tanchel Bruce , Langman Gerald , Robinson Andrew , Collard Martin , Cockcroft Peter , Ferris Charlotte , Bancroft Hollie , Kerr Amy , Middleton Gary , Webb Joanne , Kadiri Salma , Colloby Peter , Olisemeke Bernard , Wilson Rodelaine , Tomlinson Ian , McNeish Iain , Jogai Sanjay , Holden Samantha , Fernandes Tania , Hampton Blanche , McKenzie Mairead , Hackshaw Allan , Sharp Abby , Chan Kitty , Farrelly Laura , Bridger Hayley , Leslie Rachel , Jamal-Hanjani Mariam , Swanton Charles , Rubin Mark A , Wyatt Alexander W , Beltran Himisha , Attard Gerhardt , Demichelis Francesca 
Published: May 2022

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 &lt;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.