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Low-cost and clinically applicable copy number profiling using repeat DNA

By S Abujudeh, SS Zeki, MCV van Lanschot, M Pusung, JMJ Weaver, X Li, A Noorani, AJ Metz, J Bornschein, L Bower, A Miremadi, RC Fitzgerald, ER Morrissey, Andy G. Lynch, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS)Consortium, Rebecca C. Fitzgerald, Ayesha Noorani, Paul A.W. Edwards, Nicola Grehan, Barbara Nutzinger, Caitriona Hughes, Elwira Fidziukiewicz, Jan Bornschein, Shona MacRae, Jason Crawte, Alex Northrop, Gianmarco Contino, Xiaodun Li, Rachel de la Rue, Maria O’Donovan, Ahmad Miremadi, Shalini Malhotra, Monika Tripathi, Simon Tavaré, Andy G. Lynch, Matthew Eldridge, Maria Secrier, Lawrence Bower, Ginny Devonshire, Juliane Perner, Sriganesh Jammula, Jim Davies, Charles Crichton, Nick Carroll, Peter Safranek, Andrew Hindmarsh, Vijayendran Sujendran, Stephen J. Hayes, Yeng Ang, Shaun R. Preston, Sarah Oakes, Izhar Bagwan, Vicki Save, Richard J.E. Skipworth, Ted R. Hupp, J Robert O’Neill, Olga Tucker, Andrew Beggs, Philippe Taniere, Sonia Puig, Timothy J. Underwood, Fergus Noble, Jack Owsley, Hugh Barr, Neil Shepherd, Oliver Old, Jesper Lagergren, James Gossage, Andrew Davies, Fuju Chang, Janine Zylstra, Ula Mahadeva, Vicky Goh, Francesca D. Ciccarelli, Grant Sanders, Richard Berrisford, Catherine Harden, Mike Lewis, Ed Cheong, Bhaskar Kumar, Simon L Parsons, Irshad Soomro, Philip Kaye, John Saunders, Laurence Lovat, Rehan Haidry, Laszlo Igali, Michael Scott, Sharmila Sothi, Sari Suortamo, Suzy Lishman, George B. Hanna, Christopher J. Peters, Anna Grabowska, Richard Turkington

Posted 19 Aug 2018
bioRxiv DOI: 10.1101/394429

Large-scale cancer genome studies suggest that tumors are driven by somatic copy number alterations (SCNAs) or single-nucleotide variants (SNVs). Due to the low-cost, the clinical use of genomics assays is biased towards targeted gene panels, which identify SNVs. There is a need for a comparably low-cost and simple assay for high-resolution SCNA profiling. Here we present our method, conliga, which infers SCNA profiles from a low-cost and simple assay.

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