Representative sequencing: Unbiased sampling of solid tumor tissue
In: ISSN: 2211-1247, 2020
academicJournal
Zugriff:
International audience ; Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias isinherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mmbiopsy), which becomes grossly under-powered as tumor volume scales. Here, we demonstrate representative sequencing (Rep-Seq) as a new method to achieve unbiased tumor tissue sampling. Rep-Seq uses fixed residual tumor material, which is homogenized and subjected to next-generation sequencing. Analysis of intratumor tumor mutation burden (TMB) variability shows a high level of misclassification using current single-biopsy methods, with 20% of lung and 52% of bladder tumors having at least one biopsy with high TMB butlow clonal TMB overall. Misclassification rates by contrast are reduced to 2% (lung) and 4% (bladder) when a more representative sampling methodology is used. Rep-Seq offers an improved sampling protocol for tumor profiling, with significant potential for improved clinical utility and more accurate deconvolution of clonal structure.
Titel: |
Representative sequencing: Unbiased sampling of solid tumor tissue
|
---|---|
Autor/in / Beteiligte Person: | Litchfield, Kevin ; Stanislaw, Stacey ; Gallegos, Lisa ; Rowan, Andrew ; Schnidrig, Desiree ; Rosenbaum, Heidi ; Harlé, Alexandre ; Au, Lewis ; Hill, Samantha ; Tippu, Zayd ; Thomas, Jennifer ; Thompson, Lisa ; Xu, Hang ; Horswell, Stuart ; Barhoumi, Aoune ; Jones, Carol ; Leith, Katherine ; Burgess, Daniel ; Watkins, Thomas B.K. ; Birkbak, Nicolai, Juul ; Lamy, Philippe ; Nordentoft, Iver ; Dyrskjøt, Lars ; Pickering, Lisa ; Hazell, Stephen ; Jamal-Hanjani, Mariam ; Larkin, James, J ; Swanton, Charles ; Alexander, Nelson r. ; Turajlic, Samra ; Abbosh, Chris ; 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 ; Walczak, Henning ; Enver, Tariq ; Hynds, Rob ; Falzon, Mary ; Proctor, Ian ; Sinclair, Ron ; Lok, Chi-Wah ; Rhodes, Zoe ; Moore, David ; Marafioti, Teresa ; Borg, Elaine ; Mitchison, Miriam ; Khiroya, Reena ; Trevisan, Giorgia ; Ellery, Peter ; Linch, Mark ; Brandner, Sebastian ; Hiley, Crispin ; Veeriah, Selvaraju ; Razaq, Maryam ; Shaw, Heather ; Attard, Gert ; Akther, Mita Afroza ; Naceur-Lombardelli, Cristina ; Manzano, Lizi ; Al-Bakir, Maise ; Summan, Simranpreet ; Kanu, Nnenna ; Ward, Sophie ; Asghar, Uzma ; Lim, Emilia ; Gishen, Faye ; Tookman, Adrian ; Stone, Paddy ; Stirling, Caroline ; Furness, Andrew ; Edmonds, Kim ; Hunter, Nikki ; Sarker, Sarah ; Vaughan, Sarah ; Mangwende, Mary ; Pearce, Karla ; Spain, Lavinia ; Shepherd, Scott ; Yan, Haixi ; Shum, Ben ; Carlyle, Eleanor ; Hazell, Steve ; Fendler, Annika ; Byrne, Fiona ; Yousaf, Nadia ; Popat, Sanjay ; Curtis, Olivia ; Stamp, Gordon ; Toncheva, Antonia ; Nye, Emma ; Murra, Aida ; Korteweg, Justine ; Sheikh, Nahid ; Josephs, Debra ; 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 ; Stewart, Grant ; Watts, Colin ; Gilbertson, Richard ; Mcdermott, Ultan ; Tavare, Simon ; Beddowes, Emma ; Roxburgh, Patricia ; Biankin, Andrew ; Chalmers, Anthony ; Fraser, Sioban ; Oien, Karin ; Kidd, Andrew ; Blyth, Kevin ; Krebs, Matt ; Blackhall, Fiona ; Summers, Yvonne ; Dive, Caroline ; Marais, Richard ; Gomes, Fabio ; Carter, Mat ; Dransfield, Jo ; Le Quesne, John ; 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 ; Jogai, Sanjay ; Ottensmeier, Christian ; Harrison, David, L ; Loda, Massimo ; Flanagan, Adrienne ; Mckenzie, Mairead ; Hackshaw, Allan ; Ledermann, Jonathan ; Sharp, Abby ; Farrelly, Laura ; Bridger, Hayley ; Division of genetics and epidemiology ; The institute of cancer research London ; The Wellcome Trust Centre for Human Genetics Oxford ; University of Oxford ; Centre de Recherche en Automatique de Nancy (CRAN) ; Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS) ; The Royal Marsden ; University of Arizona ; University of Western Ontario, Physic and Astronomy Department ; University of Western Ontario (UWO) ; Center for Biological Sequence Analysis Lyngby ; Danmarks Tekniske Universitet = Technical University of Denmark (DTU) ; Laboratoire d'Astrophysique de Marseille (LAM) ; Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales Toulouse (CNES)-Centre National de la Recherche Scientifique (CNRS) ; Aarhus University Hospital ; Cancer Research UK Lung Cancer Centre of Excellence Londres, Royaume-Uni ; University College of London London (UCL) ; Comprehensive Cancer Center ; The Wellcome Trust Sanger Institute Cambridge ; Research Department of Pathology ; Innovation North - Faculty of Information and Technology ; Leeds Metropolitan University ; Department of histopathology ; University College Hospital ; Mammalian Genetics Laboratory ; Centre for Research on Adaptive Nanostructures and Nanodevices ; Trinity College Dublin ; Cancer Research UK London Research Institute ; Guy's and St Thomas' Hospital London ; Breakthrough Breast Cancer Centre ; London Institute of Cancer ; Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge ; University of Cambridge UK (CAM) ; Cancer Division Sydney, Australia (The Kinghorn Cancer Centre) ; Garvan Institute of medical research ; Clinical and Experimental Pharmacology Group ; Paterson Institute for Cancer Research, University of Manchester ; University of Leicester ; Experimental Cancer Medicine Centre ; University of Southampton-Faculty of Medicine ; Moses, Wittemyer, Harrison and Woodruff, P.C. |
Link: | |
Zeitschrift: | ISSN: 2211-1247, 2020 |
Veröffentlichung: | HAL CCSD ; Elsevier Inc, 2020 |
Medientyp: | academicJournal |
DOI: | 10.1016/j.celrep.2020.107550 |
Schlagwort: |
|
Sonstiges: |
|