Representative sequencing: Unbiased sampling of solid tumor tissue

Kevin Litchfield (1) , Stacey Stanislaw , Lisa Gallegos , Andrew Rowan (2) , Desiree Schnidrig , Heidi Rosenbaum , Alexandre Harlé (3) , Lewis Au (4) , Samantha Hill (5) , Zayd Tippu , Jennifer Thomas , Lisa Thompson , Hang Xu , Stuart Horswell , Aoune Barhoumi , Carol Jones (6) , Katherine Leith , Daniel Burgess , Thomas B.K. Watkins , Nicolai Juul Birkbak (7) , Philippe Lamy (8) , Iver Nordentoft , Lars Dyrskjøt (9) , Lisa Pickering , Stephen Hazell , Mariam Jamal-Hanjani (10) , James J Larkin (11) , Charles Swanton (10) , Nelson r. Alexander , Samra Turajlic , Chris Abbosh , Kai-Keen Shiu , John Bridgewater (12) , Daniel Hochhauser , Martin Forster , Siow-Ming Lee , Tanya Ahmad , Dionysis Papadatos-Pastos , Sam Janes , Peter van Loo (13) , Katey Enfield , Nicholas Mcgranahan , Ariana Huebner , Sergio Quezada , Stephan Beck , Peter Parker , Henning Walczak , Tariq Enver , Rob Hynds , Mary Falzon , Ian Proctor (14) , Ron Sinclair , Chi-Wah Lok , Zoe Rhodes , David Moore (15) , Teresa Marafioti (16) , Elaine Borg , Miriam Mitchison , Reena Khiroya , Giorgia Trevisan , Peter Ellery , Mark Linch , Sebastian Brandner (17) , Crispin Hiley , Selvaraju Veeriah , Maryam Razaq , Heather Shaw , Gert Attard , Mita Afroza Akther , Cristina Naceur-Lombardelli , Lizi Manzano , Maise Al-Bakir , Simranpreet Summan , Nnenna Kanu , Sophie Ward , Uzma Asghar , Emilia Lim , Faye Gishen , Adrian Tookman , Paddy Stone , Caroline Stirling , Andrew Furness , Kim Edmonds , Nikki Hunter , Sarah Sarker , Sarah Vaughan , Mary Mangwende , Karla Pearce , Lavinia Spain , Scott Shepherd , Haixi Yan , Ben Shum , Eleanor Carlyle , Steve Hazell , Annika Fendler , Fiona Byrne (18) , Nadia Yousaf , Sanjay Popat , Olivia Curtis , Gordon Stamp (19) , Antonia Toncheva , Emma Nye (17) , Aida Murra , Justine Korteweg , Nahid Sheikh , Debra Josephs , Ashish Chandra (20) , James Spicer , Ula Mahadeva , Anna Green , Ruby Stewart , Lara-Rose Iredale , Tina Mackay , Ben Deakin , Debra Enting , Sarah Rudman , Sharmistha Ghosh , Lena Karapagniotou , Elias Pintus , Andrew Tutt (21) , Sarah Howlett , Vasiliki Michalarea , James Brenton , Carlos Caldas (22) , Rebecca Fitzgerald , Merche Jimenez-Linan , Elena Provenzano , Alison Cluroe , Grant Stewart , Colin Watts , Richard Gilbertson , Ultan Mcdermott , Simon Tavare , Emma Beddowes , Patricia Roxburgh , Andrew Biankin (23) , Anthony Chalmers , Sioban Fraser , Karin Oien , Andrew Kidd , Kevin Blyth , Matt Krebs , Fiona Blackhall , Yvonne Summers , Caroline Dive (24) , Richard Marais (25) , Fabio Gomes , Mat Carter , Jo Dransfield , John Le Quesne (26) , Dean Fennell , Jacqui Shaw , Babu Naidu , Shobhit Baijal , Bruce Tanchel , Gerald Langman , Andrew Robinson , Martin Collard , Peter Cockcroft , Charlotte Ferris , Hollie Bancroft , Amy Kerr , Gary Middleton , Joanne Webb , Salma Kadiri , Peter Colloby , Bernard Olisemeke , Rodelaine Wilson , Ian Tomlinson (27) , Sanjay Jogai , Christian Ottensmeier (28) , David L Harrison (29) , Massimo Loda , Adrienne Flanagan , Mairead Mckenzie , Allan Hackshaw , Jonathan Ledermann , Abby Sharp , Laura Farrelly , Hayley Bridger

1 Division of genetics and epidemiology
2 The Wellcome Trust Centre for Human Genetics [Oxford]
3 CRAN - Centre de Recherche en Automatique de Nancy
4 The Royal Marsden
5 University of Arizona
6 UWO - University of Western Ontario
7 Center for Biological Sequence Analysis [Lyngby]
8 LAM - Laboratoire d'Astrophysique de Marseille
9 Aarhus University Hospital
10 Cancer Research UK Lung Cancer Centre of Excellence [Londres, Royaume-Uni]
11 Comprehensive Cancer Center
12 UCL - University College of London [London]
13 The Wellcome Trust Sanger Institute [Cambridge]
14 Research Department of Pathology
15 Innovation North - Faculty of Information and Technology
16 Department of histopathology
17 Mammalian Genetics Laboratory
18 Centre for Research on Adaptive Nanostructures and Nanodevices
19 Cancer Research UK London Research Institute
20 Guy's and St Thomas' Hospital [London]
21 Breakthrough Breast Cancer Centre
22 Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge
23 The Kinghorn Cancer Centre - Cancer Division [Sydney, Australia]
24 Clinical and Experimental Pharmacology Group
25 The institute of cancer research [London]
26 University of Leicester
27 University of Oxford
28 Experimental Cancer Medicine Centre
29 Moses, Wittemyer, Harrison and Woodruff, P.C.

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.

Domaines: Cancer

Kevin Litchfield, Stacey Stanislaw, Lisa Gallegos, Andrew Rowan, Desiree Schnidrig, et al.. Representative sequencing: Unbiased sampling of solid tumor tissue. Cell Reports, 2020, 31 (5), pp.107550. ⟨10.1016/j.celrep.2020.107550⟩. ⟨hal-02565183⟩