Cell Reports (May 2020)

Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue

  • Kevin Litchfield,
  • Stacey Stanislaw,
  • Lavinia Spain,
  • Lisa L. Gallegos,
  • Andrew Rowan,
  • Desiree Schnidrig,
  • Heidi Rosenbaum,
  • Alexandre Harle,
  • Lewis Au,
  • Samantha M. Hill,
  • Zayd Tippu,
  • Jennifer Thomas,
  • Lisa Thompson,
  • Hang Xu,
  • Stuart Horswell,
  • Aoune Barhoumi,
  • Carol Jones,
  • Katherine F. Leith,
  • Daniel L. Burgess,
  • Thomas B.K. Watkins,
  • Emilia Lim,
  • Nicolai J. Birkbak,
  • Philippe Lamy,
  • Iver Nordentoft,
  • Lars Dyrskjøt,
  • Lisa Pickering,
  • Stephen Hazell,
  • Mariam Jamal-Hanjani,
  • James Larkin,
  • Charles Swanton,
  • Nelson R. Alexander,
  • Samra Turajlic,
  • Chris Abbosh,
  • Kai-Keen Shiu,
  • John Bridgewater,
  • Daniel Hochhauser,
  • Martin Forster,
  • Siow-Ming Lee,
  • Tanya Ahmad,
  • Dionysis Papadatos-Pastos,
  • Sam Janes,
  • Peter Van Loo,
  • Katey Enfield,
  • Nicholas McGranahan,
  • Ariana Huebner,
  • Sergio Quezada,
  • Stephan Beck,
  • Peter Parker,
  • Henning Walczak,
  • Tariq Enver,
  • Rob Hynds,
  • Mary Falzon,
  • Ian Proctor,
  • Ron Sinclair,
  • Chi-wah Lok,
  • Zoe Rhodes,
  • David Moore,
  • Teresa Marafioti,
  • Elaine Borg,
  • Miriam Mitchison,
  • Reena Khiroya,
  • Giorgia Trevisan,
  • Peter Ellery,
  • Mark Linch,
  • Sebastian Brandner,
  • 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,
  • Nadia Yousaf,
  • Sanjay Popat,
  • Olivia Curtis,
  • Gordon Stamp,
  • Antonia Toncheva,
  • Emma Nye,
  • Aida Murra,
  • Justine Korteweg,
  • Nahid Sheikh,
  • Debra Josephs,
  • Ashish Chandra,
  • 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,
  • Sarah Howlett,
  • Vasiliki Michalarea,
  • James Brenton,
  • Carlos Caldas,
  • 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,
  • Anthony Chalmers,
  • Sioban Fraser,
  • Karin Oien,
  • Andrew Kidd,
  • Kevin Blyth,
  • Matt Krebs,
  • Fiona Blackhall,
  • Yvonne Summers,
  • Caroline Dive,
  • Richard Marais,
  • Fabio Gomes,
  • Mat Carter,
  • Jo Dransfield,
  • John Le Quesne,
  • 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,
  • Sanjay Jogai,
  • Christian Ottensmeier,
  • David Harrison,
  • Massimo Loda,
  • Adrienne Flanagan,
  • Mairead McKenzie,
  • Allan Hackshaw,
  • Jonathan Ledermann,
  • Abby Sharp,
  • Laura Farrelly,
  • Hayley Bridger

Journal volume & issue
Vol. 31, no. 5

Abstract

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Summary: Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), 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 but low 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.

Keywords