Using DNA sequencing data to quantify T cell fraction and therapy response

Robert B. Bentham; Kevin Litchfield; Thomas B.K. Watkins; Emilia L. Lim; Rachel Rosenthal; Carlos Martínez‐Ruiz; Crispin T. Hiley; Maise Al Bakir; Roberto Salgado; David A. Moore; Mariam Jamal‐Hanjani; Nicolai J. Birkbak; Mickael Escudero; Aengus Stewart; Andrew Rowan; Jacki Goldman; Peter Van Loo; Richard Stone; Tamara Denner; Emma Nye; Sophia Ward; Stefan Boeing; Maria Greco; Jérôme Nicod; Clare Puttick; Katey S.S. Enfield; Emma Colliver; Brittany Campbell; Alexander M. Frankell; Daniel E. Cook; Mihaela Angelova; Alastair Magness; Chris Bailey; Antonia Toncheva; Krijn K. Dijkstra; Judit Kisistók; Mateo Sokač; Oriol Pich; Jonas Demeulemeester; Elizabeth Larose Cadieux; Carla Castignani; Krupa Thakkar; Hongchang Fu; Takahiro Karasaki; Othman Al‐Sawaf; Mark S. Hill; Christopher Abbosh; Yin Wu; Selvaraju Veeriah; Robert E. Hynds; Andrew Georgiou; Mariana Werner Sunderland; James L. Reading; Sergio A. Quezada; Karl S. Peggs; Teresa Marafioti; John A. Hartley; Helen L. Lowe; Leah Ensell; Victoria J. Spanswick; Angeliki Karamani; Dhruva Biswas; Stephan Beck; Olga Chervova; Miljana Tanić; Ariana Huebner; Michelle Dietzen; James R. Black; Cristina Naceur‐Lombardelli; Mita Afroza Akther; Hao-Ran Zhai; Nnennaya Kanu; Simranpreet Summan; Francisco Gimeno-Valiente; Kezhong Chen; Elizabeth Manzano; Supreet Kaur Bola; Ehsan Ghorani; Marc Robert de Massy; Elena Hoxha; Emine Hatipoglu; Benny Chain; David R. Pearce; Javier Herrero; Simone Zaccaria; J.F. Lester; Fiona J. E. Morgan; Malgorzata Kornaszewska; Richard Attanoos; Haydn Adams; Helen Davies; Jacqui Shaw; Joan Riley; Lindsay Primrose; Dean A. Fennell; Apostolos Nakas; Sridhar Rathinam; Rachel Plummer; Rebecca Boyles; Mohamad Tufail; Amrita Bajaj; Jan Brožík; Keng Ang; Mohammed Fiyaz Chowdhry; William Monteiro; Hilary Marshall; Alan G. Dawson; Sara Busacca; Domenic Marrone; Claire Smith; Girija Anand; Sajid Khan; Gillian Price; Mohammed S. Khalil; Keith M. Kerr; Shirley Richardson; Heather Cheyne; J. Richard Miller; Keith Buchan; Mahendran Chetty; Sylvie Dubois-Marshall; Sara Lock; Kayleigh Gilbert; Babu Naidu; Gerald Langman; Hollie Bancroft; Salma Kadiri; Gary Middleton; Madava Djearaman; Aya Osman; Helen Shackleford; Akshay J. Patel; Angela Leek; Nicola Totten; Jack Davies Hodgkinson; Jane Rogan; Katrina Moore; Rachael Waddington; Raffaele Califano; Rajesh Shah; Piotr Krysiak; Kendadai Rammohan; Eustace Fontaine; Richard Booton; Matthew Evison; Stuart Moss; Juliette Novasio; Leena Dennis Joseph; Paul Bishop; Anshuman Chaturvedi; Helen Doran; Felice Granato; Vijay Joshi; Elaine Smith; Ángeles Montero; Philip Crosbie; Fiona Blackhall; Lynsey Priest; Matthew Krebs; Caroline Dive; Dominic G. Rothwell; Alastair Kerr; Elaine Kilgour; Katie Baker; Mathew Carter; Colin R. Lindsay; Fábio Gomes; Jonathan Tugwood; Jackie Pierce; Alexandra Clipson; Roland F. Schwarz; Tom L. Kaufmann; Matthew R. Huska; Zoltán Szállási; István Csabai; Miklós Dióssy; Hugo J.W.L. Aerts; Charles Fekete; Gary Royle; Catarina Veiga; Marcin Skrzypski; David Lawrence; Martin Hayward; Nikolaos Panagiotopoulos; Robert George; Davide Patrini; Mary Falzon; Elaine Borg; Reena Khiroya; Asia Ahmed; Magali N. Taylor; Junaid Choudhary; Sam M. Janes; Martin Förster; Tanya Ahmad; Siow Ming Lee; Neal Navani; Dionysis Papadatos-Pastos; Marco Scarci; Pat Gorman; Elisa Bertoja; Robert Stephens; Emilie Martinoni Hoogenboom; James W. Holding; Steve Bandula; Ricky M. Thakrar; Radhi Anand; Kayalvizhi Selvaraju; James M. Wilson; Sonya Hessey; Paul Ashford; Mansi Shah; Marcos Vasquez Duran; Mairead MacKenzie; Maggie Wilcox; Allan Hackshaw; Yenting Ngai; Abigail Sharp; Cristina Rodrigues; Oliver Pressey; Sean Smith; Nicole Gower; Harjot Kaur Dhanda; Kitty S. Chan; Sonal Chakraborty; Christian H. Ottensmeier; Serena Chee; Diana Johnson; Aiman Alzetani; Judith Cave; Lydia Scarlett; Emily Shaw; Eric Lim; Paulo De Sousa; Simon Jordan; Alexandra Rice; Hilgardt Raubenheimer; Harshil Bhayani; Morag Hamilton; Lyn Ambrose; Anand Devaraj; Hema Chavan; Sofina Begum; Silviu Buderi; Daniel Kaniu; Mpho Malima; Sarah Booth; Andrew G. Nicholson; Nadia Fernandes; Christopher Deeley; Pratibha Shah; Chiara Proli; Kelvin Lau; Michael Sheaff; Peter Schmid; Louise Lim; John Conibear; Madeleine Hewish; Sarah Danson; Jonathan Bury; John Edwards; Jennifer Hill; Sue Matthews; Yota Kitsanta; Jagan Rao; Sara Tenconi; Laura Socci; Kim Suvarna; Faith Kibutu; Patricia Fisher; Robin Young; Joann Barker; Fiona Taylor; Kirsty Lloyd; Michael Shackcloth; Julius Asante-Siaw; John R. Gosney; Teresa Light; Tracey Horey; Peter Russell; Dionysis Papadatos-Pastos; Kevin G. Blyth; Craig Dick; Andrew Kidd; Allan D. Kirk; Mo Asif; John Butler; Rocco Bilancia; Nikos Kostoulas; Mathew Thomas; Gareth A. Wilson; Charles Swanton; Nicholas McGranahan

doi:10.1038/s41586-021-03894-5

Using DNA sequencing data to quantify T cell fraction and therapy response

Robert B. Bentham(Cancer Research UK), Kevin Litchfield(Cancer Research UK), Thomas B.K. Watkins(The Francis Crick Institute), Emilia L. Lim(The Francis Crick Institute), Rachel Rosenthal(The Francis Crick Institute), Carlos Martínez‐Ruiz(Cancer Research UK), Crispin T. Hiley(The Francis Crick Institute), Maise Al Bakir(The Francis Crick Institute), Roberto Salgado(The University of Melbourne), David A. Moore(Royal London Hospital), Mariam Jamal‐Hanjani(Royal London Hospital), Nicolai J. Birkbak(The Francis Crick Institute), Mickael Escudero(The Francis Crick Institute), Aengus Stewart(The Francis Crick Institute), Andrew Rowan(The Francis Crick Institute), Jacki Goldman(The Francis Crick Institute), Peter Van Loo(The Francis Crick Institute), Richard Stone(The Francis Crick Institute), Tamara Denner(The Francis Crick Institute), Emma Nye(The Francis Crick Institute), Sophia Ward(The Francis Crick Institute), Stefan Boeing(The Francis Crick Institute), Maria Greco(The Francis Crick Institute), Jérôme Nicod(The Francis Crick Institute), Clare Puttick(The Francis Crick Institute), Katey S.S. Enfield(The Francis Crick Institute), Emma Colliver(The Francis Crick Institute), Brittany Campbell(The Francis Crick Institute), Alexander M. Frankell(The Francis Crick Institute), Daniel E. Cook(The Francis Crick Institute), Mihaela Angelova(The Francis Crick Institute), Alastair Magness(The Francis Crick Institute), Chris Bailey(The Francis Crick Institute), Antonia Toncheva(The Francis Crick Institute), Krijn K. Dijkstra(The Francis Crick Institute), Judit Kisistók(The Francis Crick Institute), Mateo Sokač(The Francis Crick Institute), Oriol Pich(The Francis Crick Institute), Jonas Demeulemeester(The Francis Crick Institute), Elizabeth Larose Cadieux(The Francis Crick Institute), Carla Castignani(The Francis Crick Institute), Krupa Thakkar(The Francis Crick Institute), Hongchang Fu(The Francis Crick Institute), Takahiro Karasaki(The Francis Crick Institute), Othman Al‐Sawaf(The Francis Crick Institute), Mark S. Hill(The Francis Crick Institute), Christopher Abbosh(London Cancer), Yin Wu(London Cancer), Selvaraju Veeriah(London Cancer), Robert E. Hynds(London Cancer), Andrew Georgiou(London Cancer), Mariana Werner Sunderland(London Cancer), James L. Reading(London Cancer), Sergio A. Quezada(London Cancer), Karl S. Peggs(London Cancer), Teresa Marafioti(London Cancer), John A. Hartley(London Cancer), Helen L. Lowe(London Cancer), Leah Ensell(London Cancer), Victoria J. Spanswick(London Cancer), Angeliki Karamani(London Cancer), Dhruva Biswas(London Cancer), Stephan Beck(London Cancer), Olga Chervova(London Cancer), Miljana Tanić(London Cancer), Ariana Huebner(London Cancer), Michelle Dietzen(London Cancer), James R. Black(London Cancer), Cristina Naceur‐Lombardelli(London Cancer), Mita Afroza Akther(London Cancer), Hao-Ran Zhai(London Cancer), Nnennaya Kanu(London Cancer), Simranpreet Summan(London Cancer), Francisco Gimeno-Valiente(London Cancer), Kezhong Chen(London Cancer), Elizabeth Manzano(London Cancer), Supreet Kaur Bola(London Cancer), Ehsan Ghorani(London Cancer), Marc Robert de Massy(London Cancer), Elena Hoxha(London Cancer), Emine Hatipoglu(London Cancer), Benny Chain(London Cancer), David R. Pearce(London Cancer), Javier Herrero(London Cancer), Simone Zaccaria(London Cancer), J.F. Lester(Swansea Bay University Health Board), Fiona J. E. Morgan(Cardiff and Vale University Health Board), Malgorzata Kornaszewska(Cardiff and Vale University Health Board), Richard Attanoos(Cardiff and Vale University Health Board), Haydn Adams(Cardiff and Vale University Health Board), Helen Davies(Cardiff and Vale University Health Board), Jacqui Shaw(University of Leicester), Joan Riley(University of Leicester), Lindsay Primrose(University of Leicester), Dean A. Fennell(University of Leicester), Apostolos Nakas(University Hospitals of Leicester NHS Trust), Sridhar Rathinam(University Hospitals of Leicester NHS Trust), Rachel Plummer(University Hospitals of Leicester NHS Trust), Rebecca Boyles(University Hospitals of Leicester NHS Trust), Mohamad Tufail(University Hospitals of Leicester NHS Trust), Amrita Bajaj(University Hospitals of Leicester NHS Trust), Jan Brožík(University Hospitals of Leicester NHS Trust), Keng Ang(University Hospitals of Leicester NHS Trust), Mohammed Fiyaz Chowdhry(University Hospitals of Leicester NHS Trust), William Monteiro(National Institute for Health and Care Research), Hilary Marshall(National Institute for Health and Care Research), Alan G. Dawson(University of Leicester), Sara Busacca(University of Leicester), Domenic Marrone(University of Leicester), Claire Smith(University of Leicester), Girija Anand(Chase Farm Hospital), Sajid Khan(Chase Farm Hospital), Gillian Price(Aberdeen Royal Infirmary), Mohammed S. Khalil(Aberdeen Royal Infirmary), Keith M. Kerr(Aberdeen Royal Infirmary), Shirley Richardson(Aberdeen Royal Infirmary), Heather Cheyne(Aberdeen Royal Infirmary), J. Richard Miller(Aberdeen Royal Infirmary), Keith Buchan(Aberdeen Royal Infirmary), Mahendran Chetty(Aberdeen Royal Infirmary), Sylvie Dubois-Marshall(Aberdeen Royal Infirmary), Sara Lock(Whittington Hospital), Kayleigh Gilbert(Whittington Hospital), Babu Naidu(University Hospitals Birmingham NHS Foundation Trust), Gerald Langman(University Hospitals Birmingham NHS Foundation Trust), Hollie Bancroft(University Hospitals Birmingham NHS Foundation Trust), Salma Kadiri(University Hospitals Birmingham NHS Foundation Trust), Gary Middleton(University Hospitals Birmingham NHS Foundation Trust), Madava Djearaman(University Hospitals Birmingham NHS Foundation Trust), Aya Osman(University Hospitals Birmingham NHS Foundation Trust), Helen Shackleford(University Hospitals Birmingham NHS Foundation Trust), Akshay J. Patel(University Hospitals Birmingham NHS Foundation Trust), Angela Leek(Cancer Research UK Manchester Centre), Nicola Totten(Cancer Research UK Manchester Centre), Jack Davies Hodgkinson(Cancer Research UK Manchester Centre), Jane Rogan(Cancer Research UK Manchester Centre), Katrina Moore(Cancer Research UK Manchester Centre), Rachael Waddington(Cancer Research UK Manchester Centre), Raffaele Califano(Manchester University NHS Foundation Trust), Rajesh Shah(Manchester University NHS Foundation Trust), Piotr Krysiak(Manchester University NHS Foundation Trust), Kendadai Rammohan(Manchester University NHS Foundation Trust), Eustace Fontaine(Manchester University NHS Foundation Trust), Richard Booton(Manchester University NHS Foundation Trust), Matthew Evison(Manchester University NHS Foundation Trust), Stuart Moss(Manchester University NHS Foundation Trust), Juliette Novasio(Manchester University NHS Foundation Trust), Leena Dennis Joseph(Manchester University NHS Foundation Trust), Paul Bishop(Manchester University NHS Foundation Trust), Anshuman Chaturvedi(Manchester University NHS Foundation Trust), Helen Doran(Manchester University NHS Foundation Trust), Felice Granato(Manchester University NHS Foundation Trust), Vijay Joshi(Manchester University NHS Foundation Trust), Elaine Smith(Manchester University NHS Foundation Trust), Ángeles Montero(Manchester University NHS Foundation Trust), Philip Crosbie(Cancer Research UK), Fiona Blackhall(Cancer Research UK), Lynsey Priest(Cancer Research UK), Matthew Krebs(Cancer Research UK), Caroline Dive(Cancer Research UK), Dominic G. Rothwell(Cancer Research UK), Alastair Kerr(Cancer Research UK), Elaine Kilgour(Cancer Research UK), Katie Baker(The Christie NHS Foundation Trust), Mathew Carter(The Christie NHS Foundation Trust), Colin R. Lindsay(The Christie NHS Foundation Trust), Fábio Gomes(The Christie NHS Foundation Trust), Jonathan Tugwood(University of Manchester), Jackie Pierce(University of Manchester), Alexandra Clipson(University of Manchester), Roland F. Schwarz(Max Delbrück Center), Tom L. Kaufmann(Max Delbrück Center), Matthew R. Huska(Max Delbrück Center), Zoltán Szállási(Danish Cancer Society), István Csabai(Eötvös Loránd University), Miklós Dióssy(Eötvös Loránd University), Hugo J.W.L. Aerts(Harvard University), Charles Fekete(Maastricht University), Gary Royle(London Cancer), Catarina Veiga(London Cancer), Marcin Skrzypski(Gdańsk Medical University), David Lawrence(Royal London Hospital), Martin Hayward(Royal London Hospital), Nikolaos Panagiotopoulos(Royal London Hospital), Robert George(Royal London Hospital), Davide Patrini(Royal London Hospital), Mary Falzon(Royal London Hospital), Elaine Borg(Royal London Hospital), Reena Khiroya(Royal London Hospital), Asia Ahmed(Royal London Hospital), Magali N. Taylor(Royal London Hospital), Junaid Choudhary(Royal London Hospital), Sam M. Janes(Royal London Hospital), Martin Förster(Royal London Hospital), Tanya Ahmad(Royal London Hospital), Siow Ming Lee(Royal London Hospital), Neal Navani(Royal London Hospital), Dionysis Papadatos-Pastos(Princess Alexandra Hospital NHS Trust), Marco Scarci(Royal London Hospital), Pat Gorman(Royal London Hospital), Elisa Bertoja(Royal London Hospital), Robert Stephens(Royal London Hospital), Emilie Martinoni Hoogenboom(Royal London Hospital), James W. Holding(Royal London Hospital), Steve Bandula(Royal London Hospital), Ricky M. Thakrar(Royal London Hospital), Radhi Anand(Royal London Hospital), Kayalvizhi Selvaraju(Royal London Hospital), James M. Wilson(Royal London Hospital), Sonya Hessey(Royal London Hospital), Paul Ashford(Royal London Hospital), Mansi Shah(Royal London Hospital), Marcos Vasquez Duran(Royal London Hospital), Mairead MacKenzie(The Patients Association), Maggie Wilcox(The Patients Association), Allan Hackshaw(Cancer Research UK), Yenting Ngai(Cancer Research UK), Abigail Sharp(Cancer Research UK), Cristina Rodrigues(Cancer Research UK), Oliver Pressey(Cancer Research UK), Sean Smith(Cancer Research UK), Nicole Gower(Cancer Research UK), Harjot Kaur Dhanda(Cancer Research UK), Kitty S. Chan(Cancer Research UK), Sonal Chakraborty(Cancer Research UK), Christian H. Ottensmeier(University Hospital Southampton NHS Foundation Trust), Serena Chee(University Hospital Southampton NHS Foundation Trust), Diana Johnson(University Hospital Southampton NHS Foundation Trust), Aiman Alzetani(University Hospital Southampton NHS Foundation Trust), Judith Cave(University Hospital Southampton NHS Foundation Trust), Lydia Scarlett(University Hospital Southampton NHS Foundation Trust), Emily Shaw(University Hospital Southampton NHS Foundation Trust), Eric Lim(Royal Brompton & Harefield NHS Foundation Trust), Paulo De Sousa(Royal Brompton & Harefield NHS Foundation Trust), Simon Jordan(Royal Brompton & Harefield NHS Foundation Trust), Alexandra Rice(Royal Brompton & Harefield NHS Foundation Trust), Hilgardt Raubenheimer(Royal Brompton & Harefield NHS Foundation Trust), Harshil Bhayani(Royal Brompton & Harefield NHS Foundation Trust), Morag Hamilton(Royal Brompton & Harefield NHS Foundation Trust), Lyn Ambrose(Royal Brompton & Harefield NHS Foundation Trust), Anand Devaraj(Royal Brompton & Harefield NHS Foundation Trust), Hema Chavan(Royal Brompton & Harefield NHS Foundation Trust), Sofina Begum(Royal Brompton & Harefield NHS Foundation Trust), Silviu Buderi(Royal Brompton & Harefield NHS Foundation Trust), Daniel Kaniu(Royal Brompton & Harefield NHS Foundation Trust), Mpho Malima(Royal Brompton & Harefield NHS Foundation Trust), Sarah Booth(Royal Brompton & Harefield NHS Foundation Trust), Andrew G. Nicholson(Royal Brompton & Harefield NHS Foundation Trust), Nadia Fernandes(Royal Brompton & Harefield NHS Foundation Trust), Christopher Deeley(Royal Brompton & Harefield NHS Foundation Trust), Pratibha Shah(Royal Brompton & Harefield NHS Foundation Trust), Chiara Proli(Royal Brompton & Harefield NHS Foundation Trust), Kelvin Lau(Barts Health NHS Trust), Michael Sheaff(Barts Health NHS Trust), Peter Schmid(Barts Health NHS Trust), Louise Lim(Barts Health NHS Trust), John Conibear(Barts Health NHS Trust), Madeleine Hewish(Ashford and St Peter's Hospitals NHS Foundation Trust), Sarah Danson(Sheffield Teaching Hospitals NHS Foundation Trust), Jonathan Bury(Sheffield Teaching Hospitals NHS Foundation Trust), John Edwards(Sheffield Teaching Hospitals NHS Foundation Trust), Jennifer Hill(Sheffield Teaching Hospitals NHS Foundation Trust), Sue Matthews(Sheffield Teaching Hospitals NHS Foundation Trust), Yota Kitsanta(Sheffield Teaching Hospitals NHS Foundation Trust), Jagan Rao(Sheffield Teaching Hospitals NHS Foundation Trust), Sara Tenconi(Sheffield Teaching Hospitals NHS Foundation Trust), Laura Socci(Sheffield Teaching Hospitals NHS Foundation Trust), Kim Suvarna(Sheffield Teaching Hospitals NHS Foundation Trust), Faith Kibutu(Sheffield Teaching Hospitals NHS Foundation Trust), Patricia Fisher(Sheffield Teaching Hospitals NHS Foundation Trust), Robin Young(Sheffield Teaching Hospitals NHS Foundation Trust), Joann Barker(Sheffield Teaching Hospitals NHS Foundation Trust), Fiona Taylor(Sheffield Teaching Hospitals NHS Foundation Trust), Kirsty Lloyd(Sheffield Teaching Hospitals NHS Foundation Trust), Michael Shackcloth(University of Liverpool), Julius Asante-Siaw(University of Liverpool), John R. Gosney(University of Liverpool), Teresa Light(Princess Alexandra Hospital NHS Trust), Tracey Horey(Princess Alexandra Hospital NHS Trust), Peter Russell(Princess Alexandra Hospital NHS Trust), Dionysis Papadatos-Pastos(Princess Alexandra Hospital NHS Trust), Kevin G. Blyth(NHS Greater Glasgow and Clyde), Craig Dick(NHS Greater Glasgow and Clyde), Andrew Kidd(NHS Greater Glasgow and Clyde), Allan D. Kirk(Golden Jubilee National Hospital), Mo Asif(Golden Jubilee National Hospital), John Butler(Golden Jubilee National Hospital), Rocco Bilancia(Golden Jubilee National Hospital), Nikos Kostoulas(Golden Jubilee National Hospital), Mathew Thomas(Golden Jubilee National Hospital), Gareth A. Wilson, Charles Swanton(The Francis Crick Institute), Nicholas McGranahan(Cancer Research UK)

Nature

September 8, 2021

10.1038/s41586-021-03894-5

Cited by 73Open Access

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