MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution

Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UKClare Puttick, Michelle M. Leung, Andrew Rowan, Oriol Pich, Carlos Martinez-Ruiz, Krijn K. Dijkstra, James R. M. Black, Rachel Rosenthal, David A. Moore, Gareth A. Wilson, Rachel Rosenthal, Andrew Rowan, Chris Bailey, Claudia Lee, Emma Colliver, Katey S. S. Enfield, Mark S. Hill, Mihaela Angelova, Oriol Pich, Dhruva Biswas, Clare Puttick, Roberto Vendramin, Cian Murphy, Maria Zagorulya, Michelle M. Leung, Emilia L. Lim, James R. sM Black, Maise Al Bakir, Ariana Huebner, Kristiana Grigoriadis, Takahiro Karasaki, Alexander M. Frankell, Crispin T. Hiley, Sophia Ward, Sian Harries, Olivia Lucas, David A. Moore, Nicolai J. Birkbak, Carlos Martínez-Ruiz, Charles Swanton, Jayant K. Rane & Charles SwantonCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UKClare Puttick, Thomas P. Jones, Michelle M. Leung, Carlos Martinez-Ruiz, Robert Bentham, James R. M. Black, Clare Puttick, Thomas P. Jones, Michelle M. Leung, Nicholas McGranahan, James R. sM Black, Ariana Huebner, Kristiana Grigoriadis, Carlos Martínez-Ruiz, Kerstin Thol, Robert Bentham, Charles Swanton, Charles Swanton & Nicholas McGranahanCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UKClare Puttick, Thomas P. Jones, Michelle M. Leung, Felipe Galvez-Cancino, Oriol Pich, Carlos Martinez-Ruiz, Robert Bentham, Krijn K. Dijkstra, James R. M. Black, Nnennaya Kanu, David A. Moore, Mariam Jamal-Hanjani, Sergio A. Quezada, Oriol Pich, Dhruva Biswas, Clare Puttick, Roberto Vendramin, Thomas P. Jones, Michelle M. Leung, Nicholas McGranahan, Jeanette Kittel, Kerstin Haase, Kexin Koh, Rachel Scott, Christopher Abbosh, Corentin Richard, Cristina Naceur-Lombardelli, Francisco Gimeno-Valiente, Krupa Thakkar, Mariana Werner Sunderland, Monica Sivakumar, Nnennaya Kanu, Ieva Usaite, Sadegh Saghafinia, Selvaraju Veeriah, Sharon Vanloo, Bushra Mussa, Michalina Magala, Elizabeth Keene, Emilia L. Lim, James R. sM Black, Maise Al Bakir, Ariana Huebner, Kristiana Grigoriadis, Takahiro Karasaki, Alexander M. Frankell, Crispin T. Hiley, Sophia Ward, Sian Harries, Olivia Lucas, David A. Moore, Nicolai J. Birkbak, Carlos Martínez-Ruiz, Kerstin Thol, Robert Bentham, Wing Kin Liu, Abigail Bunkum, Sonya Hessey, Martin D. Forster, Siow Ming Lee, Mariam Jamal-Hanjani, Despoina Karagianni, Sergio A. Quezada, Supreet Kaur Bola, Kevin Litchfield, Simone Zaccaria & Nicholas McGranahanCancer Immunology Unit, Immune Regulation and Tumour Immunotherapy Laboratory, Research Department of Haematology, University College London Cancer Institute, London, UKFelipe Galvez-Cancino, Jiali Liu, Sergio A. Quezada, Sergio A. Quezada & Supreet Kaur BolaCancer Cell Biology Laboratory, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, ChileManuel Varas-GodoyCentro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, ChileManuel Varas-GodoyDepartment of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The NetherlandsKrijn K. DijkstraOncode Institute, Utrecht, The NetherlandsKrijn K. DijkstraTumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UKKevin Litchfield, Roberto Vendramin & Kevin LitchfieldDivision of Research, Peter MacCallum Cancer Centre, Melbourne, AustraliaRoberto Salgado & Roberto SalgadoDepartment of Pathology, ZAS Hospitals, Antwerp, BelgiumRoberto Salgado & Roberto SalgadoDepartment of Cellular Pathology, University College London Hospitals, London, UKDavid A. Moore, David A. Moore, Teresa Marafioti, Elaine Borg, Mary Falzon & Reena KhiroyaCancer Genomics Laboratory, The Francis Crick Institute, London, UKPeter Van Loo, Carla Castignani, Elizabeth Larose Cadieux & Peter Van LooDepartment of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USAPeter Van Loo & Peter Van LooDepartment of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USAPeter Van Loo & Peter Van LooCancer Metastasis Laboratory, University College London Cancer Institute, London, UKMariam Jamal-Hanjani, Jeanette Kittel, Kerstin Haase, Kexin Koh, Rachel Scott, Takahiro Karasaki, Wing Kin Liu, Abigail Bunkum, Sonya Hessey & Mariam Jamal-HanjaniDepartment of Medical Oncology, University College London Hospitals, London, UKMariam Jamal-Hanjani, Martin D. Forster, Siow Ming Lee, Mariam Jamal-Hanjani, Charles Swanton, Dionysis Papadatos-Pastos, James Wilson, Tanya Ahmad, Sarah Benafif & Charles SwantonAberdeen Royal Infirmary NHS Grampian, Aberdeen, UKHeather Cheyne, Mohammed Khalil, Shirley Richardson & Tracey CruickshankAcademic Division of Thoracic Surgery, Imperial College London, London, UKEric LimRoyal Brompton and Harefield Hospitals, part of Guy’s and St Thomas’ NHS Foundation Trust, London, UKEric Lim, Paulo De Sousa, Simon Jordan, Alexandra Rice, Hilgardt Raubenheimer, Harshil Bhayani, Lyn Ambrose, Anand Devaraj, Hemangi Chavan, Sofina Begum, Silviu I. Buderi, Daniel Kaniu, Mpho Malima, Sarah Booth, Nadia Fernandes, Pratibha Shah, Chiara Proli & Andrew G. NicholsonArtificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USAHugo J. W. L. AertsDepartment of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USAHugo J. W. L. AertsRadiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The NetherlandsHugo J. W. L. AertsBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, GermanyTom L. KaufmannBerlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin, GermanyTom L. Kaufmann & Roland F. SchwarzBioinformatics and Systems Biology, Method Development and Research Infrastructure, Robert Koch Institute, Berlin, GermanyMatthew R. HuskaBirmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UKBabu NaiduBill Lyons Informatics Centre, University College London Cancer Institute, London, UKDhruva BiswasMedical Genomics, University College London Cancer Institute, London, UKCarla Castignani, Elizabeth Larose Cadieux, Stephan Beck & Miljana TanicCancer Research Centre, University of Leicester, Leicester, UKGurdeep Matharu & Jacqui A. ShawCancer Research UK & UCL Cancer Trials Centre, London, UKAllan Hackshaw, Camilla Pilotti, Rachel Leslie, Anne-Marie Hacker, Sean Smith & Aoife WalkerDepartment of Thoracic Surgery, Respiratory Center, Toranomon Hospital, Tokyo, JapanTakahiro KarasakiAdvanced Sequencing Facility, The Francis Crick, London, UKSophia Ward & Sian HarriesComputational Cancer Genomics Research Group, University College London Cancer Institute, London, UKOlivia Lucas, Abigail Bunkum, Sonya Hessey & Simone ZaccariaUniversity College London Hospitals, London, UKOlivia Lucas, Emilie Martinoni Hoogenboom, Fleur Monk, James W. Holding, Junaid Choudhary, Kunal Bhakhri, Pat Gorman, Robert C. M. Stephens, Maria Chiara Pisciella, Steve Bandula & Yien Ning Sophia WongDepartment of Molecular Medicine, Aarhus University Hospital, Aarhus, DenmarkNicolai J. BirkbakDepartment of Clinical Medicine, Aarhus University, Aarhus, DenmarkNicolai J. BirkbakBioinformatics Research Centre, Aarhus University, Aarhus, DenmarkNicolai J. BirkbakImmune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UKDespoina KaragianniCancer Research UK Scotland Institute, Glasgow, UKJohn Le QuesneInstitute of Cancer Sciences, University of Glasgow, Glasgow, UKJohn Le QuesneNHS Greater Glasgow and Clyde Pathology Department, Queen Elizabeth University Hospital, Glasgow, UKJohn Le QuesneThe Institute of Cancer Research, London, UKKhalid AbdulJabbar & Anca GrapaCentre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, London, UKCatarina VeigaCRUK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UKJonathan Tugwood & Caroline DiveCancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UKJonathan Tugwood, Caroline Dive, Colin R. Lindsay, Fiona H. Blackhall, Yvonne Summers, Anshuman Chaturvedi, Pedro Oliveira, Katherine D. Brown, Mathew Carter & Philip CrosbieDanish Cancer Institute, Copenhagen, DenmarkZoltan Szallasi & Miklos DiossyComputational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USAZoltan Szallasi & Miklos DiossyDepartment of Bioinformatics, Semmelweis University, Budapest, HungaryZoltan SzallasiDepartment of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, HungaryMiklos DiossyDepartment of Haematology, University College London Hospitals, London, UKKarl S. PeggsCancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UKKarl S. PeggsDepartment of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UKGillian PriceUniversity of Aberdeen, Aberdeen, UKGillian Price & Keith M. KerrDepartment of Medical Physics and Bioengineering, University College London Cancer Institute, London, UKGary Royle & Charles-Antoine Collins-FeketeThe Whittington Hospital NHS Trust, London, UKSarah Benafif, Jack French & Kayleigh GilbertDepartment of Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UKJudith CaveDepartment of Pathology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UKKeith M. KerrDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USAThomas B. K. WatkinsDepartment of Radiology, University College London Hospitals, London, UKAlexander James Procter, Asia Ahmed, Magali N. Taylor & Arjun NairUCL Respiratory, Department of Medicine, University College London, London, UKArjun NairDepartment of Thoracic Surgery, University College London Hospital NHS Trust, London, UKDavid Lawrence & Davide PatriniDivision of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UKColin R. Lindsay, Fiona H. Blackhall, Yvonne Summers & Matthew G. KrebsExperimental Histopathology, The Francis Crick Institute, London, UKEmma Nye & Richard Kevin StoneGarvan Institute of Medical Research, Darlinghurst, New South Wales, AustraliaHanyun ZhangGenomics Science Technology Platform, The Francis Crick Institute, London, UKJerome NicodGolden Jubilee National Hospital, Clydebank, UKAlan Kirk, Mo Asif, Rocco Bilancia, Nikos Kostoulas, Jennifer Whiteley & Mathew ThomasGuy’s and St Thomas’ NHS Foundation Trust, London, UKAkshay J. PatelIndependent Cancer Patient’s Voice, London, UKDavid Chuter & Mairead MacKenzieInstitute for Computational Cancer Biology, Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, GermanyRoland F. SchwarzInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UKAndrew KiddInstitute of Nuclear Medicine, Division of Medicine, University College London, London, UKFrancesco FraioliInstitute of Structural and Molecular Biology, University College London, London, UKPaul AshfordIntegrated Radiology Department, North-Buda St. John’s Central Hospital, Budapest, HungaryZoltan KaplarInstitute of Nuclear Medicine, University College London Hospitals, London, UKZoltan KaplarIntegrative Cancer Genomics Laboratory, VIB Center for Cancer Biology, Leuven, BelgiumJonas DemeulemeesterVIB Center for AI & Computational Biology, Leuven, BelgiumJonas DemeulemeesterLeicester Medical School, University of Leicester, Leicester, UKClaire WilsonLiverpool Heart and Chest Hospital, Liverpool, UKMichael J. ShackclothLungs for Living Research Centre, UCL Respiratory, Department of Medicine, University College London, London, UKSam M. Janes, Neal Navani & Ricky M. ThakrarDepartment of Thoracic Medicine, University College London Hospitals, London, UKNeal Navani & Ricky M. ThakrarManchester Cancer Research Centre Biobank, Manchester, UKAngela Leek, Jack Davies Hodgkinson & Nicola TottonManchester University NHS Foundation Trust, Manchester, UKAntonio Paiva-CorreiaExperimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, SerbiaMiljana TanicNHS Greater Glasgow and Clyde, Glasgow, UKCraig DickPrincess Alexandra Hospital, The Princess Alexandra Hospital NHS Trust, Harlow, UKLily Robinson & Peter RussellNational Heart and Lung Institute, Imperial College, London, UKAndrew G. NicholsonRoyal Free London NHS Foundation Trust, London, UKEkaterini BoletiRoyal Surrey Hospital, Royal Surrey Hospitals NHS Foundation Trust, Guildford, UKMadeleine HewishUniversity of Surrey, Guildford, UKMadeleine HewishSchool of Cancer Sciences, University of Glasgow, Glasgow, UKKevin G. BlythBeatson Institute for Cancer Research, University of Glasgow, Glasgow, UKKevin G. BlythQueen Elizabeth University Hospital, Glasgow, UKKevin G. BlythSingleton Hospital, Swansea Bay University Health Board, Swansea, UKJason F. LesterThe Christie NHS Foundation Trust, Manchester, UKAnshuman Chaturvedi, Pedro Oliveira, Katherine D. Brown & Mathew CarterThe Francis Crick Institute, London, UKAlastair Magness, Clare E. Weeden, Eva Grönroos, Jacki Goldman, Mickael Escudero, Philip Hobson, Stefan Boeing, Tamara Denner, Vittorio Barbè, Wei-Ting Lu, William Hill, Yutaka Naito, Zoe Ramsden, George Kassiotis & Imran NooraniDepartment of Infectious Disease, Faculty of Medicine, Imperial College London, London, UKGeorge KassiotisDepartment of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UKImran NooraniThe NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UKAiman AlzetaniThe University of Texas MD Anderson Cancer Center, Houston, TX, USAYinyin Yuan & Xiaoxi PanUniversity College London Cancer Institute, London, UKAngela Dwornik, Angeliki Karamani, Benny Chain, David R. Pearce, Felip Gálvez-Cancino, Georgia Stavrou, Gerasimos-Theodoros Mastrokalos, Helen L. Lowe, Ignacio Garcia Matos, James L. Reading, John A. Hartley, Kayalvizhi Selvaraju, Kezhong Chen, Leah Ensell, Mansi Shah, Maria Litovchenko, Piotr Pawlik, Samuel Gamble, Seng Kuong Anakin Ung, Victoria Spanswick, Yin Wu, Jayant K. Rane, Othman Al-Sawaf & Olga ChervovaDepartment I of Internal Medicine, University Hospital of Cologne, Cologne, GermanyOthman Al-SawafUniversity College London Department of Epidemiology and Health Care, London, UKOlga ChervovaNational Cancer Centre, Singapore City, SingaporeYien Ning Sophia WongUniversity Hospital Birmingham NHS Foundation Trust, Birmingham, UKAya Osman, Mandeesh Sangha, Gerald Langman, Helen Shackleford, Madava Djearaman & Gary MiddletonInstitute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UKGary MiddletonUniversity Hospital Southampton NHS Foundation Trust, Southampton, UKSerena Chee & Patricia GeorgUniversity Hospitals of Leicester NHS Trust, Leicester, UKAmrita Bajaj, Apostolos Nakas, Azmina Sodha-Ramdeen, Mohamad Tufail, Molly Scotland, Rebecca Boyles, Sridhar Rathinam, Sean Dulloo & Dean A. FennellUniversity of Leicester, Leicester, UKDomenic Marrone, Sean Dulloo & Dean A. FennellUniversity of Sheffield, Sheffield, UKSarah DansonSheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UKSarah DansonWythenshawe Hospital, Manchester University NHS Foundation Trust, Wythenshawe, UKElaine Smith, Eustace Fontaine, Felice Granato, Juliette Novasio, Kendadai Rammohan, Leena Joseph, Paul Bishop, Rajesh Shah, Vijay Joshi & Philip CrosbieDivision of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UKPhilip CrosbieImmune Regulation and Immune Interactions Group, Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UKFelipe Galvez-CancinoC.P. performed pipeline development, analysis and wrote the manuscript. T.P.J. performed pipeline development. M.M.L. performed analysis and wrote the manuscript. F.G.C., J.L., M.V.G. and A.R. designed and performed wet lab validation. O.P., C.M.-R., R.B., K.K.D., J.R.M.B. and R.R. provided bioinformatic support. N.K., K.L., R.S., D.A.M., P.V.L., M.J.-H. and S.A.Q. supervised the study. C.S. and N.M. supervised the study and wrote the manuscript.