J
John A. Foekens
Researcher at Erasmus University Medical Center
Publications - 72
Citations - 13774
John A. Foekens is an academic researcher from Erasmus University Medical Center. The author has contributed to research in topics: Breast cancer & Metastasis. The author has an hindex of 29, co-authored 72 publications receiving 11373 citations. Previous affiliations of John A. Foekens include Broad Institute & German Cancer Research Center.
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Journal ArticleDOI
Signatures of mutational processes in human cancer
Ludmil B. Alexandrov,Serena Nik-Zainal,Serena Nik-Zainal,David C. Wedge,Samuel Aparicio,Sam Behjati,Sam Behjati,Andrew V. Biankin,Graham R. Bignell,Niccolo Bolli,Niccolo Bolli,Åke Borg,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,Sandrine Boyault,Birgit Burkhardt,Adam Butler,Carlos Caldas,Helen Davies,Christine Desmedt,Roland Eils,Jorunn E. Eyfjord,John A. Foekens,Mel Greaves,Fumie Hosoda,Barbara Hutter,Tomislav Ilicic,Sandrine Imbeaud,Sandrine Imbeaud,Marcin Imielinsk,Natalie Jäger,David T. W. Jones,David T. Jones,Stian Knappskog,Stian Knappskog,Marcel Kool,Sunil R. Lakhani,Carlos López-Otín,Sancha Martin,Nikhil C. Munshi,Nikhil C. Munshi,Hiromi Nakamura,Paul A. Northcott,Marina Pajic,Elli Papaemmanuil,Angelo Paradiso,John V. Pearson,Xose S. Puente,Keiran Raine,Manasa Ramakrishna,Andrea L. Richardson,Andrea L. Richardson,Julia Richter,Philip Rosenstiel,Matthias Schlesner,Ton N. Schumacher,Paul N. Span,Jon W. Teague,Yasushi Totoki,Andrew Tutt,Rafael Valdés-Mas,Marit M. van Buuren,Laura van ’t Veer,Anne Vincent-Salomon,Nicola Waddell,Lucy R. Yates,Icgc PedBrain,Jessica Zucman-Rossi,Jessica Zucman-Rossi,P. Andrew Futreal,Ultan McDermott,Peter Lichter,Matthew Meyerson,Matthew Meyerson,Sean M. Grimmond,Reiner Siebert,Elias Campo,Tatsuhiro Shibata,Stefan M. Pfister,Stefan M. Pfister,Peter J. Campbell,Peter J. Campbell,Peter J. Campbell,Michael R. Stratton,Michael R. Stratton +84 more
TL;DR: It is shown that hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types, and this results reveal the diversity of mutational processes underlying the development of cancer.
Journal ArticleDOI
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Serena Nik-Zainal,Serena Nik-Zainal,Helen Davies,Johan Staaf,Manasa Ramakrishna,Dominik Glodzik,Xueqing Zou,Inigo Martincorena,Ludmil B. Alexandrov,Sancha Martin,David C. Wedge,Peter Van Loo,Young Seok Ju,Michiel M. Smid,Arie B. Brinkman,Sandro Morganella,Miriam Ragle Aure,Ole Christian Lingjærde,Anita Langerød,Markus Ringnér,Sung-Min Ahn,Sandrine Boyault,Jane E. Brock,Annegien Broeks,Adam Butler,Christine Desmedt,Luc Dirix,Serge Dronov,Aquila Fatima,John A. Foekens,Moritz Gerstung,Gerrit Gk Hooijer,Se Jin Jang,David Jones,Hyung-Yong Kim,Tari Ta King,Savitri Krishnamurthy,Hee Jin Lee,Jeong-Yeon Lee,Yang Li,Stuart McLaren,Andrew Menzies,Ville Mustonen,Sarah O’Meara,Iris Pauporté,Xavier Pivot,Colin Ca Purdie,Keiran Raine,Kamna Ramakrishnan,Germán Fg Rodríguez-González,Gilles Romieu,Anieta M. Sieuwerts,Peter Pt Simpson,Rebecca Shepherd,Lucy Stebbings,Olafur Oa Stefansson,Jon W. Teague,Stefania Tommasi,Isabelle Treilleux,Gert Van den Eynden,Peter B. Vermeulen,Anne Vincent-Salomon,Lucy R. Yates,Carlos Caldas,Laura Van't Veer,Andrew Tutt,Andrew Tutt,Stian Knappskog,Benita Kiat Tee Bk Tan,Jos Jonkers,Åke Borg,Naoto T. Ueno,Christos Sotiriou,Alain Viari,P. Andrew Futreal,Peter J. Campbell,Paul N. Span,Steven Van Laere,Sunil R. Lakhani,Jorunn E. Eyfjord,Alastair M Thompson,Ewan Birney,Hendrik G. Stunnenberg,Marc J. van de Vijver,John W.M. Martens,Anne Lise Børresen-Dale,Andrea L. Richardson,Gu Kong,Gilles Thomas,Michael R. Stratton +89 more
TL;DR: This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
Journal ArticleDOI
Gene expression-based classification of non-small cell lung carcinomas and survival prediction.
Jun Hou,Joachim G.J.V. Aerts,Bianca den Hamer,Wilfred F. J. van IJcken,Michael A. den Bakker,Peter Riegman,Cor van der Leest,Peter J. van der Spek,John A. Foekens,Henk C. Hoogsteden,Frank Grosveld,Sjaak Philipsen +11 more
TL;DR: The gene signatures identified are promising tools for histo-pathological classification of non-small cell lung cancer, and may improve the prediction of clinical outcome.
Journal ArticleDOI
Selection of Bone Metastasis Seeds by Mesenchymal Signals in the Primary Tumor Stroma
Xiang Zhang,Xin Jin,Srinivas Malladi,Yilong Zou,Yong H. Wen,Edi Brogi,Marcel Smid,John A. Foekens,Joan Massagué,Joan Massagué +9 more
TL;DR: The evidence suggests that stromal signals resembling those of a distant organ select for cancer cells that are primed for metastasis in that organ, thus illuminating the evolution of metastatic traits in a primary tumor and its distant metastases.
Journal ArticleDOI
Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
Jose M. C. Tubio,Yang Li,Young Seok Ju,Inigo Martincorena,Susanna L. Cooke,Marta Tojo,Gunes Gundem,Christodoulos P. Pipinikas,Jorge Zamora,Keiran Raine,Andrew Menzies,Pablo Román-García,Anthony Fullam,Moritz Gerstung,Adam Shlien,Patrick S. Tarpey,Elli Papaemmanuil,Stian Knappskog,Stian Knappskog,Stian Knappskog,Peter Van Loo,Peter Van Loo,Manasa Ramakrishna,Helen Davies,John Marshall,David C. Wedge,Jon W. Teague,Adam Butler,Serena Nik-Zainal,Serena Nik-Zainal,Ludmil B. Alexandrov,Sam Behjati,Lucy R. Yates,Niccolo Bolli,Niccolo Bolli,Laura Mudie,Claire Hardy,Sancha Martin,Stuart McLaren,Sarah O’Meara,Elizabeth Anderson,Mark Maddison,Stephen J. Gamble,Christopher S. Foster,Anne Y. Warren,Hayley C. Whitaker,Daniel Brewer,Daniel Brewer,Rosalind A. Eeles,Colin Cooper,Colin Cooper,David E. Neal,Andy G. Lynch,Tapio Visakorpi,William B. Isaacs,Laura Van't Veer,Carlos Caldas,Christine Desmedt,Christos Sotiriou,Samuel Aparicio,John A. Foekens,Jorunn E. Eyfjord,Sunil R. Lakhani,Sunil R. Lakhani,Gilles Thomas,Ola Myklebost,Paul N. Span,Anne Lise Børresen-Dale,Andrea L. Richardson,Marc J. van de Vijver,Anne Vincent-Salomon,Gert Van den Eynden,Adrienne M. Flanagan,Adrienne M. Flanagan,P. Andrew Futreal,P. Andrew Futreal,Sam M. Janes,G. Steven Bova,Michael R. Stratton,Ultan McDermott,Peter J. Campbell,Peter J. Campbell +81 more
TL;DR: It is found that 3′ transduction activity in a patient’s tumor was always associated with hypomethylation of that element, and in some cases transduction events can scatter exons, genes, and regulatory elements widely across the genome.