Scientific publications
The Hartwig Medical Database in scientific journals
Overview by year
2025 (17)
The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Takafumi N. Yamaguchi, Kathleen E. Houlahan, Helen Zhu, Natalie Kurganovs, Julie Livingstone, Natalie S. Fox, Jiapei Yuan, Jocelyn Sietsma Penington, Chol-Hee Jung, Tommer Schwarz, Weerachai Jaratlerdsiri, Job Van Riet, Peter Georgeson, Stefano Mangiola, Kodi Taraszka, Robert Lesurf, Jue Jiang, Ken Chow, Lawrence E. Heisler, Yu-Jia Shiah, Susmita G. Ramanand, Michael J. Clarkson, Anne Nguyen, Shadrielle Melijah G. Espiritu, Ryan Stuchbery, Richard Jovelin, Vincent Huang, Connor Bell, Edward O'Connor, Patrick J. McCoy, Christopher M. Lalansingh, Marek Cmero, Adriana Salcedo, Eva K.F. Chan, Lydia Y. Liu, Phillip D. Stricker, Vinayak Bhandari, Riana M.S. Bornman, Dorota Hs. Sendorek, Andrew Lonie, Stephenie D. Prokopec, Michael Fraser, Justin S. Peters, Adrien Foucal, Shingai B A. Mutambirwa, Lachlan Mcintosh, Michèle Orain, Matthew Wakefield, Valérie Picard, Daniel J. Park, Hélène Hovington, Michael Kerger, Alain Bergeron, Veronica Sabelnykova, Ji-Heui Seo, Mark M. Pomerantz, Noah Zaitlen, Sebastian M. Waszak, Alexander Gusev, Louis Lacombe, Yves Fradet, Andrew Ryan, Amar U. Kishan, Martijn P. Lolkema, Joachim Weischenfeldt, Bernard Têtu, Anthony J. Costello, Vanessa M. Hayes, Rayjean J. Hung, Housheng H. He, John D. McPherson, Bogdan Pasaniuc, Theodorus Van Der Kwast, Anthony T. Papenfuss, Matthew L. Freedman, Bernard J. Pope, Robert G. Bristow, Ram S. Mani, Niall M. Corcoran, Jüri Reimand, Christopher M. Hovens & Paul C. Boutros
Cancer Discovery, 2025, DOI
A commonly inherited human PCSK9 germline variant drives breast cancer metastasis via LRP1 receptor
Wenbin Mei, Schayan Faraj Tabrizi, Christopher Godina, Anthea F. Lovisa, Karolin Isaksson, Helena Jernström & Sohail F. Tavazoie
Cell, 2025, DOI
Whole genome sequencing-based analysis of genetic predisposition to adult glioblastoma
Mark P. Van Opijnen, Devin R. Van Valkengoed, Joep De Ligt, Filip Y. F. De Vos, Marike L. D. Broekman, Edwin Cuppen & Roelof Koster
npj Genomic Medicine, 2025, DOI
Checkpoint Blockade Combinations in High Tumor Mutational Burden/Load Tumors: Insights from the Atezolizumab + Bevacizumab and Nivolumab + Ipilimumab Cohorts in DRUP
Karlijn Verkerk, Soemeya F. Haj Mohammad, Laurien J. Zeverijn, Birgit S. Geurts, Ilse A.C. Spiekman, Florentine A.J. Verbeek, Hans Timmer, Maud A. Van Maren, V. Van Der Noort, Miguel Parra Martinez, Paul Roepman, Anne M.L. Jansen, Wendy W.J. De Leng, Serena Marchetti, Kim Monkhorst, Henk M.W. Verheul, Hans Gelderblom & Emile E. Voest
Clinical Cancer Research, 2025, DOI
Patient-Derived Organoids Predict Treatment Response in Metastatic Colorectal Cancer
Lidwien P. Smabers, G. Emerens Wensink, Carla S. Verissimo, Mayke Doorn, Tao Yang, Timo Voskuilen, Maarten A. Huismans, Liselot B.J. Valkenburg-van Iersel, Geert A. Cirkel, Elske C. Gootjes, Henk M.W. Verheul, Frank J. Jeurissen, Guus M. Bol, Hilde H. Nienhuis, Manon N.G.J.A. Braat, Edwin Cuppen, Robert G.J. Vries, Frederieke H. Van Der Baan, Sjoerd G. Elias, Onno Kranenburg, Miriam Koopman, Sylvia F. Boj & Jeanine M.L. Roodhart
Clinical Cancer Research, 2025, DOI
Genomic distinctions in adolescent and young adult cancer: A comprehensive review
Jeffrey Van Putten, Lina H. Lankhorst, Adrianus Johannes De Langen, Anthonie J. Van Der Wekken, Jeanine Roodhart, Karen Bolhuis, Sjoukje F. Oosting, Marloes Van Dongen, Marleen Kok, Marjolein Geurts, Johan A.F. Koekkoek, Edwin Cuppen, Hilde H. Nienhuis & Winette T.A. Van Der Graaf
Cancer Treatment Reviews, 2025, DOI
Clinical Benefit From Molecularly Guided Cancer Care: A Matching-Adjusted Indirect Comparison of Larotrectinib Versus Standard of Care
Carsten Bokemeyer, Keith R. Abrams, Jesus Garcia-Foncillas, Antoine Italiano, Ulrik Lassen, Louise Linsell, Marisca Marian, Noman Paracha, Sean D. Sullivan, Nicoletta Brega & Juliette Thompson
JCO Precision Oncology, 2025, DOI
Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals
Guillermo Palou-Márquez & Fran Supek
Genome Biology, 2025, DOI
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data
Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio Gonzalez, Gregory D. Sepich-Poore, Kyuto Sonehara, Mohsen Zakeri, Yang Chen, Amanda Hazel Dilmore, Neil Damle, Sergio E. Baranzini, George Hightower, Teruaki Nakatsuji, Richard L. Gallo, Ben Langmead, Yukinori Okada, Kit Curtius & Rob Knight
Nature Communications, 2025, DOI
Novel Molecular Biomarkers to Guide Treatment Decision-making in Metastatic Urothelial Cancer-A Patient Cohort Analysis
Debbie G. J. Robbrecht, Youssra Salhi, John W. M. Martens, Maureen J. B. Aarts, Paul Hamberg, Michiel S. van der Heijden, Jens Voortman, Niven Mehra, Hans M. Westgeest, Ronald de Wit, Reno Debets, Joost L. Boormans & J. Alberto Nakauma-González
European Urology Oncology, 2025, DOI
Analysis of IDH1 and IDH2 mutations as causes of the hypermethylator phenotype in colorectal cancer
Joseph C Ward, Melissa Morgan, James Wood, Connor Woolley, Albert Antao Nobre De Menezes, Alina Finch, Kitty Sherwood, Qiwen Huang, Chloe S Henry, Juan Fernández‐Tajes, Ignacio Soriano, Steve Thorn, Isabelle Legge, James McCullagh, David Kerr, Rachel Kerr, Rahul K Hejmadi, Mark J Arends, The S:CORT Consortium, Enric Domingo, Timothy Maughan, Chiara Bardella & Ian Tomlinson
The Journal of Pathology, 2025, DOI
Complex rearrangements fuel ER+ and HER2+ breast tumours
Kathleen E. Houlahan, Lise Mangiante, Cristina Sotomayor-Vivas, Alvina Adimoelja, Seongyeol Park, Aziz Khan, Sophia J. Pribus, Zhicheng Ma, Jennifer L. Caswell-Jin & Christina Curtis
Nature, 2025, DOI
A redefined InDel taxonomy provides insights into mutational signatures
Gene Ching Chiek Koh, Arjun Scott Nanda, Giuseppe Rinaldi, Soraya Boushaki, Andrea Degasperi, Cherif Badja, Andrew Marcel Pregnall, Salome Jingchen Zhao, Lucia Chmelova, Daniella Black, Laura Heskin, João Dias, Jamie Young, Yasin Memari, Scott Shooter, Jan Czarnecki, Matthew Arthur Brown, Helen Ruth Davies, Xueqing Zou & Serena Nik-Zainal
Nature Genetics, 2025, DOI
Genetic immune escape in cancer: timing and implications for treatment
Francisco Martínez-Jiménez & Diego Chowell
Trends in Cancer, 2025, DOI
KRAS mutation status integrated with RNA subtyping improves prognostic modeling in FOLFIRINOX-treated metastatic pancreatic cancer
Marjolein F. Lansbergen, Mark P.G. Dings, Jan Koster, Mariette Labots, Emile D. Kerver, Anouk Jochems, Marjolein Y.V. Homs, Judith De Vos-Geelen, Mathijs P. Hendriks, Michael W.T. Tanck, Johanna W. Wilmink, Hanneke W.M. Van Laarhoven & Maarten F. Bijlsma
Med, 2025, DOI
Towards Recommendations for Cost-Effectiveness Analysis of Predictive, Prognostic, and Serial Biomarker Tests in Oncology
Astrid Kramer, Lucas F. Van Schaik, Daan Van Den Broek, Gerrit A. Meijer, Iñaki Gutierrez Ibarluzea, Lorea Galnares Cordero, Remond J. A. Fijneman, Marjolijn J. L. Ligtenberg, Ed Schuuring, Wim H. Van Harten, Veerle M. H. Coupé, Valesca P. Retèl & the COIN Consortium
PharmacoEconomics, 2025, DOI
The viral landscape in metastatic solid cancers
2024 (22)
Combining genomic biomarkers to guide immunotherapy in non-small cell lung cancer
Joris Van De Haar, Joanne M. Mankor, Karlijn Hummelink, Kim Monkhorst, Egbert F. Smit, Lodewyk F.A. Wessels, Edwin Cuppen, Joachim G.J.V. Aerts & Emile E. Voest
Clinical Cancer Research, 2024, DOI
EXO1 protects BRCA1-deficient cells against toxic DNA lesions
Bert Van De Kooij, Anne Schreuder, Raphael Pavani, Veronica Garzero, Sidrit Uruci, Tiemen J. Wendel, Arne Van Hoeck, Marta San Martin Alonso, Marieke Everts, Dana Koerse, Elsa Callen, Jasper Boom, Hailiang Mei, Edwin Cuppen, Martijn S. Luijsterburg, Marcel A.T.M. Van Vugt, André Nussenzweig, Haico Van Attikum & Sylvie M. Noordermeer
Molecular Cell, 2024, DOI
Impact of genetic counseling strategy on diagnostic yield and workload for genome-sequencing-based tumor diagnostics
Roelof Koster, Luuk J. Schipper, Noor A.A. Giesbertz, Daphne Van Beek, Matías Mendeville, Kris G. Samsom, Efraim H. Rosenberg, Frans B.L. Hogervorst, Paul Roepman, Mirjam C. Boelens, Linda J.W. Bosch, Jose G. Van Den Berg, Gerrit A. Meijer, Emile E. Voest, Edwin Cuppen, Marielle W.G. Ruijs, Tom Van Wezel, Lizet Van Der Kolk & Kim Monkhorst
Genetics in Medicine, 2024, DOI
Transcription and DNA replication collisions lead to large tandem duplications and expose targetable therapeutic vulnerabilities in cancer
Yang Yang, Michelle L. Badura, Patrick C. O'Leary, Henry M. Delavan, Troy M. Robinson, Emily A. Egusa, Xiaoming Zhong, Jason T. Swinderman, Haolong Li, Meng Zhang, Minkyu Kim, Alan Ashworth, Felix Y. Feng, Jonathan Chou & Lixing Yang
Nature Cancer, 2024, DOI
Five latent factors underlie response to immunotherapy
Joseph Usset, Axel Rosendahl Huber, Maria A. Andrianova, Eduard Batlle, Joan Carles, Edwin Cuppen, Elena Elez, Enriqueta Felip, Marina Gómez-Rey, Deborah Lo Giacco, Francisco Martinez-Jimenez, Eva Muñoz-Couselo, Lillian L. Siu, Josep Tabernero, Ana Vivancos, Ferran Muiños, Abel Gonzalez-Perez & Nuria Lopez-Bigas
Nature Genetics, 2024, DOI
Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer
Axel Rosendahl Huber, Cayetano Pleguezuelos-Manzano, Jens Puschhof, Joske Ubels, Charelle Boot, Aurelia Saftien, Mark Verheul, Laurianne T. Trabut, Niels Groenen, Markus Van Roosmalen, Kyanna S. Ouyang, Henry Wood, Phil Quirke, Gerrit Meijer, Edwin Cuppen, Hans Clevers & Ruben Van Boxtel
Cancer Cell, 2024, DOI
Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms
Eline J. M. Bertrums, Jurrian K. De Kanter, Lucca L. M. Derks, Mark Verheul, Laurianne Trabut, Markus J. Van Roosmalen, Henrik Hasle, Evangelia Antoniou, Dirk Reinhardt, Michael N. Dworzak, Nora Mühlegger, Marry M. Van Den Heuvel-Eibrink, C. Michel Zwaan, Bianca F. Goemans & Ruben Van Boxtel
Nature Communications, 2024, DOI
Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity
Kathleen E. Houlahan, Aziz Khan, Noah F. Greenwald, Cristina Sotomayor Vivas, Robert B. West, Michael Angelo & Christina Curtis
Science, 2024, DOI
Mitochondrial DNA mutations drive aerobic glycolysis to enhance checkpoint blockade response in melanoma
Mahnoor Mahmood, Eric Minwei Liu, Amy L. Shergold, Elisabetta Tolla, Jacqueline Tait-Mulder, Alejandro Huerta-Uribe, Engy Shokry, Alex L. Young, Sergio Lilla, Minsoo Kim, Tricia Park, Sonia Boscenco, Javier L. Manchon, Crístina Rodríguez-Antona, Rowan C. Walters, Roger J. Springett, James N. Blaza, Louise Mitchell, Karen Blyth, Sara Zanivan, David Sumpton, Edward W. Roberts, Ed Reznik & Payam A. Gammage
Nature Cancer, 2024, DOI
Mapping extrachromosomal DNA amplifications during cancer progression
Hoon Kim, Soyeon Kim, Taylor Wade, Eunchae Yeo, Anuja Lipsa, Anna Golebiewska, Kevin C. Johnson, Sepil An, Junyong Ko, Yoonjoo Nam, Hwa Yeon Lee, Seunghyun Kang, Heesuk Chung, Simone P. Niclou, Hyo-Eun Moon, Sun Ha Paek, Vineet Bafna, Jens Luebeck & Roel G. W. Verhaak
Nature Genetics, 2024, DOI
Transcriptome-based classification to predict FOLFIRINOX response in a real-world metastatic pancreatic cancer cohort
Marjolein F. Lansbergen, Mark P.G. Dings, Paul Manoukian, Arantza Fariña, Cynthia Waasdorp, Gerrit K.J. Hooijer, Joanne Verheij, Jan Koster, Danny A. Zwijnenburg, Johanna W. Wilmink, Jan Paul Medema, Frederike Dijk, Hanneke W.M. Van Laarhoven & Maarten F. Bijlsma
Translational Research, 2024, DOI
Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations
Elizaveta Besedina & Fran Supek
Nature Communications, 2024, DOI
Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature
J. Alberto Nakauma-González, Maud Rijnders, Minouk T.W. Noordsij, John W.M. Martens, Astrid A.M. Van Der Veldt, Martijn P.J. Lolkema, Joost L. Boormans & Harmen J.G. Van De Werken
Cell Genomics, 2024, DOI
Estimating the Prognostic Value of the NTRK Fusion Biomarker for Comparative Effectiveness Research in The Netherlands
Irene Santi, Heleen Vellekoop, Matthijs M Versteegh, Simone A Huygens, Winand N. M. Dinjens & Maureen Rutten-van Mölken
Molecular Diagnosis & Therapy, 2024, DOI
Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma
Francisco Aya, Pablo Lanuza-Gracia, Abel González-Pérez, Sophie Bonnal, Estefania Mancini, Nuria López-Bigas, Ana Arance & Juan Valcárcel
Cell Reports, 2024, DOI
A pan-cancer analysis of the microbiome in metastatic cancer
Thomas W. Battaglia, Iris L. Mimpen, Joleen J.H. Traets, Arne Van Hoeck, Laurien J. Zeverijn, Birgit S. Geurts, Gijs F. De Wit, Michaël Noë, Ingrid Hofland, Joris L. Vos, Sten Cornelissen, Maartje Alkemade, Annegien Broeks, Charlotte L. Zuur, Edwin Cuppen, Lodewyk Wessels, Joris Van De Haar & Emile Voest
Cell, 2024, DOI
The multitarget faecal immunochemical test for improving stool-based colorectal cancer screening programmes: a Dutch population-based, paired-design, intervention study
Pieter H A Wisse, Willemijn De Klaver, Francine Van Wifferen, Frejanne G Van Maaren-Meijer, Huub E Van Ingen, Lana Meiqari, Iris Huitink, Mariska Bierkens, Margriet Lemmens, Marjolein J E Greuter, Monique E Van Leerdam, Manon C W Spaander, Evelien Dekker, Veerle M H Coupé, Beatriz Carvalho, Meike De Wit & Gerrit A Meijer
The Lancet Oncology, 2024, DOI
Gene-expression-based T-Cell-to-Stroma Enrichment (TSE) score predicts response to immune checkpoint inhibitors in urothelial cancer
Maud Rijnders, J. Alberto Nakauma-González, Debbie G. J. Robbrecht, Alberto Gil-Jimenez, Hayri E. Balcioglu, Astrid A. M. Oostvogels, Maureen J. B. Aarts, Joost L. Boormans, Paul Hamberg, Michiel S. Van Der Heijden, Bernadett E. Szabados, Geert J. L. H. Van Leenders, Niven Mehra, Jens Voortman, Hans M. Westgeest, Ronald De Wit, Astrid A. M. Van Der Veldt, Reno Debets & Martijn P. Lolkema
Nature Communications, 2024, DOI
Mapping extrachromosomal DNA amplifications during cancer progression
Hoon Kim, Soyeon Kim, Taylor Wade, Eunchae Yeo, Anuja Lipsa, Anna Golebiewska, Kevin C. Johnson, Sepil An, Junyong Ko, Yoonjoo Nam, Hwa Yeon Lee, Seunghyun Kang, Heesuk Chung, Simone P. Niclou, Hyo-Eun Moon, Sun Ha Paek, Vineet Bafna, Jens Luebeck & Roel G. W. Verhaak
Nature Genetics, 2024, DOI
Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature
J. Alberto Nakauma-González, Maud Rijnders, Minouk T. W. Noordsij, John W. M. Martens, Astrid A. M. van der Veldt, Martijn P. J. Lolkema, Joost L. Boormans & Harmen J. G. van de Werken
Cell Genomics, 2024, DOI
Transcriptome-based classification to predict FOLFIRINOX response in a real-world metastatic pancreatic cancer cohort
Marjolein F. Lansbergen, Mark P.G. Dings, Paul Manoukian, Arantza Fariña, Cynthia Waasdorp, Gerrit K.J. Hooijer, Joanne Verheij, Jan Koster, Danny A. Zwijnenburg, Johanna W. Wilmink, Jan Paul Medema, Frederike Dijk, Hanneke W.M. Van Laarhoven & Maarten F. Bijlsma
Translational Research, 2024, DOI
Long deletion signatures in repetitive genomic regions track somatic evolution and enable sensitive detection of microsatellite instability
Qingli Guo, Jacob Househam, Eszter Lakatos, Salpie Nowinski, Ibrahim Al Bakir, Heather Grant, Vickna Balarajah, Christine S. Hughes, Luis Zapata, Hemant M. Kocher, Andrea Sottoriva, Ann-Marie Baker, Ville Mustonen & Trevor A. Graham
, 2024, DOI
2023 (18)
ERα-associated translocations underlie oncogene amplifications in breast cancer
Jake June-Koo Lee, Youngsook Lucy Jung, Taek-Chin Cheong, Jose Espejo Valle-Inclan, Chong Chu, Doga C. Gulhan, Viktor Ljungström, Hu Jin, Vinayak V. Viswanadham, Emma V. Watson, Isidro Cortés-Ciriano, Stephen J. Elledge, Roberto Chiarle, David Pellman & Peter J. Park
Nature, 2023, DOI
Genetic immune escape landscape in primary and metastatic cancer
Francisco Martínez-Jiménez, Peter Priestley, Charles Shale, Jonathan Baber, Erik Rozemuller & Edwin Cuppen
Nature Genetics, 2023, DOI
Efficacy, safety and biomarker analysis of durvalumab in patients with mismatch-repair deficient or microsatellite instability-high solid tumours
Birgit S. Geurts, Thomas W. Battaglia, J. Maxime Van Berge Henegouwen, Laurien J. Zeverijn, Gijs F. De Wit, Louisa R. Hoes, Hanneke Van Der Wijngaart, Vincent Van Der Noort, Paul Roepman, Wendy W. J. De Leng, Anne M. L. Jansen, Frans L. Opdam, Maja J. A. De Jonge, Geert A. Cirkel, Mariette Labots, Ann Hoeben, Emile D. Kerver, Adriaan D. Bins, Frans G.L. Erdkamp, Johan M. Van Rooijen, Danny Houtsma, Mathijs P. Hendriks, Jan-Willem B. De Groot, Henk M. W. Verheul, Hans Gelderblom & Emile E. Voest
BMC Cancer, 2023, DOI
Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns
Simon Grund Sørensen, Amruta Shrikhande, Gustav Alexander Poulsgaard, Mikkel Hovden Christensen, Johanna Bertl, Britt Elmedal Laursen, Eva R Hoffmann & Jakob Skou Pedersen
eLife, 2023, DOI
Using genomic scars to select immunotherapy beneficiaries in advanced non-small cell lung cancer
H. C. Donker, B. Van Es, M. Tamminga, G. A. Lunter, L. C. L. T. Van Kempen, E. Schuuring, T. J. N. Hiltermann & H. J. M. Groen
Scientific Reports, 2023, DOI
A Compendium of AR Splice Variants in Metastatic Castration-Resistant Prostate Cancer
Khrystany T. Isebia, Martijn P. Lolkema, Guido Jenster, Ronald De Wit, John W. M. Martens & Job Van Riet
International Journal of Molecular Sciences, 2023, DOI
Discovering cryptic splice mutations in cancers via a deep neural network framework
Raphaël Teboul, Michalina Grabias, Jessica Zucman-Rossi & Eric Letouzé
NAR Cancer, 2023, DOI
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors
Luis Zapata, Giulio Caravagna, Marc J. Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A. Chan, Trevor A. Graham & Andrea Sottoriva
Nature Genetics, 2023, DOI
Copy number footprints of platinum-based anticancer therapies
Santiago Gonzalez, Nuria Lopez-Bigas, Abel Gonzalez-Perez & Dmitry A. Gordenin
PLOS Genetics, 2023, DOI
Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning
Anouk C. De Jong, Alexandra Danyi, Job Van Riet, Ronald De Wit, Martin Sjöström, Felix Feng, Jeroen De Ridder & Martijn P. Lolkema
Nature Communications, 2023, DOI
Tobacco Smoking-Related Mutational Signatures in Classifying Smoking-Associated and Nonsmoking-Associated NSCLC
Sophie M. Ernst, Joanne M. Mankor, Job Van Riet, Jan H. Von Der Thüsen, Hendrikus J. Dubbink, Joachim G.J.V. Aerts, Adrianus J. De Langen, Egbert F. Smit, Anne-Marie C. Dingemans & Kim Monkhorst
Journal of Thoracic Oncology, 2023, DOI
Pan-cancer whole-genome comparison of primary and metastatic solid tumours
Francisco Martínez-Jiménez, Ali Movasati, Sascha Remy Brunner, Luan Nguyen, Peter Priestley, Edwin Cuppen & Arne Van Hoeck
Nature, 2023, DOI
The ratio of adaptive to innate immune cells differs between genders and associates with improved prognosis and response to immunotherapy
Johanne Ahrenfeldt, Ditte S. Christensen, Andreas B. Østergaard, Judit Kisistók, Mateo Sokač, Nicolai J. Birkbak & Albert Rübben
PLOS ONE, 2023, DOI
Identifying somatic changes in drug transporters using whole genome and transcriptome sequencing data of advanced tumors
Wesley S. Van De Geer, Ron H.J. Mathijssen, Job Van Riet, Neeltje Steeghs, Mariette Labots, Carla Van Herpen, Lot A. Devriese, Vivianne C.G. Tjan-Heijnen, Emile E. Voest, Stefan Sleijfer, John W.M. Martens, Edwin Cuppen, Harmen J.G. Van De Werken & Sander Bins
Biomedicine & Pharmacotherapy, 2023, DOI
Heritable defects in telomere and mitotic function selectively predispose to sarcomas
Mandy L. Ballinger, Swetansu Pattnaik, Piyushkumar A. Mundra, Milita Zaheed, Emma Rath, Peter Priestley, Jonathan Baber, Isabelle Ray-Coquard, Nicholas Isambert, Sylvain Causeret, Winette T. A. Van Der Graaf, Ajay Puri, Florence Duffaud, Axel Le Cesne, Beatrice Seddon, Coonoor Chandrasekar, Joshua D. Schiffman, Andrew S. Brohl, Paul A. James, Jean-Emmanuel Kurtz, Nicolas Penel, Ola Myklebost, Leonardo A. Meza-Zepeda, Hilda Pickett, Maya Kansara, Nicola Waddell, Olga Kondrashova, John V. Pearson, Andrew P. Barbour, Shuai Li, Tuong L. Nguyen, Diane Fatkin, Robert M. Graham, Eleni Giannoulatou, Melissa J. Green, Warren Kaplan, Shyamsundar Ravishankar, Joseph Copty, Joseph E. Powell, Edwin Cuppen, Kristel Van Eijk, Jan Veldink, Jin-Hee Ahn, Jeong Eun Kim, R. Lor Randall, Kathy Tucker, Ian Judson, Rajiv Sarin, Thomas Ludwig, Emmanuelle Genin, Jean-Francois Deleuze, the French Exome Project Consortium, Michelle Haber, Glenn Marshall, Murray J. Cairns, Jean-Yves Blay, the International Sarcoma Kindred Study & David M. Thomas
Science, 2023, DOI
Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice
Kris G. Samsom, Linda J. W. Bosch, Luuk J. Schipper, Daoin Schout, Paul Roepman, Mirjam C. Boelens, Ferry Lalezari, Elisabeth G. Klompenhouwer, Adrianus J. De Langen, Tineke E. Buffart, Berit M. H. Van Linder, Kelly Van Deventer, Kay Van Den Burg, Unga Unmehopa, Efraim H. Rosenberg, Roelof Koster, Frans B. L. Hogervorst, José G. Van Den Berg, Immy Riethorst, Lieke Schoenmaker, Daphne Van Beek, Ewart De Bruijn, Jacobus J. M. Van Der Hoeven, Hans Van Snellenberg, Lizet E. Van Der Kolk, Edwin Cuppen, Emile E. Voest, Gerrit A. Meijer & Kim Monkhorst
Nature Protocols, 2023, DOI
Mutational processes of tobacco smoking and APOBEC activity generate protein-truncating mutations in cancer genomes
Nina Adler, Alexander T. Bahcheli, Kevin C. L. Cheng, Khalid N. Al-Zahrani, Mykhaylo Slobodyanyuk, Diogo Pellegrina, Daniel Schramek & Jüri Reimand
Science Advances, 2023, DOI
Tumour mutations in long noncoding RNAs enhance cell fitness
Roberta Esposito, Andrés Lanzós, Tina Uroda, Sunandini Ramnarayanan, Isabel Büchi, Taisia Polidori, Hugo Guillen-Ramirez, Ante Mihaljevic, Bernard Mefi Merlin, Lia Mela, Eugenio Zoni, Lusine Hovhannisyan, Finn McCluggage, Matúš Medo, Giulia Basile, Dominik F. Meise, Sandra Zwyssig, Corina Wenger, Kyriakos Schwarz, Adrienne Vancura, Núria Bosch-Guiteras, Álvaro Andrades, Ai Ming Tham, Michaela Roemmele, Pedro P. Medina, Adrian F. Ochsenbein, Carsten Riether, Marianna Kruithof-de Julio, Yitzhak Zimmer, Michaela Medová, Deborah Stroka, Archa Fox & Rory Johnson
Nature Communications, 2023, DOI
2022 (38)
DBFE: Distribution-based feature extraction from copy number and structural variants in whole-genome data
Maciej Piernik, Dariusz Brzezinski, Pawel Sztromwasser, Klaudia Pacewicz, Weronika Majer-Burman, Michal Gniot, Dawid Sielski, Alicja Wozna & Pawel Zawadzki
, 2022, DOI
Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach
Marzena Wojtaszewska, Rafał Stępień, Alicja Woźna, Maciej Piernik, Pawel Sztromwasser, Maciej Dąbrowski, Michał Gniot, Sławomir Szymański, Maciej Socha, Piotr Kasprzak, Rafał Matkowski & Paweł Zawadzki
Molecular Diagnosis & Therapy, 2022, DOI
Personalised selection of experimental treatment in patients with advanced solid cancer is feasible using whole-genome sequencing
Melinda A. Pruis, Floris H. Groenendijk, K. Sangeeta Badloe, Andrea Van Puffelen, Debbie Robbrecht, Winand N. M. Dinjens, Stefan Sleijfer, Anne-Marie C. Dingemans, Jan H. Von Der Thüsen, Paul Roepman & Martijn P. Lolkema
British Journal of Cancer, 2022, DOI
Patients with Rare Cancers in the Drug Rediscovery Protocol (DRUP) Benefit from Genomics-Guided Treatment
Louisa R. Hoes, Jade M. Van Berge Henegouwen, Hanneke Van Der Wijngaart, Laurien J. Zeverijn, Daphne L. Van Der Velden, Joris Van De Haar, Paul Roepman, Wendy J. De Leng, Anne M.L. Jansen, Erik Van Werkhoven, Vincent Van Der Noort, Alwin D.R. Huitema, Eelke H. Gort, Jan Willem B. De Groot, Emile D. Kerver, Derk Jan De Groot, Frans Erdkamp, Laurens V. Beerepoot, Mathijs P. Hendriks, Egbert F. Smit, Winette T.A. Van Der Graaf, Carla M.L. Van Herpen, Mariette Labots, Ann Hoeben, Hans Morreau, Martijn P. Lolkema, Edwin Cuppen, Hans Gelderblom, Henk M.W. Verheul & Emile E. Voest
Clinical Cancer Research, 2022, DOI
Trastuzumab and pertuzumab combination therapy for advanced pre-treated HER2 exon 20-mutated non-small cell lung cancer
J.M. Van Berge Henegouwen, M. Jebbink, L.R. Hoes, H. Van Der Wijngaart, L.J. Zeverijn, D.L. Van Der Velden, P. Roepman, W.W.J. De Leng, A.M.L. Jansen, E. Van Werkhoven, V. Van Der Noort, A.J. Van Der Wekken, A.J. De Langen, E.E. Voest, H.M.W. Verheul, E.F. Smit & H. Gelderblom
European Journal of Cancer, 2022, DOI
The genomic and transcriptomic landscape of advanced renal cell cancer for individualized treatment strategies
K. De Joode, W.S. Van De Geer, G.J.L.H. Van Leenders, P. Hamberg, H.M. Westgeest, A. Beeker, S.F. Oosting, J.M. Van Rooijen, L.V. Beerepoot, M. Labots, R.H.J. Mathijssen, M.P. Lolkema, E. Cuppen, S. Sleijfer, H.J.G. Van De Werken & A.A.M. Van Der Veldt
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Cell cycle alterations associate with a redistribution of mutation rates across chromosomal domains in human cancers
Marina Salvadores & Fran Supek
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Accurate and sensitive mutational signature analysis with MuSiCal
Hu Jin, Doga C. Gulhan, Daniel Ben-Isvy, David Geng, Viktor Ljungstrom & Peter J. Park
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Hotspot propensity across mutational processes
Claudia Arnedo-Pac, Ferran Muiños, Abel Gonzalez-Perez & Nuria Lopez-Bigas
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Genome-wide mapping of somatic mutation rates uncovers drivers of cancer
Maxwell A. Sherman, Adam U. Yaari, Oliver Priebe, Felix Dietlein, Po-Ru Loh & Bonnie Berger
Nature Biotechnology, 2022, DOI
Lost by Transcription: Fork Failures, Elevated Expression, and Clinical Consequences Related to Deletions in Metastatic Colorectal Cancer
Marcel Smid, Saskia M. Wilting & John W. M. Martens
International Journal of Molecular Sciences, 2022, DOI
Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas
Wesley S Van De Geer, Youri Hoogstrate, Kaspar Draaisma, Pierre A Robe, Sander Bins, Ron H J Mathijssen, Pim French, Harmen J G Van De Werken & Filip Y F De Vos
Neuro-Oncology Advances, 2022, DOI
Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma
James T. Topham, Erica S. Tsang, Joanna M. Karasinska, Andrew Metcalfe, Hassan Ali, Steve E. Kalloger, Veronika Csizmok, Laura M. Williamson, Emma Titmuss, Karina Nielsen, Gian Luca Negri, Sandra E. Spencer Miko, Gun Ho Jang, Robert E. Denroche, Hui-li Wong, Grainne M. O’Kane, Richard A. Moore, Andrew J. Mungall, Jonathan M. Loree, Faiyaz Notta, Julie M. Wilson, Oliver F. Bathe, Patricia A. Tang, Rachel Goodwin, Gregg B. Morin, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J. M. Jones, David F. Schaeffer & Daniel J. Renouf
Nature Communications, 2022, DOI
Impact of molecular tumour board discussion on targeted therapy allocation in advanced prostate cancer
Peter H. J. Slootbeek, Iris S. H. Kloots, Minke Smits, Inge M. Van Oort, Winald R. Gerritsen, Jack A. Schalken, Marjolijn J. L. Ligtenberg, Katrien Grünberg, Leonie I. Kroeze, Haiko J. Bloemendal & Niven Mehra
British Journal of Cancer, 2022, DOI
Apolipoprotein B mRNA-Editing Catalytic Polypeptide-Like–Induced Protein Changes in Estrogen Receptor–Positive, Human Epidermal Growth Factor Receptor 2–Negative Breast Cancer Throughout Disease Progression
Manouk K. Bos, Marcel Smid, Stefan Sleijfer & John W. M. Martens
JCO Precision Oncology, 2022, DOI
High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer
Marta Palafox, Laia Monserrat, Meritxell Bellet, Guillermo Villacampa, Abel Gonzalez-Perez, Mafalda Oliveira, Fara Brasó-Maristany, Nusaibah Ibrahimi, Srinivasaraghavan Kannan, Leonardo Mina, Maria Teresa Herrera-Abreu, Andreu Òdena, Mònica Sánchez-Guixé, Marta Capelán, Analía Azaro, Alejandra Bruna, Olga Rodríguez, Marta Guzmán, Judit Grueso, Cristina Viaplana, Javier Hernández, Faye Su, Kui Lin, Robert B. Clarke, Carlos Caldas, Joaquín Arribas, Stefan Michiels, Alicia García-Sanz, Nicholas C. Turner, Aleix Prat, Paolo Nuciforo, Rodrigo Dienstmann, Chandra S. Verma, Nuria Lopez-Bigas, Maurizio Scaltriti, Monica Arnedos, Cristina Saura & Violeta Serra
Nature Communications, 2022, DOI
Feasibility of whole‐genome sequencing‐based tumor diagnostics in routine pathology practice
Kris G Samsom, Luuk J Schipper, Paul Roepman, Linda Jw Bosch, Ferry Lalezari, Elisabeth G Klompenhouwer, Adrianus J De Langen, Tineke E Buffart, Immy Riethorst, Lieke Schoenmaker, Daoin Schout, Vincent Van Der Noort, Jose G Van Den Berg, Ewart De Bruijn, Jacobus Jm Van Der Hoeven, Hans Van Snellenberg, Lizet E Van Der Kolk, Edwin Cuppen, Emile E Voest, Gerrit A Meijer & Kim Monkhorst
The Journal of Pathology, 2022, DOI
Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer
Chris J. De Witte, Joachim Kutzera, Arne Van Hoeck, Luan Nguyen, Ingrid A. Boere, Mathilde Jalving, Petronella B. Ottevanger, Christa Van Schaik-van De Mheen, Marion Stevense, Wigard P. Kloosterman, Ronald P. Zweemer, Edwin Cuppen & Petronella O. Witteveen
Cancers, 2022, DOI
Study protocol of the GLOW study: maximising treatment options for recurrent glioblastoma patients by whole genome sequencing-based diagnostics—a prospective multicenter cohort study
Mark P. Van Opijnen, Marike L. D. Broekman, Filip Y. F. De Vos, Edwin Cuppen, Jacobus J. M. Van Der Hoeven, Myra E. Van Linde, Annette Compter, Laurens V. Beerepoot, Martin J. Van Den Bent, Maaike J. Vos, Helle-Brit Fiebrich, Johan A. F. Koekkoek, Ann Hoeben, Kuan H. Kho, Chantal M. L. Driessen, Hanne-Rinck Jeltema, Pierre A. J. T. Robe & Sybren L. N. Maas
BMC Medical Genomics, 2022, DOI
Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features
Luan Nguyen, Arne Van Hoeck & Edwin Cuppen
Nature Communications, 2022, DOI
Comprehensive Molecular Characterization Reveals Genomic and Transcriptomic Subtypes of Metastatic Urothelial Carcinoma
J. Alberto Nakauma-González, Maud Rijnders, Job Van Riet, Michiel S. Van Der Heijden, Jens Voortman, Edwin Cuppen, Niven Mehra, Sandra Van Wilpe, Sjoukje F. Oosting, L. Lucia Rijstenberg, Hans M. Westgeest, Ellen C. Zwarthoff, Ronald De Wit, Astrid A.M. Van Der Veldt, Harmen J.G. Van De Werken, Martijn P.J. Lolkema & Joost L. Boormans
European Urology, 2022, DOI
Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer
Judith M. Vlaar, Anouska Borgman, Eric Kalkhoven, Denise Westland, Nicolle Besselink, Charles Shale, Bishoy M. Faltas, Peter Priestley, Ewart Kuijk & Edwin Cuppen
Scientific Reports, 2022, DOI
Complete genomic characterization in patients with cancer of unknown primary origin in routine diagnostics
L.J. Schipper, K.G. Samsom, P. Snaebjornsson, T. Battaglia, L.J.W. Bosch, F. Lalezari, P. Priestley, C. Shale, A.J. Van Den Broek, N. Jacobs, P. Roepman, J.J.M. Van Der Hoeven, N. Steeghs, M.A. Vollebergh, S. Marchetti, E. Cuppen, G.A. Meijer, E.E. Voest & K. Monkhorst
ESMO Open, 2022, DOI
Functional RECAP (REpair CAPacity) assay identifies homologous recombination deficiency undetected by DNA-based BRCAness tests
Titia G. Meijer, Luan Nguyen, Arne Van Hoeck, Anieta M. Sieuwerts, Nicole S. Verkaik, Marjolijn M. Ladan, Kirsten Ruigrok-Ritstier, Carolien H. M. Van Deurzen, Harmen J. G. Van De Werken, Esther H. Lips, Sabine C. Linn, Yasin Memari, Helen Davies, Serena Nik-Zainal, Roland Kanaar, John W. M. Martens, Edwin Cuppen, Agnes Jager & Dik C. Van Gent
Oncogene, 2022, DOI
Temporal Dissection of Altered Pathways during the Evolution of Cancer
Johanne Ahrenfeldt, Ditte S. Christensen, Mateo Sokač, Judit Kisistók, Nicholas McGranahan & Nicolai J. Birkbak
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Genome-wide analysis of somatic noncoding mutation patterns in cancer
Felix Dietlein, Alex B. Wang, Christian Fagre, Anran Tang, Nicolle J. M. Besselink, Edwin Cuppen, Chunliang Li, Shamil R. Sunyaev, James T. Neal & Eliezer M. Van Allen
Science, 2022, DOI
Truncated FGFR2 is a clinically actionable oncogene in multiple cancers
Daniel Zingg, Jinhyuk Bhin, Julia Yemelyanenko, Sjors M. Kas, Frank Rolfs, Catrin Lutz, Jessica K. Lee, Sjoerd Klarenbeek, Ian M. Silverman, Stefano Annunziato, Chang S. Chan, Sander R. Piersma, Timo Eijkman, Madelon Badoux, Ewa Gogola, Bjørn Siteur, Justin Sprengers, Bim De Klein, Richard R. De Goeij-de Haas, Gregory M. Riedlinger, Hua Ke, Russell Madison, Anne Paulien Drenth, Eline Van Der Burg, Eva Schut, Linda Henneman, Martine H. Van Miltenburg, Natalie Proost, Huiling Zhen, Ellen Wientjens, Roebi De Bruijn, Julian R. De Ruiter, Ute Boon, Renske De Korte-Grimmerink, Bastiaan Van Gerwen, Luis Féliz, Ghassan K. Abou-Alfa, Jeffrey S. Ross, Marieke Van De Ven, Sven Rottenberg, Edwin Cuppen, Anne Vaslin Chessex, Siraj M. Ali, Timothy C. Burn, Connie R. Jimenez, Shridar Ganesan, Lodewyk F. A. Wessels & Jos Jonkers
Nature, 2022, DOI
Substitution mutational signatures in whole-genome–sequenced cancers in the UK population
Andrea Degasperi, Xueqing Zou, Tauanne Dias Amarante, Andrea Martinez-Martinez, Gene Ching Chiek Koh, João M. L. Dias, Laura Heskin, Lucia Chmelova, Giuseppe Rinaldi, Valerie Ya Wen Wang, Arjun S. Nanda, Aaron Bernstein, Sophie E. Momen, Jamie Young, Daniel Perez-Gil, Yasin Memari, Cherif Badja, Scott Shooter, Jan Czarnecki, Matthew A. Brown, Helen R. Davies, Genomics England Research Consortium†, Serena Nik-Zainal, J. C. Ambrose, P. Arumugam, R. Bevers, M. Bleda, F. Boardman-Pretty, C. R. Boustred, H. Brittain, M. J. Caulfield, G. C. Chan, T. Fowler, A. Giess, A. Hamblin, S. Henderson, T. J. P. Hubbard, R. Jackson, L. J. Jones, D. Kasperaviciute, M. Kayikci, A. Kousathanas, L. Lahnstein, S. E. A. Leigh, I. U. S. Leong, F. J. Lopez, F. Maleady-Crowe, M. McEntagart, F. Minneci, L. Moutsianas, M. Mueller, N. Murugaesu, A. C. Need, P. O‘Donovan, C. A. Odhams, C. Patch, D. Perez-Gil, M. B. Pereira, J. Pullinger, T. Rahim, A. Rendon, T. Rogers, K. Savage, K. Sawant, R. H. Scott, A. Siddiq, A. Sieghart, S. C. Smith, A. Sosinsky, A. Stuckey, M. Tanguy, A. L. Taylor Tavares, E. R. A. Thomas, S. R. Thompson, A. Tucci, M. J. Welland, E. Williams, K. Witkowska & S. M. Wood
Science, 2022, DOI
A multi-platform reference for somatic structural variation detection
Jose Espejo Valle-Inclan, Nicolle J.M. Besselink, Ewart De Bruijn, Daniel L. Cameron, Jana Ebler, Joachim Kutzera, Stef Van Lieshout, Tobias Marschall, Marcel Nelen, Peter Priestley, Ivo Renkens, Margaretha G.M. Roemer, Markus J. Van Roosmalen, Aaron M. Wenger, Bauke Ylstra, Remond J.A. Fijneman, Wigard P. Kloosterman & Edwin Cuppen
Cell Genomics, 2022, DOI
Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care
Edwin Cuppen, Olivier Elemento, Richard Rosenquist, Svetlana Nikic, Maarten IJzerman, Isabelle Durand Zaleski, Geert Frederix, Lars-Åke Levin, Charles G. Mullighan, Reinhard Buettner, Trevor J. Pugh, Sean Grimmond, Carlos Caldas, Fabrice Andre, Ilse Custers, Elias Campo, Hans Van Snellenberg, Anna Schuh, Hidewaki Nakagawa, Christof Von Kalle, Torsten Haferlach, Stefan Fröhling & Vaidehi Jobanputra
JCO Precision Oncology, 2022, DOI
Clinical Impact of Prospective Whole Genome Sequencing in Sarcoma Patients
Luuk J. Schipper, Kim Monkhorst, Kris G. Samsom, Linda J.W. Bosch, Petur Snaebjornsson, Hester Van Boven, Paul Roepman, Lizet E. Van Der Kolk, Winan J. Van Houdt, Winette T.A. Van Der Graaf, Gerrit A. Meijer & Emile E. Voest
Cancers, 2022, DOI
Unscrambling cancer genomes via integrated analysis of structural variation and copy number
Charles Shale, Daniel L. Cameron, Jonathan Baber, Marie Wong, Mark J. Cowley, Anthony T. Papenfuss, Edwin Cuppen & Peter Priestley
Cell Genomics, 2022, DOI
Analytical demands to use whole-genome sequencing in precision oncology
Manja Meggendorfer, Vaidehi Jobanputra, Kazimierz O. Wrzeszczynski, Paul Roepman, Ewart De Bruijn, Edwin Cuppen, Reinhard Buttner, Carlos Caldas, Sean Grimmond, Charles G. Mullighan, Olivier Elemento, Richard Rosenquist, Anna Schuh & Torsten Haferlach
Seminars in Cancer Biology, 2022, DOI
Clinical utility of whole-genome sequencing in precision oncology
Richard Rosenquist, Edwin Cuppen, Reinhard Buettner, Carlos Caldas, Helene Dreau, Olivier Elemento, Geert Frederix, Sean Grimmond, Torsten Haferlach, Vaidehi Jobanputra, Manja Meggendorfer, Charles G. Mullighan, Sarah Wordsworth & Anna Schuh
Seminars in Cancer Biology, 2022, DOI
Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology
Vaidehi Jobanputra, Kazimierz O. Wrzeszczynski, Reinhard Buttner, Carlos Caldas, Edwin Cuppen, Sean Grimmond, Torsten Haferlach, Charles Mullighan, Anna Schuh & Olivier Elemento
Seminars in Cancer Biology, 2022, DOI
Delivering precision oncology to patients with cancer
Joaquin Mateo, Lotte Steuten, Philippe Aftimos, Fabrice André, Mark Davies, Elena Garralda, Jan Geissler, Don Husereau, Iciar Martinez-Lopez, Nicola Normanno, Jorge S. Reis-Filho, Stephen Stefani, David M. Thomas, C. Benedikt Westphalen & Emile Voest
Nature Medicine, 2022, DOI
Genome‐wide aneuploidy detected by mFast‐SeqS in circulating cell‐free DNA is associated with poor response to pembrolizumab in patients with advanced urothelial cancer
Pauline A. J. Mendelaar, Debbie G. J. Robbrecht, Maud Rijnders, Ronald De Wit, Vanja De Weerd, Teoman Deger, Hans M. Westgeest, Maureen J. B. Aarts, Jens Voortman, John W. M. Martens, Astrid A. M. Van Der Veldt, José Alberto Nakauma‐González, Saskia M. Wilting & Martijn Lolkema
Molecular Oncology, 2022, DOI
Meta-analysis of preclinical pharmacogenomic studies to discover robust and translatable biomarkers of drug response
Petr Smirnov, Sisira Kadambat Nair, Farnoosh Abbas-Aghababazadeh, Nikta Feizi, Ian Smith, Trevor J. Pugh & Benjamin Haibe-Kains
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2021 (31)
The Management of Neuroendocrine Tumors of the Lung in MEN1: Results From the Dutch MEN1 Study Group
Medard F M Van Den Broek, Joanne M De Laat, Rachel S Van Leeuwaarde, Annenienke C Van De Ven, Wouter W De Herder, Olaf M Dekkers, Madeleine L Drent, Michiel N Kerstens, Peter H Bisschop, Bas Havekes, Wenzel M Hackeng, Lodewijk A A Brosens, Menno R Vriens, Wieneke A Buikhuisen & Gerlof D Valk
The Journal of Clinical Endocrinology & Metabolism, 2021, DOI
Generating human prostate cancer organoids from leukapheresis enriched circulating tumour cells
Lisanne Mout, Lisanne F. Van Dessel, Jaco Kraan, Anouk C. De Jong, Rui P.L. Neves, Sigrun Erkens-Schulze, Corine M. Beaufort, Anieta M. Sieuwerts, Job Van Riet, Thomas L.C. Woo, Ronald De Wit, Stefan Sleijfer, Paul Hamberg, Yorick Sandberg, Peter A.W. Te Boekhorst, Harmen J.G. Van De Werken, John W.M. Martens, Nikolas H. Stoecklein, Wytske M. Van Weerden & Martijn P. Lolkema
European Journal of Cancer, 2021, DOI
Clinical outcomes and molecular profiling of advanced metastatic castration-resistant prostate cancer patients treated with 225Ac-PSMA-617 targeted alpha-radiation therapy
Maarten J. Van Der Doelen, Niven Mehra, Inge M. Van Oort, Monika G. Looijen-Salamon, Marcel J.R. Janssen, José A.E. Custers, Peter H.J. Slootbeek, Leonie I. Kroeze, Frank Bruchertseifer, Alfred Morgenstern, Uwe Haberkorn, Clemens Kratochwil, James Nagarajah & Winald R. Gerritsen
Urologic Oncology: Seminars and Original Investigations, 2021, DOI
Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning
Soufiane M. C. Mourragui, Marco Loog, Daniel J. Vis, Kat Moore, Anna G. Manjon, Mark A. Van De Wiel, Marcel J. T. Reinders & Lodewyk F. A. Wessels
Proceedings of the National Academy of Sciences, 2021, DOI
The impact of rare germline variants on human somatic mutation processes
Mischan Vali Pour, Ben Lehner & Fran Supek
, 2021, DOI
11-Ketotestosterone: the resilience of a potent androgen in prostate cancer patients after castration
Gido Snaterse, Lisanne F. Van Dessel, Job Van Riet, Angela E. Taylor, Michelle Van Der Vlugt-Daane, Paul Hamberg, Ronald De Wit, Jenny A. Visser, Wiebke Arlt, Martijn P. Lolkema & Johannes Hofland
JCI Insight, 2021, DOI
Early Cost Effectiveness of Whole-Genome Sequencing as a Clinical Diagnostic Test for Patients with Inoperable Stage IIIB,C/IV Non-squamous Non-small-Cell Lung Cancer
Martijn J. H. G. Simons, Valesca P. Retèl, Bram L. T. Ramaekers, Rogier Butter, Joanne M. Mankor, Marthe S. Paats, Joachim G. J. V. Aerts, Zakile A. Mfumbilwa, Paul Roepman, Veerle M. H. Coupé, Carin A. Uyl-de Groot, Wim H. Van Harten & Manuela A. Joore
PharmacoEconomics, 2021, DOI
Patients with Biallelic BRCA1/2 Inactivation Respond to Olaparib Treatment Across Histologic Tumor Types
Hanneke Van Der Wijngaart, Louisa R. Hoes, J. Maxime Van Berge Henegouwen, Daphne L. Van Der Velden, Laurien J. Zeverijn, Paul Roepman, Erik Van Werkhoven, Wendy W.J. De Leng, Anne M.L. Jansen, Niven Mehra, Debbie G.J. Robbrecht, Mariette Labots, Derk Jan A. De Groot, Ann Hoeben, Paul Hamberg, Hans Gelderblom, Emile E. Voest & Henk M.W. Verheul
Clinical Cancer Research, 2021, DOI
Impact of DNA damage repair defects and aggressive variant features on response to carboplatin‐based chemotherapy in metastatic castration‐resistant prostate cancer
Peter H. J. Slootbeek, Marleen L. Duizer, Maarten J. Van Der Doelen, Iris S. H. Kloots, Malou C. P. Kuppen, Hans M. Westgeest, Carin A. Uyl‐de Groot, Samhita Pamidimarri Naga, Marjolijn J. L. Ligtenberg, Inge M. Van Oort, Winald R. Gerritsen, Jack A. Schalken, Leonie I. Kroeze, Haiko J. Bloemendal & Niven Mehra
International Journal of Cancer, 2021, DOI
The evolution of hematopoietic cells under cancer therapy
Oriol Pich, Albert Cortes-Bullich, Ferran Muiños, Marta Pratcorona, Abel Gonzalez-Perez & Nuria Lopez-Bigas
Nature Communications, 2021, DOI
Mutational signatures impact the evolution of anti-EGFR antibody resistance in colorectal cancer
Andrew Woolston, Louise J. Barber, Beatrice Griffiths, Oriol Pich, Nuria Lopez-Bigas, Nik Matthews, Sheela Rao, David Watkins, Ian Chau, Naureen Starling, David Cunningham & Marco Gerlinger
Nature Ecology & Evolution, 2021, DOI
A kinome-centered CRISPR-Cas9 screen identifies activated BRAF to modulate enzalutamide resistance with potential therapeutic implications in BRAF-mutated prostate cancer
Sander A. L. Palit, Jeroen Van Dorp, Daniel Vis, Cor Lieftink, Simon Linder, Roderick Beijersbergen, Andries M. Bergman, Wilbert Zwart & Michiel S. Van Der Heijden
Scientific Reports, 2021, DOI
In silico saturation mutagenesis of cancer genes
Ferran Muiños, Francisco Martínez-Jiménez, Oriol Pich, Abel Gonzalez-Perez & Nuria Lopez-Bigas
Nature, 2021, DOI
Evaluation of the Khorana, PROTECHT, and 5‐SNP scores for prediction of venous thromboembolism in patients with cancer
Noori A.M. Guman, Roos J. Van Geffen, Frits I. Mulder, Thijs F. Van Haaps, Vahram Hovsepjan, Mariette Labots, Geert A. Cirkel, Filip Y.F.L. De Vos, Albert J. Ten Tije, Laurens V. Beerepoot, Vivianne C.G. Tjan‐Heijnen, Hanneke W.M. Van Laarhoven, Paul Hamberg, Annelie J.E. Vulink, Maartje Los, Aeilko H. Zwinderman, Bart Ferwerda, Martijn P.J.K. Lolkema, Neeltje Steeghs, Harry R. Büller, Pieter W. Kamphuisen & Nick Van Es
Journal of Thrombosis and Haemostasis, 2021, DOI
Learning mutational signatures and their multidimensional genomic properties with TensorSignatures
Harald Vöhringer, Arne Van Hoeck, Edwin Cuppen & Moritz Gerstung
Nature Communications, 2021, DOI
Network-Based Analysis to Identify Drivers of Metastatic Prostate Cancer Using GoNetic
Louise De Schaetzen Van Brienen, Giles Miclotte, Maarten Larmuseau, Jimmy Van Den Eynden & Kathleen Marchal
Cancers, 2021, DOI
Driver mutations occur frequently in metastases of well‐differentiated small intestine neuroendocrine tumours
Kris G Samsom, Sonja Levy, Linde M Van Veenendaal, Paul Roepman, Liudmila L Kodach, Neeltje Steeghs, Gerlof D Valk, M Wouter Dercksen, Koert F D Kuhlmann, Wieke H M Verbeek, Gerrit A Meijer, Margot E T Tesselaar & José G Van Den Berg
Histopathology, 2021, DOI
Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features
Pauline A. J. Mendelaar, Marcel Smid, Job Van Riet, Lindsay Angus, Mariette Labots, Neeltje Steeghs, Mathijs P. Hendriks, Geert A. Cirkel, Johan M. Van Rooijen, Albert J. Ten Tije, Martijn P. Lolkema, Edwin Cuppen, Stefan Sleijfer, John W. M. Martens & Saskia M. Wilting
Nature Communications, 2021, DOI
RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer
Teodora Radonic, W.R.R. Geurts-Giele, Kris G. Samsom, Guido M.J. M. Roemen, Jan H. Von Der Thüsen, Erik Thunnissen, Isabelle C. Meijssen, Hein F.B. M. Sleddens, Winand N.M. Dinjens, Mirjam C. Boelens, Karin Weijers, Ernst Jan M. Speel, Stephen P. Finn, Cathal O’Brien, Tom Van Wezel, Danielle Cohen, Kim Monkhorst, Paul Roepman & H.J. Dubbink
Journal of Thoracic Oncology, 2021, DOI
A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage
Xueqing Zou, Gene Ching Chiek Koh, Arjun Scott Nanda, Andrea Degasperi, Katie Urgo, Theodoros I. Roumeliotis, Chukwuma A. Agu, Cherif Badja, Sophie Momen, Jamie Young, Tauanne Dias Amarante, Lucy Side, Glen Brice, Vanesa Perez-Alonso, Daniel Rueda, Celine Gomez, Wendy Bushell, Rebecca Harris, Jyoti S. Choudhary, Genomics England Research Consortium, John C. Ambrose, Prabhu Arumugam, Emma L. Baple, Marta Bleda, Freya Boardman-Pretty, Jeanne M. Boissiere, Christopher R. Boustred, Helen Brittain, Mark J. Caulfield, Georgia C. Chan, Clare E. H. Craig, Louise C. Daugherty, Anna De Burca, Andrew Devereau, Greg Elgar, Rebecca E. Foulger, Tom Fowler, Pedro Furió-Tarí, Adam Giess, Joanne M. Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, James E. Holman, Tim J. P. Hubbard, Kristina IbáÑEz, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Athanasios Kousathanas, Lea Lahnstein, Kay Lawson, Sarah E. A. Leigh, Ivonne U. S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Joanne Mason, Ellen M. McDonagh, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Pter O’Donovan, Chris A. Odhams, Andrea Orioli, Christine Patch, Mariana Buongermino Pereira, Daniel Perez-Gil, Dimitris Polychronopoulos, John Pullinger, Tahrima Rahim, Augusto Rendon, Pablo Riesgo-Ferreiro, Tim Rogers, Mina Ryten, Kevin Savage, Kushmita Sawant, Richard H. Scott, Afshan Siddiq, Alexander Sieghart, Damian Smedley, Katherine R. Smith, Samuel C. Smith, Alona Sosinsky, William Spooner, Helen E. Stevens, Alexander Stuckey, Razvan Sultana, Mélanie Tanguy, Ellen R. A. Thomas, Simon R. Thompson, Carolyn Tregidgo, Arianna Tucci, Emma Walsh, Sarah A. Watters, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, Magdalena Zarowiecki, Josef Jiricny, William C. Skarnes & Serena Nik-Zainal
Nature Cancer, 2021, DOI
Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics
Paul Roepman, Ewart De Bruijn, Stef Van Lieshout, Lieke Schoenmaker, Mirjam C. Boelens, Hendrikus J. Dubbink, Willemina R.R. Geurts-Giele, Floris H. Groenendijk, Manon M.H. Huibers, Mariëtte E.G. Kranendonk, Margaretha G.M. Roemer, Kris G. Samsom, Marloes Steehouwer, Wendy W.J. De Leng, Alexander Hoischen, Bauke Ylstra, Kim Monkhorst, Jacobus J.M. Van Der Hoeven & Edwin Cuppen
The Journal of Molecular Diagnostics, 2021, DOI
VIRUSBreakend: Viral Integration Recognition Using Single Breakends
Daniel L Cameron, Nina Jacobs, Paul Roepman, Peter Priestley, Edwin Cuppen, Anthony T Papenfuss & Tobias Marschall
Bioinformatics, 2021, DOI
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Daniel L. Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclan, Nicolle Besselink, Arne Van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley & Anthony T. Papenfuss
Genome Biology, 2021, DOI
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer
Emre Kocakavuk, Kevin J. Anderson, Frederick S. Varn, Kevin C. Johnson, Samirkumar B. Amin, Erik. P. Sulman, Martijn P. Lolkema, Floris P. Barthel & Roel G. W. Verhaak
Nature Genetics, 2021, DOI
Limited evolution of the actionable metastatic cancer genome under therapeutic pressure
Joris Van De Haar, Louisa R. Hoes, Paul Roepman, Martijn P. Lolkema, Henk M. W. Verheul, Hans Gelderblom, Adrianus J. De Langen, Egbert F. Smit, Edwin Cuppen, Lodewyk F. A. Wessels & Emile E. Voest
Nature Medicine, 2021, DOI
Early technology assessment of using whole genome sequencing in personalized oncology
Martijn Simons, Michiel Van De Ven, Veerle Coupé, Manuela Joore, Maarten IJzerman, Erik Koffijberg, Geert Frederix, Carin Uyl - De Groot, Edwin Cuppen, Wim Van Harten & Valesca Retèl
Expert Review of Pharmacoeconomics & Outcomes Research, 2021, DOI
Prospective experimental treatment of colorectal cancer patients based on organoid drug responses
S.N. Ooft, F. Weeber, L. Schipper, K.K. Dijkstra, C.M. McLean, S. Kaing, J. Van De Haar, W. Prevoo, E. Van Werkhoven, P. Snaebjornsson, L.R. Hoes, M. Chalabi, D. Van Der Velden, M. Van Leerdam, H. Boot, C. Grootscholten, A.D.R. Huitema, H.J. Bloemendal, E. Cuppen & E.E. Voest
ESMO Open, 2021, DOI
The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets
Job Van Riet, Harmen J. G. Van De Werken, Edwin Cuppen, Ferry A. L. M. Eskens, Margot Tesselaar, Linde M. Van Veenendaal, Heinz-Josef Klümpen, Marcus W. Dercksen, Gerlof D. Valk, Martijn P. Lolkema, Stefan Sleijfer & Bianca Mostert
Nature Communications, 2021, DOI
Micro-costing diagnostics in oncology: from single-gene testing to whole- genome sequencing
Clémence T. B. Pasmans, Bastiaan B. J. Tops, Elisabeth M. P. Steeghs, Veerle M. H. Coupé, Katrien Grünberg, Eiko K De Jong, Ed M. D. Schuuring, Stefan M. Willems, Marjolijn J. L. Ligtenberg, Valesca P. Retèl, Hans Van Snellenberg, Ewart De Bruijn, Edwin Cuppen & Geert W. J. Frederix
Expert Review of Pharmacoeconomics & Outcomes Research, 2021, DOI
Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning
Marleen M. Nieboer, Luan Nguyen & Jeroen De Ridder
Scientific Reports, 2021, DOI
Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients
Jurrian K. De Kanter, Flavia Peci, Eline Bertrums, Axel Rosendahl Huber, Anaïs Van Leeuwen, Markus J. Van Roosmalen, Freek Manders, Mark Verheul, Rurika Oka, Arianne M. Brandsma, Marc Bierings, Mirjam Belderbos & Ruben Van Boxtel
Cell Stem Cell, 2021, DOI
2020 (12)
Impact of DNA damage repair defects on response to radium-223 and overall survival in metastatic castration-resistant prostate cancer
Maarten J. Van Der Doelen, Pedro Isaacsson Velho, Peter H.J. Slootbeek, Samhita Pamidimarri Naga, Maren Bormann, Sjoerd Van Helvert, Leonie I. Kroeze, Inge M. Van Oort, Winald R. Gerritsen, Emmanuel S. Antonarakis & Niven Mehra
European Journal of Cancer, 2020, DOI
A compendium of mutational cancer driver genes
Francisco Martínez-Jiménez, Ferran Muiños, Inés Sentís, Jordi Deu-Pons, Iker Reyes-Salazar, Claudia Arnedo-Pac, Loris Mularoni, Oriol Pich, Jose Bonet, Hanna Kranas, Abel Gonzalez-Perez & Nuria Lopez-Bigas
Nature Reviews Cancer, 2020, DOI
The Immunogenic Potential of Recurrent Cancer Drug Resistance Mutations: An In Silico Study
Marco Punta, Victoria A. Jennings, Alan A. Melcher & Stefano Lise
Frontiers in Immunology, 2020, DOI
svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
Marleen M. Nieboer & Jeroen De Ridder
Bioinformatics, 2020, DOI
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers
David Mas-Ponte & Fran Supek
Nature Genetics, 2020, DOI
Pervasive chromosomal instability and karyotype order in tumour evolution
Thomas B. K. Watkins, Emilia L. Lim, Marina Petkovic, Sergi Elizalde, Nicolai J. Birkbak, Gareth A. Wilson, David A. Moore, Eva Grönroos, Andrew Rowan, Sally M. Dewhurst, Jonas Demeulemeester, Stefan C. Dentro, Stuart Horswell, Lewis Au, Kerstin Haase, Mickael Escudero, Rachel Rosenthal, Maise Al Bakir, Hang Xu, Kevin Litchfield, Wei Ting Lu, Thanos P. Mourikis, Michelle Dietzen, Lavinia Spain, George D. Cresswell, Dhruva Biswas, Philippe Lamy, Iver Nordentoft, Katja Harbst, Francesc Castro-Giner, Lucy R. Yates, Franco Caramia, Fanny Jaulin, Cécile Vicier, Ian P. M. Tomlinson, Priscilla K. Brastianos, Raymond J. Cho, Boris C. Bastian, Lars Dyrskjøt, Göran B. Jönsson, Peter Savas, Sherene Loi, Peter J. Campbell, Fabrice Andre, Nicholas M. Luscombe, Neeltje Steeghs, Vivianne C. G. Tjan-Heijnen, Zoltan Szallasi, Samra Turajlic, Mariam Jamal-Hanjani, Peter Van Loo, Samuel F. Bakhoum, Roland F. Schwarz, Nicholas McGranahan & Charles Swanton
Nature, 2020, DOI
Study protocol: Whole genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE)
Kris G. Samsom, Linda J. W. Bosch, Luuk J. Schipper, Paul Roepman, Ewart De Bruijn, Louisa R. Hoes, Immy Riethorst, Lieke Schoenmaker, Lizet E. Van Der Kolk, Valesca P. Retèl, Geert W. J. Frederix, Tineke E. Buffart, Jacobus J. M. Van Der Hoeven, Emile E. Voest, Edwin Cuppen, Kim Monkhorst & Gerrit A. Meijer
BMC Medical Genomics, 2020, DOI
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes and Clinical Translation Working Group, Fatima Al-Shahrour, Gurnit Atwal, Peter J. Bailey, Andrew V. Biankin, Paul C. Boutros, Peter J. Campbell, David K. Chang, Susanna L. Cooke, Vikram Deshpande, Bishoy M. Faltas, William C. Faquin, Levi Garraway, Gad Getz, Sean M. Grimmond, Syed Haider, Katherine A. Hoadley, Wei Jiao, Vera B. Kaiser, Rosa Karlic, Mamoru Kato, Kirsten Kübler, Alexander J. Lazar, Constance H. Li, David N. Louis, Adam Margolin, Sancha Martin, Hardeep K. Nahal-Bose, G. Petur Nielsen, Serena Nik-Zainal, Larsson Omberg, Christine P’ng, Marc D. Perry, Paz Polak, Esther Rheinbay, Mark A. Rubin, Colin A. Semple, Dennis C. Sgroi, Tatsuhiro Shibata, Reiner Siebert, Jaclyn Smith, Lincoln D. Stein, Miranda D. Stobbe, Ren X. Sun, Kevin Thai, Derek W. Wright, Chin-Lee Wu, Ke Yuan, Junjun Zhang, Alexandra Danyi, Jeroen De Ridder, Carla Van Herpen, Martijn P. 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Nature Cancer, 2020, DOI
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Nature Genetics, 2019, DOI
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Nature, 2019, DOI
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Targeted Treatment Options of Recurrent Radioactive Iodine Refractory Hürthle Cell Cancer
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The complete DNA test allows for personalized treatment and so limits the chance of undesirable side effects.
Patient