Wetenschappelijke publicaties

Publicaties en pre-publicaties waarbij gebruik is gemaakt van de Hartwig Medical Database

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2024 (7)

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: 10.1016/j.celrep.2024.114048

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: 10.1016/j.cell.2024.03.021

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: 10.1016/j.gim.2023.101032

The multitarget faecal immunochemical test for improving stool-based colorectal cancer screening programmes: a Dutch population-based, paired-design, intervention study

Wisse PHA, de Klaver W, van Wifferen F, van Maaren-Meijer FG, van Ingen HE, Meiqari L, Huitink I, Bierkens M, Lemmens M, Greuter MJE, van Leerdam ME, Spaander MCW, Dekker E, Coupé VMH, Carvalho B, de Wit M, Meijer GA

Lancet Oncology, February 2024, DOI: 10.1016/S1470-2045(23)00651-4

Gene-expression-based T-Cell-to-Stroma Enrichment (TSE) score predicts response to immune checkpoint inhibitors in urothelial cancer

Rijnders M, Nakauma-González JA, Robbrecht DGJ, Gil-Jimenez A, Balcioglu HE, Oostvogels AAM, Aarts MJB, Boormans JL, Hamberg P, van der Heijden MS, Szabados BE, van Leenders GJLH, Mehra N, Voortman J, Westgeest HM, de Wit R, van der Veldt AAM, Debets R, Lolkema MP

Nature Communications, February 2024, DOI: 10.1038/s41467-024-45714-0

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, Februari 1, 2024, https://doi.org/10.1158/1078-0432.CCR-23-4027

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, February 24, 2024, https://doi.org/10.1016/j.molcel.2023.12.039

2023 (20)

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: 10.1038/s41596-023-00933-5

Tumour mutations in long noncoding RNAs enhance cell fitness

Roberta Esposito, Andrés Lanzós, Taisia Polidori, Hugo Guillen-Ramirez, Bernard Mefi Merlin, Lia Mela, Eugenio Zoni, Isabel Büchi, Lusine Hovhannisyan, Finn McCluggage, Matúš Medo, Giulia Basile, Dominik F. Meise, Sunandini Ramnarayanan, Sandra Zwyssig, Corina Wenger, Kyriakos Schwarz, Adrienne Vancura, Núria Bosch-Guiteras, Marianna Kruithof-de Julio, Yitzhak Zimmer, Michaela Medová, Deborah Stroka, Archa Fox, Rory Johnson

Nature Communications, 2023, DOI: 10.1038/s41467-023-39160-7

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: 10.3390/ijms24066009

Copy number footprints of platinum-based anticancer therapies

Santiago Gonzalez, Nuria Lopez-Bigas, Abel Gonzalez-Perez, Dmitry A. Gordenin

PLOS Genetics, 2023, DOI: 10.1371/journal.pgen.1010634

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: 10.1093/narcan/zcad014

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: 10.1038/s41586-023-06057-w

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: 10.1186/s12885-023-10663-2

Genetic immune escape landscape in primary and metastatic cancer

Francisco Martínez-Jiménez, Peter Priestley, Charles Shale, Jonathan Baber, Erik Rozemuller, Edwin Cuppen

Nature Genetics, May 10 2023, DOI: 10.1038/s41588-023-01367-1

Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity

Kathleen E. Houlahan, Aziz Khan, Noah F Greenwald, Robert B. West, Michael Angelo, Christina Curtis

NA, 2023, DOI: 10.1101/2023.03.15.532870

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, NA NA, Michelle Haber, Glenn Marshall, Murray J. Cairns, Jean-Yves Blay, NA NA, David M. Thomas

Science, 2023, DOI: 10.1126/science.abj4784

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: 10.1038/s41588-023-01313-1

Mutational processes of tobacco smoking and APOBEC activity generate protein-truncating mutations in cancer genomes

Nina Adler, Alexander T. Bahcheli, Kevin Cheng, Khalid N. Al-Zahrani, Mykhaylo Slobodyanyuk, Diogo Pellegrina, Daniel Schramek, Jüri Reimand

NA, 2023, DOI: 10.1101/2023.03.19.533271

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: 10.7554/eLife.81224

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, May 10 2023, DOI: 10.1038/s41586-023-06054-z

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: 10.1038/s41467-023-37647-x

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: 10.1371/journal.pone.0281375

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: 10.1016/j.jtho.2022.11.030

Tumour mitochondrial DNA mutations drive aerobic glycolysis to enhance checkpoint blockade

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, J.L. Manchon, Crístina Rodríguez-Antona, Rowan C. Walters, Roger J. Springett, James N. Blaza, Sara Zanivan, David Sumpton, Edward W. Roberts, Ed Reznik, Payam A. Gammage

NA, 2023, DOI: 10.1101/2023.03.21.533091

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: 10.1038/s41598-023-32499-3

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, March 2023, DOI: https://doi.org/10.1016/j.biopha.2022.114210

2022 (38)

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: 10.1038/s41591-022-01717-2

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: 10.1007/s40291-021-00571-1

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: 10.1016/j.ejca.2022.05.009

Temporal Dissection of Altered Pathways during the Evolution of Cancer

Johanne Ahrenfeldt, Ditte S. Christensen, Mateo Sokač, Judit Kisistók, Nicholas McGranahan, Nicolai J. Birkbak

NA, 2022, DOI: 10.20944/preprints202210.0470.v1

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: 10.1186/s12920-022-01343-4

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: 10.3390/ijms23095080

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: 10.1038/s41467-022-33718-7

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: 10.1200/PO.22.00245

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: 10.1038/s41416-021-01663-9

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: 10.1038/s41467-022-32828-6

Germline determinants of the prostate tumor genome

Kathleen E. Houlahan, Jiapei Yuan, Tommer Schwarz, Julie Livingstone, Natalie S. Fox, Weerachai Jaratlerdsiri, Job Van Riet, Kodi Taraszka, Natalie Kurganovs, Helen Zhu, Jocelyn Sietsma Penington, Chol-Hee Jung, Takafumi N Yamaguchi, Jue Jiang, Lawrence E Heisler, Richard Jovelin, Susmita G Ramanand, Connor Bell, Edward O’Connor, Shingai B.A. Mutambirwa, Ji-Heui Seo, Anthony J. Costello, Mark M. Pomerantz, Bernard J. Pope, Noah Zaitlen, Amar U. Kishan, Niall M. Corcoran, Robert G. Bristow, Sebastian M. Waszak, Riana M.S. Bornman, Alexander Gusev, Martijn P. Lolkema, Joachim Weischenfeldt, Rayjean J. Hung, Housheng H. He, Vanessa M. Hayes, Bogdan Pasaniuc, Matthew L. Freedman, Christopher M. Hovens, Ram S. Mani, Paul C. Boutros

NA, 2022, DOI: 10.1101/2022.11.16.516773

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: 10.1038/s41587-022-01353-8

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

NA, 2022, DOI: 10.1101/2022.02.09.479712

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: 10.1016/j.semcancer.2021.06.018

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: 10.1016/j.semcancer.2021.07.003

Cell cycle alterations associate with a redistribution of mutation rates across chromosomal domains in human cancers

Marina Salvadores, Fran Supek

NA, 2022, DOI: 10.1101/2022.10.24.513586

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: 10.1200/PO.21.00190

Accurate and sensitive mutational signature analysis with MuSiCal

Hu Jin, Doga C. Gulhan, Daniel Ben-Isvy, David Geng, Viktor Ljungstrom, Peter J. Park

NA, 2022, DOI: 10.1101/2022.04.21.489082

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: 10.1016/j.xgen.2022.100139

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, September 2022, DOI: 10.1016/j.semcancer.2021.06.009

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, December 1, 2022, PMID: 36463731

Hotspot propensity across mutational processes

Claudia Arnedo-Pac, Ferran Muiños, Abel Gonzalez-Perez & Nuria Lopez-Bigas

BioRxiv, September 19 2022, doi: https://doi.org/10.1101/2022.09.14.507952

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, August 10, 2022

Personalized selection of experimental treatment in patients with advanced solid cancer is feasible using Whole Genome Sequencing

M.A. Pruis, F.H. Groenendijk, K.S. Badloe, A. van Puffelen, D. Robbrecht, W.N.M. Dinjens, S. Sleijfer, A.C. Dingemans, J.H. von der Thüsen, P. Roepman, M.P. Lolkema

British Journal of Cancer (BJC), May 23, 2022, PMID: 35606463

The genomic and transcriptomic landscape of advanced renal cell cancer to individualize 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

BioRxiv, April 22, 2022, DOI: https://doi.org/10.1101/2022.04.22.488773

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

Science

April 21, 2022

DOI: 10.1126/science.abl9283

Genome-wide analysis of somatic noncoding mutation patterns in cancer

Felix Dietlein, Alex B. Wang, Fagre, Anran Tang, Nicolle J. M. Besselink, Cuppen, Chunliang Li, R. Sunyaev, T. Neal, Eliezer M. Van Allen

Science

April 8, 2022

DOI: 10.1126/science.abg5601

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, March 22, 2022, DOI: https://doi.org/10.1016/j.xgen.2022.100112

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 and Petronella O. Witteveen

Cancers

March 15, 2022

PMID: 35326660

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 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, J Alberto Nakauma-González, Saskia M Wilting, Martijn Lolkema

Molecular Oncology, February 19, 2022, PMID: 35181986

Comprehensive Molecular Characterization Reveals Genomic and Transcriptomic Subtypes of Metastatic Urothelial Carcinoma

J. Alberto Nakauma-Gonzáleza, Maud Rijnders, Job van Riet, Michiel S.van der Heijden, Jens Voortman, EdwinCuppen, Niven Mehra, Sandra van Wilpe, Sjoukje F.Oosting, 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,

January 25, 2022

PMID: 35086719

Genomics – Guided Treatment of Rare Cancer Patients in DRUP

L.R. Hoes, J.M. van Berge Henegouwen, H. van der Wijngaart, L.J. Zeverijn, D.L. van der Velden, J. van de Haar, P. Roepman, W.W.J. de Leng, A.M.L. Jansen, E. van Werkhoven, V. van der Noort, A.D.R. Huitema, E.H. Gort, J.W.B. de Groot, E.D. Kerver, D.J. de Groot, F. Erdkamp, L.V. Beerepoot, M.P. Hendriks, E.F. Smit, W.T.A. van der Graaf, C.M.L. van Herpen, M. Labots, A. Hoeben, H. Morreau, M.P. Lolkema, E. Cuppen, H. Gelderblom, H.M.W. Verheul, E.E. Voest

Clinical Cancer Research

January 19, 2022

PMID: 35046062

Clinical impact of prospective whole genome sequencing in sarcoma patients

L.J. Schipper, K. Monkhorst, K.G. Samsom, L.J.W. Bosch, P. Snaebjornsson, H. van Boven, P. Roepman, L.E. van der Kolk, W.J. van Houdt, W.T.A. van der Graaf, G.A. Meijer, E.E. Voest

Cancers (Basel), MDPI

January 16, 2022

PMID: 35053600

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, December 2022, PMID: 35047820

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, July 11, 2022

PMID: 35817764

Feasibility of whole genome sequencing based tumor diagnostics in routine pathology practice

Kris G. Samsom, Luuk J. Schipper, Paul Roepman, Linda J.W. 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 J.M. 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, July 6, 2022

PMID: 35792649

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

June 16, 2022

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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 and Dik C. van Gent

Oncogene, Jun 3, 2022, DOI: https://doi.org/10.1038/s41388-022-02363-1

2021 (30)

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: 10.1016/j.ejca.2021.03.023

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: 10.1210/clinem/dgaa800

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, April 19, 2021, DOI: 10.1016/j.esmoop.2021.100103

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, October 21, 2021, DOI: 10.3390/cancers13215291

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, May 20, 2021, DOI: 10.1038/s41559-021-01470-8

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, May 6, 2021, DOI: 10.1080/14737167.2021.1917385

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: 10.1002/ijc.33306

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, June 1, 2021, DOI: 10.1080/14737167.2021.1917386

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, August 18, 2021, DOI: 10.1007/s40273-021-01073-y

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, October 2021, DOI: 10.1016/j.urolonc.2020.12.002

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, May 11, 2021, DOI: 10.1172/jci.insight.148507

In silico saturation mutagenesis of cancer genes

Ferran Muiños, Francisco Martínez-Jiménez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-Bigas

Nature

July 8, 2021

PMID: 34321661

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

Nature

July 1, 2021

PMID: 34211036

Learning mutational signatures and their multidimensional genomic properties with TensorSignatures

Harald Vöhringer, Arne Van Hoeck, Edwin Cuppen, Moritz Gerstung

Nature Communications

June 15, 2021

PMID: 34131135

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

May 27, 2021

PMID: 34045764

VIRUSBreakend: Viral Integration Recognition Using Single Breakends

Daniel L. Cameron, Nina Jacobs, Paul Roepman, Peter Priestley, Edwin Cuppen, Anthony T. Papenfuss

Bioinformatics

May 11, 2021

PMID: 33973999

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 RR. Geurts-Giele, Floris H. Groenendijk, Manon MH. Huibers, Mariëtte EG. Kranendonk, Margaretha GM. Roemer, Kris G. Samsom, Marloes Steehouwer, Wendy WJ. de Leng, Alexander Hoischen, Bauke Ylstra, Kim Monkhorst, Jacobus JM. van der Hoeven, Edwin Cuppen

The Journal of Moleculair Diagnostics,

May 5, 2021

PMID: 33964451

"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, Josef Jiricny, William C. Skarnes & Serena Nik-Zainal

Nature Cancer

April 26, 2021

PMID: 34164627

RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer

Teodora Radonic, MD, PhD, W. R. R. Geurts-Giele, PhD,b Kris G. Samsom, MD, Guido M. J. M. Roemen, BSc,Jan H. von der Thüsen, MD, PhD, Erik Thunnissen, MD, PhD, Isabelle C. Meijssen, MSc, Hein F. B. M. Sleddens, BSc, Winand N. M. Dinjens, Prof, Mirjam C. Boelens, PhD, Karin Weijers, MSc,Ernst Jan M. Speel, Prof,d, Stephen P. Finn, Prof, Cathal O’Brien, PhD, Tom van Wezel, PhD, Danielle Cohen, MD, PhD, Kim Monkhorst, MD, PhD, Paul Roepman, PhD,j H. J. Dubbink, PhD

Journal of Thoracic Oncology

February 12, 2021

PMID: 33588111

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

January 25, 2021

PMID: 33495476

Driver mutations occur frequently in metastases of well‐differentiated small intestine neuroendocrine tumours

Samsom K G, Levy S, van Veenendaal L M, Roepman P, Kodach L L, Steeghs N, Valk G D, Dercksen M W, Kuhlmann K F D, Verbeek W H M, Meijer G A, Tesselaar M E T & van den Berg J G Histopathology, 2021, PMID: 32931025

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, eMarcel J. T. Reinders, Lodewyk F. A. Wessels

Proceedings of the National Academy of Sciences of the United States of America (PNAS)

December 7, 2021

PMID: 34873056

Patients with bi-allelic 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

American Association for Cancer Research – AACR

September 2, 2021

PMID: 34475104

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 – jth

Augustus 16, 2021

PMID: 34409743

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

Augustus 10, 2021

PMID: 34376657

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

Augustus 9, 2021

PMID: 34373653

The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtypeheterogeneity 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

July 29, 2021

PMID: 34326338

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

Nature

July 13, 2021

PMID: 34257393

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, July 12, 2021, PMID: 34253237

The impact of rare germline variants on human somatic mutation processes

Mischan Vali-Pour, Ben Lehner & Fran Supek Nature Communications, November 14, 2021 PMID: 35764656

2020 (12)

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, November 10, 2020, DOI: 10.1186/s12920-020-00814-w

Impact of panel design and cut-off on tumour mutational burden assessment in metastatic solid tumour samples

Mankor JM, Paats MS, Groenendijk FH, Roepman P, Dinjens WNM, Dubbink HJ, Sleijfer S, CPCT Consortium, Cuppen E, Lolkema MPJK BJC British Journal of Cancer, March 12, 2020, PMID: 32094484

A mutational signature in human colorectal cancer induced by genotoxic pks+ E. coli

Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood H, Nomburg JL, Gurjao C, Manders F, Dalmasso G, Stege P, Paganelli F, Geurts MH, Beumer J, Mizutani T, van der Linden R, van Elst S, The Genomics England Consortium, Top J, Willems R, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R, Clevers H

Nature

February 27, 2020

PMID: 32106218

GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number

Cameron DL, Baber J, Shale C, Papenfuss AT, Espejo Valle-Inclan J, Besselink N, Cuppen E, Priestley P

BJC British Journal of Cancer

February 25, 2020

DOI: 10.1038/s41416-020-0762-5

A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies

Andrea Degasperi, Tauanne Dias Amarante, Jan Czarnecki, Scott Shooter, Xueqing Zou, Dominik Glodzik, Sandro Morganella, Arjun S. Nanda, Cherif Badja, Gene Koh, Sophie E. Momen, Ilias Georgakopoulos-Soares, João M. L. Dias, Jamie Young, Yasin Memari, Helen Davies & Serena Nik-Zainal

Nature Cancer

February 17, 2020

PMID: 32118208

A deep learning system accurately classify primary and metastatic cancers using passenger mutation patterns

Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium

Nat Commun.

January 22, 2020

PMID: 32024849

svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning

Marleen M. Nieboer, Jeroen de Ridder

Bioinformatics

December 1, 2020

PMID: 33381833

Pervasive Chromosomal Instability and Karyotype Order In Tumour Evolution

Thomas BK 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 PM 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 CG Tjan-Heijnen, Zoltan Szallasi, Samra Turajlic, Mariam Jamal-Hanjani, Peter Van Loo, Samuel F Bakhoum, Roland F Schwarz, Nicholas McGranahan, Charles Swanton

Nature

November 5, 2020

PMID: 32879494

Pan-cancer landscape of homologous recombination deficiency.

Nguyen L, van Hoeck A, Cuppen E

Nature Communications

November 1, 2020

PMID: 33149131

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

October 8, 2020

PMID: 33133066

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

August 10, 2020

PMID: 32778778

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers.

Ponte, D and Supek, F

Nature Genetics

August 1, 2020

PMID: 32747826

2019 (10)

Molecular tumour boards and molecular diagnostics for patients with cancer in the Netherlands: experiences, challenges, and aspirations

Annelieke E. C. A. B. Willemsen, Sarah Krausz, Marjolijn J. L. Ligtenberg, Katrien Grünberg, Harry J. M. Groen, Emile E. Voest, Edwin P. J. G. Cuppen, Hanneke W. M. Van Laarhoven, Carla M. L. Van Herpen

British Journal of Cancer, 2019, DOI: 10.1038/s41416-019-0489-3

Pancreatic cancer organoids recapitulate disease and allow personalized drug screening

Driehuis E, van Hoeck A, Moore K, Kolders S, Francies HE, Gulersonmez MC, Stigter ECA, Burgering B, Geurts V, Gracanin A, Bounova G, Morsink FH, Vries R, Boj S, van Es J, Offerhaus GJA, Kranenburg O, Garnett MJ, Wessels L, Cuppen E, Brosens LAA, Clevers H

Proceedings of the National Academy of Sciences of the U S A.

December 9, 2019

PMID: 31818951

The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact

van Dessel LF, van Riet J, Smits M, Zhu Y, Hamberg P, van der Heijden MS, Bergman AM, van Oort IM, de Wit R, Voest EE, Steeghs N, Yamaguchi TN, Livingstone J, Boutros PC, Martens JWM, Sleijfer S, Cuppen E, Zwart W, van de Werken HJG, Mehra N, Lolkema MP

Nat Commun.

November 20, 2019

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PMCID: PMC6868175

The mutational footprints of cancer therapies

Pich O, Muiños F, Lolkema MP, Steeghs N, Gonzalez-Perez A, Lopez-Bigas N

Nat Genet.

November 18, 2019

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Pan-cancer whole-genome analyses of metastatic solid tumours

Priestley P, Baber J, Lolkema MP, Steeghs N, de Bruijn E, Shale C, Duyvesteyn K, Haidari S, van Hoeck A, Onstenk W, Roepman P, Voda M, Bloemendal HJ, Tjan-Heijnen VCG, van Herpen CML, Labots M, Witteveen PO, Smit EF, Sleijfer S, Voest EE, Cuppen E

Nature

October 23, 2019

PMID: 31645765

5-Fluorouracil treatment induces characteristic T>G mutations in human cancer

Christensen S, Van der Roest B, Besselink N, Janssen R, Boymans S, Martens JWM, Yaspo ML, Priestley P, Kuijk E, Cuppen E, Van Hoeck A

Nat Commun.

October 8, 2019

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The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies.

Angus L, Smid M, Wilting SM, van Riet J, Van Hoeck A, Nguyen L, Nik-Zainal S, Steenbruggen TG, Tjan-Heijnen VCG, Labots M, van Riel JMGH, Bloemendal HJ, Steeghs N, Lolkema MP, Voest EE, van de Werken HJG, Jager A, Cuppen E, Sleijfer S, Martens JWM

Nature Genetics

September 30, 2019

PMID: 31570896

The Drug Rediscovery protocol facilitates the expanded use of existing anticancer drugs

van der Velden DL, Hoes LR, van der Wijngaart H, van Berge Henegouwen JM, van Werkhoven E, Roepman P, Schilsky RL, de Leng WWJ, Huitema ADR, Nuijen B, Nederlof PM, van Herpen CML, de Groot DJA, Devriese LA, Hoeben A, de Jonge MJA, Chalabi M, Smit EF, de Langen AJ, Mehra N, Labots M, Kapiteijn E, Sleijfer S, Cuppen E, Verheul HMW, Gelderblom H, Voest EE

Nature

September 30, 2019

PMID: 31570881

Targeted Treatment Options of Recurrent Radioactive Iodine Refractory Hürthle Cell Cancer

Aydemirli MD, Corver W, Beuk R, Roepman P, Solleveld-Westerink N, van Wezel T, Kapiteijn E, Morreau H

MDPI

August 15, 2019

PMID: 31443247

Tumor mutational landscape is a record of the pre-malignant state

Kirsten Kübler, Rosa Karlić, Nicholas J. Haradhvala, Kyungsik Ha, Jaegil Kim, Maja Kuzman, Wei Jiao, Sitanshu Gakkhar, Kent W. Mouw, Lior Z. Braunstein, Olivier Elemento, Andrew V. Biankin, Ilse Rooman, Mendy Miller, Wouter R. Karthaus, Christopher D. Nogiec, Edouard Juvenson, Edward Curry, Mari Mino- Kenudson, Leif W. Ellisen, Robert Brown, Alexander Gusev, Cristian Tomasetti, Martijn P. Lolkema, Neeltje Steeghs, Carla van Herpen, Hong-Gee Kim, Hwajin Lee, Kristian Vlahoviček, Bradley E. Bernstein, Charles L. Sawyers, Katherine A. Hoadley, Edwin Cuppen, Amnon Koren, Peter F. Arndt, David N. Louis, Lincoln D. Stein, William D. Foulkes, Paz Polak, Gad Getz, on behalf of the PCAWG Pathology and Clinical Correlates Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network

BioRxiv

January 11, 2019

DOI: /10.1101/517565v1

2016 (1)

Next-generation sequencing in NSCLC and melanoma patients: a cost and budget impact analysis

Rosa Van Amerongen, Valesca P Retèl, Veerle Mh Coupé, Petra M Nederlof, Maartje J Vogel, Wim H Van Harten

ecancermedicalscience, October 28 2016, DOI: 10.3332/ecancer.2016.684

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Minister van Volksgezondheid, Welzijn en Sport (VWS)

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