Publications with Hartwig Medical Foundaton data in 2019

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. 2019 Nov;575(7781):210-216. doi: 10.1038/s41586-019-1689-y. Epub 2019 Oct 23. PMID: 31645765


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. 2019 Oct;574(7776):127-131. doi: 10.1038/s41586-019-1600-x. Epub 2019 Sep 30. PMID: 31570881


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.

Nature Communications. 2019 Oct 8;10(1):4571. doi: 10.1038/s41467-019-12594-8. PMID: 31594944


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. 2019 Oct;51(10):1450-1458. doi: 10.1038/s41588-019-0507-7. Epub 2019 Sep 30. PMID: 31570896


The mutational footprints of cancer therapies

Oriol Pich, Ferran Muiños, Martijn Paul Lolkema, Neeltje Steeghs, Abel Gonzalez-Perez, Nuria Lopez-Bigas

Nature Genetics. Nov 18, bioRxiv 683268; https://www.nature.com/articles/s41588-019-0525-5


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

Lisanne F. van Dessel, Job van Riet, Minke Smits, Yanyun Zhu, Paul Hamberg, Michiel S. van der Heijden, Andries M. Bergman, Inge M. van Oort, Ronald de Wit, Emile E. Voest, Neeltje Steeghs, Takafumi N. Yamaguchi, Julie Livingstone, Paul C. Boutros, John W.M. Martens, Stefan Sleijfer, Edwin Cuppen, Wilbert Zwart, Harmen J.G. van de Werken, Niven Mehra, Martijn P. Lolkema

Nature Communications. Dec 2019, bioRxiv 546051; https://www.nature.com/articles/s41467-019-13084-7


A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations

Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P Lolkema, Neeltje Steeghs, Gad Getz, Quaid D Morris, Lincoln D. Stein, PCAWG Pathology & Clinical Correlates Working Grp, ICGC/TCGA Pan-cancer Analysis of Whole Genomes Network

bioRxiv 214494; https://www.biorxiv.org/content/10.1101/214494v3

Or watch on ISCB channel on YouTube


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 517565; https://www.biorxiv.org/content/10.1101/517565v1


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

Daniel L. Cameron, Jonathan Baber, Charles Shale, Anthony T. Papenfuss, Jose Espejo Valle-Inclan, Nicolle Besselink, Edwin Cuppen, Peter Priestley

bioRxiv 781013; https://www.biorxiv.org/content/10.1101/781013v1