3D medical background with DNA strands
3D medical background with DNA strands
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Publicaties

(09-09-2021; versie 19: Publicaties i.h.k.v. CPCT)

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

Evaluation of the Khorana, PROTECHT, and 5-SNP scores for prediction of venous thromboembolism in patients with cancer

PubMed

https://pubmed.ncbi.nlm.nih.gov/34409743/

Preprint:

August 19, 2021

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

Limited evolution of the actionable metastatic cancer genome under therapeutic pressure

PubMed

https://pubmed.ncbi.nlm.nih.gov/34373653/

Preprint:

August 9, 2021

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

The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets

Nature Communications

https://www.nature.com/articles/s41467-021-24812-3

Published:

July 29, 2021

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 Retèlon behalf of the TANGO consortium

Early technology assessment of using whole genome sequencing in personalised oncology

Taylor & Francis Online

https://www.tandfonline.com/doi/full/10.1080/14737167.2021.1917386  

Published:

April 29, 2021

***This article is in preprint and has not been certified by peer review***

Lindsay Angus, Marcel Smid, Saskia M. Wilting, Manouk K. Bos, Neeltje Steeghs, Inge R.H.M. Konings, Vivianne C.G. Tjan-Heijnen, Johanna M.G.H. van Riel, Agnes J. van de Wouw, CPCT Consortium, Edwin Cuppen, Martijn P. Lolkema, Agnes Jager, Stefan Sleijfer, John W.M. Martens

Genomic alterations associated with estrogen receptor pathway activity in metastatic breast cancer have a differential impact on downstream ER signaling.

Clinical and Translational Medicine

https:…

Preprint:

March 31, 2021

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, CPCT Consortium, Martijn P.J.K. Lolkema, Edwin Cuppen, Stefan Sleijfer, John W.M. Martens & Saskia M. Wilting

Whole genome sequencing of metastatic CRC reveals prior treatment effects, metastasis-specific features, and potential clinical actionability

Nature Communications

https://www.nature.com/articles/s41467-020-20887-6

Published:

January 25, 2021

Luan Nguyen, John W.M. Martens, Arne Van Hoeck & Edwin Cuppen

Pan-cancer landscape of homologous recombination deficiency

Nature Communications

https://www.nature.com/articles/s41467-020-19406-4

https://www.biorxiv.org/content/10.1101/2020.01.13.905026v2

Published:

November 04, 2020

Martijn Simons, Bram Ramaekers, Andrea Peeters, Joanne Mankor, Marthe Paats, Joachim Aerts, Wim van Harten, Valesca Retèl, Manuela Joore

Observed versus modelled lifetime overall survival of targeted therapies and immunotherapies for advanced non-small cell lung cancer patients – A systematic review.

Critical Reviews in Oncology/Hematology

https://www.sciencedirect.com/science/article/pii/S1040842820301736?dgcid=coauthor

Published:

September 23, 2020

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

Pervasive Chromosomal Instability and Karyotype Order In Tumour Evolution

Nature

https://doi.org/10.1038/s41586-020-2698-6

Published:

September 02, 2020

Cayetano Pleguezuelos-Manzano, Jens Puschhof, Axel Rosendahl Huber, Arne van Hoeck, Henry M. Wood, Jason Nomburg, Carino Gurjao, Freek Manders, Guillaume Dalmasso, Paul B. Stege, Fernanda L. Paganelli, Maarten H. Geurts, Joep Beumer, Tomohiro Mizutani, Reinier van der Linden, Stefan van Elst, Genomics England Research Consortium, Janetta Top, Rob J.L. Willems, Marios Giannakis, Richard Bonnet, Phil Quirke, Matthew Meyerson, Edwin Cuppen, Ruben van Boxtel, Hans Clevers

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli.

Nature

https://www.nature.com/articles/s41586-020-2080-8

Published:

February 27, 2020

Joanne M. Mankor, Marthe S. Paats, Floris H. Groenendijk, Paul Roepman, Winand N. M. Dinjens, Hendrikus J. Dubbink, Stefan Sleijfer, CPCT Consortium, Edwin Cuppen & Martijn P.J.K. Lolkema

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

British journal of cancer

https://www.nature.com/articles/s41416-020-0762-5#auth-6

Published:

February 25, 2020

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 Net

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

Nature Communications

https://www.nature.com/articles/s41467-019-13825-8

Published:

February 05, 2020

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

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

Nature Commununications

https://www.nature.com/articles/s41467-019-13084-7

Published:

November 20, 2019

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

The mutational footprints of cancer therapies.

Nature Genetics

https://www.nature.com/articles/s41588-019-0525-5

Published:

November 18, 2019

Peter Priestley, Jonathan Baber, Martijn P. Lolkema, Neeltje Steeghs, Ewart de Bruijn, Charles Shale, Korneel Duyvesteyn, Susan Haidari, Arne van Hoeck, Wendy Onstenk, Paul Roepman, Mircea Voda, Haiko J. Bloemendal, Vivianne C. G. Tjan-Heijnen, Carla M. L. van Herpen, Mariette Labots, Petronella O. Witteveen, Egbert F. Smit, Stefan Sleijfer, Emile E. Voest & Edwin Cuppen

Pan-cancer whole-genome analyses of metastatic solid tumors.

Nature

https://www.nature.com/articles/s41586-019-1689-y (October 23, 2020)

https://www.biorxiv.org/content/10.1101/2020.01.13.905026v2 (June 19, 2020)

Published:

October 23, 2019

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.

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

Nature Communications

https://www.nature.com/articles/s41467-019-12594-8

Published:

October 08, 2019

Lindsay Angus, Marcel Smid, Saskia M. Wilting, Job van Riet, Arne Van Hoeck, Luan Nguyen, Serena Nik-Zainal, Tessa G. Steenbruggen, Vivianne C.G. Tjan-Heijnen, Mariette Labots, Johanna M.G.H. van Riel, Haiko J. Bloemendal, Neeltje Steeghs, Martijn P. Lolkema, Emile E. Voest, Harmen J.G. van de Werken, Agnes Jager, Edwin Cuppen, Stefan Sleijfer and John W.M. Martens

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

Nature Genetics

https://www.nature.com/articles/s41588-019-0507-7

Published:

September 30, 2019

D.L. van der Velden, L.R. Hoes, H. van der Wijngaart, J.M. van Berge Henegouwen, E. van Werkhoven, P. Roepman, R.L. Schilsky, W.W.J. de Leng, A.D.R. Huitema, B. Nuijen, P.M. Nederlof, C.M.L. van Herpen, D.J.A. de Groot, L.A. Devriese, A. Hoeben, M.J.A. de Jonge, M. Chalabi, E.F. Smit, A.J. de Langen, N. Mehra, M. Labots, E. Kapiteijn, S. Sleijfer, E. Cuppen, H.M.W. Verheul, H. Gelderblom and E.E. Voest

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

Nature

https://www.nature.com/articles/s41586-019-1600-x

Published:

September 30, 2019

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

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

bioRxiv 781013

https://doi.org/10.1101/781013

Published:

September 25, 2019

Ausems MGEM, Oosterwijk JC, Nielsen M, Lolkema MP, Hoogerbrugge N, Ligtenberg MJL.

Genetic testing in patients with cancer, new developments.

Ned Tijdschr Geneeskd.

https://www.ncbi.nlm.nih.gov/m/pubmed/31140768

Published:

May 20, 2019

Giesbertz NAA, van Harten MH, Bredenoord AL.

A duty of recontact in genetics: context matters.

Nature Reviews Genetics

https://doi.org/10.1038/s41576-019-0121-7

Published:

April 01, 2019

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

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

bioRxiv 517565

https://doi.org/10.1101/517565

Published:

January 11, 2019

Bijlsma RM, Wouters RHP, Wessels H, May AM, Ausems MGEM, Voest EE, Bredenoord AL.

Managing unsolicited findings in genomics: A qualitative interview study with cancer patients.

Psychooncology

https://pubmed.ncbi.nlm.nih.gov/29471587/

Published:

February 22, 2018

Bijlsma RM, Wessels H, Wouters RHP, May AM, Ausems MGEM, Voest EE, Bredenoord AL.

Cancer patients’ intentions towards receiving unsolicited genetic information obtained using next-generation sequencing.

Fam Cancer

https://pubmed.ncbi.nlm.nih.gov/28852913/

Published:

April 17, 2018

Weeber F, Cirkel GA, Hoogstraat M, Bins S, Gadellaa-van Hooijdonk CGM, Ooft S, van Werkhoven E, Willems SM, van Stralen M, Veldhuis WB, Besselink NJM, Horlings HM, Steeghs N, de Jonge MJ, Langenberg MHG, Wessels LFA, Cuppen EPJG, Schellens JH, Sleijfer S, Lolkema MP, Voest EE.

Predicting clinical benefit from everolimus in patients with advanced solid tumors, the CPCT-03 study.

Oncotarget

https://pubmed.ncbi.nlm.nih.gov/28903445/

Published:

March 8, 2017

Bins S, Cirkel GA, Gadellaa-van Hooijdonk CG, Weeber F, Nijman IJ, Bruggink AH, van Diest PJ, Willems SM, Veldhuis WB, van den Heuvel MM, de Knegt RJ, Koudijs MJ, van Werkhoven E, Mathijssen RH, Cuppen E, Sleijfer S, Schellens JH, Voest EE, Langenberg MH, de Jonge MJ, Steeghs N, Lolkema MP.

Implementation of a Multicenter Biobanking Collaboration for Next-Generation Sequencing-Based Biomarker Discovery Based on Fresh Frozen Pretreatment Tumor Tissue Biopsies.

The Oncologist

https://theoncologist.onlinelibrary.wiley.com/doi/full/10.1634/theoncologist.2016-0085

Published:

January 17, 2017

Rhodé M Bijlsma, Annelien L Bredenoord, Christa G Gadellaa-Hooijdonk, Martijn PJ Lolkema, Stefan Sleijfer, Emile E Voest, Margreet GEM Ausems and Neeltje Steeghs

Unsolicited findings of next-generation sequencing for tumor analysis within a Dutch consortium: clinical daily practice reconsidered.

European Journal of Human Genetics

https://pubmed.ncbi.nlm.nih.gov/27071717/

Published:

October 24,

2016

Cirkel GA, Weeber F, Bins S, Gadellaa-van Hooijdonk CG, van Werkhoven E, Willems SM, van Stralen M, Veldhuis WB, Ubink I, Steeghs N, de Jonge MJ, Langenberg MH, Schellens JH, Sleijfer S, Lolkema MP, Voest EE

The Time To Progression Ratio: a new individualized volumetric parameter for early detection of clinical benefit of targeted therapies.

Annals of Oncology

https://www.annalsofoncology.org/article/S0923-7534(19)34751-9/fulltext

Published:

August 01, 2016

de Leng WW, Gadellaa-van Hooijdonk CG, Barendregt-Smouter FA, Koudijs MJ, Nijman I, Hinrichs JW, Cuppen E, van Lieshout S, Loberg RD, de Jonge M, Voest EE, de Weger RA, Steeghs N, Langenberg MH, Sleijfer S, Willems SM, Lolkema MP

Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material.

PLoS One

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149405

Published:

February 26, 2016

Hoogstraat M1, Gadellaa-van Hooijdonk CG, Ubink I, Besselink NJ, Pieterse M, Veldhuis W, van Stralen M, Meijer EF, Willems SM, Hadders MA, Kuilman T, Krijgsman O, Peeper DS, Koudijs MJ, Cuppen E, Voest EE, Lolkema MP

Detailed imaging and genetic analysis reveal a secondary BRAF(L505H) resistance mutation and extensive intrapatient heterogeneity in metastatic BRAF mutant melanoma patients treated with vemurafenib.

Pigment Cell Melanoma Res.

https://pubmed.ncbi.nlm.nih.gov/25515853/

Published:

May 28, 2015

Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O.

CopywriteR: DNA copy number detection from off-target sequence data.

Genome Biology

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0617-1

Published:

February 27, 2015

Marlous Hoogstraat, John W J Hinrichs, Nicolle J M Besselink, Joyce H Radersma-van Loon, Carmen M A de Voijs, Ton Peeters, Isaac J Nijman, Roel A de Weger, Emile E Voest, Stefan M Willems, Edwin Cuppen, Marco J Koudijs

Simultaneous detection of clinically relevant mutations and amplifications for cancer diagnostics using Next Generation Sequencing.

The Journal of molecular diagnostics

https://pubmed.ncbi.nlm.nih.gov/25445215/

Published:

January 17, 2015

Beaufort CM, Helmijr JC, Piskorz AM, Hoogstraat M, Ruigrok-Ritstier K, Besselink N, Murtaza M, van IJcken WF, Heine AA, Smid M, Koudijs MJ, Brenton JD, Berns EM, Helleman J.

Ovarian cancer cell line panel (OCCP): clinical importance of in vitro morphological subtypes.

PLoS One

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103988

Published:

September 17, 2014

Hoogstraat M, de Pagter MS, Cirkel GA, van Roosmalen MJ, Harkins TT, Duran K, Kreeftmeijer J, Renkens I, Witteveen PO, Lee CC, Nijman IJ, Guy T, van ’t Slot R, Jonges TN, Lolkema MP, Koudijs MJ, Zweemer RP, Voest EE, Cuppen E, Kloosterman WP.

The genomic and transcriptomic dynamics of treatment-naïve epithelial ovarian cancer.

Genome Res.

https://pubmed.ncbi.nlm.nih.gov/24221193/

Published:

February 24, 2014

Sander Bins, Jan H.M. Schellens, Emile E. Voest, Stefan Sleijfer

Geneesmiddelenonderzoek in de Oncologie, vorderingen in het genoomtijdperk.

Nederlands Tijdschrift voor Geneeskunde

https://www.ntvg.nl/artikelen/geneesmiddelenonderzoek-de-oncologie

Published:

February 19, 2014

Geert A Cirkel, Christa G Gadellaa-van Hooijdonk, Marco J Koudijs, Stefan M Willems, Emile E Voest

Tumor heterogeneity and personalized cancer medicine: are we being outnumbered?

Future Oncology

https://pubmed.ncbi.nlm.nih.gov/24559448/

Published:

February 10, 2014

Lolkema MP, Gadellaa-van Hooijdonk CG, Bredenoord AL, Kapitein P, Roach N, Cuppen E, Knoers NV, Voest EE.

Ethical, legal, and counseling challenges surrounding the return of genetic results in oncology.

Journal of Clinicla Oncology

https://ascopubs.org/doi/10.1200/JCO.2012.45.2789

Published:

May 20, 2013

Lips E, Magali M, Mulder L. et al.

Next-generation sequencing to find predictors for chemotherapy response in triple-negative breast cancer.

Journal of Clinical Oncology

https://ascopubs.org/doi/10.1200/jco.2013.31.15_suppl.1010

Published:

May 20, 2013

Vermaat JS, Nijman IJ, Koudijs MJ, Gerritse FL, Scherer SJ, Mokry M, Roessingh WM, Lansu N, de Bruijn E, van Hillegersberg R, van Diest PJ, Cuppen E, Voest EE.

Primary colorectal cancers and their subsequent hepatic metastases are genetically different: implications for selection of patients for targeted treatment.

Clin Cancer Res.

https://clincancerres.aacrjournals.org/content/18/3/688

Published:

February 01, 2012

Harakalova M, Mokry M, Hrdlickova B, Renkens I, Duran K, van Roekel H, Lansu N, van Roosmalen M, de Bruijn E, Nijman IJ, Kloosterman WP, Cuppen E

Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing.

Nature Protocols

https://www.nature.com/articles/nprot.2011.396

Published:

November 03, 2011

Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, Vermaat JS, van Roosmalen MJ, van Lieshout S, Nijman IJ, Roessingh W, van ’t Slot R, van de Belt J, Guryev V, Koudijs M, Voest E, Cuppen E

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer.

Genome Biology

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-10-r103

Published:

October 19, 2011

C.G.M. Gadellaa-van Hooijdonk, M.J. Koudijs, E.P.J.G. Cuppen, P.J. van Diest, J.W.M. Martens, S. Sleijfer, J.H.M. Schellens, E.E. Voest en M.P.J.K. Lolkema

Van DNA-afwijkingen tot therapie: selectie voor geïndividualiseerde kankerbehandeling.

Ned. Tijdschr. Oncol.

https://www.ariez.nl/wp-content/uploads/2018/08/325-1.pdf

Published:

August, 2011

Nijman IJ, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E.

Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples.

Nature Methods

https://www.nature.com/articles/nmeth.1516

Published: October 17, 2010