Wetenschappelijke publicaties - Hartwig Medical Foundation (2024)

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, fa*gre, 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 PriestleyCell 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 VosNeuro-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

DOI: https://doi.org/10.1101/2021.11.09.468005

Functional RECAP (REpair CAPacity) assay identifies hom*ologous 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

Wetenschappelijke publicaties - Hartwig Medical Foundation (2024)
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