E Cuppen

Affiliations
  • Oncode Institute, Utrecht, The Netherlands; Division of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands; Hartwig Medical Foundation, Amsterdam, The Netherlands.

Publications (66)

Patient-Derived Ovarian Cancer Organoids Mimic Clinical Response and Exhibit Heterogeneous Inter- and Intrapatient Drug Responses.

Cell reports
Avec: Chris Jenske de Witte , Jose Espejo Valle-Inclan , Nizar Hami , Kadi Lõhmussaar , Oded Kopper , Celien Philomena Henrieke Vreuls , Geertruida Nellie Jonges , Paul van Diest , Luan Nguyen , Hans Clevers , Wigard Pieter Kloosterman , Edwin Cuppen , Hugo Johannes Gerhardus Snippert , Ronald Peter Zweemer , Petronella Oda Witteveen , Ellen Stelloo

SARS-CoV-2 productively infects human gut enterocytes.

Science (New York, N.Y.)
Avec: Mart M Lamers , Joep Beumer , Jelte van der Vaart , Kèvin Knoops , Jens Puschhof , Tim I Breugem , Raimond B G Ravelli , J Paul van Schayck , Anna Z Mykytyn , Hans Q Duimel , Elly van Donselaar , Samra Riesebosch , Helma J H Kuijpers , Debby Schipper , Willine J van de Wetering , Miranda de Graaf , Marion Koopmans , Edwin Cuppen , Peter J Peters , Bart L Haagmans , Hans Clevers

Long-term expanding human airway organoids for disease modeling.

The EMBO journal
Avec: Norman Sachs , Angelos Papaspyropoulos , Domenique D Zomer-van Ommen , Inha Heo , Lena Böttinger , Dymph Klay , Fleur Weeber , Guizela Huelsz-Prince , Nino Iakobachvili , Gimano D Amatngalim , Joep de Ligt , Arne van Hoeck , Natalie Proost , Marco C Viveen , Anna Lyubimova , Luc Teeven , Sepideh Derakhshan , Jeroen Korving , Harry Begthel , Johanna F Dekkers , Kuldeep Kumawat , Emilio Ramos , Matthijs Fm van Oosterhout , G Johan Offerhaus , Dominique J Wiener , Eduardo P Olimpio , Krijn K Dijkstra , Egbert F Smit , Maarten van der Linden , Sridevi Jaksani , Marieke van de Ven , Jos Jonkers , Anne C Rios , Emile E Voest , Coline Hm van Moorsel , Cornelis K van der Ent , Edwin Cuppen , Alexander van Oudenaarden , Frank E Coenjaerts , Linde Meyaard , Louis J Bont , Peter J Peters , Sander J Tans , Jeroen S van Zon , Sylvia F Boj , Robert G Vries , Jeffrey M Beekman , Hans Clevers

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

British journal of cancer
Avec: Joanne M Mankor , Marthe S Paats , Floris H Groenendijk , Paul Roepman , Winand N M Dinjens , Hendrikus J Dubbink , Stefan Sleijfer , Auteur inconnu , Edwin Cuppen , Martijn P J K Lolkema

Precancerous liver diseases do not cause increased mutagenesis in liver stem cells.

Communications biology
Avec: Luan Nguyen , Myrthe Jager , Ruby Lieshout , Petra E de Ruiter , Mauro D Locati , Nicolle Besselink , Bastiaan van der Roest , Roel Janssen , Sander Boymans , Jeroen de Jonge , Jan N M IJzermans , Michail Doukas , Monique M A Verstegen , Ruben van Boxtel , Luc J W van der Laan , Edwin Cuppen , Ewart Kuijk

Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features.

Nature communications
Avec: Luan Nguyen , Arne Van Hoeck , Edwin Cuppen

Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue.

Nature communications
Avec: Ewart Kuijk , Onno Kranenburg , Edwin Cuppen , Arne Van Hoeck

Study protocol of the GLOW study: maximising treatment options for recurrent glioblastoma patients by whole genome sequencing-based diagnostics-a prospective multicenter cohort study.

BMC medical genomics
Avec: 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

Understanding Value Change in the Energy Transition: Exploring the Perspective of Original Institutional Economics.

Science and engineering ethics
Avec: Aad Correljé , Udo Pesch , Eefje Cuppen

The genome-wide mutational consequences of DNA hypomethylation.

Scientific reports
Avec: Nicolle Besselink , Janneke Keijer , Carlo Vermeulen , Sander Boymans , Jeroen de Ridder , Arne van Hoeck , Edwin Cuppen , Ewart Kuijk

The role of molecular biomarkers in recurrent glioblastoma trials: an assessment of the current trial landscape of genome-driven oncology.

Medical oncology (Northwood, London, England)
Avec: Mark P van Opijnen , Filip Y F de Vos , Edwin Cuppen , Marjolein Geurts , Sybren L N Maas , Marike L D Broekman

Pancreatic cancer organoids recapitulate disease and allow personalized drug screening.

Proceedings of the National Academy of Sciences of the United States of America
Avec: Else Driehuis , Arne van Hoeck , Kat Moore , Sigrid Kolders , Hayley E Francies , M Can Gulersonmez , Edwin C A Stigter , Boudewijn Burgering , Veerle Geurts , Ana Gracanin , Gergana Bounova , Folkert H Morsink , Robert Vries , Sylvia Boj , Johan van Es , G Johan A Offerhaus , Onno Kranenburg , Mathew J Garnett , Lodewyk Wessels , Edwin Cuppen , Lodewijk A A Brosens , Hans Clevers

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

Nature communications
Avec: Sharon Christensen , Bastiaan Van der Roest , Nicolle Besselink , Roel Janssen , Sander Boymans , John W M Martens , Marie-Laure Yaspo , Peter Priestley , Ewart Kuijk , Edwin Cuppen , Arne Van Hoeck

Biallelic variants in POLR3GL cause endosteal hyperostosis and oligodontia.

European journal of human genetics : EJHG
Avec: Paulien A Terhal , Judith M Vlaar , Sjors Middelkamp , Rutger A J Nievelstein , Peter G J Nikkels , Jamila Ross , Marijn Créton , Jeroen W Bos , Elsbeth S M Voskuil-Kerkhof , Edwin Cuppen , Nine Knoers , Koen L I van Gassen

Early divergence of mutational processes in human fetal tissues.

Science advances
Avec: Ewart Kuijk , Francis Blokzijl , Myrthe Jager , Nicolle Besselink , Sander Boymans , Susana M Chuva de Sousa Lopes , Ruben van Boxtel , Edwin Cuppen

Publisher Correction: The mutational impact of culturing human pluripotent and adult stem cells.

Nature communications
Avec: Ewart Kuijk , Myrthe Jager , Bastiaan van der Roest , Mauro D Locati , Arne Van Hoeck , Jerome Korzelius , Roel Janssen , Nicolle Besselink , Sander Boymans , Ruben van Boxtel , Edwin Cuppen

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.

Genome biology
Avec: 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

Prospective experimental treatment of colorectal cancer patients based on organoid drug responses.

ESMO open
Avec: 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

Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics.

The Journal of molecular diagnostics : JMD
Avec: 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

Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology.

Seminars in cancer biology
Avec: Vaidehi Jobanputra , Kazimierz O Wrzeszczynski , Reinhard Buttner , Carlos Caldas , Edwin Cuppen , Sean Grimmond , Torsten Haferlach , Charles Mullighan , Anna Schuh , Olivier Elemento

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

Nature communications
Avec: 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

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

European urology
Avec: 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

Complete genomic characterization in patients with cancer of unknown primary origin in routine diagnostics.

ESMO open
Avec: 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

Genetic immune escape landscape in primary and metastatic cancer.

Nature genetics
Avec: Francisco Martínez-Jiménez , Peter Priestley , Charles Shale , Jonathan Baber , Erik Rozemuller , Edwin Cuppen

Impact of genetic counselling strategy on diagnostic yield and workload for genome sequencing-based tumour diagnostics.

Genetics in medicine : official journal of the American College of Medical Genetics
Avec: 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

Multi-omic analysis identifies hypoalbuminemia as independent biomarker of poor outcome upon PD-1 blockade in metastatic melanoma.

Scientific reports
Avec: Lindsay V M Leek , Jessica C L Notohardjo , Karlijn de Joode , Eline L Velker , John B A G Haanen , Karijn P M Suijkerbuijk , Maureen J B Aarts , Jan Willem B de Groot , Ellen Kapiteijn , Franchette W P J van den Berkmortel , Hans M Westgeest , Tanja D de Gruijl , Valesca P Retel , Edwin Cuppen , Astrid A M van der Veldt , Mariette Labots , Emile E Voest , Joris van de Haar , Alfons J M van den Eertwegh

Whole genome sequencing in (recurrent) glioblastoma: challenges related to informed consent procedures and data sharing.

Acta neurochirurgica
Avec: Mira C Hasner , Mark P van Opijnen , Filip Y F de Vos , Edwin Cuppen , Marike L D Broekman

Sperm DNA damage causes genomic instability in early embryonic development.

Science advances
Avec: Sjors Middelkamp , Helena T A van Tol , Diana C J Spierings , Sander Boymans , Victor Guryev , Bernard A J Roelen , Peter M Lansdorp , Edwin Cuppen , Ewart W Kuijk

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

Nature communications
Avec: 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

Tubuloids derived from human adult kidney and urine for personalized disease modeling.

Nature biotechnology
Avec: Frans Schutgens , Maarten B Rookmaaker , Thanasis Margaritis , Anne Rios , Carola Ammerlaan , Jitske Jansen , Linda Gijzen , Marianne Vormann , Annelotte Vonk , Marco Viveen , Fjodor Yousef Yengej , Sepide Derakhshan , Karin M de Winter-de Groot , Benedetta Artegiani , Ruben van Boxtel , Edwin Cuppen , Antoni P A Hendrickx , Marry M van den Heuvel-Eibrink , Ellen Heitzer , Henriette Lanz , Jeffrey Beekman , Jean-Luc Murk , Rosalinde Masereeuw , Frank Holstege , Jarno Drost , Marianne C Verhaar , Hans Clevers

Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants.

Genome medicine
Avec: Sjors Middelkamp , Judith M Vlaar , Jacques Giltay , Jerome Korzelius , Nicolle Besselink , Sander Boymans , Roel Janssen , Lisanne de la Fonteijne , Ellen van Binsbergen , Markus J van Roosmalen , Ron Hochstenbach , Daniela Giachino , Michael E Talkowski , Wigard P Kloosterman , Edwin Cuppen

Single-cell derived tumor organoids display diversity in HLA class I peptide presentation.

Nature communications
Avec: Laura C Demmers , Kai Kretzschmar , Arne Van Hoeck , Yotam E Bar-Epraïm , Henk W P van den Toorn , Mandy Koomen , Gijs van Son , Joost van Gorp , Apollo Pronk , Niels Smakman , Edwin Cuppen , Hans Clevers , Albert J R Heck , Wei Wu

Functional RECAP (REpair CAPacity) assay identifies homologous recombination deficiency undetected by DNA-based BRCAness tests.

Oncogene
Avec: 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

Clinical utility of whole-genome sequencing in precision oncology.

Seminars in cancer biology
Avec: 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

Learning mutational signatures and their multidimensional genomic properties with TensorSignatures.

Nature communications
Avec: Harald Vöhringer , Arne Van Hoeck , Edwin Cuppen , Moritz Gerstung

Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns.

Nature genetics
Avec: Yannik Bollen , Ellen Stelloo , Petra van Leenen , Myrna van den Bos , Bas Ponsioen , Bingxin Lu , Markus J van Roosmalen , Ana C F Bolhaqueiro , Christopher Kimberley , Maximilian Mossner , William C H Cross , Nicolle J M Besselink , Bastiaan van der Roest , Sander Boymans , Koen C Oost , Sippe G de Vries , Holger Rehmann , Edwin Cuppen , Susanne M A Lens , Geert J P L Kops , Wigard P Kloosterman , Leon W M M Terstappen , Chris P Barnes , Andrea Sottoriva , Trevor A Graham , Hugo J G Snippert

MutationalPatterns: the one stop shop for the analysis of mutational processes.

BMC genomics
Avec: Freek Manders , Arianne M Brandsma , Jurrian de Kanter , Mark Verheul , Rurika Oka , Markus J van Roosmalen , Bastiaan van der Roest , Arne van Hoeck , Edwin Cuppen , Ruben van Boxtel

Truncated FGFR2 is a clinically actionable oncogene in multiple cancers.

Nature
Avec: 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

Pan-cancer whole-genome comparison of primary and metastatic solid tumours.

Nature
Avec: Francisco Martínez-Jiménez , Ali Movasati , Sascha Remy Brunner , Luan Nguyen , Peter Priestley , Edwin Cuppen , Arne Van Hoeck

Identifying somatic changes in drug transporters using whole genome and transcriptome sequencing data of advanced tumors.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
Avec: 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

Next generation sequencing of high-grade adult-type diffuse glioma in the Netherlands: interlaboratory variation in the primary diagnostic and recurrent setting.

Journal of neuro-oncology
Avec: Mark P van Opijnen , Marike L D Broekman , Edwin Cuppen , Hendrikus J Dubbink , Arja Ter Elst , Ronald van Eijk , Angelika Mühlebner , Casper Jansen , Robert van der Geize , Ernst-Jan M Speel , Patricia J T A Groenen , Filip Y F de Vos , Pieter Wesseling , Wendy W J de Leng , Sybren L N Maas

A pan-cancer analysis of the microbiome in metastatic cancer.

Cell
Avec: 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

Study protocol: Whole genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE).

BMC medical genomics
Avec: 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

Pan-cancer landscape of homologous recombination deficiency.

Nature communications
Avec: Luan Nguyen , John W M Martens , Arne Van Hoeck , Edwin Cuppen

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer.

Genome research
Avec: Myrthe Jager , Francis Blokzijl , Ewart Kuijk , Johanna Bertl , Maria Vougioukalaki , Roel Janssen , Nicolle Besselink , Sander Boymans , Joep de Ligt , Jakob Skou Pedersen , Jan Hoeijmakers , Joris Pothof , Ruben van Boxtel , Edwin Cuppen

Portrait of a cancer: mutational signature analyses for cancer diagnostics.

BMC cancer
Avec: Arne Van Hoeck , Niels H Tjoonk , Ruben van Boxtel , Edwin Cuppen

Challenges in Establishing Pure Lung Cancer Organoids Limit Their Utility for Personalized Medicine.

Cell reports
Avec: Krijn K Dijkstra , Kim Monkhorst , Luuk J Schipper , Koen J Hartemink , Egbert F Smit , Sovann Kaing , Rosa de Groot , Monika C Wolkers , Hans Clevers , Edwin Cuppen , Emile E Voest

Mutational signature in colorectal cancer caused by genotoxic pks

Nature
Avec: 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 , Yi Miao , Reinier van der Linden , Stefan van der Elst , Auteur inconnu , K Christopher Garcia , Janetta Top , Rob J L Willems , Marios Giannakis , Richard Bonnet , Phil Quirke , Matthew Meyerson , Edwin Cuppen , Ruben van Boxtel , Hans Clevers

Analytical demands to use whole-genome sequencing in precision oncology.

Seminars in cancer biology
Avec: 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

Genome-wide analysis of somatic noncoding mutation patterns in cancer.

Science (New York, N.Y.)
Avec: 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

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

The Journal of pathology
Avec: 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

Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer.

Scientific reports
Avec: Judith M Vlaar , Anouska Borgman , Eric Kalkhoven , Denise Westland , Nicolle Besselink , Charles Shale , Bishoy M Faltas , Peter Priestley , Ewart Kuijk , Edwin Cuppen

Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care.

JCO precision oncology
Avec: 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

Genomic Alterations Associated with Estrogen Receptor Pathway Activity in Metastatic Breast Cancer Have a Differential Impact on Downstream ER Signaling.

Cancers
Avec: 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

EXO1 protects BRCA1-deficient cells against toxic DNA lesions.

Molecular cell
Avec: 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

Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice.

Nature protocols
Avec: 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

Five latent factors underlie response to immunotherapy.

Nature genetics
Avec: 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

The mutational impact of culturing human pluripotent and adult stem cells.

Nature communications
Avec: Ewart Kuijk , Myrthe Jager , Bastiaan van der Roest , Mauro D Locati , Arne Van Hoeck , Jerome Korzelius , Roel Janssen , Nicolle Besselink , Sander Boymans , Ruben van Boxtel , Edwin Cuppen

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

Nature communications
Avec: Wei Jiao , Gurnit Atwal , Paz Polak , Rosa Karlic , Edwin Cuppen , Auteur inconnu , Alexandra Danyi , Jeroen de Ridder , Carla van Herpen , Martijn P Lolkema , Neeltje Steeghs , Gad Getz , Quaid D Morris , Lincoln D Stein , Auteur inconnu

Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients.

Science translational medicine
Avec: Salo N Ooft , Fleur Weeber , Krijn K Dijkstra , Chelsea M McLean , Sovann Kaing , Erik van Werkhoven , Luuk Schipper , Louisa Hoes , Daniel J Vis , Joris van de Haar , Warner Prevoo , Petur Snaebjornsson , Daphne van der Velden , Michelle Klein , Myriam Chalabi , Henk Boot , Monique van Leerdam , Haiko J Bloemendal , Laurens V Beerepoot , Lodewyk Wessels , Edwin Cuppen , Hans Clevers , Emile E Voest

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

Nature
Avec: 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 , E E Voest

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

Nature genetics
Avec: 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 , John W M Martens

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

Nature
Avec: 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

The molecular genetic make-up of male breast cancer.

Endocrine-related cancer
Avec: Cathy B Moelans , Joep de Ligt , Petra van der Groep , Pjotr Prins , Nicolle J M Besselink , Marlous Hoogstraat , Natalie D Ter Hoeve , Miangela M Lacle , Robert Kornegoor , Carmen C van der Pol , Wendy W J de Leng , Ellis Barbé , Bert van der Vegt , John Martens , Peter Bult , Vincent T H B M Smit , Marco J Koudijs , Isaac J Nijman , Emile E Voest , Pier Selenica , Britta Weigelt , Jorge S Reis-Filho , Elsken van der Wall , Edwin Cuppen , Paul J van Diest

Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features.

Nature communications
Avec: 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

Human extrahepatic and intrahepatic cholangiocyte organoids show region-specific differentiation potential and model cystic fibrosis-related bile duct disease.

Scientific reports
Avec: Monique M A Verstegen , Floris J M Roos , Ksenia Burka , Helmuth Gehart , Myrthe Jager , Maaike de Wolf , Marcel J C Bijvelds , Hugo R de Jonge , Arif I Ardisasmita , Nick A van Huizen , Henk P Roest , Jeroen de Jonge , Michael Koch , Francesco Pampaloni , Sabine A Fuchs , Imre F Schene , Theo M Luider , Hubert P J van der Doef , Frank A J A Bodewes , Ruben H J de Kleine , Bart Spee , Gert-Jan Kremers , Hans Clevers , Jan N M IJzermans , Edwin Cuppen , Luc J W van der Laan

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