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2020

IBD-Associated Dysplastic Lesions Show More Chromosomal Instability Than Sporadic Adenomas

Wanders, L. K., Cordes, M., Voorham, Q., Sie, D., de Vries, S. D., d’Haens, G. R. A. M., de Boer, N. K. H., Ylstra, B., van Grieken, N. C. T., Meijer, G. A., Dekker, E. & Carvalho, B., Feb 2020, In : Inflammatory Bowel Diseases. 26, 2, p. 167-180 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

2019

ACE: Absolute Copy number Estimation from low-coverage whole-genome sequencing data

Poell, J. B., Mendeville, M., Sie, D., Brink, A., Brakenhoff, R. H. & Ylstra, B., 15 Aug 2019, In : Bioinformatics. 35, 16, p. 2847-2849

Research output: Contribution to journalArticleAcademicpeer-review

Clonality analysis of pulmonary tumors by genome-wide copy number profiling

Vincenten, J. P. L., van Essen, H. F., Lissenberg-Witte, B. I., Bulkmans, N. W. J., Krijgsman, O., Sie, D., Eijk, P. P., Smit, E. F., Ylstra, B. & Thunnissen, E., 2019, In : PLoS ONE. 14, 10, e0223827.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Colorectal metastasis to the gallbladder mimicking a primary gallbladder malignancy: histopathological and molecular characteristics

de Bitter, T. J. J., van der Linden, R. L. A., van Vliet, S., Weren, F., Sie, D., Ylstra, B., van der Linden, H. C., Knijn, N., Ligtenberg, M. J. L., van der Post, R. S., Simmer, F. & Nagtegaal, I. D., 1 Jan 2019, In : Histopathology. 75, 3, p. 394-404 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Fetal fraction evaluation in non-invasive prenatal screening (NIPS)

Hestand, M. S., Bessem, M., van Rijn, P., de Menezes, R. X., Sie, D., Bakker, I., Boon, E. M. J., Sistermans, E. A. & Weiss, M. M., 1 Feb 2019, In : European Journal of Human Genetics. 27, 2, p. 198-202 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

Genome-wide microRNA analysis of HPV-positive self-samples yields novel triage markers for early detection of cervical cancer

Snoek, B. C., Verlaat, W., Babion, I., Novianti, P. W., van de Wiel, M. A., Wilting, S. M., van Trommel, N. E., Bleeker, M. C. G., Massuger, L. F. A. G., Melchers, W. J. G., Sie, D., Heideman, D. A. M., Snijders, P. J. F., Meijer, C. J. L. M. & Steenbergen, R. D. M., 15 Jan 2019, In : International Journal of Cancer. 144, 2, p. 372-379 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

2018

Combination of a six microRNA expression profile with four clinicopathological factors for response prediction of systemic treatment in patients with advanced colorectal cancer

Neerincx, M., Poel, D., Sie, D. L. S., van Grieken, N. C. T., Shankaraiah, R. C., van der Wolf-de Lijster, F. S. W., van Waesberghe, J-H. T. M., Burggraaf, J-D., Eijk, P. P., Verhoef, C., Ylstra, B., Meijer, G. A., van de Wiel, M. A., Buffart, T. E. & Verheul, H. M. W., 2018, In : PLoS ONE. 13, 8, p. e0201809

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Consensus molecular subtype classification of colorectal adenomas

Komor, M. A., Bosch, L. J. W., Bounova, G., Bolijn, A. S., Delis-van Diemen, P. M., Rausch, C., Hoogstrate, Y., Stubbs, A. P., de Jong, M., Jenster, G., van Grieken, N. C. T., Carvalho, B., Wessels, L. F. A., Jimenez, C. R., Fijneman, R. J. A., Meijer, G. A. & In collaboration with the NGS-ProToCol Consortium:, 2018, In : Journal of Pathology. 246, 3, p. 266-276

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Copy number signatures and mutational processes in ovarian carcinoma

Macintyre, G., Goranova, T. E., De Silva, D., Ennis, D., Piskorz, A. M., Eldridge, M., Sie, D., Lewsley, L. A., Hanif, A., Wilson, C., Dowson, S., Glasspool, R. M., Lockley, M., Brockbank, E., Montes, A., Walther, A., Sundar, S., Edmondson, R., Hall, G. D., Clamp, A. & 19 others, Gourley, C., Hall, M., Fotopoulou, C., Gabra, H., Paul, J., Supernat, A., Millan, D., Hoyle, A., Bryson, G., Nourse, C., Mincarelli, L., Sanchez, L. N., Ylstra, B., Jimenez-Linan, M., Moore, L., Hofmann, O., Markowetz, F., McNeish, I. A. & Brenton, J. D., 1 Sep 2018, In : Nature Genetics. 50, 9, p. 1262-1270 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Molecular heterogeneity in human papillomavirus-dependent and -independent vulvar carcinogenesis

Swarts, D. R. A., Voorham, Q. J. M., van Splunter, A. P., Wilting, S. M., Sie, D., Pronk, D., van Beurden, M., Heideman, D. A. M., Snijders, P. J. F., Meijer, C. J. L. M., Steenbergen, R. D. M. & Bleeker, M. C. G., 2018, In : Cancer Medicine. 7, 9, p. 4542-4553

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2017

Functional Screening Identifies Human miRNAs that Modulate Adenovirus Propagation in Prostate Cancer Cells

Hodzic, J., Sie, D., Vermeulen, A. & Van Beusechem, V. W., 1 Sep 2017, In : Human Gene Therapy. 28, 9, p. 766-780 15 p.

Research output: Contribution to journalArticleAcademicpeer-review

2016

Condensin II mutation causes T-cell lymphoma through tissue-specific genome instability

Woodward, J., Taylor, G. C., Soares, D. C., Boyle, S., Sie, D., Read, D., Chathoth, K., Vukovic, M., Tarrats, N., Jamieson, D., Campbell, K. J., Blyth, K., Acosta, J. C., Ylstra, B., Arends, M. J., Kranc, K. R., Jackson, A. P., Bickmore, W. A. & Woods, A. J., 1 Oct 2016, In : Genes and Development. 30, 19, p. 2173-2186

Research output: Contribution to journalArticleAcademicpeer-review

Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients

van den Broek, E., Krijgsman, O., Sie, D., Tijssen, M., Mongera, S., van de Wiel, M. A., Belt, E. J. T., den Uil, S. H., Bril, H., Stockmann, H. B. A. C., Ylstra, B., Carvalho, B., Meijer, G. A. & Fijneman, R. J. A., 8 Nov 2016, In : Oncotarget. 7, 45, p. 73876-73887

Research output: Contribution to journalArticleAcademicpeer-review

MiR expression profiles can predict response to systemic treatment in patients with advanced colorectal cancer

Poel, D., Neerincx, M., Sie, D. L. S., van Grieken, N. C. T., Shankaraiah, R., van der Wolf, F. S. W., van Waesberghe, J. H. T. M., Burggraaf, J. D., Eijk, P. P., Ylstra, B., Verhoef, C., van de Wiel, M. A., Verheul, H. M. W. & Buffart, T. E., Jul 2016, In : Cancer Research. 76

Research output: Contribution to journalArticleAcademicpeer-review

Non-classic EGFR mutations in a cohort of Dutch EGFR-mutated NSCLC patients and outcomes following EGFR-TKI treatment

Kuiper, J. L., Hashemi, S. M. S., Thunnissen, E., Snijders, P. J. F., Grünberg, K., Bloemena, E., Sie, D., Postmus, P. E., Heideman, D. A. M. & Smit, E. F., 6 Dec 2016, In : British Journal of Cancer. 115, 12, p. 1504-1512 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

2015

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life

Faddeeva-Vakhrusheva, A., Studer, R. A., Kraaijeveld, K., Sie, D. L. S., Ylstra, B., Mariën, J., op den Camp, H. M. J., Datema, E., den Dunnen, J. T., van Straalen, N. M. & Roelofs, D., 2015, In : PLoS ONE. 10, 6, e0130600.

Research output: Contribution to journalArticleAcademicpeer-review

High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer

van den Broek, E., Dijkstra, M. J. J., Krijgsman, O., Sie, D. L. S., Haan, J. C., Traets, J. J. H., van de Wiel, M. A., Nagtegaal, I. D., Punt, C. J. A., Carvalho, B., Ylstra, B., Abeln, S., Meijer, G. A. & Fijneman, R. J. A., 2015, In : PLoS ONE. 10, 9, e0138141.

Research output: Contribution to journalArticleAcademicpeer-review

Landscape of chromosomal copy number aberrations in gangliogliomas and dysembryoplastic neuroepithelial tumours

Prabowo, A. S., van Thuijl, H. F., Scheinin, I., Sie, D. L. S., van Essen, H. F., Iyer, A. M., Spliet, W. G. M., Ferrier, C. H., van Rijen, P. C., Veersema, T. J., Thom, M., Schouten-van Meeteren, A. Y. N., Reijneveld, J. C., Ylstra, B., Wesseling, P. & Aronica, E., 2015, In : Neuropathology and Applied Neurobiology. 41, 6, p. 743-755

Research output: Contribution to journalArticleAcademicpeer-review

MiR expression profiles of paired primary colorectal cancer and metastases by next-generation sequencing

Neerincx, M., Sie, D. L. S., van de Wiel, M. A., van Grieken, N. C. T., Burggraaf, J. D., Dekker, H., Eijk, P. P., Ylstra, B., Verhoef, C., Meijer, G. A., Buffart, T. E. & Verheul, H. M. W., 2015, In : Oncogenesis. 4, e170.

Research output: Contribution to journalArticleAcademicpeer-review

Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes

Massink, M. P. G., Kooi, E. I., van Mil, S. E., Jordanova, E. S., Ameziane, N., Dorsman, J. C., van Beek, D. M., van der Voorn, J. P., Sie, D. L. S., Ylstra, B., van Deurzen, C. L. H. M., Martens, J. W., Smid, M., Sieuwerts, A. M., de Weerd, V., Foekens, J. A., van den Ouweland, A. M. W., van Dyk, E., Nederlof, P. M., Waisfisz, Q. & 1 others, Meijers-Heijboer, H., 2015, In : Molecular oncology. 9, 4, p. 877-888

Research output: Contribution to journalArticleAcademicpeer-review

Somatic mutation in PIK3CA is a late event in cervical carcinogenesis

Verlaat, W., Snijders, P. J. F., van Moorsel, M. I. H., Bleeker, M. C. G., Rozendaal, L., Sie, D. L. S., Ylstra, B., Meijer, C. J. L. M., Steenbergen, R. D. M. & Heideman, D. A. M., 2015, In : The Journal of Pathology: Clinical Research. 1, 4, p. 207-211

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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2014

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Scheinin, I., Sie, D. L. S., Bengtsson, H., van de Wiel, M. A., Olshen, A. B., van Thuijl, H. F., van Essen, H. F., Eijk, P. P., Rustenburg, F., Meijer, G. A., Reijneveld, J. C., Wesseling, P., Pinkel, D., Albertson, DG. & Ylstra, B., 2014, In : Genome Research. 24, 12, p. 2022-2032

Research output: Contribution to journalArticleAcademicpeer-review

No evidence for active human papillomavirus (HPV) in fields surrounding HPV-positive oropharyngeal tumors

Rietbergen, M. M., Braakhuis, B. J. M., Moukhtari, N., Bloemena, E., van den Brink, A., Sie, D. L. S., Ylstra, B., de Jong, R. J. B., Snijders, P. J. F., Brakenhoff, R. H. & Leemans, C. R., 2014, In : Journal of Oral Pathology and Medicine. 43, 2, p. 137-142

Research output: Contribution to journalArticleAcademicpeer-review

Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes

Lalic, D., Hackenberg, M., Bijnsdorp, I. V., van Eijndhoven, M. A. J., Sadek, P., Sie, D. L. S., Zini, N., Middeldorp, J. M., Ylstra, B., Menezes, R., Wurdinger, T., Meijer, G. A. & Pegtel, D. M., 2014, In : Cell Reports. 8, 6, p. 1649-1658

Research output: Contribution to journalArticleAcademicpeer-review

Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology

Sie, D. L. S., Snijders, P. J. F., Meijer, G. A., Doeleman, M. W., van Moorsel, M. I. H., van Essen, H. F., Eijk, P. P., Grunberg, K., van Grieken, N. C. T., Thunnissen, E., Verheul, H. M., Smit, E. F., Ylstra, B. & Heideman, D. A. M., 2014, In : Cellular Oncology. 37, 5, p. 353-361

Research output: Contribution to journalArticleAcademicpeer-review

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

van de Wiel, M. A., Neerincx, M., Buffart, T. E., Sie, D. L. S. & Verheul, H. M., 2014, In : BMC Bioinformatics. 15, p. 116 116.

Research output: Contribution to journalArticleAcademicpeer-review

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis

Holstege, H., Pfeiffer, W., Sie, D. L. S., Hulsman, M., Nicholas, T. J., Lee, C. C., Ross, T., Lin, J., Miller, M. A., Ylstra, B., Meijers-Heijboer, H. E., Brugman, M. H., Staal, F. J. T., Holstege, G., Reinders, M. J. T., Harkins, T. T., Levy, S. & Sistermans, E. A., 2014, In : Genome Research. 24, 5, p. 733-742

Research output: Contribution to journalArticleAcademicpeer-review

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

van Thuijl, H. F., Scheinin, I., Sie, D. L. S., Alentorn, A., van Essen, H. F., Cordes, M., Fleischeuer, R., Beute, G., van den Brink, W. A., Meijer, G. A., Havenith, M., Idbaih, A., Hoang-Xuan, K., Mokhtari, K., Verhaak, R. G. W., van der Valk, P., van de Wiel, M. A., Heimans, J. J., Aronica, E., Reijneveld, J. C. & 2 others, Wesseling, P. & Ylstra, B., 2014, In : Genome Biology. 15, 9, 471.

Research output: Contribution to journalArticleAcademicpeer-review

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

de Vree, P. J. P., de Wit, E., Yilmaz, M., de Heijning, M. V., Klous, P., Verstegen, M. J. A. M., Wan, Y., Teunissen, H., Krijger, P. H. L., Geeven, G., Eijk, P. P., Sie, D. L. S., Ylstra, B., Hulsman, L. O. M., van Dooren, M. F., van Zutven, L. J. C. M., van den Ouweland, A., Verbeek, S., van Dijk, K. W., Cornelissen, M. & 19 others, Das, A. T., Ben, B., Sikkema-Raddatz, B., Berg, E., van der Vlies, P., Weening, D., den Dunnen, J. T., Matusiak, M., Lamkanfi, M., Ligtenberg, M. J. L., ter Brugge, P., Jonkers, J., Foekens, J. A., Martens, J. W., van der Luijt, R., van Amstel, H. K. P., van Min, M., Splinter, E. & de Laat, W., 2014, In : Nature Biotechnology. 32, 10, p. 1019-1025

Research output: Contribution to journalArticleAcademicpeer-review

2013

EGFR mutation analysis in sputum of lung cancer patients: A multitechnique study

Hubers, A. J., Heideman, D. A. M., Yatabe, Y., Wood, M. D., Tull, J., Taron, M., Molina, M. A., Mayo, C., Bertran-Alamillo, J., Herder, G. J. M., Koning, R., Sie, D. L. S., Ylstra, B., Meijer, G. A., Snijders, P. J. F., Witte, B. I., Postmus, P. E., Smit, E. F. & Thunnissen, E., 2013, In : Lung Cancer. 82, 1, p. 38-43

Research output: Contribution to journalArticleAcademicpeer-review

Novel cases of D-2-hydroxyglutaric aciduria with IDH1 or IDH2 mosaic mutations identified by amplicon deep sequencing

Nota, B., Hamilton, E. M. C., Sie, D. L. S., Ozturk, S., van Dooren, S. J. M., Ojeda, M. R. F., Jakobs, C. A. J. M., Christensen, E., Kirk, E. P., Sykut-Cegielska, J., Lund, A. M., van der Knaap, M. S. & Salomons, G. S., 2013, In : Journal of Medical Genetics. 50, 11, p. 754-759

Research output: Contribution to journalArticleAcademicpeer-review

2012

Diagnosis of fanconi anemia: mutation analysis by next-generation sequencing

Ameziane, N., Sie, D. L. S., Dentro, S., Ariyurek, Y., Kerkhoven, L., Joenje, H., Dorsman, J. C., Ylstra, B., Gille, J. J. P., Sistermans, E. A. & de Winter, J. P., 2012, In : Anemia. 2012, 132856.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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HELLP babies link a novel lincRNA to the trophoblast cell cycle

van Dijk, M., Thulluru, H. K., Mulders, J., Michel, O. J., Poutsma, A., Windhorst, S., Kleiverda, G., Sie, D. L. S., Lachmeijer, A. M. A. & Oudejans, C. B. M., 2012, In : Journal of Clinical Investigation. 122, 11, p. 4003-4011

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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Search for a gene expression signature of breast cancer local recurrence in young women

Servant, N., Bollet, M. A., Halfwerk, H., Bleakley, K., Kreike, B., Jacob, L., Sie, D., Kerkhoven, R. M., Hupé, P., Hadhri, R., Fourquet, A., Bartelink, H., Barillot, E., Sigal-Zafrani, B. & van de Vijver, M. J., 15 Mar 2012, In : Clinical Cancer Research. 18, 6, p. 1704-15 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

2011

A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover

Verzijlbergen, K. F., van Welsem, T., Sie, D., Lenstra, T. L., Turner, D. J., Holstege, F. C. P., Kerkhoven, R. M. & van Leeuwen, F., Oct 2011, In : PLoS Genetics. 7, 10, p. e1002284

Research output: Contribution to journalArticleAcademicpeer-review

High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors

Koudijs, M. J., Klijn, C., van der Weyden, L., Kool, L., Hoeve, J. J., Sie, D. L. S., Prasetyanti, P. R., Schut, E., Kas, S., Whipp, T., Cuppen, E., Wessels, L., Adams, D. J. & Jonkers, J., 2011, In : Genome Research. 21, 12, p. 2181-2189

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Farazi, T. A., Horlings, H. M., Hoeve, J. J., Mihailovic, A., Halfwerk, H., Morozov, P., Brown, M., Hafner, M., Reyal, F., van Kouwenhove, M., Kreike, B., Sie, D. L. S., Hovestadt, V., Wessels, L. F., van de Vijver, M. J. & Tuschl, T., 2011, In : Cancer Research. 71, 13, p. 4443-4453

Research output: Contribution to journalArticleAcademicpeer-review

To DNA or not to DNA? That Is the Question, When It Comes to Molecular Subtyping for the Clinic!

Smeets, S. J., Harjes, U., van Wieringen, W. N., Meijer, G. A., Sie, D. L. S. & Ylstra, B., 2011, In : Clinical Cancer Research. 17, 15, p. 4959-4964

Research output: Contribution to journalArticleAcademicpeer-review

2010

Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes

Kool, J., Uren, A. G., Martins, C. P., Sie, D., de Ridder, J., Turner, G., van Uitert, M., Matentzoglu, K., Lagcher, W., Krimpenfort, P., Gadiot, J., Pritchard, C., Lenz, J., Lund, A. H., Jonkers, J., Rogers, J., Adams, D. J., Wessels, L., Berns, A. & van Lohuizen, M., 15 Jan 2010, In : Cancer Research. 70, 2, p. 520-31 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

One naive T cell, multiple fates in CD8+ T cell differentiation

Gerlach, C., van Heijst, J. W. J., Swart, E., Sie, D., Armstrong, N., Kerkhoven, R. M., Zehn, D., Bevan, M. J., Schepers, K. & Schumacher, T. N. M., 7 Jun 2010, In : Journal of Experimental Medicine. 207, 6, p. 1235-46 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

2009

Recruitment of antigen-specific CD8+ T cells in response to infection is markedly efficient

van Heijst, J. W. J., Gerlach, C., Swart, E., Sie, D., Nunes-Alves, C., Kerkhoven, R. M., Arens, R., Correia-Neves, M., Schepers, K. & Schumacher, T. N. M., 4 Sep 2009, In : Science. 325, 5945, p. 1265-9 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

2008

Dissecting T cell lineage relationships by cellular barcoding

Schepers, K., Swart, E., van Heijst, J. W. J., Gerlach, C., Castrucci, M., Sie, D., Heimerikx, M., Velds, A., Kerkhoven, R. M., Arens, R. & Schumacher, T. N. M., 29 Sep 2008, In : Journal of Experimental Medicine. 205, 10, p. 2309-18 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

Uren, A. G., Kool, J., Matentzoglu, K., de Ridder, J., Mattison, J., van Uitert, M., Lagcher, W., Sie, D., Tanger, E., Cox, T., Reinders, M., Hubbard, T. J., Rogers, J., Jonkers, J., Wessels, L., Adams, D. J., van Lohuizen, M. & Berns, A., 16 May 2008, In : Cell. 133, 4, p. 727-41 15 p.

Research output: Contribution to journalArticleAcademicpeer-review

The T7-primer is a source of experimental bias and introduces variability between microarray platforms

Kerkhoven, R. M., Sie, D., Nieuwland, M., Heimerikx, M., De Ronde, J., Brugman, W. & Velds, A., 23 Apr 2008, In : PLoS ONE. 3, 4, p. e1980

Research output: Contribution to journalArticleAcademicpeer-review