Publications by authors named "Bauke Ylstra"

100Publications

Circulating tumor DNA analysis of EGFR-mutant non-small cell lung cancer patients receiving osimertinib following previous tyrosine kinase inhibitor treatment.

Lung Cancer 2020 07 11;145:173-180. Epub 2020 May 11.

Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.lungcan.2020.04.039DOI Listing
July 2020

Circulating Tumor DNA Analysis: Clinical Implications for Colorectal Cancer Patients. A Systematic Review.

JNCI Cancer Spectr 2019 Sep 19;3(3):pkz042. Epub 2019 Jun 19.

Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1093/jncics/pkz042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7050033PMC
September 2019

Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts.

Proc Natl Acad Sci U S A 2019 03 8;116(13):6140-6145. Epub 2019 Mar 8.

Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;

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http://dx.doi.org/10.1073/pnas.1813417116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442578PMC
March 2019

ACE: absolute copy number estimation from low-coverage whole-genome sequencing data.

Bioinformatics 2019 08;35(16):2847-2849

Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty1055DOI Listing
August 2019

Establishment and Genetic Landscape of Precancer Cell Model Systems from the Head and Neck Mucosal Lining.

Mol Cancer Res 2019 01 17;17(1):120-130. Epub 2018 Sep 17.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology-Head and Neck Surgery, Cancer Center Amsterdam, Amsterdam, the Netherlands.

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http://mcr.aacrjournals.org/lookup/doi/10.1158/1541-7786.MCR
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http://dx.doi.org/10.1158/1541-7786.MCR-18-0445DOI Listing
January 2019

Loss of Chromosome 18q11.2-q12.1 Is Predictive for Survival in Patients With Metastatic Colorectal Cancer Treated With Bevacizumab.

J Clin Oncol 2018 07 24;36(20):2052-2060. Epub 2018 May 24.

Erik van Dijk, Hedde D. Biesma, Martijn Cordes, Maarten Neerincx, Paul P. Eijk, Henk M.W. Verheul, Nicole C.T. van Grieken, and Bauke Ylstra, Vrije Universiteit Medical Center; Gerrit A. Meijer, Netherlands Cancer Institute; Cornelis J.A. Punt, Academic Medical Center, Amsterdam; Miriam Koopman, University Medical Center Utrecht, Utrecht, the Netherlands; Dominiek Smeets and Diether Lambrechts, KU Leuven, Leuven, Belgium; Sudipto Das, Orna Bacon, Jochen H.M. Prehn, Bryan T. Hennessey, Darran P. O'Connor, and Annette T. Byrne, Royal College of Surgeons in Ireland; Verena Murphy, Cancer Trials Ireland; Anna Barat, Deborah A. McNamara, and Elaine W. Kay, Beaumont Hospital; Bozena Fender and William M. Gallagher, OncoMark Ltd; Rut Klinger and William M. Gallagher, University College Dublin, Dublin, United Kingdom; Johannes Betge, Timo Gaiser, and Matthias P.A. Ebert, University Hospital Mannheim, Mannheim, Germany; and Fotios Loupakis, Veneto Institute of Oncology IOV-IRCCS Padua, Italy.

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http://dx.doi.org/10.1200/JCO.2017.77.1782DOI Listing
July 2018

High number of chromosomal copy number aberrations inversely relates to t(11;19)(q21;p13) translocation status in mucoepidermoid carcinoma of the salivary glands.

Oncotarget 2017 Sep 20;8(41):69456-69464. Epub 2017 Apr 20.

Department of Oral and Maxillofacial Surgery and Oral Pathology VU University Medical Center, Academic Centre for Dentistry Amsterdam (ACTA) Amsterdam, The Netherlands.

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http://dx.doi.org/10.18632/oncotarget.17282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642491PMC
September 2017

Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets.

Cancer Cell 2017 08;32(2):238-252.e9

Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Brain Tumor Center Amsterdam, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13(th) Street, Charlestown, MA 02129, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381325PMC
August 2017

Postmortem Examination of an Aggressive Case of Medullary Thyroid Carcinoma Characterized by Catastrophic Genomic Abnormalities.

JCO Precis Oncol 2017 5;1. Epub 2017 Jun 5.

, , , , , , , , , , , and , University College Dublin, Belfield; , , , and , Royal College of Surgeons in Ireland; , , , , , , and , Mater Misericordiae University Hospital; , Beaumont Hospital, Dublin, Ireland; and , Vrije Universiteit Medical Center, Amsterdam, the Netherlands; and , Vesailus Research Center, Vlaams Instituut voor Biotechnologie, Katholieke Universiteit, Leuven, Belgium.

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http://dx.doi.org/10.1200/PO.16.00063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7446351PMC
June 2017

Somatic mutation in PIK3CA is a late event in cervical carcinogenesis.

J Pathol Clin Res 2015 Oct 21;1(4):207-11. Epub 2015 Sep 21.

Department of Pathology VU University Medical Center Amsterdam The Netherlands.

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http://dx.doi.org/10.1002/cjp2.27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939891PMC
October 2015

Sequencing Structural Variants in Cancer for Precision Therapeutics.

Trends Genet 2016 09 29;32(9):530-542. Epub 2016 Jul 29.

Cancer Research UK Cambridge Institute, University of Cambridge, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.07.002DOI Listing
September 2016

RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.

Cancer Cell 2015 Nov 29;28(5):666-676. Epub 2015 Oct 29.

Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands; Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; thromboDx B.V., 1098 EA Amsterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2015.09.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644263PMC
November 2015

Endogenous C1-inhibitor production and expression in the heart after acute myocardial infarction.

Cardiovasc Pathol 2016 Jan-Feb;25(1):33-9. Epub 2015 Sep 25.

Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands; Institute for Cardiovascular Research, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.carpath.2015.09.006DOI Listing
October 2016

Diagnostic challenges in survivors of early stage lung cancer.

Lung Cancer 2015 Nov 24;90(2):212-6. Epub 2015 Aug 24.

Department of Radiation Oncology, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.lungcan.2015.08.013DOI Listing
November 2015

Variant Rett syndrome in a girl with a pericentric X-chromosome inversion leading to epigenetic changes and overexpression of the MECP2 gene.

Int J Dev Neurosci 2015 Nov 10;46:82-7. Epub 2015 Aug 10.

Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.ijdevneu.2015.07.010DOI Listing
November 2015

Defects in the Fanconi Anemia Pathway and Chromatid Cohesion in Head and Neck Cancer.

Cancer Res 2015 Sep 29;75(17):3543-53. Epub 2015 Jun 29.

Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-0528DOI Listing
September 2015

Transformation to a squamous cell carcinoma phenotype of an EGFR-mutated NSCLC patient after treatment with an EGFR-tyrosine kinase inhibitor.

J Clin Pathol 2015 Apr 6;68(4):320-1. Epub 2015 Feb 6.

Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands Department of Pulmonary Diseases, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1136/jclinpath-2015-202866DOI Listing
April 2015

FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations.

Cancer Inform 2014 1;13:153-6. Epub 2014 Dec 1.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://journals.sagepub.com/doi/10.4137/CIN.S19519
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http://dx.doi.org/10.4137/CIN.S19519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4251178PMC
December 2014

Breast cancers with a BRCA1-like DNA copy number profile recur less often than expected after high-dose alkylating chemotherapy.

Clin Cancer Res 2015 Feb 5;21(4):763-70. Epub 2014 Dec 5.

Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands. Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-14-1894DOI Listing
February 2015

Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas.

Gut 2015 Nov 10;64(11):1721-31. Epub 2014 Nov 10.

Department of Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore.

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http://dx.doi.org/10.1136/gutjnl-2014-308252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4680172PMC
November 2015

Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes.

Cell Rep 2014 Sep 18;8(6):1649-1658. Epub 2014 Sep 18.

Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands; Exosomes Research Group, VU University Medical Center, 1007MB Amsterdam, the Netherlands. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(14)00703-7.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471400703
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http://dx.doi.org/10.1016/j.celrep.2014.08.027DOI Listing
September 2014

Focal chromosomal copy number aberrations in cancer-Needles in a genome haystack.

Biochim Biophys Acta 2014 Nov 7;1843(11):2698-2704. Epub 2014 Aug 7.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bbamcr.2014.08.001DOI Listing
November 2014

Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases.

PLoS One 2014 1;9(8):e103177. Epub 2014 Aug 1.

Division of Molecular Pathology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands; Division of Medical Oncology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103177PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118860PMC
April 2015

M-CSF priming of osteoclast precursors can cause osteoclastogenesis-insensitivity, which can be prevented and overcome on bone.

J Cell Physiol 2015 Jan;230(1):210-25

Department of Periodontology, University of Amsterdam VU University, MOVE Research Institute, Amsterdam, The Netherlands; Department of Oral Cell Biology, University of Amsterdam VU University, MOVE Research Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/jcp.24702DOI Listing
January 2015

Gene-dosage dependent overexpression at the 13q amplicon identifies DIS3 as candidate oncogene in colorectal cancer progression.

Genes Chromosomes Cancer 2014 Apr 29;53(4):339-48. Epub 2014 Jan 29.

Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/gcc.22144DOI Listing
April 2014

Clinical value of chromosome arms 19q and 11p losses in low-grade gliomas.

Neuro Oncol 2014 Mar 12;16(3):400-8. Epub 2013 Dec 12.

Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière (CRICM), UMRS 975, Inserm U 975, CNRS, UMR 7225, Université Pierre et Marie Curie, Paris, France (A.A., Y.M, C.C., B.B., K.M., K.H.-X., M.S., J.-Y.D., A.I.); Department of Neuropathology (H.A., K.M.); Department of Neurology 2-Mazarin (F.L.-D., K.H.-X., M.S., J.-Y.D., A.I.); Department of Neurosurgery, AP-HP, Groupe Hospitalier Pitié-Salpêtriére, Paris, France (L.C.); Department of Neurology (H.F.v.T., J.C.R.); Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands (I.S., P.W., B.Y.); Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands (P.W.).

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http://dx.doi.org/10.1093/neuonc/not227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922518PMC
March 2014

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

J Oral Pathol Med 2014 Feb 11;43(2):137-42. Epub 2013 Oct 11.

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1111/jop.12123DOI Listing
February 2014

Identification of lethal microRNAs specific for head and neck cancer.

Clin Cancer Res 2013 Oct 13;19(20):5647-57. Epub 2013 Aug 13.

Authors' Affiliations: Departments of Otolaryngology/Head-Neck Surgery, Epidemiology and Biostatistics, and Pathology, VU University Medical Center; Department of Mathematics, VU University; Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam; and InteRNA Technologies BV, Utrecht, The Netherlands.

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http://clincancerres.aacrjournals.org/content/early/2013/09/
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http://clincancerres.aacrjournals.org/content/early/2013/08/
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http://clincancerres.aacrjournals.org/cgi/doi/10.1158/1078-0
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http://dx.doi.org/10.1158/1078-0432.CCR-12-2295DOI Listing
October 2013

An exploration of pathways involved in lung carcinoid progression using gene expression profiling.

Carcinogenesis 2013 Dec 8;34(12):2726-37. Epub 2013 Aug 8.

Department of Molecular Cell Biology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, PO Box 616, 6200 MD Maastricht, The Netherlands.

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http://dx.doi.org/10.1093/carcin/bgt271DOI Listing
December 2013

Benefit of a second opinion: intrapulmonary metastases or multiple primary tumors?

J Thorac Oncol 2013 Jun;8(6):e54-6

Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1097/JTO.0b013e31828c28c6DOI Listing
June 2013

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures.

Nat Struct Mol Biol 2013 Mar 17;20(3):387-95. Epub 2013 Feb 17.

Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.

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http://dx.doi.org/10.1038/nsmb.2509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689368PMC
March 2013

Genetic variation in parthenogenetic collembolans is associated with differences in fitness and cadmium-induced transcriptome responses.

Environ Sci Technol 2013 Jan 7;47(2):1155-62. Epub 2013 Jan 7.

Department of Animal Ecology, Institute of Ecological Science, VU University, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/es303983zDOI Listing
January 2013

Detection limits of DNA copy number alterations in heterogeneous cell populations.

Cell Oncol (Dordr) 2013 Feb 2;36(1):27-36. Epub 2012 Nov 2.

Department of Pathology, VU University Medical Center, MB, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s13402-012-0108-2DOI Listing
February 2013

Focal aberrations indicate EYA2 and hsa-miR-375 as oncogene and tumor suppressor in cervical carcinogenesis.

Genes Chromosomes Cancer 2013 Jan 14;52(1):56-68. Epub 2012 Sep 14.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://doi.wiley.com/10.1002/gcc.22006
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http://dx.doi.org/10.1002/gcc.22006DOI Listing
January 2013

Low-grade and high-grade mammary carcinomas in WAP-T transgenic mice are independent entities distinguished by Met expression.

Int J Cancer 2013 Mar 26;132(6):1300-10. Epub 2012 Sep 26.

Department of Clinical Chemistry/Central Laboratories, Center for Diagnostic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.

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http://dx.doi.org/10.1002/ijc.27783DOI Listing
March 2013

An 82-year-old woman with small-cell lung cancer: relapse after 9 years or a new primary?

J Thorac Oncol 2012 Aug;7(8):e3-5

Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1097/JTO.0b013e31825bceadDOI Listing
August 2012

Chromosome 5q loss in colorectal flat adenomas.

Clin Cancer Res 2012 Sep 3;18(17):4560-9. Epub 2012 Jul 3.

Departments of Pathology, Epidemiology and Biostatistics, Gynaecology, and Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-11-2385DOI Listing
September 2012

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

Anemia 2012 3;2012:132856. Epub 2012 Jun 3.

Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands.

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http://dx.doi.org/10.1155/2012/132856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374947PMC
August 2012

Vitamin D and the mammary gland: a review on its role in normal development and breast cancer.

Breast Cancer Res 2012 May 31;14(3):211. Epub 2012 May 31.

IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr Roberto Frias, s/n, 4200-465, Porto, Portugal.

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http://dx.doi.org/10.1186/bcr3178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446331PMC
May 2012

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.

BMC Bioinformatics 2012 May 4;13:80. Epub 2012 May 4.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-13-80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475006PMC
May 2012

HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia.

BMC Cancer 2012 Jan 24;12:36. Epub 2012 Jan 24.

Department of Pathology, Unit of Molecular Pathology, VU University Medical Center, PO box 7057, 1007 MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2407-12-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305644PMC
January 2012

Chromosome 20p11 gains are associated with liver-specific metastasis in patients with colorectal cancer.

Gut 2013 Jan 20;62(1):94-101. Epub 2012 Jan 20.

Department of Pathology, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://gut.bmj.com/lookup/doi/10.1136/gutjnl-2011-301587
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http://dx.doi.org/10.1136/gutjnl-2011-301587DOI Listing
January 2013

CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material.

Genes Chromosomes Cancer 2012 Apr 8;51(4):344-52. Epub 2011 Dec 8.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/gcc.21920DOI Listing
April 2012