Bauke Ylstra

Summary

Affiliation: VU University Medical Center
Country: The Netherlands

Publications

  1. pmc Human and mouse oligonucleotide-based array CGH
    Paul van den IJssel
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Nucleic Acids Res 33:e192. 2005
  2. pmc Phenotypic and functional consequences of haploinsufficiency of genes from exocyst and retinoic acid pathway due to a recurrent microdeletion of 2p13.2
    Jiadi Wen
    Child and Family Research Institute, Department of Pathology, University of British Columbia, Vancouver, BC, Canada
    Orphanet J Rare Dis 8:100. 2013
  3. pmc Vitamin D and the mammary gland: a review on its role in normal development and breast cancer
    Nair Lopes
    IPATIMUP Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr Roberto Frias, S N, 4200 465, Porto, Portugal
    Breast Cancer Res 14:211. 2012
  4. pmc Relevance of PTEN loss in brain metastasis formation in breast cancer patients
    Harriet Wikman
    Institute of Tumor Biology, University Medical Center Hamburg Eppendorf, Martinistreet 52, 20246 Hamburg, Germany
    Breast Cancer Res 14:R49. 2012
  5. pmc High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
  6. pmc Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility
    Koen Bossers
    Neuroregeneration Laboratory, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands
    BMC Genomics 11:112. 2010
  7. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
  8. pmc BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)
    Bauke Ylstra
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    Nucleic Acids Res 34:445-50. 2006
  9. pmc Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer
    Saskia M Wilting
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 47:890-905. 2008
  10. doi request reprint Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomics
    Joost J Oudejans
    Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
    Genes Chromosomes Cancer 48:250-60. 2009

Detail Information

Publications97

  1. pmc Human and mouse oligonucleotide-based array CGH
    Paul van den IJssel
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Nucleic Acids Res 33:e192. 2005
    ....
  2. pmc Phenotypic and functional consequences of haploinsufficiency of genes from exocyst and retinoic acid pathway due to a recurrent microdeletion of 2p13.2
    Jiadi Wen
    Child and Family Research Institute, Department of Pathology, University of British Columbia, Vancouver, BC, Canada
    Orphanet J Rare Dis 8:100. 2013
    ..However, at the cellular level, the functional consequences of recurrent genomic abnormalities and how they can be linked to the phenotype are much less investigated...
  3. pmc Vitamin D and the mammary gland: a review on its role in normal development and breast cancer
    Nair Lopes
    IPATIMUP Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr Roberto Frias, S N, 4200 465, Porto, Portugal
    Breast Cancer Res 14:211. 2012
    ..Accordingly, we review data on the influence of vitamin D in the development of normal breast and the expression of vitamin D-related proteins (VDR, CYP27B1 and CYP24A21) in benign mammary lesions and ductal carcinomas in situ...
  4. pmc Relevance of PTEN loss in brain metastasis formation in breast cancer patients
    Harriet Wikman
    Institute of Tumor Biology, University Medical Center Hamburg Eppendorf, Martinistreet 52, 20246 Hamburg, Germany
    Breast Cancer Res 14:R49. 2012
    ..Therefore, our aim was to identify molecular markers associated with the development of brain metastases in breast cancer...
  5. pmc High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
    ..To date, most genome-wide array comparative genomic hybridization studies have used tumor panels of relatively large tumor size and high Nottingham Prognostic Index (NPI) that are not as representative of breast cancer demographics...
  6. pmc Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility
    Koen Bossers
    Neuroregeneration Laboratory, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands
    BMC Genomics 11:112. 2010
    ..Furthermore, we compared performance of both ratio- and intensity-based analyses in terms of reproducibility and sensitivity for differential gene expression...
  7. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
    ..g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes...
  8. pmc BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)
    Bauke Ylstra
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    Nucleic Acids Res 34:445-50. 2006
    ..This review compares the different platforms and will attempt to shine a light on the 'BAC to the future' of the array CGH technique...
  9. pmc Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer
    Saskia M Wilting
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 47:890-905. 2008
    ..In conclusion, integrated chromosomal and transcriptional profiling identified chromosomal hotspots at 1q, 3q, 11q, and 20q with altered gene expression within large commonly altered chromosomal regions in cervical cancer...
  10. doi request reprint Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomics
    Joost J Oudejans
    Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
    Genes Chromosomes Cancer 48:250-60. 2009
    ..In summary, using integrative genomics novel onco and tumor suppressor genes were identified in DLBCL that were not recognized by expression profiling alone...
  11. doi request reprint High-risk human papillomavirus-positive lung cancer: molecular evidence for a pattern of pulmonary metastasis
    Robert A A van Boerdonk
    Department of Pathology, Academic Center for Dentistry Amsterdam ACTA, VU University Medical Center, Amsterdam, The Netherlands
    J Thorac Oncol 8:711-8. 2013
    ..Since a causal contribution of hrHPV infection to lung cancer (LC) is still a matter of debate, a comprehensive study was performed to delineate hrHPV involvement in LC, using a Dutch study population...
  12. doi request reprint Focal aberrations indicate EYA2 and hsa-miR-375 as oncogene and tumor suppressor in cervical carcinogenesis
    Mariska Bierkens
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 52:56-68. 2013
    ..Our data provide a proof of concept that chromosomal aberrations are actively contributing to HPV-induced carcinogenesis and identify EYA2 and hsa-miR-375 as oncogene and tumor suppressor gene, respectively...
  13. doi request reprint DNA copy number aberrations in endobronchial lesions: a validated predictor for cancer
    Robert A A van Boerdonk
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Thorax 69:451-7. 2014
    ..This classifier could assist in selecting subjects with endobronchial lesions who might benefit from more aggressive therapeutic intervention or surveillance. ..
  14. pmc Integration of gene dosage and gene expression in non-small cell lung cancer, identification of HSP90 as potential target
    Marielle I Gallegos Ruiz
    Department of Medical Oncology, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
    PLoS ONE 3:e0001722. 2008
    ..Understanding the molecular events in non-small cell lung cancer (NSCLC) is essential to improve early diagnosis and treatment for this disease...
  15. ncbi request reprint Gene expression analysis of collembola in cadmium containing soil
    Benjamin Nota
    Department of Animal Ecology, Institute of Ecological Science, VU Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
    Environ Sci Technol 42:8152-7. 2008
    ..This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil, and provides a mechanistic basis for the development of a gene expression soil quality test...
  16. doi request reprint Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas
    Saskia M Wilting
    Departments of Pathology and Mathematics, VU University Medical Center, Amsterdam, The Netherlands, and Department of Obstetrics and Gynaecology, Erasmus University Medical Center, Rotterdam, The Netherlands
    Cancer Res 69:647-55. 2009
    ..These findings suggest that biomarkers associated with gains at chromosomes 1, 3q, and 20 are potential hallmarks of advanced p16(INK4a)-positive CIN2/3 lesions with a high short-term risk of progression...
  17. doi request reprint Gene-dosage dependent overexpression at the 13q amplicon identifies DIS3 as candidate oncogene in colorectal cancer progression
    Florence L M de Groen
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 53:339-48. 2014
    ..The functional relevance of this copy number aberration was corroborated for DIS3, thereby identifying this gene as novel candidate oncogene contributing to the 13q-driven adenoma to carcinoma progression...
  18. pmc Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene
    Benjamin Nota
    VU University Amsterdam, Institute of Ecological Science, Department of Animal Ecology, 1081 HV, Amsterdam, The Netherlands
    BMC Genomics 10:236. 2009
    ..Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida...
  19. pmc Losses of chromosome 5q and 14q are associated with favorable clinical outcome of patients with gastric cancer
    Tineke E Buffart
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Oncologist 17:653-62. 2012
    ..We hypothesize that, by identification of subgroups, individual treatment strategies can be selected to improve clinical outcome and to reduce unnecessary treatment toxicity for patients with gastric cancer...
  20. pmc Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism
    Beatriz Carvalho
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Cell Oncol (Dordr) 35:53-63. 2012
    ..It is estimated that only about 5% of adenomas do progress to a carcinoma...
  21. doi request reprint Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection
    Mariska Bierkens
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Int J Cancer 131:E579-85. 2012
    ..Hence, CIN3 with a longer duration of existence are likely more prone to have an increased short-term risk of cervical cancer...
  22. pmc HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia
    Mariska Bierkens
    Department of Pathology, Unit of Molecular Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    BMC Cancer 12:36. 2012
    ..The current study aimed to investigate whether CIN2/3 with different hrHPV types vary with respect to their chromosomal profiles, both in terms of the number of aberrations and chromosomal loci affected...
  23. pmc DNA copy number profiles of gastric cancer precursor lesions
    Tineke E Buffart
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    BMC Genomics 8:345. 2007
    ..e. intestinal-type and pyloric gland adenomas, would carry different patterns of DNA copy number changes, possibly reflecting distinct genetic pathways of gastric carcinogenesis in these two adenoma types...
  24. pmc DNA quality assessment for array CGH by isothermal whole genome amplification
    Tineke E Buffart
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Cell Oncol 29:351-9. 2007
    ..The aim of this study was to accurately determine the quality of FFPE DNA input in order to predict quality of array CGH outcome...
  25. doi request reprint Across array comparative genomic hybridization: a strategy to reduce reference channel hybridizations
    Tineke E Buffart
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 47:994-1004. 2008
    ..In summary, across array CGH avoids redundant hybridizations of the same reference material in every experiment either allowing hybridization of two test samples on one array or producing both CNA and CNV profiles simultaneously...
  26. pmc Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck
    Saskia M Wilting
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    BMC Med Genomics 2:32. 2009
    ..The latter differ from hrHPV-negative HNSCCs at the clinical and molecular level...
  27. doi request reprint Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas
    Hedy Vékony
    Department of Oral and Maxillofacial Surgery Oral Pathology, Academic Centre for Dentistry ACTA, VU University Medical Center, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 48:202-12. 2009
    ..Both unsupervised and supervised analysis of the genomic profiles revealed chromosome arm 8q to be involved in the malignant phenotype of salivary gland myoepitheliomas...
  28. doi request reprint Detection limits of DNA copy number alterations in heterogeneous cell populations
    Oscar Krijgsman
    Department of Pathology, VU University Medical Center, MB, Amsterdam, The Netherlands
    Cell Oncol (Dordr) 36:27-36. 2013
    ..The detection limits reported are a compound of analytical software and laboratory techniques and do not account for the number of probes in relation to sample homogeneity...
  29. ncbi request reprint CGHcall: calling aberrations for array CGH tumor profiles
    Mark A van de Wiel
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands
    Bioinformatics 23:892-4. 2007
    ..By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information...
  30. doi request reprint CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material
    Oscar Krijgsman
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Genes Chromosomes Cancer 51:344-52. 2012
    ..Copy number analysis using DNA derived from FFPE archival material is feasible using all three high-resolution copy number platforms and shows reproducible results, also with DNA input amounts lower than recommended...
  31. doi request reprint Gene expression analysis reveals a gene set discriminatory to different metals in soil
    Benjamin Nota
    Department of Animal Ecology, Institute of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands
    Toxicol Sci 115:34-40. 2010
    ....
  32. doi request reprint Chromosome 20p11 gains are associated with liver-specific metastasis in patients with colorectal cancer
    Leonie J M Mekenkamp
    Department of Pathology, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
    Gut 62:94-101. 2013
    ..This study aimed to identify clinicopathological features and chromosomal aberrations of primary tumours associated with organ-specific CRC metastasis...
  33. pmc High resolution analysis of DNA copy-number aberrations of chromosomes 8, 13, and 20 in gastric cancers
    Tineke E Buffart
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007, Amsterdam, The Netherlands
    Virchows Arch 455:213-23. 2009
    ..ZNF217 and TNFRSF6B are associated with important clinicopathological variables, including lymph node status...
  34. pmc CGHpower: exploring sample size calculations for chromosomal copy number experiments
    Ilari Scheinin
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    BMC Bioinformatics 11:331. 2010
    ..Several approaches for sample size determination have been developed for expression array studies, but so far none has been proposed for array comparative genomic hybridization (aCGH)...
  35. doi request reprint High-level copy number gains of established and potential drug target genes in gastric cancer as a lead for treatment development and selection
    Mariette Labots
    Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
    Cell Oncol (Dordr) 37:41-52. 2014
    ..g. previously been shown for HER2. The aim of the present study was to identify putative drug targets in patients with gastric cancer by applying this strategy...
  36. ncbi request reprint Chromosome 5q loss in colorectal flat adenomas
    Quirinus J M Voorham
    Departments of Pathology, Epidemiology and Biostatistics, Gynaecology, and Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
    Clin Cancer Res 18:4560-9. 2012
    ..Here, we aimed to compare one of the molecular changes most explicitly associated with adenoma to carcinoma progression, that is, chromosomal instability, between flat and polypoid colorectal adenomas...
  37. pmc Gastric cancers of Western European and African patients show different patterns of genomic instability
    Tineke E Buffart
    Dept of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    BMC Med Genomics 4:7. 2011
    ..We aim to study genomic instability patterns of gastric cancers obtained from patients from United Kingdom (UK) and South Africa (SA), in an attempt to support the African enigma hypothesis at the biological level...
  38. doi request reprint Trifluorothymidine resistance is associated with decreased thymidine kinase and equilibrative nucleoside transporter expression or increased secretory phospholipase A2
    Olaf H Temmink
    Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    Mol Cancer Ther 9:1047-57. 2010
    ..Mol Cancer Ther; 9(4); 1047-57. (c)2010 AACR...
  39. pmc Genomic landscape of metastatic colorectal cancer
    Josien C Haan
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    Nat Commun 5:5457. 2014
    ..1-q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of mCRC reveals a number of DNA copy number aberrations associated with response to drug therapy. ..
  40. doi request reprint Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology
    Daoud Sie
    Departments of Pathology, VU University Medical Center, PO Box 7057, 1007, MB, Amsterdam, The Netherlands
    Cell Oncol (Dordr) 37:353-61. 2014
    ..The current study presents a comprehensive analysis of TruSeq Amplicon Cancer Panel-based NGS using a MiSeq Personal sequencer (TSACP-MiSeq-NGS) for somatic mutation profiling...
  41. pmc Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis
    Serge J Smeets
    Section Tumor Biology, Department of Otolaryngology Head Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
    Cell Oncol 31:291-300. 2009
    ..In conclusion, the discovery of these new classes of oral and oropharyngeal cancer with unique genetic and clinical characteristics has important consequences for future basic and clinical studies...
  42. pmc Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses
    Wessel N van Wieringen
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
    BMC Bioinformatics 13:80. 2012
    ..Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms...
  43. pmc Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down
    Jose L Costa
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    BMC Genomics 10:499. 2009
    ..In contrast, the molecular mechanism of 1,25D for the regulation of calcium homeostasis has principally been resolved, demonstrating a pivotal role for the vitamin D receptor (VDR)...
  44. doi request reprint Smoothing waves in array CGH tumor profiles
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands
    Bioinformatics 25:1099-104. 2009
    ..Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult...
  45. ncbi request reprint Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancer
    Jillian de Wilde
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Int J Cancer 122:877-88. 2008
    ..In summary, we identified 32 candidate biomarkers for deregulated hTERT mRNA expression, which may enable the identification of cervical premalignant lesions that are at highest risk to progress to invasive cancer...
  46. pmc High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer
    Evert van den Broek
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    PLoS ONE 10:e0138141. 2015
    ..This study aimed to perform a systematic analysis of genes that are affected by CNA-associated chromosomal breaks in colorectal cancer (CRC) and to determine the clinical relevance of recurrent breakpoint genes...
  47. pmc 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
    Ilari Scheinin
    Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands Department of Pathology, Haartman Institute and HUSLAB, FIN 00014 University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
    Genome Res 24:2022-32. 2014
    ..The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost...
  48. pmc Chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts and differences are typically non-recurrent
    Leonie J M Mekenkamp
    Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    PLoS ONE 9:e86833. 2014
    ..We conclude, based on detailed analysis and large independent datasets, that chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts, and differences are typically non-recurrent. ..
  49. pmc Mixed gastric carcinomas show similar chromosomal aberrations in both their diffuse and glandular components
    Beatriz Carvalho
    Department of Pathology, VUMC VU University Medical Centre, Amsterdam, The Netherlands
    Cell Oncol 28:283-94. 2006
    ..This supports the idea that the phenotypic divergence within mixed gastric carcinomas is not caused by DNA chromosomal aberrations...
  50. doi request reprint Genetic variation in parthenogenetic collembolans is associated with differences in fitness and cadmium-induced transcriptome responses
    Benjamin Nota
    Department of Animal Ecology, Institute of Ecological Science, VU University, Amsterdam, The Netherlands
    Environ Sci Technol 47:1155-62. 2013
    ..This sheds new light on the sources of biological variability in test results, even when the test organisms are thought to be genetically homogeneous because of their parthenogenetic reproduction...
  51. doi request reprint Transcriptional plasticity of a soil arthropod across different ecological conditions
    Tjalf E de Boer
    Department of Ecological Science, VU University, Amsterdam, The Netherlands
    Mol Ecol 20:1144-54. 2011
    ..candida strongly responds. The broad range of conditions over which this soil-living detritivore is able to survive and reproduce, indicates a strategy of high plasticity, which comes with extensive gene expression regulation...
  52. pmc Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features
    Marcel Kool
    Department of Human Genetics, Academic Medical Center, Amsterdam, The Netherlands
    PLoS ONE 3:e3088. 2008
    ..This illustrates the potential benefits of a robust classification of medulloblastoma patients and a detailed knowledge of associated biological mechanisms...
  53. doi request reprint High-resolution array comparative genomic hybridization in sporadic and celiac disease-related small bowel adenocarcinomas
    Begona Diosdado
    Departments of Pathology and Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
    Clin Cancer Res 16:1391-401. 2010
    ..The molecular pathogenesis of small intestinal adenocarcinomas is not well understood. Understanding the molecular characteristics of small bowel adenocarcinoma may lead to more effective patient treatment...
  54. doi request reprint Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients
    Evert van den Broek
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Oncotarget . 2016
    ..We conclude that among multiple genomic alterations in CRC, strongest associations with clinical outcome were observed for common mutations in APC...
  55. pmc NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines
    Tineke E Buffart
    Dept Pathology, VU University Medical Center, Amsterdam, The Netherlands
    BMC Med Genomics 2:39. 2009
    ....
  56. doi request reprint DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancer
    Robert A A van Boerdonk
    VU University Medical Center, Department of Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
    Am J Respir Crit Care Med 184:948-56. 2011
    ..Autofluorescence bronchoscopy (AFB) is a valid strategy for detecting premalignant endobronchial lesions. However, no biomarker can reliably predict lung cancer risk of subjects with AFB-visualized premalignant lesions...
  57. doi request reprint Salivary gland carcinosarcoma: oligonucleotide array CGH reveals similar genomic profiles in epithelial and mesenchymal components
    Hedy Vékony
    Department of Oral and Maxillofacial Surgery Oral Pathology, Academic Centre for Dentistry ACTA, VU University Medical Center VUmc, Amsterdam, The Netherlands
    Oral Oncol 45:259-65. 2009
    ..Furthermore, specific amplifications of a mucin and a Polycomb group gene imply these proteins in the tumorigenesis of carcinosarcomas...
  58. doi request reprint Candidate driver genes in focal chromosomal aberrations of stage II colon cancer
    Rebecca P M Brosens
    Department of Surgery, VU University Medical Centre, Amsterdam, The Netherlands
    J Pathol 221:411-24. 2010
    ..DNA copy number status of these genes correlates with mRNA expression and some are associated with clinical outcome...
  59. doi request reprint Stimulated gene expression profiles as a blood marker of major depressive disorder
    Sabine Spijker
    Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
    Biol Psychiatry 68:179-86. 2010
    ..Major depressive disorder (MDD) is a moderately heritable disorder with a high lifetime prevalence. At present, laboratory blood tests to support MDD diagnosis are not available...
  60. pmc Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression
    Anke H Sillars-Hardebol
    Department of Pathology Tumor Profiling Unit, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
    Tumour Biol 31:89-96. 2010
    ....
  61. doi request reprint Preprocessing and downstream analysis of microarray DNA copy number profiles
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
    Brief Bioinform 12:10-21. 2011
    ..Finally, we look ahead: what should we prepare for and which methodology-related topics may deserve attention in the near future?..
  62. doi request reprint Focal chromosomal copy number aberrations in cancer-Needles in a genome haystack
    Oscar Krijgsman
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands Electronic address
    Biochim Biophys Acta 1843:2698-2704. 2014
    ..However, focal CNAs lack a consensus definition; therefore, we propose one based on pragmatic considerations. We also describe different strategies to identify focal CNAs and procedures to distinguish them from large CNAs and CNVs...
  63. ncbi request reprint In vivo induction of resistance to gemcitabine results in increased expression of ribonucleotide reductase subunit M1 as the major determinant
    Andries M Bergman
    Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
    Cancer Res 65:9510-6. 2005
    ..This study is the first in vivo evidence for a key role for RRM1 in acquired gemcitabine resistance...
  64. doi request reprint EGFR mutation analysis in sputum of lung cancer patients: a multitechnique study
    A Jasmijn Hubers
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Lung Cancer 82:38-43. 2013
    ..The aim of the present study was to determine whether EGFR mutation analysis is attainable on sputum samples, employing different assays in a multicenter study...
  65. doi request reprint No evidence for active human papillomavirus (HPV) in fields surrounding HPV-positive oropharyngeal tumors
    Michelle M Rietbergen
    Department of Otolaryngology Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
    J Oral Pathol Med 43:137-42. 2014
    ..Therefore, the presence of transcriptionally active HPV was analyzed in the mucosa surrounding HPV-positive OPSCCs...
  66. doi request reprint A novel method to identify syncytiotrophoblast-derived RNA products representative of trisomy 21 placental RNA in maternal plasma
    Attie T J J Go
    Department of Obstetrics Gynecology, VU University Medical Center, Amsterdam, The Netherlands
    Methods Mol Biol 444:291-302. 2008
    ....
  67. ncbi request reprint Microarray analysis of bleomycin-exposed lymphoblastoid cells for identifying cancer susceptibility genes
    Jacqueline Cloos
    Section Tumor Biology, Department of Otolaryngology Head Neck Surgery, VU University Medical Center, P O Box 7057, 1007 MB Amsterdam, The Netherlands
    Mol Cancer Res 4:71-7. 2006
    ..g., BUB1 and DUSP4). This difference in expression profiles between mutagen-sensitive and mutagen-insensitive individuals justifies further studies aimed at elucidating the genes responsible for the development of sporadic cancers...
  68. ncbi request reprint DNA copy number gains at loci of growth factors and their receptors in salivary gland adenoid cystic carcinoma
    Hedy Vékony
    Department of Oral and Maxillofacial Surgery Oral Pathology, Academic Centre for Dentistry Amsterdam, The Netherlands
    Clin Cancer Res 13:3133-9. 2007
    ..This study aimed at unraveling common genetic abnormalities associated with ACC. Additionally, chromosomal changes were correlated with patient characteristics and survival...
  69. pmc Immortalization capacity of HPV types is inversely related to chromosomal instability
    Denise M Schütze
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Oncotarget 7:37608-37621. 2016
    ..This may in part explain the observed differences in HPV-type prevalence in cervical cancers and emphasizes that changes in the host cell genome contribute to HPV-induced carcinogenesis...
  70. doi request reprint Defects in the Fanconi Anemia Pathway and Chromatid Cohesion in Head and Neck Cancer
    Chantal Stoepker
    Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
    Cancer Res 75:3543-53. 2015
    ..Inactivation of known Fanconi anemia and chromatid cohesion genes does explain CIN in the minority of cases. These findings point to phenotypes that may be highly relevant in treatment response of HNSCC...
  71. doi request reprint Breast cancers with a BRCA1-like DNA copy number profile recur less often than expected after high-dose alkylating chemotherapy
    Philip C Schouten
    Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
    Clin Cancer Res 21:763-70. 2015
    ....
  72. ncbi request reprint Determination of amplicon boundaries at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization
    Marjan M Weiss
    Department of Gastroenterology, VU University Medical Centre, Amsterdam, The Netherlands
    J Pathol 200:320-6. 2003
    ..In the present study, an amplicon at 20q13.2 has been narrowed down to 800 kb which is likely to harbour one or more putative oncogenes relevant to gastric carcinogenesis, for which ZNF217 and CYP24 are good candidates...
  73. pmc Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus
    Gea Beunders
    Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
    Am J Hum Genet 92:210-20. 2013
    ..The zebrafish model provides a valuable tool for investigating the etiology of AUTS2 syndrome and facilitating gene-function analysis in the future...
  74. doi request reprint Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta
    Dick Roelofs
    Institute of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands
    Mol Ecol 18:3227-39. 2009
    ..We confirmed the micro-evolutionary processes occurring in soil arthropod populations and suggest a major contribution of gene regulation to the evolution of a stress-adapted phenotype...
  75. ncbi request reprint Genomic stability and functional activity may be lost in telomerase-transduced human CD8+ T lymphocytes
    Marco W J Schreurs
    Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
    Blood 106:2663-70. 2005
    ....
  76. pmc Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases
    Marieke A Vollebergh
    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
    PLoS ONE 9:e103177. 2014
    ....
  77. pmc Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis
    Henne Holstege
    Department of Clinical Genetics, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
    Genome Res 24:733-42. 2014
    ..Together, this suggests that the finite lifespan of HSCs, rather than somatic mutation effects, may lead to hematopoietic clonal evolution at extreme ages. ..
  78. ncbi request reprint ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data
    Wessel N van Wieringen
    Department of Mathematics, Vrije Universiteit De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
    Bioinformatics 22:1919-20. 2006
    ..ACE-it links the chromosomal position of the gene dosage measured by array CGH to the genes measured by the expression array. ACE-it uses this link to statistically test whether gene dosage affects RNA expression...
  79. ncbi request reprint Genetic heterogeneity in patients with multiple neoplastic lung lesions: a report of three cases
    Marielle I Gallegos Ruiz
    Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
    J Thorac Oncol 2:12-21. 2007
    ..A better understanding of the molecular alterations present in the different lesions may help in defining this relation...
  80. pmc Increased expression of matrix extracellular phosphoglycoprotein (MEPE) in cortical bone of the rat tibia after mechanical loading: identification by oligonucleotide microarray
    Christianne M A Reijnders
    Department of Internal Medicine, Endocrine Section, VU University Medical Center, Amsterdam, The Netherlands
    PLoS ONE 8:e79672. 2013
    ..The modulation of MEPE expression may indicate a connection between bone mineralization and bone formation after mechanical stimulation. ..
  81. doi request reprint Molecular basis of bortezomib resistance: proteasome subunit beta5 (PSMB5) gene mutation and overexpression of PSMB5 protein
    Ruud Oerlemans
    Department of Rheumatology, VUMC Institute for Cancer and Immunology, VU University Medical Center, Amsterdam, The Netherlands
    Blood 112:2489-99. 2008
    ..Collectively, these findings establish a novel mechanism of bortezomib resistance associated with the selective overexpression of a mutant PSMB5 protein...
  82. ncbi request reprint Microarray analysis reveals pivotal divergent mRNA expression profiles early in the development of either compensated ventricular hypertrophy or heart failure
    Henk P J Buermans
    Laboratory for Physiology, VU University Medical Center, Amsterdam, The Netherlands
    Physiol Genomics 21:314-23. 2005
    ..These data reveal genes that may provide markers for the early prediction of clinical outcome as well as potential targets for early intervention...
  83. ncbi request reprint Resolving the resolution of array CGH
    Bradley P Coe
    British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
    Genomics 89:647-53. 2007
    ..Calculation of these metrics is automated through the development of a Java-based application, "ResCalc," which is applicable to any array CGH platform...
  84. ncbi request reprint Weighted clustering of called array CGH data
    Wessel N van Wieringen
    Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands
    Biostatistics 9:484-500. 2008
    ..We illustrate WECCA using an application to a breast cancer data set, where WECCA finds a clustering that relates better with survival than the original one...
  85. doi request reprint Array comparative genomic hybridization copy number profiling: a new tool for translational research in solid malignancies
    José Luis Costa
    Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
    Semin Radiat Oncol 18:98-104. 2008
    ....
  86. ncbi request reprint CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data
    Mark A van de Wiel
    Department of Mathematics and Computer Science, Technische Universiteit Eindhoven PO Box 513, 5600 MB, Eindhoven, The Netherlands
    Bioinformatics 21:3193-4. 2005
    ..We compute P-values, based on the Wilcoxon test with ties, to compare two conditions with array comparative genomic hybridization data, and we provide a simple interface to export and plot these P-values...
  87. ncbi request reprint Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event
    Anna L Paterson
    Hutchison MRC Research Centre, Department of Pathology, University of Cambridge, Cambridge, UK
    Genes Chromosomes Cancer 46:427-39. 2007
    ..This article contains supplementary material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat...
  88. ncbi request reprint Breakpoint identification and smoothing of array comparative genomic hybridization data
    Kees Jong
    Faculty of Sciences, Vrije Universiteit, De Boelelaan 1117, Amsterdam 1081HV, The Netherlands
    Bioinformatics 20:3636-7. 2004
    ..aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data...
  89. doi request reprint Comment re: a comparison of DNA copy number profiling platforms
    Bradley P Coe
    Cancer Res 68:4010; author reply 4010. 2008
  90. doi request reprint Inhibition of gastric cancer invasion and metastasis by PLA2G2A, a novel beta-catenin/TCF target gene
    Kumaresan Ganesan
    Cellular and Molecular Research, National Cancer Center, Genome Institute of Singapore, Singapore, Singapore
    Cancer Res 68:4277-86. 2008
    ..Our results highlight the complexity of PLA2G2A regulation and provide functional evidence for PLA2G2A as an important regulator of invasion and metastasis in GC...
  91. doi request reprint Mutation of C/EBPalpha predisposes to the development of myeloid leukemia in a retroviral insertional mutagenesis screen
    Marie S Hasemann
    Section for Gene Therapy Research, Department of Clinical Biochemistry, Copenhagen University Hospital, Juliane Maries Vej 20 9322, DK2100 Copenhagen, Denmark
    Blood 111:4309-21. 2008
    ....
  92. pmc Recruitment to the nuclear periphery can alter expression of genes in human cells
    Lee E Finlan
    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 4:e1000039. 2008
    ..This is compatible with the suggestion that re-localisation of genes relative to the peripheral zone of the nucleus could be used by metazoans to modulate the expression of selected genes during development and differentiation...
  93. ncbi request reprint Oligonucleotide array comparative genomic hybridization
    Paul van den Ijssel
    Methods Mol Biol 396:207-21. 2007
    ..The protocol allows as little as 300 ng of input DNA, which makes the procedure valuable for small clinical samples and is also functional for DNA samples obtained from archival tissues...
  94. ncbi request reprint ErbB2 activation of ESX gene expression
    Richard M Neve
    Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA
    Oncogene 21:3934-8. 2002
    ..These results indicate that the ESX promoter represents a transcriptional target of ErbB2, and ESX expression may represent a downstream mediator of ErbB2 signaling and ErbB2-induced gene expression...
  95. ncbi request reprint Expression microarray analysis and oligo array comparative genomic hybridization of acquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations
    Mark A van de Wiel
    Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
    Cancer Res 65:10208-13. 2005
    ....
  96. ncbi request reprint Altered promoter usage characterizes monoallelic transcription arising with ERBB2 amplification in human breast cancers
    Christopher C Benz
    Buck Institute for Age Research, Novato, CA 94945, USA
    Genes Chromosomes Cancer 45:983-94. 2006
    ....
  97. ncbi request reprint High resolution microarray CGH and MLPA analysis for improved genotype/phenotype evaluation of two childhood genetic disorder cases: ring chromosome 19 and partial duplication 2q
    Mario A J A Hermsen
    Department Otorinolayngology, Instituto Universitario de Oncologia del Principado de Asturias IUOPA, Hospital Central de Asturias, Unidad Administrativa del IUOPA, University of Oviedo, Asturias, Spain
    Eur J Med Genet 48:310-8. 2005
    ..These two examples illustrate the additional value of new, high resolution genetic analysis techniques for a better characterization of the genotype/phenotype relationship in childhood chromosomal disorders...