Jo Vandesompele

Summary

Affiliation: Ghent University
Country: Belgium

Publications

  1. doi request reprint Target enrichment using parallel nanoliter quantitative PCR amplification
    Bram De Wilde
    Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
    BMC Genomics 15:184. 2014
  2. pmc Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas
    Frank Westermann
    Department of Tumor Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
    Genome Biol 9:R150. 2008
  3. pmc Selection of reference genes for quantitative real-time PCR in equine in vivo and fresh and frozen-thawed in vitro blastocysts
    Katrien Smits
    Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
    BMC Res Notes 2:246. 2009
  4. pmc Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans
    David Hoogewijs
    Department of Biology and Center for Molecular Phylogeny and Evolution, Ghent University, B 9000 Ghent, Belgium
    BMC Mol Biol 9:9. 2008
  5. pmc A dual fluorescent multiprobe assay for prion protein genotyping in sheep
    Mario Van Poucke
    Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B 9820 Merelbeke, Belgium
    BMC Infect Dis 5:13. 2005
  6. pmc Differential mucosal expression of Th17-related genes between the inflamed colon and ileum of patients with inflammatory bowel disease
    Sara Bogaert
    Department of Gastroenterology, Ghent University, Ghent, Belgium
    BMC Immunol 11:61. 2010
  7. pmc Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos
    Karen Goossens
    Department of Animal Nutrition, Genetics, Breeding and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B 9820 Merelbeke, Belgium
    BMC Dev Biol 5:27. 2005
  8. pmc Quantitative real time polymerase chain reaction for measurement of human interleukin-5 receptor alpha spliced isoforms mRNA
    Claudina Pérez
    Faculty of Medicine and Health Sciences, Department of Otorhynolaringology, Ghent University Hospital De Pintelaan 185, 9000 Ghent, Belgium
    BMC Biotechnol 3:17. 2003
  9. pmc Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline
    Joachim M De Schrijver
    Laboratory for Bioinformatics and Computational Genomics, Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium
    BMC Bioinformatics 11:269. 2010
  10. ncbi request reprint Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma
    Jo Vandesompele
    Center for Medical Genetics Ghent CMGG, Ghent University Hospital, MRB, De Pintelaan 185, B 9000 Ghent, Belgium
    J Clin Oncol 23:2280-99. 2005

Detail Information

Publications102 found, 100 shown here

  1. doi request reprint Target enrichment using parallel nanoliter quantitative PCR amplification
    Bram De Wilde
    Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
    BMC Genomics 15:184. 2014
    ..The need for well validated, high quality enrichment platforms to complement the bench-top next generation sequencing devices is high...
  2. pmc Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas
    Frank Westermann
    Department of Tumor Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
    Genome Biol 9:R150. 2008
    ..In this study, we asked whether distinct transcriptional MYCN or c-MYC activities are associated with specific neuroblastoma phenotypes...
  3. pmc Selection of reference genes for quantitative real-time PCR in equine in vivo and fresh and frozen-thawed in vitro blastocysts
    Katrien Smits
    Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
    BMC Res Notes 2:246. 2009
    ..In this study a set of reliable reference genes was identified for equine in vivo and fresh and frozen-thawed in vitro embryos...
  4. pmc Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans
    David Hoogewijs
    Department of Biology and Center for Molecular Phylogeny and Evolution, Ghent University, B 9000 Ghent, Belgium
    BMC Mol Biol 9:9. 2008
    ..The aim of this study was to establish a reliable set of reference genes for gene expression analysis in C. elegans...
  5. pmc A dual fluorescent multiprobe assay for prion protein genotyping in sheep
    Mario Van Poucke
    Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B 9820 Merelbeke, Belgium
    BMC Infect Dis 5:13. 2005
    ....
  6. pmc Differential mucosal expression of Th17-related genes between the inflamed colon and ileum of patients with inflammatory bowel disease
    Sara Bogaert
    Department of Gastroenterology, Ghent University, Ghent, Belgium
    BMC Immunol 11:61. 2010
    ..Inflammation was quantified by measuring expression of the inflammatory mediators IL8 and TNF...
  7. pmc Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos
    Karen Goossens
    Department of Animal Nutrition, Genetics, Breeding and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B 9820 Merelbeke, Belgium
    BMC Dev Biol 5:27. 2005
    ..Normalization of the data using unstable controls can result in erroneous conclusions, especially when only one reference gene is used...
  8. pmc Quantitative real time polymerase chain reaction for measurement of human interleukin-5 receptor alpha spliced isoforms mRNA
    Claudina Pérez
    Faculty of Medicine and Health Sciences, Department of Otorhynolaringology, Ghent University Hospital De Pintelaan 185, 9000 Ghent, Belgium
    BMC Biotechnol 3:17. 2003
    ..The aim of this study was to develop a reliable and sensitive real-time quantitative PCR assay to analyse the expression level of each isoform...
  9. pmc Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline
    Joachim M De Schrijver
    Laboratory for Bioinformatics and Computational Genomics, Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium
    BMC Bioinformatics 11:269. 2010
    ..Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions...
  10. ncbi request reprint Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma
    Jo Vandesompele
    Center for Medical Genetics Ghent CMGG, Ghent University Hospital, MRB, De Pintelaan 185, B 9000 Ghent, Belgium
    J Clin Oncol 23:2280-99. 2005
    ..In this study, we aimed for comprehensive genetic subgroup discovery and assessment of independent prognostic markers based on genome-wide aberrations detected by comparative genomic hybridization (CGH)...
  11. ncbi request reprint High resolution tiling-path BAC array deletion mapping suggests commonly involved 3p21-p22 tumor suppressor genes in neuroblastoma and more frequent tumors
    Jasmien Hoebeeck
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Int J Cancer 120:533-8. 2007
    ..3 in more frequent tumors including lung and breast cancer. As such, similar tumor suppressor genes may play a critical role in development or progression of a variety of neoplasms, including neuroblastoma...
  12. pmc Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
    BMC Genomics 5:11. 2004
    ..In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes...
  13. pmc Positional and functional mapping of a neuroblastoma differentiation gene on chromosome 11
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B 9000 Ghent, Belgium
    BMC Genomics 6:97. 2005
    ..We decided to further exploit this model system as a means to identify candidate tumour suppressor or differentiation genes located on chromosome 11...
  14. pmc CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23
    Evi Michels
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    BMC Cancer 8:173. 2008
    ..Despite intensive mapping efforts to localize the culprit 11q tumour suppressor gene, this search has been unsuccessful thus far as no sufficiently small critical region could be delineated for selection of candidate genes...
  15. doi request reprint Chromosome 3p microsatellite allelotyping in neuroblastoma: a report on the technical hurdles
    Jasmien Hoebeeck
    Center for Medical Genetics, Ghent University Hospital, Belgium
    Cancer Invest 27:857-68. 2009
    ..To provide functional support for the implication of 3p tumor suppressor genes in this childhood malignancy, we performed a microcell-mediated chromosome 3 transfer in neuroblastoma cells...
  16. pmc Molecular dissection of isolated disease features in mosaic neurofibromatosis type 1
    Ophélia Maertens
    Center for Medical Genetics, Department of Dermatology, Ghent University Hospital, Ghent, Belgium
    Am J Hum Genet 81:243-51. 2007
    ....
  17. pmc methBLAST and methPrimerDB: web-tools for PCR based methylation analysis
    Filip Pattyn
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
    BMC Bioinformatics 7:496. 2006
    ..Consequently, standard BLAST sequence homology searches cannot be applied to search for specific methylation primers...
  18. doi request reprint Aberrant methylation of candidate tumor suppressor genes in neuroblastoma
    Jasmien Hoebeeck
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Cancer Lett 273:336-46. 2009
    ....
  19. pmc Regulatory microRNA network identification in bovine blastocyst development
    Karen Goossens
    Department of Nutrition, Genetics and Ethology, Ghent University, Merelbeke, Belgium
    Stem Cells Dev 22:1907-20. 2013
    ..The results of this study expand our knowledge about the miRNA signature of the bovine blastocyst and of the interactions between miRNAs and cell fate regulating transcription factors...
  20. pmc Cancer gene prioritization for targeted resequencing using FitSNP scores
    Annelies Fieuw
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    PLoS ONE 7:e31333. 2012
    ..In this study, a successful strategy for prioritizing candidate genes for targeted resequencing of cancer genomes is presented...
  21. pmc A constitutional translocation t(1;17)(p36.2;q11.2) in a neuroblastoma patient disrupts the human NBPF1 and ACCN1 genes
    Karl Vandepoele
    Department for Molecular Biomedical Research, VIB, Ghent, Belgium
    PLoS ONE 3:e2207. 2008
    ..The disruption of both NBPF1 and ACCN1 genes in this neuroblastoma patient indicates that these genes might suppress development of neuroblastoma and possibly other tumor types...
  22. ncbi request reprint The von Hippel-Lindau tumor suppressor gene expression level has prognostic value in neuroblastoma
    Jasmien Hoebeeck
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Int J Cancer 119:624-9. 2006
    ....
  23. ncbi request reprint Real-time quantitative PCR as an alternative to Southern blot or fluorescence in situ hybridization for detection of gene copy number changes
    Jasmien Hoebeeck
    Center for Medical Genetics, Ghent University Hospital, Belgium
    Methods Mol Biol 353:205-26. 2007
    ..We illustrate the approach by describing a validated assay for the detection of germline VHL exon deletions and for determination of MYCN copy numbers in tumor samples...
  24. ncbi request reprint ArrayCGH-based classification of neuroblastoma into genomic subgroups
    Evi Michels
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Genes Chromosomes Cancer 46:1098-108. 2007
    ..Further multicentric studies on large tumor series are warranted in order to improve therapeutic stratification in conjunction with other features such as age at diagnosis, tumor stage, and gene expression signatures...
  25. pmc Identification and expression analysis of genes associated with bovine blastocyst formation
    Karen Goossens
    Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
    BMC Dev Biol 7:64. 2007
    ..This information could lead to improvements of in vitro embryo production procedures...
  26. doi request reprint Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis
    Frauke Coppieters
    Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
    Genet Med 14:576-85. 2012
    ..Here, we developed a comprehensive molecular test for LCA based on targeted MPS of all exons of 16 known LCA genes...
  27. ncbi request reprint Translocation-excision-deletion-amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1
    Nadine Van Roy
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Genes Chromosomes Cancer 45:107-17. 2006
    ..Furthermore, it illustrates the power of presently available tools for detailed analysis of the complex rearrangements that accompany amplicon formation...
  28. pmc Focal DNA copy number changes in neuroblastoma target MYCN regulated genes
    Candy Kumps
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    PLoS ONE 8:e52321. 2013
    ....
  29. doi request reprint Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma
    Sara De Brouwer
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Int J Cancer 130:2591-8. 2012
    ..The strict MYCN-mediated regulation of DKK3 is suggestive for an important downstream function of the MYCN protein and thus warrants further investigations to unravel the role of DKK3 in NB...
  30. doi request reprint miRNA expression profiling enables risk stratification in archived and fresh neuroblastoma tumor samples
    Katleen De Preter
    Center for Medical Genetics Department of Paediatric Hematology and Oncology, Ghent University Hospital, Ghent, Belgium
    Clin Cancer Res 17:7684-92. 2011
    ..In this study, we aimed to establish and validate a prognostic miRNA signature for children with NB and tested it in both fresh frozen and archived formalin-fixed paraffin-embedded (FFPE) samples...
  31. doi request reprint Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas
    Annelies Fieuw
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Int J Cancer 130:2599-606. 2012
    ....
  32. pmc arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays
    Bjorn Menten
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    BMC Bioinformatics 6:124. 2005
    ..One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment...
  33. doi request reprint Meta-mining of neuroblastoma and neuroblast gene expression profiles reveals candidate therapeutic compounds
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Clin Cancer Res 15:3690-6. 2009
    ..In this study, we aimed to identify new treatment options for neuroblastoma based on integrative genomic analysis...
  34. pmc External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data
    Joelle Vermeulen
    Center for Medical Genetics, Ghent University Hospital, Belgium
    Nucleic Acids Res 37:e138. 2009
    ....
  35. pmc The microRNA body map: dissecting microRNA function through integrative genomics
    Pieter Mestdagh
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium and Life Technologies, Foster City, CA, USA
    Nucleic Acids Res 39:e136. 2011
    ..The miRNA bodymap project provides users with a single one-stop data-mining solution and has great potential to become a community resource...
  36. pmc Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan, B 9000 Ghent, Belgium
    Genome Biol 7:R84. 2006
    ..This study provides the first genome-wide mRNA expression profile of these human fetal sympathetic neuroblasts. To this purpose, small islets of normal neuroblasts were isolated by laser microdissection from human fetal adrenal glands...
  37. ncbi request reprint Real-time quantitative allele discrimination assay using 3' locked nucleic acid primers for detection of low-percentage mosaic mutations
    Ophélia Maertens
    Center for Medical Genetics, Ghent University Hospital, B 9000 Ghent, Belgium
    Anal Biochem 359:144-6. 2006
  38. ncbi request reprint Comprehensive NF1 screening on cultured Schwann cells from neurofibromas
    Ophélia Maertens
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Hum Mutat 27:1030-40. 2006
    ..41/81). Differences in somatic inactivation mechanism might therefore exist between NF1 microdeletion patients and the general NF1 population...
  39. doi request reprint Comparison of miRNA profiles of microdissected Hodgkin/Reed-Sternberg cells and Hodgkin cell lines versus CD77+ B-cells reveals a distinct subset of differentially expressed miRNAs
    Pieter Van Vlierberghe
    Centre for Medical Genetics CMGG, Ghent University Hospital, Ghent, Belgium
    Br J Haematol 147:686-90. 2009
    ..Our data suggest that miRNAs are implicated in the pathogenesis of Hodgkin lymphoma and prompt further investigations concerning their role in cHL...
  40. ncbi request reprint methGraph: a genome visualization tool for PCR-based methylation assays
    Steve Lefever
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Epigenetics 5:159-63. 2010
    ..The generated high-quality figures can easily be customized and exported for use in publications or presentations. methGraph is available at http://mellfire.ugent.be/methgraph/...
  41. pmc RTPrimerDB: the real-time PCR primer and probe database, major update 2006
    Filip Pattyn
    Center for Medical Genetics Ghent CMGG, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
    Nucleic Acids Res 34:D684-8. 2006
    ....
  42. ncbi request reprint Identification of 2 putative critical segments of 17q gain in neuroblastoma through integrative genomics
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Int J Cancer 122:1177-82. 2008
    ..e. a region on 17q21.32 immediately distal to the most distal breakpoint (in cases with single regions of gain) and 17q24.1, a region coinciding with breakpoints leading to superimposed gain...
  43. doi request reprint Meta-analysis of neuroblastomas reveals a skewed ALK mutation spectrum in tumors with MYCN amplification
    Sara De Brouwer
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Clin Cancer Res 16:4353-62. 2010
    ..We carried out a meta-analysis of 709 neuroblastoma tumors to determine their frequency and mutation spectrum in relation to genomic and clinical parameters, and studied the prognostic significance of ALK copy number and expression...
  44. pmc High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA
    Pieter Mestdagh
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Nucleic Acids Res 36:e143. 2008
    ..The high specificity of RT-qPCR together with a superior sensitivity makes this approach the method of choice for high-throughput miRNA expression profiling...
  45. ncbi request reprint Small-molecule MDM2 antagonists as a new therapy concept for neuroblastoma
    Tom Van Maerken
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Cancer Res 66:9646-55. 2006
    ..The observed treatment effects without the need of imposing a genotoxic burden suggest that selective MDM2 antagonists might be beneficial for treatment of neuroblastoma patients with and without MYCN amplification...
  46. ncbi request reprint Identification of an unbalanced X-autosome translocation by array CGH in a boy with a syndromic form of chondrodysplasia punctata brachytelephalangic type
    Bjorn Menten
    Centre for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    Eur J Med Genet 48:301-9. 2005
    ..This study confirms the power of array CGH in the detection of subtle or submicroscopic chromosomal changes...
  47. doi request reprint Antitumor activity of the selective MDM2 antagonist nutlin-3 against chemoresistant neuroblastoma with wild-type p53
    Tom Van Maerken
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    J Natl Cancer Inst 101:1562-74. 2009
    ..Mutational inactivation of p53 is rare in neuroblastoma tumors at diagnosis and occurs in only a subset of multidrug-resistant neuroblastomas...
  48. pmc Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    Nucleic Acids Res 36:e43. 2008
    ..esat.kuleuven.be/~bioiuser/pge). We validated PGE on published lists of differentially expressed genes. These analyses showed significant overrepresentation of known aberrant chromosomal regions...
  49. doi request reprint Functional analysis of the p53 pathway in neuroblastoma cells using the small-molecule MDM2 antagonist nutlin-3
    Tom Van Maerken
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    Mol Cancer Ther 10:983-93. 2011
    ..These insights may prove useful for the clinical translation of evolving strategies aimed at p53 reactivation and for the development of new therapeutic approaches...
  50. pmc No evidence for involvement of SDHD in neuroblastoma pathogenesis
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital, K5, De Pintelaan 185, B 9000 Ghent, Belgium
    BMC Cancer 4:55. 2004
    ..In this study, we sought for evidence for involvement of SDHD in neuroblastoma...
  51. ncbi request reprint Rapid detection of VHL exon deletions using real-time quantitative PCR
    Jasmien Hoebeeck
    Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Lab Invest 85:24-33. 2005
    ..5 h), accurate and sensitive (ng amount of input DNA) exon deletion screening in routine DNA diagnosis of VHL disease. Similar assays can be designed for deletion screening in other genetic disorders...
  52. ncbi request reprint Application of laser capture microdissection in genetic analysis of neuroblastoma and neuroblastoma precursor cells
    Katleen De Preter
    Department of Medical Genetics, Ghent University Hospital, 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
    Cancer Lett 197:53-61. 2003
    ....
  53. pmc N-cadherin in neuroblastoma disease: expression and clinical significance
    Tim Lammens
    Department of Pediatric Hematology Oncology, Ghent University Hospital, Ghent, Belgium
    PLoS ONE 7:e31206. 2012
    ..Our results suggest that N-cadherin signaling may play a role in neuroblastoma disease, marking involvement of metastasis and determining neuroblastoma cell viability...
  54. pmc A novel and universal method for microRNA RT-qPCR data normalization
    Pieter Mestdagh
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent, Belgium
    Genome Biol 10:R64. 2009
    ..We demonstrate that the mean expression value outperforms the current normalization strategy in terms of better reduction of technical variation and more accurate appreciation of biological changes...
  55. ncbi request reprint EVI1 is consistently expressed as principal transcript in common and rare recurrent 3q26 rearrangements
    Bruce Poppe
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Genes Chromosomes Cancer 45:349-56. 2006
    ..Our results underscore the feasibility of FISH as an adjunct to PCR for the identification of EVI1 deranged leukemias and identified EVI1 as the principal transcript expressed in these malignancies...
  56. doi request reprint Improved molecular diagnostics of idiopathic short stature and allied disorders: quantitative polymerase chain reaction-based copy number profiling of SHOX and pseudoautosomal region 1
    Barbara D'haene
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    J Clin Endocrinol Metab 95:3010-8. 2010
    ..Deletions spanning or surrounding the SHOX gene account for a significant proportion of patients with idiopathic short stature (ISS) and allied disorders, such as Leri-Weill dyschondrosteosis...
  57. pmc Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study
    Joelle Vermeulen
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Lancet Oncol 10:663-71. 2009
    ..More accurate prognostic assessment of patients with neuroblastoma is required to better inform the choice of risk-related therapy. The aim of this study is to develop and validate a gene-expression signature to improve outcome prediction...
  58. pmc Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
    Genome Biol 3:RESEARCH0034. 2002
    ....
  59. doi request reprint Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma
    Katleen De Preter
    Center for Medical Genetics Ghent, Ghent University Hospital, 2nd Floor, Room 120 038, De Pintelaan 185, MRB2, 9000 Ghent, Belgium
    Cancer Lett 269:111-6. 2008
    ..The mini-arrays were validated on neuroblastoma samples and comparison with high-resolution whole-genome arrayCGH data yielded complete concordant results...
  60. pmc RTPrimerDB: the portal for real-time PCR primers and probes
    Steve Lefever
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Gent, Belgium
    Nucleic Acids Res 37:D942-5. 2009
    ..RTPrimerDB is a one-stop portal for high-quality and highly annotated real-time PCR assays...
  61. pmc Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics
    Kim De Leeneer
    Center for Medical Genetics, Ghent University, Ghent, Belgium
    PLoS ONE 6:e25531. 2011
    ....
  62. doi request reprint Whole-genome RT-qPCR microRNA expression profiling
    Pieter Mestdagh
    Center for Medical Genetics, Ghent University, De Pintelaan 185, Ghent 9000, Belgium
    Methods Mol Biol 815:121-30. 2012
    ..Owing to their small size (20-22 nucleotides), accurate quantification of miRNA expression is particularly challenging. In this chapter, we present different RT-qPCR technologies that enable whole genome miRNA expression quantification...
  63. pmc qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
    Jan Hellemans
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan, B 9000 Ghent, Belgium
    Genome Biol 8:R19. 2007
    ..These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data...
  64. pmc Measurable impact of RNA quality on gene expression results from quantitative PCR
    Joelle Vermeulen
    Centre for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    Nucleic Acids Res 39:e63. 2011
    ..This study forms the basis for further rational assessment of reverse transcription quantitative PCR based results in relation to RNA quality...
  65. ncbi request reprint ID2 expression in neuroblastoma does not correlate to MYCN levels and lacks prognostic value
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital, Belgium
    Oncogene 22:456-60. 2003
    ..Importantly, we could not confirm the reported prognostic power of ID2-expression in neuroblastoma. These data, obtained in two independent laboratories, challenge the previously proposed ID2-MYCN relation...
  66. pmc Report of a female patient with mental retardation and tall stature due to a chromosomal rearrangement disrupting the OPHN1 gene on Xq12
    Bjorn Menten
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Eur J Med Genet 50:446-54. 2007
    ..3 breakpoint was assigned to a non-coding segment within a gene dense region. Disruption of OPHN1 by the Xq12 breakpoint was considered the major cause of the abnormal phenotype observed in the proband...
  67. pmc Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform
    Sarah De Keulenaer
    NXTGNT, Ghent University, Ghent, Belgium
    BMC Med Genomics 5:17. 2012
    ..In this study we used a semi-automated PCR amplification and NGS in order to combine high sensitivity, speed and cost efficiency...
  68. doi request reprint Identification of miR-145 as a key regulator of the pigmentary process
    Peter Dynoodt
    Department of Dermatology, Ghent University Hospital, Ghent, Belgium
    J Invest Dermatol 133:201-9. 2013
    ..The significant down- or upregulation of major pigmentation genes, after modulating miR-145 expression, suggests a key role for miR-145 in regulating melanogenesis...
  69. pmc Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A
    Tim Erkens
    Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
    BMC Biotechnol 6:41. 2006
    ....
  70. doi request reprint How to do successful gene expression analysis using real-time PCR
    Stefaan Derveaux
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Methods 50:227-30. 2010
    ....
  71. pmc The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy
    Nadine Van Roy
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B 9000 Ghent, Belgium
    Genome Med 1:74. 2009
    ..The recent successes in unraveling the genetic basis of neuroblastoma are now opening opportunities for development of targeted therapies...
  72. doi request reprint Accurate outcome prediction in neuroblastoma across independent data sets using a multigene signature
    Katleen De Preter
    Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
    Clin Cancer Res 16:1532-41. 2010
    ..Although numerous studies have shown that outcome might be predicted using gene expression signatures, independent cross-platform validation is often lacking...
  73. ncbi request reprint Gene-expression profiling reveals distinct expression patterns for Classic versus Variant Merkel cell phenotypes and new classifier genes to distinguish Merkel cell from small-cell lung carcinoma
    Mireille Van Gele
    Center for Medical Genetics, Ghent University Hospital, Ghent B 9000, Belgium
    Oncogene 23:2732-42. 2004
    ..Real-time quantitative RT-PCR analysis of these genes on 26 additional MCC and SCLC samples confirmed their diagnostic classification potential, opening opportunities for new investigations into these aggressive cancers...
  74. pmc Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma
    Candy Kumps
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    BMC Genomics 11:298. 2010
    ..Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors...
  75. pmc RDML: structured language and reporting guidelines for real-time quantitative PCR data
    Steve Lefever
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Nucleic Acids Res 37:2065-9. 2009
    ..We here also propose data related guidelines as a subset of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to guarantee inclusion of key data information when reporting experimental results...
  76. ncbi request reprint Evidence for involvement of a tumor suppressor gene on 1p in malignant peripheral nerve sheath tumors
    Nadine Van Roy
    Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Cancer Genet Cytogenet 143:120-4. 2003
    ..These findings together with data from the literature suggest that loss of a tumor suppressor gene located within distal 1p is implicated in the pathogenesis of MPNST...
  77. ncbi request reprint Predicting outcomes for children with neuroblastoma
    Joelle Vermeulen
    Center for Medical Genetics, Ghent University Hospital, Ghent, B 9000, Belgium
    Discov Med 10:29-36. 2010
    ..Various studies have put forward new prognostic markers, including copy number aberrations, gene expression signatures, and epigenetic markers...
  78. doi request reprint MicroRNA expression in induced sputum of smokers and patients with chronic obstructive pulmonary disease
    Geert R Van Pottelberge
    Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
    Am J Respir Crit Care Med 183:898-906. 2011
    ..MicroRNAs (miRNAs) have the ability to regulate these processes by interfering with gene transcription and translation...
  79. ncbi request reprint The human FOXL2 mutation database
    Diane Beysen
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Hum Mutat 24:189-93. 2004
    ..Moreover, it will allow us to establish more accurate genotype-phenotype correlations, since clinical information is contained in the database...
  80. ncbi request reprint Elimination of primer-dimer artifacts and genomic coamplification using a two-step SYBR green I real-time RT-PCR
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital, B 9000 Ghent, Belgium
    Anal Biochem 303:95-8. 2002
  81. ncbi request reprint Localization of the 17q breakpoint of a constitutional 1;17 translocation in a patient with neuroblastoma within a 25-kb segment located between the ACCN1 and TLK2 genes and near the distal breakpoints of two microdeletions in neurofibromatosis type 1 pat
    Nadine Van Roy
    Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Genes Chromosomes Cancer 35:113-20. 2002
    ....
  82. pmc RTPrimerDB: the real-time PCR primer and probe database
    Filip Pattyn
    Centre for Medical Genetics, Gent University Hospital, 1K5, De Pintelaan 185, B 9000 Gent, Belgium
    Nucleic Acids Res 31:122-3. 2003
    ..Real-time PCR primer/probe records are available at http://www.realtimeprimerdatabase.ht.st...
  83. doi request reprint Neuroblastoma genetics and phenotype: a tale of heterogeneity
    Frank Speleman
    Center for Medical Genetics, Ghent University Hospital MRB, De Pintelaan 185, B 9000 Ghent, Belgium
    Semin Cancer Biol 21:238-44. 2011
    ..Here we will summarize the current state-of-the-art of these studies with focus on genome wide DNA copy number and gene expression analyses in relation to the relevance for present and future clinical management of NB patients...
  84. ncbi request reprint Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay
    Katleen De Preter
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Mod Pathol 15:159-66. 2002
    ..In addition to MYCN copy number evaluation, DDX1 and NAG gene copy numbers were determined using a similar Q-PCR strategy. Survival analysis pointed out that DDX1 and/or NAG amplification has no additional adverse effect on prognosis...
  85. doi request reprint Accurate and objective copy number profiling using real-time quantitative PCR
    Barbara D'haene
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Methods 50:262-70. 2010
    ..The provided guidelines will most certainly improve the quality and reliability of your qPCR-based copy number screening...
  86. ncbi request reprint Impact of RNA quality on reference gene expression stability
    Claudina Angela Perez-Novo
    Department of Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
    Biotechniques 39:52, 54, 56. 2005
  87. ncbi request reprint Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis
    Jan Hellemans
    Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
    Nat Genet 36:1213-8. 2004
    ..XMAN1, the Xenopus laevis ortholog, antagonizes BMP signaling during embryogenesis. In this study, LEMD3 interacted with BMP and activin-TGFbeta receptor-activated Smads and antagonized both signaling pathways in human cells...
  88. ncbi request reprint Potential application of ELAVL4 real-time quantitative reverse transcription-PCR for detection of disseminated neuroblastoma cells
    Katrien Swerts
    Department of Pediatric Hematology and Oncology, Ghent University Hospital, Ghent, Belgium
    Clin Chem 52:438-45. 2006
    ..Standard cytomorphologic examination of BM aspirates is sensitive enough to detect single tumor cells. Consequently, more sensitive and specific detection methods are indispensable...
  89. doi request reprint Positive correlation between relative mRNA expression of PRNP and SPRN in cerebral and cerebellar cortex of sheep
    Evelyne Lampo
    Department of Nutrition, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B 9820 Merelbeke, Belgium
    Mol Cell Probes 23:60-4. 2009
    ..0001) and cerebellum (p<0.001). This positive correlation might indicate co-regulation between these genes. Further investigation on the causal nature of this correlation may provide new insights into prion pathogenesis...
  90. ncbi request reprint Quantification of NF1 transcripts reveals novel highly expressed splice variants
    Ina Vandenbroucke
    Centre for Medical Genetics, Ghent University Hospital 0K5, De Pintelaan 185, Belgium
    FEBS Lett 522:71-6. 2002
    ..NF1-DeltaE43 lacks a nuclear targeting sequence and might be functionally different from full-length NF1. These novel NF1 splice variants might expand our understanding of the role of neurofibromin...
  91. ncbi request reprint Pathological splice mutations outside the invariant AG/GT splice sites of BRCA1 exon 5 increase alternative transcript levels in the 5' end of the BRCA1 gene
    Kathleen Claes
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent, Belgium
    Oncogene 21:4171-5. 2002
    ..We hypothesize that disruption of alternative transcript ratios of BRCA1 may be a dominant mechanism affecting predisposition to hereditary breast and/or ovarian cancer...
  92. ncbi request reprint No evidence for correlation of DDX1 gene amplification with improved survival probability in patients with MYCN-amplified neuroblastomas
    Katleen De Preter
    J Clin Oncol 23:3167-8; author reply 3168-70. 2005
  93. ncbi request reprint Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome
    Alexander Schramm
    Division of Hematology and Oncology, University Children s Hospital Essen, Essen, Germany
    Clin Cancer Res 13:1459-65. 2007
    ..To assess the feasibility of predicting neuroblastoma outcome using highly parallel quantitative real-time PCR data...
  94. ncbi request reprint Expression analyses identify MLL as a prominent target of 11q23 amplification and support an etiologic role for MLL gain of function in myeloid malignancies
    Bruce Poppe
    Centre for Medical Genetics, University Hospital Ghent, Belgium
    Blood 103:229-35. 2004
    ..In addition, our results indicate that the transcriptional program associated with MLL rearrangements and MLL overexpression displays significant similarities...
  95. ncbi request reprint A brief commentary on "Chromosomal aberrations in neuroblastoma cell lines identified by cross species color banding and chromosome painting"
    Jo Vandesompele
    Cancer Genet Cytogenet 135:196. 2002
  96. ncbi request reprint Neuroblastoma cells with overexpressed MYCN retain their capacity to undergo neuronal differentiation
    Anders Edsjö
    Department of Laboratory Medicine, Molecular Medicine, Lund University, University Hospital MAS, S 20502 Malmo, Sweden
    Lab Invest 84:406-17. 2004
    ....
  97. ncbi request reprint Aberrant splicing of the PTPRD gene mimics microdeletions identified at this locus in neuroblastomas
    Prakash Nair
    Department of Pediatrics, Greehey Children s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
    Genes Chromosomes Cancer 47:197-202. 2008
    ....
  98. ncbi request reprint Expression profiling suggests underexpression of the GABA(A) receptor subunit delta in the fragile X knockout mouse model
    Ilse Gantois
    Department of Medical Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
    Neurobiol Dis 21:346-57. 2006
    ..We consider their differential expression as provisional. It is possible that these differentially expressed genes play an important role in the cognitive and behavioral problems observed in the fragile X syndrome...
  99. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  100. ncbi request reprint Rapid and easy prenatal diagnosis of sickle cell anemia using double-dye LNA probe technology
    Hakim E Housni
    Br J Haematol 136:509-10. 2007
  101. doi request reprint Standardization of real-time PCR gene expression data from independent biological replicates
    Erik Willems
    Del E Webb Neuroscience, Aging, and Stem Cell Research Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    Anal Biochem 379:127-9. 2008
    ....