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Dive into the research topics where Sarah Vergult is active.

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Featured researches published by Sarah Vergult.


Nature Methods | 2013

The need for transparency and good practices in the qPCR literature

Stephen A. Bustin; Vladimir Benes; Jeremy A. Garson; Jan Hellemans; Jim F. Huggett; Mikael Kubista; Reinhold Mueller; Tania Nolan; Michael W. Pfaffl; Gregory L. Shipley; Carl T. Wittwer; Peter Schjerling; Philip J. R. Day; Mónica Abreu; Begoña Aguado; Jean-François Beaulieu; Anneleen Beckers; Sara Bogaert; John A. Browne; Fernando Carrasco-Ramiro; Liesbeth Ceelen; Kate L. Ciborowski; Pieter Cornillie; Stephanie Coulon; Ann Cuypers; Sara De Brouwer; Leentje De Ceuninck; Jurgen De Craene; Hélène De Naeyer; Ward De Spiegelaere

Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.


American Journal of Human Genetics | 2014

Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems.

Anneke T. Vulto-van Silfhout; Shivakumar Rajamanickam; Philip J. Jensik; Sarah Vergult; Nina De Rocker; Kathryn J. Newhall; Ramya Raghavan; Sara N. Reardon; Kelsey Jarrett; Tara McIntyre; Joseph Bulinski; Stacy L. Ownby; Jodi I. Huggenvik; G. Stanley McKnight; Gregory M. Rose; Xiang Cai; Andy Willaert; Christiane Zweier; Sabine Endele; Joep de Ligt; Bregje W.M. van Bon; Dorien Lugtenberg; Petra de Vries; Joris A. Veltman; Hans van Bokhoven; Han G. Brunner; Anita Rauch; Arjan P.M. de Brouwer; Gemma L. Carvill; Alexander Hoischen

Recently, we identified in two individuals with intellectual disability (ID) different de novo mutations in DEAF1, which encodes a transcription factor with an important role in embryonic development. To ascertain whether these mutations in DEAF1 are causative for the ID phenotype, we performed targeted resequencing of DEAF1 in an additional cohort of over 2,300 individuals with unexplained ID and identified two additional individuals with de novo mutations in this gene. All four individuals had severe ID with severely affected speech development, and three showed severe behavioral problems. DEAF1 is highly expressed in the CNS, especially during early embryonic development. All four mutations were missense mutations affecting the SAND domain of DEAF1. Altered DEAF1 harboring any of the four amino acid changes showed impaired transcriptional regulation of the DEAF1 promoter. Moreover, behavioral studies in mice with a conditional knockout of Deaf1 in the brain showed memory deficits and increased anxiety-like behavior. Our results demonstrate that mutations in DEAF1 cause ID and behavioral problems, most likely as a result of impaired transcriptional regulation by DEAF1.


Human Mutation | 2015

Two Siblings with Homozygous Pathogenic Splice‐Site Variant in Mitochondrial Asparaginyl–tRNA Synthetase (NARS2)

Arnaud Vanlander; Björn Menten; Joél Smet; Linda De Meirleir; Tom Sante; Boel De Paepe; Sara Seneca; Sarah F. Pearce; Christopher A. Powell; Sarah Vergult; Alex Michotte; Elien De Latter; Lies Vantomme; Michal Minczuk; Rudy Van Coster

A homozygous missense mutation (c.822G>C) was found in the gene encoding the mitochondrial asparaginyl–tRNA synthetase (NARS2) in two siblings born to consanguineous parents. These siblings presented with different phenotypes: one had mild intellectual disability and epilepsy in childhood, whereas the other had severe myopathy. Biochemical analysis of the oxidative phosphorylation (OXPHOS) complexes in both siblings revealed a combined complex I and IV deficiency in skeletal muscle. In‐gel activity staining after blue native‐polyacrylamide gel electrophoresis confirmed the decreased activity of complex I and IV, and, in addition, showed the presence of complex V subcomplexes. Considering the consanguineous descent, homozygosity mapping and whole‐exome sequencing were combined revealing the presence of one single missense mutation in the shared homozygous region. The c.822G>C variant affects the 3′ splice site of exon 7, leading to skipping of the whole exon 7 and a part of exon 8 in the NARS2 mRNA. In EBV‐transformed lymphoblasts, a specific decrease in the amount of charged mt‐tRNAAsn was demonstrated as compared with controls. This confirmed the pathogenic nature of the variant. To conclude, the reported variant in NARS2 results in a combined OXPHOS complex deficiency involving complex I and IV, making NARS2 a new member of disease‐associated aaRS2.


Human Reproduction | 2012

Array comparative genomic hybridization in male infertility

Katrien Stouffs; D. Vandermaelen; A Massart; Björn Menten; Sarah Vergult; Herman Tournaye; Willy Lissens

BACKGROUND Male infertility caused by a maturation arrest of spermatogenesis is a condition with an abrupt stop in spermatogenesis, mostly at the level of primary spermatocytes. The etiology remains largely unknown. METHODS We focused on patients with a complete arrest at the spermatocyte level (n = 9) and used array comparative genomic hybridization to screen for deletions or duplications that might be associated with maturation arrest. Interesting copy number variations (CNVs) were further examined by using quantitative PCR. Where appropriate, the expression pattern was analyzed in multiple human tissues including the testis. RESULTS A total of 227 CNVs were detected in the patient group. After the elimination of CNVs that were also present in the control group or that were not likely to be involved in male infertility, the remaining 11 regions were investigated more in detail. We first determined the expression pattern of seven genes, for which expression had not been reported to be investigated in testicular tissue, after which one region could be eliminated. Next, all 10 promising candidate regions were analyzed by quantitative PCR in a control population. CONCLUSIONS Eight deletions/duplications were absent in our control group, and therefore might be linked with the male infertility in our patients. One of these alterations, however, has been detected in a proven fertile father group. Further research is necessary to determine the relationship between the observed genomic alterations and maturation arrest of spermatogenesis. Furthermore, several of the above genes have not been studied at the functional level and consequently, more research is required to determine their role in spermatogenesis.


European Journal of Human Genetics | 2012

17q24.2 microdeletions: a new syndromal entity with intellectual disability, truncal obesity, mood swings and hallucinations

Sarah Vergult; Andrew Dauber; Barbara Delle Chiaie; Marleen Simon; Ali Rihani; Bart Loeys; Joel N. Hirschhorn; Jean Pfotenhauer; John A. Phillips; Shehla Mohammed; Caroline Mackie Ogilvie; John A. Crolla; Geert Mortier; Bjoern Menten

Although microdeletions of the long arm of chromosome 17 are being reported with increasing frequency, deletions of chromosome band 17q24.2 are rare. Here we report four patients with a microdeletion encompassing chromosome band 17q24.2 with a smallest region of overlap of 713 kb containing five Refseq genes and one miRNA. The patients share the phenotypic characteristics, such as intellectual disability (4/4), speech delay (4/4), truncal obesity (4/4), seizures (2/4), hearing loss (3/4) and a particular facial gestalt. Hallucinations and mood swings were also noted in two patients. The PRKCA gene is a very interesting candidate gene for many of the observed phenotypic features, as this gene plays an important role in many cellular processes. Deletion of this gene might explain the observed truncal obesity and could also account for the hallucinations and mood swings seen in two patients, whereas deletion of a CACNG gene cluster might be responsible for the seizures observed in two patients. In one of the patients, the PRKAR1A gene responsible for Carney Complex and the KCNJ2 gene causal for Andersen syndrome are deleted. This is the first report of a patient with a whole gene deletion of the KCNJ2 gene.


European Journal of Human Genetics | 2015

Genomic aberrations of the CACNA2D1 gene in three patients with epilepsy and intellectual disability

Sarah Vergult; Annelies Dheedene; Alfred Meurs; Franny Faes; Bertrand Isidor; Sandra Janssens; Agnès Gautier; Cédric Le Caignec; Björn Menten

Voltage-gated calcium channels have an important role in neurotransmission. Aberrations affecting genes encoding the alpha subunit of these channels have been associated with epilepsy and neuropsychiatric disorders such as autism or schizophrenia. Here we report three patients with a genomic aberration affecting the CACNA2D1 gene encoding the α2δ subunit of these voltage-gated calcium channels. All three patients present with epilepsy and intellectual disability pinpointing the CACNA2D1 gene as an interesting candidate gene for these clinical features. Besides these characteristics, patient 2 also presents with obesity with hyperinsulinism, which is very likely to be caused by deletion of the CD36 gene.


International Journal of Cancer | 2012

Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas

Annelies Fieuw; Candy Kumps; Alexander Schramm; Filip Pattyn; Björn Menten; Francesca Antonacci; Peter H. Sudmant; Johannes H. Schulte; N. Van Roy; Sarah Vergult; Patrick G. Buckley; A. De Paepe; Rosa Noguera; Rogier Versteeg; Raymond L. Stallings; Angelika Eggert; Jo Vandesompele; K. De Preter; Frank Speleman

Neuroblastoma is an aggressive embryonal tumor that accounts for ∼15% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p = 5.61 × 10−5). Using ultra‐high resolution (∼115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5‐kb region, of which eight were found in a 7‐kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4‐Mb proximal. The commonly deleted region contains one miRNA (hsa‐mir‐1537), four transcribed ultra conserved region elements (uc.43‐uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.


Scientific Reports | 2016

Identification of long non-coding RNAs involved in neuronal development and intellectual disability

Eva D’haene; Eva Jacobs; Pieter-Jan Volders; Tim De Meyer; Björn Menten; Sarah Vergult

Recently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.


PLOS ONE | 2014

ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation

Tom Sante; Sarah Vergult; Pieter-Jan Volders; Wigard P. Kloosterman; Geert Trooskens; Katleen De Preter; Annelies Dheedene; Franki Speleman; Tim De Meyer; Björn Menten

Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/


PLOS ONE | 2010

Identification of Two Critically Deleted Regions within Chromosome Segment 7q35-q36 in EVI1 Deregulated Myeloid Leukemia Cell Lines

An De Weer; Bruce Poppe; Sarah Vergult; Pieter Van Vlierberghe; Marjan Petrick; Robrecht De Bock; Yves Benoit; Lucien Noens; Anne De Paepe; Nadine Van Roy; Björn Menten; Franki Speleman

Chromosomal rearrangements involving the EVI1 proto-oncogene are a recurrent finding in myeloid leukemias and are indicative of a poor prognosis. Rearrangements of the EVI1 locus are often associated with monosomy 7 or cytogenetic detectable deletions of part of 7q. As EVI1 overexpression alone is not sufficient to induce leukemia, loss of a 7q tumour suppressor gene might be a required cooperating event. To test this hypothesis, we performed high-resolution array comparative genomic hybridization analysis of twelve EVI1 overexpressing patients and three EVI1 deregulated cell lines to search for 7q submicroscopic deletions. This analysis lead to the delineation of two critical regions, one of 0.39 Mb on 7q35 containing the CNTNAP2 gene and one of 1.33 Mb on chromosome bands 7q35–q36 comprising nine genes in EVI1 deregulated cell lines. These findings open the way to further studies aimed at identifying the culprit EVI1 implicated tumour suppressor genes on 7q.

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Björn Menten

Ghent University Hospital

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Eva Jacobs

Ghent University Hospital

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Eva D'haene

Ghent University Hospital

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Rudy Van Coster

Ghent University Hospital

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Joél Smet

Ghent University Hospital

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Elise Vantroys

Ghent University Hospital

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