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In de Wat met-reeks draait alles om hete hangijzers. De Wat met-reeks wil het maatschappelijke debat over belangrijke thema's die de mens raken op een kritische manier wetenschappelijk onderbouwen. De publicaties scheiden feiten van fictie, reiken de nodige voorgeschiedenis aan, wijzen ons op de dilemma's en bieden een duidelijk toekomstperspectief. Wat met genetica? Een snelle technische vooruitgang maakt dat een volledige analyse van iemands genoom vandaag nog slechts enkele duizenden euro's kost. En de prijs daalt verder. Dit gegeven heeft niet enkel een enorme impact op wetenschappelijk onderzoek en genetische diagnostiek. Het stelt ook de maatschappij voor nieuwe uitdagingen. - Hoeveel weten we? - Wie zullen we testen? - Wanneer is zo’n test echt nodig? - Hoe zal genoomonderzoek de gezondheidszorg beïnvloeden? - Waarom zal genoomonderzoek ook de maatschappij veranderen? De vooruitzichten zijn veelbelovend, maar hoe leiden we deze revolutie in goede banen? Wat met genetica? buigt zich over de plaats, het nut en de toekomst van genoomonderzoek. 1. Wat met genetica en genomica ? - 2. Hoeveel weten we (niet) ? - 3. Hoe zal genomica de gezondheidszorg veranderen ? 4. Hoe kunnen we genomica maatschappelijk inpassen ? - 5. Welke invloed zal genomica nog hebben ?

Genetics --- Genomics --- Forecasting --- Academic collection --- 061 Ethische problemen --- Genetica --- Genetisch onderzoek --- Provincie West-Vlaanderen --- Erfelijkheidsleer

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Chromosomal microarray analysis has gradually replaced conventional karyotyping over recent years in the postnatal setting which has revolutionized whole genome screening for genomic imbalances in patients. We sought to evaluate the benefits and the challenges of applying chromosomal microarrays to prenatal diagnosis for referrals with abnormal ultrasound findings. Our findings, presented in Chapter 3, demonstrate a diagnostic yield of ~10%. Importantly, ~3% are caused by submicroscopic CNVs which would go undetected by conventional karyotyping alone. Furthermore, the higher resolution offered by chromosomal microarray analysis led to important additional information in ~4% of patients. Of particular interest we discover a novel and unexpected advantage of arrays; a 500kb paternal insertional translocation is the likely driver of a de novo unbalanced translocation, thus improving recurrence risk calculation in this family. Our study has, in part, paved the way for the recent ‘Summary Guidelines for Prenatal Chromosomal Microarray Analysis and Genetic Counselling’ from the Belgian Society for Human Genetics [http://www.beshg.be/download/annex_2_summary_of_array_and_prenatal_guidelines_20130502.pdf]. The implementation of prenatal chromosomal microarray analysis as the first tier test in place of conventional karyotyping brings the standard of prenatal diagnosis in line with that which is provided for postnatal genetic diagnosis. Congenital diaphragmatic hernia (CDH) is a life-threatening prenatal disorder detectable by ultrasound during pregnancy. We sought to further unravel the genetic factors underlying isolated CDH by the design of a custom microarray covering genomic loci recurrently associated with CDH and candidate CDH genes. Our retrospective screen of 79 isolated CDH patients using this custom microarray is presented in Chapter 4. This study identified a novel duplication of the EFNB1 gene in a male patient which was considered likely to be pathogenic. Since our publication, a second case of a male CDH patient with duplication of EFNB1 was reported, thus reinforcing EFNB1 dosage sensitivity as a cause of isolated CDH. In order to further identify (novel) CNVs and genes associated with isolated CDH, we undertook a prospective prenatal study using chromosomal microarrays with genome-wide coverage in 75 foetuses with isolated CDH, which is presented in Chapter 4. This study revealed submicroscopic de novo pathogenic CNVs in 9.3% and rare inherited variants which may be involved in CDH in a further 4% of foetuses. This diagnostic yield is significantly higher than the ~3% rate of pathogenic submicroscopic CNVs which we observed in our prenatal study using the same microarray platform. Isolated CDH thus represents a valid cohort for CNV screening in the prenatal phase, and suggests that the clinical utility of conventional karyotyping is questionable for this group of patients. This study allowed us to further refine the critical region at 15q26 to only 2 genes, pinpointing NR2F2 as the causal gene. We add further evidence for the 15q25.2 and 16p11.2 recurrent microdeletions as CDH loci, and we identify novel CNVs not previously observed in association with CDH, including a duplication of 4p15.2-p14.We next evaluated the use of exome sequencing for the investigation of isolated CDH and non-isolated CDH where a genetic cause was suspected. Our results show that exome sequencing represents an effective technique with which to investigate familial CDH, described in Chapter 5. In the first family studied, we identified a nonsense mutation in ZFPM2 in 2 individuals with isolated CDH, as well as a sibling with a congenital heart defect. Surprisingly, the mutation was shown to be transmitted from the unaffected mother, and is also carried by the maternal grandfather and the maternal sister, both of whom are also asymptomatic. This intriguing finding highlights the complexity of CDH, reinforcing the involvement of additional as yet unidentified (epi)genetic factors in CDH penetrance. In a second family with 2 male foetuses with MCA, we identify a mutation in the X-linked PORCN gene inherited from an unaffected mother who was shown to have extreme skewing of X-inactivation. This further implicates Wnt signaling as playing a role in CDH, as well as multiple aspects of foetal development. In a third consanguineous family we identify a mutation in PIGN in a foetus with MCA, inherited from carrier parents. PIGN is involved in GPI anchor synthesis and our finding adds to a growing body of evidence that defective GPI anchor synthesis causes multiple phenotypes in humans.Given the variation in severity of herniation and thus pulmonary hypoplasia, as well as differences in responses to foetal and / or neonatal therapy for CDH patients, we sought to explore whether gene expression analysis of amniotic fluid cells from CDH foetuses could identify dysregulated genes and biological pathways which may act as predictive biomarkers. In this exploratory study we applied RNA-sequencing to investigate gene expression in cultured cells sourced from amniotic fluid of isolated CDH patients, described in Chapter 6. This analysis identifies 2 potential molecular subtypes of isolated CDH, one of which is characterized by downregulation of TGFB1 and CTGF, and upregulation of TNF, IL6 and IL8. This highlights downregulation of TGFB signalling as a likely cause of much of of the downstream dysregulation in gene expression observed, including that of CTGF which has been previously implicated in the nitrofen rodent model of CDH. Furthermore, this group of patients shows an apparent inflammatory response indicated by the upregulation of TNF, IL6 and IL8 which may in turn exacerbate postnatal pulmonary hypertension. These findings direct future targeted studies in a larger cohort of isolated CDH patients to determine the clinical significance and therapeutic potential.

Academic collection --- Theses

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Het 22q11.2 deletie syndroom (22q11.2DS) is het meest voorkomende microdeletie syndroom met een incidentie van ongeveer 1 op 4000 geboortes. Deze deletie wordt veroorzaakt door niet-allelische homologe recombinatie (NAHR) tussen ‘low copy repeats’ (LCRs) binnen de 22q11.2 regio. Er bestaat een grote fenotypische variabiliteit en meer dan 180 symptomen werden reeds in verband gebracht met deze genetische aandoening. De belangrijkste symptomen omvatten aangeboren hartafwijkingen, immunodeficiëntie, afwijkingen van het gehemelte, psychiatrische aandoeningen en typische gelaatskenmerken. In deze studie gaan we uit van de hypothese dat verschillende breekpunten binnen éénzelfde LCR aanleiding kunnen geven tot een verschillend fenotype. Door middel van ‘molecular combing’, en hybridisatie van fluorescent gemerkte probes willen we nagegaan of er inderdaad verschillende breekpunten binnen éénzelfde LCR bestaan. Bovendien kan met deze methode de opbouw van de 22q11.2 regio, bestaande uit verschillende duplicatie eenheden, gevisualiseerd worden en kan variatie in de regio in beeld gebracht worden. Deze studie heeft aangetoond dat de gebruikte techniek geschikt is voor het bepalen van breekpunten bij verschillende 22q11.2 deleties en voor het opsporen van variatie binnen de 22q11.2 regio. We kunnen besluiten dat binnen LCR-A minstens twee verschillende breekpunten werden teruggevonden bij de vier onderzochte probands. Binnen LCR-D werden geen verschillende breekpunten gevonden. Verder werden een aantal inversie polymorfismen gevonden binnen de 22q11.2 regio. Ten slotte blijkt de structuur van LCR-A niet volledig overeen te komen met de structuur die in het referentiegenoom wordt weergegeven.

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Introduction: Genetic abnormalities are of big clinical importance in human embryos. They exist in many different types and occur with varying incidences. The available data are mostly derived from genome analysis of preimplantation embryos from the IVF population. Most IVF cycles are performed for couples with fertility problems and these embryos may not be representative for the general reproductive population. In fact, surprisingly little is known about the occurrence of genetic abnormalities in embryos from the general reproductive population. Methods: In this study, we analyzed the incidence and origin of various common and rare genetic abnormalities in 1994 cleavage- and blastocyst stage embryos from a PGT-M population using siCHILD/haplarithmisis. Results: We observed an abnormality in 42.1% of embryos with a statistically significant difference (P < 0.00001) between D3 (44.0%) and D5-6 (15.5%) embryos. Whole-chromosome imbalances, particularly monosomies, were the most common at 34.1% and 21.9% of embryos respectively. We detected segmental aneuploidies in 10.9% of embryos and found a moderate correlation (R²=0.69) between incidence and chromosomal length. We also observed a statistically non-significant bias favoring paternal segmental imbalances, particularly deletions, over maternal imbalances. Ploidy abnormalities were present in 2.0% of embryos of which 79% would have been missed by conventional methods. Discussion: The incidences of whole-chromosome aneuploidies we found are lower than those reported elsewhere, highlighting the differences between the IVF and general reproductive population. By using a large sample size and techniques with a high diagnostic accuracy, we believe our results are a close approximation of the true incidence of genetic abnormalities in embryos from the general reproductive population.