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De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10-5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10-4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility. © 2022, The Author(s).

Contains fulltext : 87530.pdf (Publisher’s version ) (Closed access) Massively parallel sequencing has tremendous diagnostic potential but requires enriched templates for sequencing. Here we report the validation of an array-based sequence capture method in genetically heterogeneous disorders. The model disorder selected was AR ataxia, using five subjects with known mutations and two unaffected controls. The genomic sequences of seven disease genes, together with two control loci were targeted on a 2-Mb sequence-capture array. After enrichment, the patients' DNA samples were analyzed using one-quarter Roche GS FLX Titanium sequencing run, resulting in an average of 65 Mb of sequence data per patient. This was sufficient for an average 25-fold coverage/base in all targeted regions. Enrichment showed high specificity; on average, 80% of uniquely mapped reads were on target. Importantly, this approach enabled automated detection of deletions and hetero- and homozygous point mutations for 6/7 mutant alleles, and greater than 99% accuracy for known SNP variants. Our results also clearly show reduced coverage for sequences in repeat-rich regions, which significantly impacts the reliable detection of genomic variants. Based on these findings we recommend a minimal coverage of 15-fold for diagnostic implementation of this technology. We conclude that massive parallel sequencing of enriched samples enables personalized diagnosis of heterogeneous genetic disorders and qualifies for rapid diagnostic implementation. 01 april 2010

Contains fulltext : 153601.pdf (Publisher’s version ) (Closed access) The Radboud University Medical Center was among the first to implement two-step exome sequencing in clinical genetic diagnostics. This study is the first to evaluate patient experiences with gene panels based on exome sequencing, using quantified psychological variables: acceptance, psychological distress, expectations of heredity and unsolicited findings. Between August 2011 and July 2012, 177 patients diagnosed with early-onset colorectal/kidney cancer, deafness, blindness or movement disorder consented to diagnostic exome sequencing offered by clinical geneticists. Baseline questionnaires were sent to 141 adults, returned by 111 with median age of 49 [22-79] years and positive family history in 81%. Follow-up included 91 responders at median 4 [2-22] weeks after results from known gene panels per diagnosis group; exome-wide analysis is ongoing. Confirmed or possibly pathogenic mutations were found in 31% with one unsolicited finding (oncogenetic panel). Most patients (92%) were satisfied. There were no significant changes in heredity-specific distress (18% at baseline, 17% at follow-up) and expectations of heredity. Fewer patients expected unsolicited findings at follow-up (29% vs 18%, p = 0.01). Satisfaction and distress were equal in those with vs without mutations. In conclusion, most adults accepted and were satisfied with gene panels based on diagnostic exome sequencing, few reporting distress.

Contains fulltext : 47561.pdf (Publisher’s version ) (Closed access) Small, submicroscopic, genomic deletions and duplications (1 kb to 10 Mb) constitute up to 15% of all mutations underlying human monogenic diseases. Novel genomic technologies such as microarray-based comparative genomic hybridization (array CGH) allow the mapping of genomic copy number alterations at this submicroscopic level, thereby directly linking disease phenotypes to gene dosage alterations. At present, the entire human genome can be scanned for deletions and duplications at over 30,000 loci simultaneously by array CGH ( approximately 100 kb resolution), thus entailing an attractive gene discovery approach for monogenic conditions, in particular those that are associated with reproductive lethality. Here, we review the present and future potential of microarray-based mapping of genes underlying monogenic diseases and discuss our own experience with the identification of the gene for CHARGE syndrome. We expect that, ultimately, genomic copy number scanning of all 250,000 exons in the human genome will enable immediate disease gene discovery in cases exhibiting single exon duplications and/or deletions.

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Item does not contain fulltext The genetic causes of mental retardation are highly heterogeneous and for a large proportion unknown. Mutations as well as large chromosomal abnormalities are known to contribute to mental retardation, and recently more subtle structural genomic variations have been shown to contribute significantly to this common and complex disorder. Genomic microarrays with increasing resolution levels have revealed the presence of rare de novo CNVs in approximately 15% of all mentally retarded patients. Microarray-based CNV screening is rapidly replacing conventional karyotyping in the diagnostic workflow, resulting in an increased diagnostic yield as well as biological insight into this disorder. In this chapter, an overview is given of the detection and interpretation of copy number variations in mental retardation, with a focus on diagnostic applications. In addition, a detailed protocol is provided for the diagnostic interpretation of copy-number variations in mental retardation.

Contains fulltext : 97490.pdf (Publisher’s version ) (Open Access)

Item does not contain fulltext We report on a follow-up evaluation of a male with a phenotype including craniosynostosis, periventricular nodular heterotopia, and neurodevelopmental delay. He was initially assigned a clinical diagnosis of Fontaine-Farriaux syndrome (FFS) as an infant although now, with improved delineation of this entity, it is evident that this diagnosis is not applicable to this individual. Array comparative genomic hybridization has demonstrated a 300 kb interstitial deletion on Xp22.11 affecting all or part of three annotated genes, ZFX, PDK3, and PCYT1B in this subject. The deletion was inherited from the phenotypically normal mother who also exhibited markedly skewed X-inactivation. These findings implicate hemizygosity for one or all three of these genes as the cause of this phenotype. (c) 2011 Wiley Periodicals, Inc.

Contains fulltext : 89449.pdf (Publisher’s version ) (Closed access) The chromosomal band 17q21.31, containing the microtubule-associated protein tau (MAPT) gene, is a hotspot for chromosomal rearrangements. It is known to contain a common inversion polymorphism of approximately 900 kb in populations with European ancestry. The inverted configuration is linked to a distinct MAPT haplotype, H2, which is relatively common in Europeans but nearly absent in Asian and African populations. Recent studies have demonstrated that the H2 haplotype is ancestral in hominoids, and under positive selection in Europeans. This haplotype is also linked to events leading to the 17q21.31 microdeletion syndrome, one of the most common causes of 'idiopathic' mental retardation in people of European descent. We performed direct analysis of the chromosome structure by fluorescence in situ hybridization and observed heterozygosity of the inversion status for the H2 chromosomes, but not for the H1 haplotype. Inversion heterozygosity was also observed in a mother homozygous for the H2 haplotype, who transmitted the chromosome with the deletion to a proband with 17q21.31 microdeletion syndrome. Our results highlight an allele-specific sensitivity to chromosome rearrangements and suggest that it is the heterozygosity of inversion status that predisposes to the 17q21.31 microdeletion syndrome.

Contains fulltext : 51503.pdf (Publisher’s version ) (Closed access) We describe our findings in a 46,XY female with a clinical features of Genitopatellar syndrome (GPS) and confirmed hermaphroditism with ovotestes, and five additional patients with GPS. GPS is a genetic disorder characterized by renal and genital anomalies, joint dislocation, aplastic or hypoplastic and often displaced patellae, minor facial anomalies, and mental retardation. The genital anomalies clearly distinguish GPS from nail-patella syndrome (NPS) that has similar features, but additionally shows hypoplastic finger- and toenails as found in the 46,XY female. In our patients no mutation was found in the coding regions of WNT4, WNT7A, TBX4, and LMX1B. Fluorescent in situ hybridization (FISH) and array-based comparative genome hybridization (aCGH) analysis showed a 3 Mb deletion of LMX1B, NR6A1, and NR5A1 (SF1) in the 46,XY female. This is the first report of a microdeletion causing haploinsuffiency of LMX1B and NR5A1. The deletion of LMX1B is responsible for the knee anomalies and the deletion of NR5A1 likely causes the sex reversal. Cytogenetic analysis of the five additional patients with diagnosed GPS failed to identify a similar microdeletion, or inversion of a potentially regulatory element between the two genes. This suggests that the locus 9q33-9q34 can be excluded for GPS and that the presented case is unique in its combination of GPS and NPS features caused by a microdeletion associated with loss of function of LMX1B and NR5A1.

Contains fulltext : 51726.pdf (Publisher’s version ) (Closed access)

Contains fulltext : 51728.pdf (Publisher’s version ) (Closed access) Partial deletions of the long arm of chromosome 18 lead to variable phenotypes. Common clinical features include a characteristic face, short stature, congenital aural atresia (CAA), abnormalities of the feet, and mental retardation (MR). The presence or absence of these clinical features may depend on the size and position of the deleted region. Conversely, it is also known that patients whose breakpoints are localized within the same chromosome band may exhibit distinct phenotypes. New molecular techniques such as array CGH allow for a more precise determination of breakpoints in cytogenetic syndromes, thus leading to better-defined genotype-phenotype correlations. In order to update the phenotypic map for chromosome 18q deletions, we applied a tiling resolution chromosome 18 array to determine the exact breakpoints in 29 patients with such deletions. Subsequently, we linked the genotype to the patient's phenotype and integrated our results with those previously published. Using this approach, we were able to refine the critical regions for microcephaly (18q21.33), short stature (18q12.1-q12.3, 18q21.1-q21.33, and 18q22.3-q23), white matter disorders and delayed myelination (18q22.3-q23), growth hormone insufficiency (18q22.3-q23), and CAA (18q22.3). Additionally, the overall level of MR appeared to be mild in patients with deletions distal to 18q21.33 and severe in patients with deletions proximal to 18q21.31. The critical region for the 'typical' 18q-phenotype is a region of 4.3 Mb located within 18q22.3-q23. Molecular characterization of more patients will ultimately lead to a further delineation of the critical regions and thus to the identification of candidate genes for these specific traits.

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Contains fulltext : 50829.pdf (Publisher’s version ) (Closed access) In a female patient with mild mental retardation an interstitial subtelomeric 9q34.3 deletion was identified by a multiplex ligation-dependent probe amplification (MLPA) based screen for subtelomeric abnormalities. Further characterization of the deletion by high-resolution tiling path array-based comparative genomic hybridization (array CGH) revealed a size of 2.2 Mb. The woman lacked the typical 9qter deletion phenotype characteristics, which is inline with the finding that both Eu-HMTase1 (EHMT) genes were present. However, she presented with mild mental retardation, some mild facial dysmorphisms and aplasia cutis. This is another example of an interstitial subtelomeric deletion, which underscores that further characterizing the precise nature of the deletion is of clinical importance. Moreover, it confirms the importance of the Eu-HMTase1 gene as the major causative factor of the classical 9qter syndrome phenotype.

Tele-operated unmanned aerial vehicles (UAVs) have no operators on board and therefore enable extension of the present sensing and communication capabilities in civil and military missions, without unnecessarily endangering personnel or deploying expensive material. One should also realize that tele-operation from a control centre may result in new and formerly unknown human factors problems. For this reason, TNO Human Factors has been performing UAV related research for more than ten years, focusing on the identification of possible human factors problems in UAV supervisory control. The present paper gives an overview of exploratory human-machine interface optimization studies, and reports the findings to overcome specific problems that are inherent in remote camera and platform operation. Important points of departure for the studies are a UAV mission analysis and an assessed order of possible missions. Since important mission elements involve target location, classification (target acquisition), and damage assessment, operator-in-the-loop performance remains an important issue, depending on the level of automation. We acquired more knowledge on the functioning of the human operator dealing with remote sensing and control, with the emphasis on aspects related to automation and interface aspects. For automation this involved, among others, the distribution of tasks between the human operator and the unmanned system, automation and operator situation awareness, the effects of automation breakdowns and adaptive automation. The interface aspects mainly involved the viewing systems and control devices that form the interface between the remote operator and the UAV. This concerned, among others: image characteristics of the remote sensor, application and consequences of head-slaved viewing systems, effects of time delays, control device configurations and the application of force feedback. The paper discusses a series of studies that focuses on the negative effects of degraded information, and the possibilities to compensate these effects by innovative human-machine interface designs supporting the operator in charge. Important point of departure was that the improvements did not result in additional claims on the capacity of the up/down data-link. The applied techniques included the use of graphic overlays, ecological interface design, head-coupled control, and the use of prediction techniques. The results show that carefully designed human-machine interfaces are able to partially compensate specific image degradations while operator performance may significantly increase. Further experimental research focused on sub-optimal operator performance when UAV remote information is handled on board a moving platform, e.g., a helicopter. We tested methods to increase spatial awareness. The paper gives an overview of the studies and presents the main results.

TM bijdragen aan dit rapport: chapter 1: Introduction, chapter 3.3.1: Cognitive Load, chapter 4.1.2: Cardiorespiratory Measures

This paper summarizes a Cognitive Task Load (CTL) model, which describes the effects of (envisioned) task allocations and support functions on operator performance and mental effort. The CTL-model distinguishes three load factors: the classical measure percentage time occupied, the number of task-set switches and the level of information processing. Recently, the model has been used to guide several system development processes. We present a validation study and an example application for the analysis of envisioned task distributions and support functions on a ship. This CTLanalysis provided requirements for dynamic task allocation and a first design of support functions that extend human capacities for the three factors of the CTL model.

The manual control of the camera of an unmanned aerial vehicle (UAV) can be difficult due to several factors such as 1) time delays between steering input and changes of the monitor content, 2) low update rates of the camera images and 3) lack of situation awareness due to the remote position of the operator and the small field of view of the camera images. Therefore, it is important to assist the operator with adequate tools. We constructed and evaluated a perspective (3D) digital map with information about the predicted viewing direction of the camera. In an experiment, participants inspected roads and edges of wood with and without the 3D map. A 2D map with the same information as the 3D map was available in all conditions. With the 3D map, the participants: 1) were able to inspect larger areas, especially when the task became more difficult due to time delays and low update rates, 2) were better able to perform an additional task, and 3) reported lower workload compared to the condition without the 3D map. These subjective workload results were not supported by objective (physiological) workload measures. Analysis of eye movements showed that the 3D map was used very frequently, especially in conditions with time delays and low update rates.

The paper provides an example of a method to get insight into workload changes over time, executed tasks and situation awareness (SA) in complex task environments. The method is applied to measure the workload of a helicopter crew. The method has three components: 1) task analysis, 2) video recordings of the tasks and 3) analysis of the video tapes by the crew members. A computer program was developed for the third part of the method. The crew members had to indicate the tasks that were executed during the mission and they had to indicate the workload during the mission at fixed time intervals. The results showed, among others, that the relation between number of tasks that were executed concurrently and the workload was low for the crew members of which the tasks were mainly cognitive demanding. Workload for these crew members were more related to the level of SA. The workload was high during periods of low SA. Workload for the crew member of which the tasks were less cognitive demanding was more related to the number of tasks that were executed concurrently and less by the level of SA.

The sensitivity of physiological measures to mental workload has been investigated in a flight simulator. Twelve pilots had to fly through a tunnel with different levels of difficulty. Additionally, they had to perform a memory task with four levels of difficulty. The easiest memory task was combined with the easiest tunnel task and the most difficult memory task with the most difficult tunnel task. Between the tunnel tasks, subjects had to fly a pursuit task in which a target jet had to be followed. Rest periods before and after the experiment were used as a baseline for the physiolog-ical measures. Mental workload was measured with heart period, continuous blood pressure, respiration and eye blinks. Heart rate variability, blood pressure variability and the gain between systolic blood pressure and heart period (modulus) was derived from the measures. All measures showed differences between rest and flight, and between the pursuit and the tunnel task. Only heart period was sensitive to the different levels in the tunnel task. Since heart rate variability was affected by respiration, it could only be interpreted together with the respiratory data. The modulus, how-ever, was hardly influenced by respiration and therefore, appears te be a better measure than heart rate variability. From the respiratory parameters, the duration of a respiratory cycle was the most sensitive to changes in workload. The time in between two successive eye blinks (blink interval) increased and the blink duration decreased as more visual information had to be processed. Increas-ing the difficulty of the memory task leaded to a decrement in blink interval, probably caused by subvocal activity during the rehearsal of the letters. Blink duration was not influenced by memory load.

Hartslag, bloeddruk en oogknippers geven goed verschillende niveaus van mentale inspanning weer. Hartslagvariabiliteit kan tijdens het uitvoeren van complexe taken verstoord worden door ademhaling.

Contains fulltext : 233754.pdf (Publisher’s version ) (Open Access) Radboud University, 18 juni 2021 Promotor : Veltman, J.A. Co-promotores : Vissers, L.E.L.M., Ramos, L. 336 p.

Contains fulltext : 236701.pdf (Publisher’s version ) (Open Access) Radboud University, 27 oktober 2021 Promotores : Braat, D.D.M., Veltman, J.A. Co-promotores : Fleischer, K., Ramos, L. 287 p.

Contains fulltext : 235388.pdf (Publisher’s version ) (Open Access) Radboud University, 25 augustus 2021 Promotores : Veltman, J.A., Vriend, G. Co-promotor : Gilissen, C.F.H.A. 185 p.

Contains fulltext : 204522.pdf (Publisher’s version ) (Open Access) Radboud University, 28 juni 2019 Promotor : Veltman, J.A. Co-promotor : Gilissen, C.F.H.A.

Contains fulltext : 207613.pdf (Publisher’s version ) (Open Access) Radboud University, 04 oktober 2019 Promotor : Veltman, J.A. Co-promotor : Gilissen, C.F.H.A.

Contains fulltext : 173265.pdf (Publisher’s version ) (Open Access) The work presented in this thesis shows that mutations arise constantly, between one generation and the next but also throughout life. This continuous occurrence of mutations leads to extraordinary genetic diversity between individuals but is also at the origin of the existence of genetically different populations of cells within a single human being. While the occurrence of novel mutations represents an important biological phenomenon in humans with a role on prenatal development, physiology and evolution, novel mutations also contribute to different forms of human disease ranging from rare and severe developmental disorders to adult-onset diseases such as cancer. The work in this thesis supports that in addition to the detection of mutations, NGS can be used as a tool to identify the timing of mutations in order to include the dimension of time in the interpretation of mutations and their possible consequences. De novo mutations have different recurrence risks depending on the exact timing at which they occurred, which can be determined by meticulous analysis with NGS methods. Indeed, genetic mosaicism resulting from mutations occurring during embryogenesis is common and, depending on their timing, postzygotic mutations can be transmitted to the next generation. Additionally, somatic mutations arise in stem cells throughout life and can be detected using highly sensitive sequencing methods. Furthermore, the timing of a mutation can also shape the resulting phenotype, as the same mutation can be involved in different disorders depending on its timing. For instance, overlapping germline and somatic mutations in SETBP1, leading to Schinzel-Giedion syndrome and to myeloid leukemia, respectively. Future work focusing on the role of timing of somatic and germline mutations will provide us with a better understanding of the effect of the expression of a mutation in the dynamic context of a cell, a tissue and a whole organism. Radboud University, 08 juni 2017 Promotor : Veltman, J.A. Co-promotores : Hoischen, A., Gilissen, C.F.H.A.

Contains fulltext : 160831.pdf (Publisher’s version ) (Open Access) Radboud University, 10 november 2016 Promotores : Braat, D.D.M., Veltman, J.A. Co-promotores : Fleischer, K., Ramos, L.

Contains fulltext : 145297.pdf (Publisher’s version ) (Open Access) Radboud Universiteit Nijmegen, 16 november 2015 Promotores : Drenth, J.P., Veltman, J.A. Co-promotor : Hoischen, A.

Contains fulltext : 125598.pdf (Publisher’s version ) (Open Access) Radboud Universiteit Nijmegen, 07 april 2014 Promotores : Brunner, H.G., Veltman, J.A. Co-promotores : Vissers, L.E.L.M., Hehir, J.Y.

Contains fulltext : 92728.pdf (Publisher’s version ) (Open Access) Radboud Universiteit Nijmegen, 13 januari 2012 Promotores : Brunner, H.G., Geurts van Kessel, A.H.M. Co-promotor : Veltman, J.A. 255 p.

Contains fulltext : 85870.pdf (Publisher’s version ) (Open Access) Radboud Universiteit Nijmegen, 01 april 2011 Promotores : Geurts van Kessel, A.H.M., Brunner, H.G. Co-promotor : Veltman, J.A. 136 p.

Contains fulltext : 82002.pdf (Publisher’s version ) (Open Access) Radboud Universiteit Nijmegen, 30 september 2010 Promotores : Geurts van Kessel, A.H.M., Brunner, H.G. Co-promotor : Veltman, J.A. 244 p.

Contains fulltext : 30198_molekabya.pdf (Publisher’s version ) (Open Access) Chromosomal rearrangements can lead to various serious clinical manifestations, including mental retardation and congenital malformation syndromes. Chromosomal rearrangements larger than 5-10 Mb in size can be detected by conventional karyotyping. A considerable number of clinical disorders, however, is caused by submicroscopic chromosomal rearrangements smaller than 5-10 Mb in size. To routinely detect these rearrangements, an efficient and robust genome-wide technology is needed. One such technology is array-based comparative genomic hybridization (array CGH), an approach which is also referred to as molecular karyotyping. In analogy to the application of array CGH in cancer research, we reasoned that this technology might also be suited for the detection of submicroscopic chromosomal rearrangements in patients with unexplained mental retardation and/or congenital malformation syndromes. The specific aim of this thesis was to explore the feasibility of the array CGH technology for the delineation of DNA copy number alterations for applied clinical genetic and basic genome research purposes. During the course of the project, the concept of molecular karyotyping rapidly changed the field of clinical genetics and genome research and, without any doubt, will continue to do so in the years to come. In case of clinical genetics, we conclude that molecular karyotyping has led to a significant increase in the diagnostic yield in patients with unexplained mental retardation and/or malformation syndromes; the identification of a gene underlying CHARGE syndrome, and the identification of a novel microdeletion syndrome involving chromosome 17q21.31. In case of genome research, we conclude that molecular karyotyping has led to novel insight into the occurrence of copy number variation within the human genome, and into the recombination mechanisms and genomic architectural features underlying the occurrence of copy number variation. Based on the above, we conclude that molecular karyotyping serves as a powerful tool for linking gene dosage alterations to (disease) phenotypes RU Radboud Universiteit Nijmegen, 13 september 2007 Promotor : Geurts van Kessel, A.H.M. Co-promotor : Veltman, J.A. 192 p.