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KLHL20 is part of a CUL3-RING E3 ubiquitin ligase involved in protein ubiquitination. KLHL20 functions as the substrate adaptor that recognizes substrates and mediates the transfer of ubiquitin to the substrates. Although KLHL20 regulates neurite outgrowth and synaptic development in animal models, a role in human neurodevelopment has not yet been described. We report on a neurodevelopmental disorder caused by de novo missense variants in KLHL20.Patients were ascertained by the investigators through Matchmaker Exchange. Phenotyping of patients with de novo missense variants in KLHL20 was performed.We studied 14 patients with de novo missense variants in KLHL20, delineating a genetic syndrome with patients having mild to severe intellectual disability, febrile seizures or epilepsy, autism spectrum disorder, hyperactivity, and subtle dysmorphic facial features. We observed a recurrent de novo missense variant in 11 patients (NM_014458.4:c.1069GA p.[Gly357Arg]). The recurrent missense and the 3 other missense variants all clustered in the Kelch-type β-propeller domain of the KLHL20 protein, which shapes the substrate binding surface.Our findings implicate KLHL20 in a neurodevelopmental disorder characterized by intellectual disability, febrile seizures or epilepsy, autism spectrum disorder, and hyperactivity.

BackgroundIn clinical genetics, establishing an accurate nosology requires analysis of variations in both aetiology and the resulting phenotypes. At the phenotypic level, recognising typical facial gestalts has long supported clinical and molecular diagnosis; however, the objective analysis of facial phenotypic variation remains underdeveloped. In this work, we propose exploratory strategies for assessing facial phenotypic variation within and among clinical and molecular disease entities and deploy these techniques on cross-sectional samples of four RASopathies: Costello syndrome (CS), Noonan syndrome (NS), cardiofaciocutaneous syndrome (CFC) and neurofibromatosis type 1 (NF1).MethodsFrom three-dimensional dense surface scans, we model the typical phenotypes of the four RASopathies as average ‘facial signatures’ and assess individual variation in terms of direction (what parts of the face are affected and in what ways) and severity of the facial effects. We also derive a metric of phenotypic agreement between the syndromes and a metric of differences in severity along similar phenotypes.ResultsCFC shows a relatively consistent facial phenotype in terms of both direction and severity that is similar to CS and NS, consistent with the known difficulty in discriminating CFC from NS based on the face. CS shows a consistent directional phenotype that varies in severity. Although NF1 is highly variable, on average, it shows a similar phenotype to CS.ConclusionsWe established an approach that can be used in the future to quantify variations in facial phenotypes between and within clinical and molecular diagnoses to objectively define and support clinical nosologies.

Squamous odontogenic tumors (SOT) are rare, benign, odontogenic neoplasms of the jaws. The sporadically reported cases with multifocal SOTs seem to have a marked predilection for younger African American patients. In this case report a 14-year-old Caucasian male presented with swelling of the vestibular alveolar process, slight tooth divergence, and mobility. A multifocal squamous odontogenic tumor was diagnosed and subsequently treated twice with surgical enucleation. Two and a half years earlier his mother was diagnosed and treated for a similar multifocal SOT. Next-Generation-Sequencing targeted resequencing mutational analysis of the maternal surgical specimens was performed. No potential causal mutation could be identified. Postoperative follow-up of the patient showed no recurrence of the SOT after 2 years. This case report substantiates the possibility of a familial relationship in (multifocal) SOT, possibly changing current ideas concerning the etiology and treatment of these neoplasms.

Objective The aim of this study was to analyze patients with thrombophilia who underwent oral and/or maxillofacial surgery at our center. Study Design We performed a retrospective analysis of patients with hereditary or acquired thrombophilia who had undergone oral/maxillofacial surgery between January 1, 2000 and December 31, 2019. Data regarding demographic and patient characteristics, surgical treatment modalities, antithrombotic therapies, and complications were analyzed. Results A total of 76 eligible patients (26 male, 50 female) were included in this study, with a mean follow-up period of 3.8 months (range, 0-51 months). The mean age at time of surgery was 44.7 ± 19.4 years. Seven different hereditary and acquired thrombophilia were identified: factor V Leiden (n = 31; 40.8%), prothrombin G20210A mutation (n = 5; 6.6%), protein C deficiency (n = 4; 5.3%), protein S deficiency (n = 11; 14.5%), antiphospholipid syndrome (n = 10; 13.2%), hyperhomocysteinemia (n = 8; 10.5%), and elevated factor VIII (n = 2; 2.6%). Complications occurred in 9 patients (11.8%) and included postoperative infections (n = 6; 7.9%) and postoperative bleeding (n = 3; 3.9%). Conclusion Our data suggest that oral and/or maxillofacial surgery in patients with a confirmed diagnosis of thrombophilia is not associated with a burden of thrombosis or high complication rates. Furthermore, we formulated a guideline for preoperative antithrombotic therapy for patients with thrombophilia undergoing oral and/or maxillofacial surgery.

Clinical diagnosis of syndromes benefits strongly from objective facial phenotyping. This study investigates facial dysmorphism of genetic syndromes by building and investigating a low-dimensional metric space referred to as the clinical face phenotypic space (CFPS). As a facial matching tool for clinical genetics, such CFPS can enhance clinical diagnosis. It helps to interpret facial dysmorphisms of a subject by placing them within the space of known dysmorphisms. In this paper, a triplet loss-based autoencoder developed by geometric deep learning (GDL) is trained using multi-task learning, which combines supervised and unsupervised learning approaches. Experiments are designed to illustrate the following properties of CFPSs that can aid clinicians in narrowing down their search space: A CFPS can 1) classify and cluster syndromes accurately, 2) generalize to novel syndromes, and 3) preserve the relatedness of genetic diseases, meaning that clusters of phenotypically similar disorders reflect functional relationships between genes. This model is composed of three main components: 1) an encoder based on GDL that optimize distances between individuals in the CFPS therefore adding to the classifier’s power. 2) a decoder that improves both classification and clustering performance by reconstructing a face from an embedding in a CFPS, 3) a singular value decomposition layer to maintain orthogonality and optimal variance distribution across dimensions. This allows for the selection of an optimal number of CFPS dimensions as well as improving the classification, reconstruction, and generalization capabilities of the CFPS.

Lay abstract Previous studies have reported a considerable interest in carrier screening for hereditary conditions among individuals in the general population, but actual uptake remains low. This study examines the perspectives of nonpregnant reproductive-aged women in Flanders (Belgium) regarding expanded carrier screening (ECS) for hereditary conditions to gain more insights in factors that possibly influence the opinions of reproductive-aged women. These insights are crucial to ensure a responsible implementation of ECS within healthcare services and to make sure that future parents are making informed choices when they are presented with the choice to accept or decline ECS. The results of this study can be used by healthcare providers interacting with couples planning a pregnancy to improve pre-/post-test counseling services. Which in turn can help to manage expectations and reduce misconceptions among potential users of ECS.

Craniofacial dysmorphism is associated with thousands of genetic and environmental disorders. Delineation of salient facial characteristics can guide clinicians towards a correct clinical diagnosis and understanding the pathogenesis of the disorder. Abnormal facial shape might require craniofacial surgical intervention, with the restoration of normal shape an important surgical outcome. Facial anthropometric growth curves or standards of single inter-landmark measurements have traditionally supported assessments of normal and abnormal facial shape, for both clinical and research applications. However, these fail to capture the full complexity of facial shape. With the increasing availability of 3D photographs, methods of assessment that take advantage of the rich information contained in such images are needed. In this article we derive and present open-source three-dimensional (3D) growth curves of the human face. These are sequences of age and sex-specific expected 3D facial shapes and statistical models of the variation around the expected shape, derived from 5443 3D images. We demonstrate the use of these growth curves for assessing patients and show that they identify normal and abnormal facial morphology independent from age-specific facial features. 3D growth curves can facilitate use of state-of-the-art 3D facial shape assessment by the broader clinical and biomedical research community. This advance in phenotype description will support clinical diagnosis and the understanding of disease pathogenesis including genotype-phenotype relations. ispartof: Scientific Reports vol:11 issue:1 pages:1-12 ispartof: location:England status: Published online

A de novo 0.95 Mb 8p21.3 deletion had been identified in an individual with non-syndromic autism spectrum disorder (ASD) through high-resolution copy number variant analysis. Subsequent screening of in-house and publicly available databases resulted in the identification of six additional individuals with 8p21.3 deletions. Through case-based reasoning, we conclude that 8p21.3 deletions are rare causes of non-syndromic neurodevelopmental and neuropsychiatric disorders. Based on literature data, we highlight six genes within the region of minimal overlap as potential ASD genes or genes for neuropsychiatric disorders: DMTN, EGR3, FGF17, LGI3, PHYHIP, and PPP3CC. ispartof: Neurogenetics vol:22 issue:3 pages:207-213 ispartof: location:United States status: published

Non-invasive prenatal testing has been introduced for the detection of Trisomy 13, 18, and 21. Using genome-wide screening also other "rare" autosomal trisomies (RATs) can be detected with a frequency about half the frequency of the common trisomies in the large population-based studies. Large prospective studies and clear clinical guidelines are lacking to provide adequate counseling and management to those who are confronted with a RAT as a healthcare professional or patient. In this review we reviewed the current knowledge of the most common RATs. We compiled clinical relevant parameters such as incidence, meiotic or mitotic origin, the risk of fetal (mosaic) aneuploidy, clinical manifestations of fetal mosaicism for a RAT, the effect of confined placental mosaicism on placental function and the risk of uniparental disomy (UPD). Finally, we identified gaps in the knowledge on RATs and highlight areas of future research. This overview may serve as a first guide for prenatal management for each of these RATs.

The human face is complex and multipartite, and characterization of its genetic architecture remains challenging. Using a multivariate genome-wide association study meta-analysis of 8,246 European individuals, we identified 203 genome-wide-significant signals (120 also study-wide significant) associated with normal-range facial variation. Follow-up analyses indicate that the regions surrounding these signals are enriched for enhancer activity in cranial neural crest cells and craniofacial tissues, several regions harbor multiple signals with associations to different facial phenotypes, and there is evidence for potential coordinated actions of variants. In summary, our analyses provide insights into the understanding of how complex morphological traits are shaped by both individual and coordinated genetic actions. ispartof: Nature Genetics vol:53 issue:1 ispartof: location:United States status: Published online

In pleiotropic diseases, multiple organ systems are affected causing a variety of clinical manifestations. Here, we report a pleiotropic disorder with a unique constellation of neurological, endocrine, exocrine, and haematological findings that is caused by biallelic MADD variants. MADD, the mitogen-activated protein kinase (MAPK) activating death domain protein, regulates various cellular functions, such as vesicle trafficking, activity of the Rab3 and Rab27 small GTPases, tumour necrosis factor-α (TNF-α)-induced signalling and prevention of cell death. Through national collaboration and GeneMatcher, we collected 23 patients with 21 different pathogenic MADD variants identified by next-generation sequencing. We clinically evaluated the series of patients and categorized the phenotypes in two groups. Group 1 consists of 14 patients with severe developmental delay, endo- and exocrine dysfunction, impairment of the sensory and autonomic nervous system, and haematological anomalies. The clinical course during the first years of life can be potentially fatal. The nine patients in Group 2 have a predominant neurological phenotype comprising mild-to-severe developmental delay, hypotonia, speech impairment, and seizures. Analysis of mRNA revealed multiple aberrant MADD transcripts in two patient-derived fibroblast cell lines. Relative quantification of MADD mRNA and protein in fibroblasts of five affected individuals showed a drastic reduction or loss of MADD. We conducted functional tests to determine the impact of the variants on different pathways. Treatment of patient-derived fibroblasts with TNF-α resulted in reduced phosphorylation of the extracellular signal-regulated kinases 1 and 2, enhanced activation of the pro-apoptotic enzymes caspase-3 and -7 and increased apoptosis compared to control cells. We analysed internalization of epidermal growth factor in patient cells and identified a defect in endocytosis of epidermal growth factor. We conclude that MADD deficiency underlies multiple cellular defects that can be attributed to alterations of TNF-α-dependent signalling pathways and defects in vesicular trafficking. Our data highlight the multifaceted role of MADD as a signalling molecule in different organs and reveal its physiological role in regulating the function of the sensory and autonomic nervous system and endo- and exocrine glands.

BACKGROUND Through carrier screening, prospective parents can acquire information about whether they have an increased risk of conceiving a child affected with an autosomal recessive or X-linked condition. Within the last decade, advances in genomic technologies have facilitated a shift from condition-directed carrier screening to expanded carrier screening (ECS). Following the introduction of ECS, several studies have been performed to gauge the interest in this new technology among individuals and couples in the general population. OBJECTIVE AND RATIONALE The aim of this systematic review was to synthesize evidence from empirical studies that assess the interest in ECS among individuals and couples in the general population. As the availability and accessibility of ECS grow, more couples who are a priori not at risk based on their personal or family history will be presented with the choice to accept or decline such an offer. Their attitudes and beliefs, as well as the perceived usefulness of this screening modality, will likely determine whether ECS is to become a widespread reproductive genetic test. SEARCH METHODS Four databases (Pubmed, Web of Science, CINAHL, Cochrane Library) were systematically searched to identify English language studies performed between January 2009 and January 2019 using the following search terms: carrier screening, carrier testing, attitudes, intention, interest, views, opinions, perspectives and uptake. Studies were eligible for inclusion if they reported on intentions to undergo a (hypothetical) ECS test, uptake of an actual ECS offer or both. Two researchers performed a multistep selection process independently for validation purposes. OUTCOMES Twelve empirical studies performed between 2015 and 2019 were included for analysis. The studies originated from the USA (n = 6), the Netherlands (n = 3), Belgium (n = 1), Sweden (n = 1) and Australia (n = 1). The sample size of the studies varied from 80 to 1669. In the included studies, 32%–76% of respondents were interested in a (hypothetical) ECS test, while uptake rates for actual ECS offers ranged from 8% to 50%. The highest overall uptake was observed when ECS was offered to pregnant women (50%). By contrast, studies focusing on the preconception population reported lower overall uptake rates (8–34%) with the exception of one study where women were counseled preconception in preparation for IVF (68.7%). WIDER IMPLICATIONS Our findings suggest that there may be discrepancies between prospective parents’ reported intentions to undergo ECS and their actual uptake, particularly during the preconception period. As ECS is a new and relatively unknown test for most future parents, the awareness and comprehension within the general population could be rather limited. Adequate pre- and post-test counseling services should be made available to couples offered ECS to ensure informed reproductive decision-making, together with guidelines for primary health care professionals. Due to restricted nature of the samples and methods of the underlying primary studies, some of the reported results might not be transferable to a broader population. More research is needed to see if the observed trends also apply to a broader and more diverse population.

BackgroundIntragenic NRXN1 deletions are susceptibility variants for neurodevelopmental disorders; however, their clinical interpretation is often unclear. Therefore, a literature study and an analysis of 43 previously unpublished deletions are provided.MethodsThe literature cohort covered 629 heterozygous NRXN1 deletions: 148 in controls, 341 in probands and 140 in carrier relatives, and was used for clinical hypothesis testing. Exact breakpoint determination was performed for 43 in-house deletions.ResultsThe prevalence of exonic NRXN1 deletions in controls was ~1/3000 as compared with ~1/800 in patients with neurodevelopmental/neuropsychiatric disorders. The differential distribution of deletions across the gene between controls and probands allowed to distinguish distinct areas within the gene. Exon 6–24 deletions appeared only twice in over 100000 control individuals, had an estimated penetrance for neurodevelopmental disorders of 32.43%, a de novo rate of 50% and segregated mainly with intellectual disability (ID) and schizophrenia. In contrast, exon 1–5 deletions appeared in 20 control individuals, had an estimated penetrance of 12.59%, a de novo rate of 32.5% and were reported with a broad range of neurodevelopmental phenotypes. Exact breakpoint determination revealed six recurrent intron 5 deletions.ConclusionExon 6–24 deletions have a high penetrance and are mainly associated with ID and schizophrenia. In contrast, the actual contribution of exon 1–5 deletions to a neurodevelopmental/neuropsychiatric disorder in an individual patient and family remains very difficult to assess. To enhance the clinical interpretation, this study provides practical considerations for counselling and an interactive table for comparing a deletion of interest with the available literature data.

Reproductive genetic carrier screening (RGCS) allows to identify couples who have an increased likelihood of conceiving a child affected with an autosomal recessive or X-linked monogenic condition. Multiple studies have reported on a wide and fragmented set of reasons to accept or decline RGCS. Only a few studies have been performed to assess the uptake of RGCS. Nonpregnant women visiting their gynecologist were invited to complete a questionnaire assessing perceived susceptibility, the acceptability of offering RGCS, attitudes, the intention to participate in RGCS, reasons to accept or decline RGCS, and sociodemographic characteristics. Women who showed the intention to have RGCS were asked to consider a free RGCS offer. Most women (n = 127) were between 25 and 34 years old (60%), in a relationship (91%), and wanted to have children (65%). Study participants had positive attitudes towards RGCS and the intention to consider RGCS in the future. Reasons to accept RGCS were being able to share genetic information with children or relatives (n = 104/127, 82%), to prevent the birth of a child affected with a hereditary condition (n = 103/127, 81%), and/or to know the chance of conceiving a child with a hereditary condition (n = 102/127, 80%). Reasons for declining RGCS were the possible concerns that could arise when receiving test results (n = 27/127, 21%), having no family history of hereditary disorders (n = 19/127, 15%), and not wanting to take action based on test results (n = 13/127, 10%). Among test intenders that met the inclusion criteria, 53% decided to participate in RGCS together with their male reproductive partner. More in-depth research on the decision-making process behind the choice to accept or decline an RGCS offer would be highly valuable to make sure couples are making informed reproductive choices. ispartof: JOURNAL OF GENETIC COUNSELING vol:31 issue:5 pages:1043-1053 ispartof: location:United States status: published

To review the experience with orthognathic surgery in patients with systemic diseases, syndromic conditions or an oncological history at a tertiary center.All patients who had undergone orthognathic surgery and all patients who were considered for orthognathic surgery between January 2013 and August 2020 at a tertiary center were retrospectively reviewed. Patients with cleft lip/palate and orthognathic patients requiring craniofacial surgery or reconstructive surgery were excluded. Patients with an underlying disorder were identified and divided into 3 categories: systemic disease, syndromic condition, or oncological disease treated with chemotherapy and/or radiation therapy of the head and neck. Data on intraoperative and postoperative complications until 3 months after surgery were collected for the patients who had undergone surgery. If orthognathic surgery was contraindicated, the reason was extracted from the patient's medical record.Eighty out of 1049 orthognathic patients had an underlying disorder (7.6%), including 50 patients with at least one systemic disease, 25 patients with a syndromic condition, and 5 patients with an oncological disease. A complication was encountered in respectively 5 (10%), 9 (36%), and 0 (0%) patients. Three out of 1134 patients who consulted the multidisciplinary orthognathic-orthodontic consultation had a contraindication for orthognathic surgery because of an underlying disease (0.3%).Based on our findings, intraoperative and short-term postoperative complications in patients with an underlying disorder are not frequent. Contraindications for orthognathic surgery because of a medical condition are very rare.

Through carrier screening couples at-risk of conceiving a child with an autosomal recessive or X-linked condition can be identified prior to conception. The aim of this study was to assess knowledge, attitudes and preferences regarding reproductive genetic carrier screening (RGCS) among reproductive-aged men and women in Flanders (Belgium). Women and men of reproductive age visiting their pharmacist were invited to answer a self-administered questionnaire. Prior to filling in the questionnaire, participants were asked to read an information leaflet explaining some key concepts about RGCS. Our sample included 387 individuals of reproductive age, of which 68.5% were female and 31.5% were male. Most of the participants were below 34 years old (72.9%), didn't have children (68.6%) and were currently in a relationship (69.1%). Offering RGCS to couples that want to have children was found acceptable by 86% of participants. However, fewer participants would consider RGCS for themselves in the future (61%). We observed a positive correlation between attitude score/knowledge score and the intention to have RGCS. Half of the participants (50.9%) preferred the disclosure of individual test results. Most of participants indicated that RGCS should be offered through the gynecologist (81.1%), followed by the GP (71.5%) and the Centre for Human Genetics (64.8%). About 68.9% of participants were willing to pay out-of-pocket for an RGCS test. We recommend that RGCS should ideally be implemented through a tailored implementation strategy whereby individual needs and preferences can be taken into account.

Background NRXN1 deletions are identified as one of major rare risk factors for autism spectrum disorder (ASD) and other neurodevelopmental disorders. ASD has 30% co-morbidity with epilepsy, and the latter is associated with excessive neuronal firing. NRXN1 encodes hundreds of presynaptic neuro-adhesion proteins categorized as NRXN1α/β/γ. Previous studies on cultured cells show that the short NRXN1β primarily exerts excitation effect, whereas the long NRXN1α which is more commonly deleted in patients involves in both excitation and inhibition. However, patient-derived models are essential for understanding functional consequences of NRXN1α deletions in human neurons. We recently derived induced pluripotent stem cells (iPSCs) from five controls and three ASD patients carrying NRXN1α+/- and showed increased calcium transients in patient neurons. Methods In this study we investigated the electrophysiological properties of iPSC-derived cortical neurons in control and ASD patients carrying NRXN1α+/- using patch clamping. Whole genome RNA sequencing was carried out to further understand the potential underlying molecular mechanism. Results NRXN1α + / - cortical neurons were shown to display larger sodium currents, higher AP amplitude and accelerated depolarization time. RNASeq analyses revealed transcriptomic changes with significant upregulation glutamatergic synapse and ion channels/transporter activity including voltage-gated potassium channels (GRIN1, GRIN3B, SLC17A6, CACNG3, CACNA1A, SHANK1), which are likely to couple with the increased excitability in NRXN1α + / - cortical neurons. Conclusions Together with recent evidence of increased calcium transients, our results showed that human NRXN1α + / - isoform deletions altered neuronal excitability and non-synaptic function, and NRXN1α + / - patient iPSCs may be used as an ASD model for therapeutic development with calcium transients and excitability as readouts.

Background: The introduction of multi-gene panel testing and improved awareness under patients and physicians has led to an increase of individuals with known germline pathogenic variants in hereditary breast and ovarian cancer (HBOC) genes. Significant regional differences exist in germline mutational landscape. We aimed to report the findings from multi-gene panel testing in a large Belgian cohort of individuals at risk for HBOC. Methods: All individuals who underwent multi-gene panel testing for HBOC at the Center for Human Genetics of the University Hospitals Leuven since the introduction of the panel were included (March 2016-April 2019). All included individuals were considered candidates for HBOC-panel testing by the requesting physician based on a personal or familial history of breast and/or ovarian cancer. Testing criteria from the Belgian Society of Human Genetics (www.beshg.be/download/guidelines/Guidelines_HBOC_2018.pdf) were met in the vast majority. The panel used was the BRCA Hereditary Cancer MASTR Plus® (Agilent, Belgium), with sequencing of BARD1, BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, TP53, MRE11A, RAD50, NBN, FAM175A, ATM, PALB2, STK11, MEN1, PTEN, CDH1, MUTYH, CHEK2, BLM, XRCC2, EPCAM, MLH1, MSH6, PMS2 and MSH2. Sequencing was performed by NGS on a Miseq platform (Illumina). Genomic deletions and duplications in BRCA1 and BRCA2 were investigated with multiplex ligation-dependent probe amplification. We hereby report on the frequency of pathogenic and likely pathogenic germline variants in this population. Results: In 5422 individuals who underwent multi-gene panel testing, we detected 665 pathogenic or likely pathogenic variants in 639 patients (11,7%). In 25 patients (0.46%), more than one relevant alteration was detected with double heterozygosity in 24 individuals and triple heterozygosity in one. Germline variants in BRCA1 and BRCA2 were detected in 178 (3.3%) and 144 (2.7%) patients, resulting in a fraction of 26,4% and 21,4% of detected variants respectively. Relevant alterations in CHEK2, ATM, PALB2 and TP53 were observed in 135 (2.5%), 93 (1.7%), 26 (0.5%) and 11 (0.2%) patients respectively, accounting together for 39.3% of detected variants. Alterations in BRIP1/RAD51C/RAD51D were retrieved in 64 patients (1.2%) and alterations in mismatch-repair genes MSH6/MLH1/PMS2/MSH2 were detected in 0.3% of patients. These patients where dominantly referred for familial history of ovarian cancer. Furthermore, germline alterations in PTEN, CDH1 and BLM were observed in 3, 2 and 1 cases respectively. Double heterozygosity for ATM+CHEK2 and for ATM+BRCA2 were both observed in 3 cases. In the patient with triple heterozygosity, co-occurrence of pathogenic variants in BRCA2, ATM and CHEK2 was detected. Conclusions: In a large Belgian cohort of 5422 individuals at risk for HBOC who underwent multi-gene panel testing, a pathogenic or likely pathogenic germline variant was detected in 11,7% of patients, and in 0,46% of patients double or triple heterozygosity for HBOC-variants was observed. Almost 40% of detected variants were alterations beyond BRCA correlated with hereditary breast cancer (CHEK2, ATM, PALB2 and TP53). Given the time-lag to predictive testing in families, a significant rise in healthy carriers with these non-BRCA alterations is expected in the upcoming years. Citation Format: Kevin Punie, Griet Hoste, Griet Van Buggenhout, Ellen Denayer, Hilde Brems, Hilde Peeters, Ann Smeets, Ines Nevelsteen, Patrick Neven, Jan Ardui, Renate Prevos, Machteld Keupers, Chantal Van Ongeval, Giuseppe Floris, Christine Desmedt, Hans Wildiers, Geneviève Michils, Hilde Van Esch, Eric Legius. Germline mutational landscape in 5422 individuals at risk for hereditary breast and ovarian cancer who underwent multi-gene panel testing [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-03.

UNLABELLED: Background and Objective; Genetic risk factors for childhood cancer may also influence facial morphology. 3D photography can be used in the recognition of differences in face shape among individuals. In previous research, 3D facial photography was used to identify increased facial asymmetry and greater deviation from normal facial morphology in a group of individuals with distinct morphological features who had childhood cancer compared to healthy controls. In this study, we aim to determine whether there is a difference in facial morphology between children with cancer without previously selected morphological features and healthy controls, detected with 3D facial photography. METHODS: Facial 3D photographic images were obtained of children with a newly diagnosed malignancy. The resulting sample comprised 13 different cancer types. Patients were excluded if they had a known genetic cause of the cancer. Patients were compared to healthy controls, matched for sex, age and ethnic background. The degree of asymmetry and overall deviation of an individual's face from an age and sex typical control face were measured. RESULTS: A total of 163 patients of European descent were included. No significant difference in asymmetry between patients and controls could be identified. On average, patients deviated more from an age and sex typical face than the controls. CONCLUSION: This study shows that children with cancer deviate more than controls, possibly suggesting a higher prevalence of genetic anomalies within this group. The results suggest that this is not sufficient to discriminate patients from controls. Further research is necessary to explore the patterns of individual variation among the overall deviation of patients and controls. The open access fees have been paid for this paper, so the paper is open-access in this normally closed-access journal ispartof: Computer Methods And Programs In Biomedicine vol:205 ispartof: location:Ireland status: Published online

Automatic craniomaxillofacial (CMF) three dimensional (3D) dense phenotyping promises quantification of the complete CMF shape compared to the limiting use of sparse landmarks in classical phenotyping. This study assesses the accuracy and reliability of this new approach on the human mandible. Classic and automatic phenotyping techniques were applied on 30 unaltered and 20 operated human mandibles. Seven observers indicated 26 anatomical landmarks on each mandible three times. All mandibles were subjected to three rounds of automatic phenotyping using Meshmonk. The toolbox performed non-rigid surface registration of a template mandibular mesh consisting of 17,415 quasi landmarks on each target mandible and the quasi landmarks corresponding to the 26 anatomical locations of interest were identified. Repeated-measures reliability was assessed using root mean square (RMS) distances of repeated landmark indications to their centroid. Automatic phenotyping showed very low RMS distances confirming excellent repeated-measures reliability. The average Euclidean distance between manual and corresponding automatic landmarks was 1.40 mm for the unaltered and 1.76 mm for the operated sample. Centroid sizes from the automatic and manual shape configurations were highly similar with intraclass correlation coefficients (ICC) of > 0.99. Reproducibility coefficients for centroid size were 0.90 indicating again high similarity between shapes quantified by classic or automatic phenotyping. Combined, these findings established high accuracy and repeated-measures reliability of the automatic approach. 3D dense CMF phenotyping of the human mandible using the Meshmonk toolbox introduces a novel improvement in quantifying CMF shape. Automatic craniomaxillofacial (CMF) three dimensional (3D) dense phenotyping promises quantification of the complete CMF shape compared to the limiting use of sparse landmarks in classical phenotyping. This study assesses the accuracy and reliability of this new approach on the human mandible. Classic and automatic phenotyping techniques were applied on 30 unaltered and 20 operated human mandibles. Seven observers indicated 26 anatomical landmarks on each mandible three times. All mandibles were subjected to three rounds of automatic phenotyping using Meshmonk. The toolbox performed non-rigid surface registration of a template mandibular mesh consisting of 17,415 quasi landmarks on each target mandible and the quasi landmarks corresponding to the 26 anatomical locations of interest were identified. Repeated-measures reliability was assessed using root mean square (RMS) distances of repeated landmark indications to their centroid. Automatic phenotyping showed very low RMS distances confirming excellent repeated-measures reliability. The average Euclidean distance between manual and corresponding automatic landmarks was 1.40 mm for the unaltered and 1.76 mm for the operated sample. Centroid sizes from the automatic and manual shape configurations were highly similar with intraclass correlation coefficients (ICC) of > 0.99. Reproducibility coefficients for centroid size were 0.90 indicating again high similarity between shapes quantified by classic or automatic phenotyping. Combined, these findings established high accuracy and repeated-measures reliability of the automatic approach. 3D dense CMF phenotyping of the human mandible using the Meshmonk toolbox introduces a novel improvement in quantifying CMF shape. ispartof: Scientific Reports vol:11 issue:1 ispartof: location:England status: published

Background NRXN1 deletions are identified as one of major rare risk factors for autism spectrum disorder (ASD) and other neurodevelopmental disorders. ASD has 30% co-morbidity with epilepsy, and the latter is associated with excessive neuronal firing. NRXN1 encodes hundreds of presynaptic neuro-adhesion proteins categorized as NRXN1α/β/γ. Previous studies on cultured cells show that the short NRXN1β primarily exerts excitation effect, whereas the long NRXN1α which is more commonly deleted in patients involves in both excitation and inhibition. However, patient-derived models are essential for understanding functional consequences of NRXN1α deletions in human neurons. We recently derived induced pluripotent stem cells (iPSCs) from five controls and three ASD patients carrying NRXN1α+/- and showed increased calcium transients in patient neurons. Methods In this study we investigated the electrophysiological properties of iPSC-derived cortical neurons in control and ASD patients carrying NRXN1α+/- using patch clamping. Whole genome RNA sequencing was carried out to further understand the potential underlying molecular mechanism. Results NRXN1α + / - cortical neurons were shown to display larger sodium currents, higher AP amplitude and accelerated depolarization time. RNASeq analyses revealed transcriptomic changes with significant upregulation glutamatergic synapse and ion channels/transporter activity including voltage-gated potassium channels (GRIN1, GRIN3B, SLC17A6, CACNG3, CACNA1A, SHANK1), which are likely to couple with the increased excitability in NRXN1α + / - cortical neurons. Conclusions Together with recent evidence of increased calcium transients, our results showed that human NRXN1α + / - isoform deletions altered neuronal excitability and non-synaptic function, and NRXN1α + / - patient iPSCs may be used as an ASD model for therapeutic development with calcium transients and excitability as readouts. Supplementary Information The online version contains supplementary material available at 10.1186/s12868-021-00661-0.

NCKAP1/NAP1 regulates neuronal cytoskeletal dynamics and is essential for neuronal differentiation in the developing brain. Deleterious variants in NCKAP1 have been identified in individuals with autism spectrum disorder (ASD) and intellectual disability; however, its clinical significance remains unclear. To determine its significance, we assemble genotype and phenotype data for 21 affected individuals from 20 unrelated families with predicted deleterious variants in NCKAP1. This includes 16 individuals with de novo (n = 8), transmitted (n = 6), or inheritance unknown (n = 2) truncating variants, two individuals with structural variants, and three with potentially disruptive de novo missense variants. We report a de novo and ultra-rare deleterious variant burden of NCKAP1 in individuals with neurodevelopmental disorders which needs further replication. ASD or autistic features, language and motor delay, and variable expression of intellectual or learning disability are common clinical features. Among inherited cases, there is evidence of deleterious variants segregating with neuropsychiatric disorders. Based on available human brain transcriptomic data, we show that NCKAP1 is broadly and highly expressed in both prenatal and postnatal periods and demostrate enriched expression in excitatory neurons and radial glias but depleted expression in inhibitory neurons. Mouse in utero electroporation experiments reveal that Nckap1 loss of function promotes neuronal migration during early cortical development. Combined, these data support a role for disruptive NCKAP1 variants in neurodevelopmental delay/autism, possibly by interfering with neuronal migration early in cortical development.

Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case-control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p 1.25E-06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p 3.64E-07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype-genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.

Evidence from model organisms and clinical genetics suggests coordination between the developing brain and face, but the role of this link in common genetic variation remains unknown. We performed a multivariate genome-wide association study of cortical surface morphology in 19,644 individuals of European ancestry, identifying 472 genomic loci influencing brain shape, of which 76 are also linked to face shape. Shared loci include transcription factors involved in craniofacial development, as well as members of signaling pathways implicated in brain-face cross-talk. Brain shape heritability is equivalently enriched near regulatory regions active in either forebrain organoids or facial progenitors. However, we do not detect significant overlap between shared brain-face genome-wide association study signals and variants affecting behavioral-cognitive traits. These results suggest that early in embryogenesis, the face and brain mutually shape each other through both structural effects and paracrine signaling, but this interplay may not impact later brain development associated with cognitive function. A multivariate genome-wide association study highlighting loci that influence both face and brain shape suggesting shared developmental axes during early embryogenesis. These loci did not overlap with those governing behavioral-cognitive traits or neuropsychiatric risk indicating divergence between early brain development and cognitive function. J.W. was supported by the Howard Hughes Medical Institute, a Lorry Lokey endowed professorship and a Stinehart Reed award. S.N. was supported by a Helen Hay Whitney Fellowship. The KU Leuven research team and analyses were supported by the National Institutes of Health (NIH; 1-R01-DE027023 and 2-R01-DE027023), The Research Fund KU Leuven (BOF-C1, C14/15/081 and C14/20/081) and The Research Program of the Research Foundation in Flanders (FWO; G078518N). The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government (department EWI). J.P.S. was supported by an NIH training grant (5T32HG000044-23). J.K.P. was supported by the NIH (HG008140 and HG009431). Pittsburgh personnel, data collection and analyses were supported by the National Institute of Dental and Craniofacial Research (U01-DE020078, R01-DE016148 and R01-DE027023). Funding for genotyping by the National Human Genome Research Institute (X01-HG007821 and X01-HG007485) and funding for initial genomic data cleaning by the University of Washington were provided by contract HHSN268201200008I from the National Institute for Dental and Craniofacial Research awarded to the Center for Inherited Disease Research (https://www.cidr.jhmi.edu/).J.T.was supported by the NIH (5R01-DA033431-07) and the National Science Foundation (1922598). This research has been conducted, in part, using the UKB resource under application no. 43193 (understanding the genetic architecture of human brain shape from MRI using global-to-local shape segmentations), and we are grateful for all the participants in that resource. This manuscript reflects the views of the authors and may not reflect the opinions or views of the UKB funders and investigators. Data used in the preparation of this article were obtained from the ABCD Study (https://abcdstudy.org), held in the National Institute of Mental Health Data Archive. This is a multisite, longitudinal study designed to recruit more than 10,000 children aged 9-10 years and follow them over 10 years into early adulthood. The ABCD Study is supported by the NIH and additional federal partners under award nos. U01DA041022, U01DA041028, U01DA041048, U01DA041089, U01DA041106, U01DA041117, U01DA041120, U01DA041134, U01DA041148, U01DA041156, U01DA041174, U24DA041123, U24DA041147, U01DA041093 and U01DA041025. A full list of supporters is available at https://abcdstudy.org/federal-partners.html.A list of participating sites and study investigators can be found at https://abcdstudy.org/wp-content/uploads/2019/04/Consortium_Members.pdf.ABCD consortium investigators provided data but did not necessarily participate in analysis or writing of this report. This manuscript reflects the views of the authors and may not reflect the opinions or views of the NIH or ABCD consortium investigators. Naqvi, S; Wysocka, J (corresponding author), Stanford Univ, Sch Med, Dept Chem & Syst Biol, Stanford, CA 94305 USA ; Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA ; Stanford Univ, Sch Med, Dept Biol, Stanford, CA 94305 USA. Claes, P (corresponding author), Katholieke Univ Leuven, Dept Human Genet, Leuven, Belgium. ; Univ Hosp Leuven, Med Imaging Res Ctr, Leuven, Belgium ; Katholieke Univ Leuven, ESAT PSI, Dept Elect Engn, Leuven, Belgium ; Murdoch Childrens Res Inst, Melbourne, Vic, Australia. Wysocka, J (corresponding author), Stanford Univ, Sch Med, Dept Dev Biol, Stanford, CA 94305 USA ; Stanford Univ, Sch Med, Howard Hughes Med Inst, Stanford, CA 94305 USA.

Evidence from both model organisms and clinical genetics suggests close coordination between the developing brain and face1–8, but it remains unknown whether this developmental link extends to genetic variation that drives normal-range diversity of face and brain shape. Here, we performed a multivariate genome-wide association study of cortical surface morphology in 19,644 European-ancestry individuals and identified 472 genomic loci influencing brain shape at multiple levels. We discovered a substantial overlap of these brain shape association signals with those linked to facial shape variation, with 76 common to both. These shared loci include transcription factors with cell-intrinsic roles in craniofacial development, as well as members of signaling pathways involved in brain-face crosstalk. Brain shape heritability is equivalently enriched near regulatory regions active in either brain organoids or in facial progenitor cells. However, brain shape association signals shared with face shape are distinct from those shared with behavioral-cognitive traits or neuropsychiatric disorder risk. Together, we uncover common genetic variants and candidate molecular players underlying brain-face interactions. We propose that early in embryogenesis, the face and the brain mutually shape each other through a combination of structural effects and paracrine signaling, but this interplay may have little impact on later brain development associated with cognitive function.

BACKGROUND: Craniofacial syndromes occur in approximately 1 in 5600 to 100,000 infants, often resulting in significant morbidity. Due to the heterogeneity of this patient population, no clear consensus consists on optimal treatment modalities and timing. The aim of this study was to analyze the craniofacial syndrome population that were treated at the University Hospital Leuven. METHODS: A retrospective analysis of patients with a clinical diagnosis of a craniofacial syndrome was performed. Inclusion criteria were patients with a clinical diagnosis of a craniofacial syndrome and that received treatment between "2000-2005" and "2010-2015." Patients with nonsyndromic conditions were excluded. Data regarding patient characteristics, treatment modalities, and treatment outcomes were analyzed. RESULTS: After matching the inclusion criteria, 98 eligible patients, affected by 40 different syndromes were included. In the period of "2000 to 2005," 48 patients were treated, as compared to 50 patients in the period of "2010 to 2015." A statistically significant decrease over time is seen for cleft surgery and orthodontic treatment (P = 0.0017 and P = 0.0015, respectively). No statistically significant differences were found concerning the age at which treatment was received (P = 0.42). Significant associations between treatment modalities were found for orthognathic surgery and distraction osteogenesis (P

The human face is complex and multipartite, and characterization of its genetic architecture remains intriguingly challenging. Applying GWAS to multivariate shape phenotypes, we identified 203 genomic regions associated with normal-range facial variation, 117 of which are novel. The associated regions are enriched for both genes relevant to craniofacial and limb morphogenesis and enhancer activity in cranial neural crest cells and craniofacial tissues. Genetic variants grouped by their contribution to similar aspects of facial variation show high within-group correlation of enhancer activity, and four SNP pairs display evidence of epistasis, indicating potentially coordinated actions of variants within the same cell types or tissues. In sum, our analyses provide new insights for understanding how complex morphological traits are shaped by both individual and coordinated genetic actions.

Nonsyndromic orofacial clefting is one of the most frequently occurring congenital conditions. The aim of the study was to investigate the prevalence and nature of reduced olfactory function in patients with nonsyndromic cleft lip and/or cleft palate (NSCL/P) and their unaffected first-degree relatives. Olfactory function was tested using the Sniffin' Sticks identification test in patients with NSCL/P, in their unaffected relatives, and in control subjects. MR imaging was performed to measure olfactory bulb (OB) volumes and olfactory sulcus (OS) depths. A reduced olfactory function was seen in significantly more patients with NSCL/P (p = .002) than in control subjects, regardless of the cleft type. Strikingly, unaffected relatives of patients with NSCL/P also had a higher rate of hyposmia (p = .001). In hyposmic patients, the OB volumes (left: p = .01 and right: p = .003) and the depth of the left OS (p = .02) were significantly smaller than in controls. In hyposmic relatives, both OS depths (left: p = .02 and right: p = .03) were significantly smaller. Patients with NSCL/P and their unaffected relatives have an increased prevalence of reduced olfactory function, associated with changes in the central olfactory structures.

Screening for fragile X syndrome (FXS) is essential in children with developmental delay or intellectual disability (ID). In addition, using clinical screening checklists remains of high interest in resource-limited settings. We aimed to gain insight into the prevalence of FXS and the distribution of CGG alleles and to evaluate the usefulness of three checklists in specialized institutions in Kinshasa, DR Congo. We recruited 80 males and 25 females from six specialized institutions in Kinshasa and administered a questionnaire comprising items from the following FXS checklists: Hagerman, Maes, and Guruju. FMR1 CGG repeats were assessed for every patient. About 37% of patients were referable for FX testing based on Hagerman's checklist, 35% for Maes', and 43.80% for Guruju's, but none of them was molecularly confirmed to have FXS. Thus, specificities were 62.86, 64.76, and 56.5%, respectively, for Hagerman, Maes, and Guruju, respectively. The mean CGG allele size was 28.55 ± 2.83 (ranges, 17-48). The 29 CGG was the most frequent allele (24.61%). Thus, existing checklists should not be automatically applied to Congolese patients without adjustments. The distribution of CGG repeats and the number of CGG alleles are similar to other African studies. ispartof: JOURNAL OF COMMUNITY GENETICS vol:10 issue:1 pages:153-159 ispartof: location:Germany status: published

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly. ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:103 issue:5 pages:752-768 ispartof: location:United States status: published

Nonsyndromic orofacial clefts (OFCs) are complex traits characterized by multifactorial inheritance and wide phenotypic variability. Numerous studies have shown subtle differences in the faces of unaffected relatives from cleft families compared to controls, the implication being that such outward differences are an incomplete expression reflecting an underlying genetic predisposition. Twins discordant for OFCs provide a unique opportunity to further test this idea, as the unaffected co-twin shares on average 50% (for dizygotic twins) and 100% (for monozygotic twins) of the genetic risk factors as the affected twin. We used 3D surface imaging and spatially-dense morphometry to compare facial shape in a sample of 44 unaffected co-twins and age- and sex-matched unaffected controls (n = 241). Unaffected co-twins showed statistically significant differences in the midface, lateral upper face, and forehead regions, compared to controls. Furthermore, co-twins were characterized by a distinct pattern of midfacial retrusion, broader upper faces, and greater protrusion of the mandible and brow ridges. This same general facial pattern was shown in both unaffected monozygotic and dizygotic co-twin subsets. These results provide additional support that altered facial shape is a phenotypic marker for OFC susceptibility.

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder with a complex genetic architecture. To identify genetic variants underlying ASD, we performed single-variant and gene-based genome-wide association studies using a dense genotyping array containing over 2.3 million single-nucleotide variants in a discovery sample of 160 families with at least one child affected with non-syndromic ASD using a binary (ASD yes/no) phenotype and a quantitative autistic trait. Replication of the top findings was performed in Psychiatric Genomics Consortium and Erasmus Rucphen Family (ERF) cohort study. Significant association of quantitative autistic trait was observed with the TTC25 gene at 17q21.2 (effect size=10.2, P-value=3.4 × 10-7) in the gene-based analysis. The gene also showed nominally significant association in the cohort-based ERF study (effect=1.75, P-value=0.05). Meta-analysis of discovery and replication improved the association signal (P-valuemeta=1.5 × 10-8). No genome-wide significant signal was observed in the single-variant analysis of either the binary ASD phenotype or the quantitative autistic trait. Our study has identified a novel gene TTC25 to be associated with quantitative autistic trait in patients with ASD. The replication of association in a cohort-based study and the effect estimate suggest that variants in TTC25 may also be relevant for broader ASD phenotype in the general population. TTC25 is overexpressed in frontal cortex and testis and is known to be involved in cilium movement and thus an interesting candidate gene for autistic trait.