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Abstract The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses. Here, we present a method (Chameleolyser) that accurately identifies single nucleotide variants and small insertions/deletions (SNVs/Indels), copy number variants and ectopic gene conversion events in duplicated genomic regions using whole-exome sequencing data. Application to a cohort of 41,755 exome samples yields 20,432 rare homozygous deletions and 2,529,791 rare SNVs/Indels, of which we show that 338,084 are due to gene conversion events. None of the SNVs/Indels are detectable using regular analysis techniques. Validation by high-fidelity long-read sequencing in 20 samples confirms >88% of called variants. Focusing on variation in known disease genes leads to a direct molecular diagnosis in 25 previously undiagnosed patients. Our method can readily be applied to existing exome data.

Abstract Allele-specific expression (ASE) analysis detects the relative abundance of alleles at heterozygous loci as a proxy for cis-regulatory variation, which affects the personal transcriptome and proteome. This study describes the development and application of an ASE analysis pipeline on a unique cohort of 87 well phenotyped and RNA sequenced patients from the Maastricht Cardiomyopathy Registry with dilated cardiomyopathy (DCM), a complex genetic disorder with a remaining gap in explained heritability. Regulatory processes for which ASE is a proxy might explain this gap. We found an overrepresentation of known DCM-associated genes among the significant results across the cohort. In addition, we were able to find genes of interest that have not been associated with DCM through conventional methods such as genome-wide association or differential gene expression studies. The pipeline offers RNA sequencing data processing, individual and population level ASE analyses as well as group comparisons and several intuitive visualizations such as Manhattan plots and protein–protein interaction networks. With this pipeline, we found evidence supporting the case that cis-regulatory variation contributes to the phenotypic heterogeneity of DCM. Additionally, our results highlight that ASE analysis offers an additional layer to conventional genomic and transcriptomic analyses for candidate gene identification and biological insight.

Abstract A growing number of children born are conceived through in vitro fertilisation (IVF), which has been linked to an increased risk of adverse perinatal outcomes, as well as altered growth profiles and cardiometabolic differences in the resultant individuals. Some of these outcomes have also been shown to be influenced by the use of different IVF culture media and this effect is hypothesised to be mediated epigenetically, e.g. through the methylome. As such, we profiled the umbilical cord blood methylome of IVF neonates that underwent preimplantation embryo development in two different IVF culture media (G5 or HTF), using the Infinium Human Methylation EPIC BeadChip. We found no significant methylation differences between the two groups in terms of: (i) systematic differences at CpG sites or regions, (ii) imprinted sites/genes or birth weight-associated sites, (iii) stochastic differences presenting as DNA methylation outliers or differentially variable sites, and (iv) epigenetic gestational age acceleration.

Summary: TSPEAR variants cause autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown. The clinical features, the mutation spectrum, and the underlying mechanisms of ARED14 are poorly understood. Combining data from new and previously published individuals established that ARED14 is primarily characterized by dental anomalies such as conical tooth cusps and hypodontia, like those seen in individuals with WNT10A-related odontoonychodermal dysplasia. AlphaFold-predicted structure-based analysis showed that most of the pathogenic TSPEAR missense variants likely destabilize the β-propeller of the protein. Analysis of 100000 Genomes Project (100KGP) data revealed multiple founder TSPEAR variants across different populations. Mutational and recombination clock analyses demonstrated that non-Finnish European founder variants likely originated around the end of the last ice age, a period of major climatic transition. Analysis of gnomAD data showed that the non-Finnish European population TSPEAR gene-carrier rate is ∼1/140, making it one of the commonest AREDs. Phylogenetic and AlphaFold structural analyses showed that TSPEAR is an ortholog of drosophila Closca, an extracellular matrix-dependent signaling regulator. We, therefore, hypothesized that TSPEAR could have a role in enamel knot, a structure that coordinates patterning of developing tooth cusps. Analysis of mouse single-cell RNA sequencing (scRNA-seq) data revealed highly restricted expression of Tspear in clusters representing enamel knots. A tspeara−/−;tspearb−/− double-knockout zebrafish model recapitulated the clinical features of ARED14 and fin regeneration abnormalities of wnt10a knockout fish, thus suggesting interaction between tspear and wnt10a. In summary, we provide insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.

Members of the CHD chromatin remodeler family are implicated in human pathologies, however CHD6 remained poorly studied. Here, the authors show that CHD6 binds to and regulates autophagy and stress response genes across cell types. They identify a clinical mutation that affects its ability to recruit cofactors, leading to impaired autophagy induction and DNA repair.

Monoamine neurotransmitter abundance affects motor control, emotion, and cognitive function and is regulated by monoamine oxidases. Among these, Monoamine oxidase A (MAOA) catalyzes the degradation of dopamine, norepinephrine, and serotonin into their inactive metabolites. Loss-of-function mutations in the X-linked MAOA gene have been associated with Brunner syndrome, which is characterized by various forms of impulsivity, maladaptive externalizing behavior, and mild intellectual disability. Impaired MAOA activity in individuals with Brunner syndrome results in bioamine aberration, but it is currently unknown how this affects neuronal function, specifically in dopaminergic (DA) neurons. Here we generated human induced pluripotent stem cell (hiPSC)-derived DA neurons from three individuals with Brunner syndrome carrying different mutations and characterized neuronal properties at the single cell and neuronal network level in vitro. DA neurons of Brunner syndrome patients showed reduced synaptic density but exhibited hyperactive network activity. Intrinsic functional properties and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-mediated synaptic transmission were not affected in DA neurons of individuals with Brunner syndrome. Instead, we show that the neuronal network hyperactivity is mediated by upregulation of the GRIN2A and GRIN2B subunits of the N-methyl-d-aspartate receptor (NMDAR), resulting in increased NMDAR-mediated currents. By correcting a MAOA missense mutation with CRISPR/Cas9 genome editing we normalized GRIN2A and GRIN2B expression, NMDAR function and neuronal population activity to control levels. Our data suggest that MAOA mutations in Brunner syndrome increase the activity of dopaminergic neurons through upregulation of NMDAR function, which may contribute to the etiology of Brunner syndrome associated phenotypes.

Abstract Background Spinal dysraphism with a hamartomatous growth (appendix) of the spinal cord is better known as herniated spinal cord. There are many arguments in favour of considering it a developmental defect. From this point of view, it is a type of neural tube disorder. Neural tube disorders can be caused by multiple factors, including a genetic factor. A common genetic defect in patients with a spinal dysraphism with a hamartomatous growth of the spinal cord is sought for. Case presentation In two patients with a symptomatic lesion and referred to an academic hospital a genetic analysis was performed after informed consent. Whole-exome analysis was performed. : Whole-exome analysis did not result in identification of a clinically relevant genetic variant. Conclusions This the first study to investigate the genetic contribution to spinal dysraphism with a hamartomatous growth (appendix) of the spinal cord. We could not establish a genetic cause for this entity. This conclusion cannot be definitive due to the small sample size. However, the incidental occurrence, the lack of reports of inheritance of this disorder and the absence of contribution to syndromal disorders favours a defect of normal development of the spinal cord.

Abstract Background Massively parallel genetic sequencing allows rapid testing of known intellectual disability (ID) genes. However, the discovery of novel syndromic ID genes requires molecular confirmation in at least a second or a cluster of individuals with an overlapping phenotype or similar facial gestalt. Using computer face-matching technology we report an automated approach to matching the faces of non-identical individuals with the same genetic syndrome within a database of 3681 images [1600 images of one of 10 genetic syndrome subgroups together with 2081 control images]. Using the leave-one-out method, two research questions were specified: 1) Using two-dimensional (2D) photographs of individuals with one of 10 genetic syndromes within a database of images, did the technology correctly identify more than expected by chance: i) a top match? ii) at least one match within the top five matches? or iii) at least one in the top 10 with an individual from the same syndrome subgroup? 2) Was there concordance between correct technology-based matches and whether two out of three clinical geneticists would have considered the diagnosis based on the image alone? Results The computer face-matching technology correctly identifies a top match, at least one correct match in the top five and at least one in the top 10 more than expected by chance (P

Sindromul Bardet-Biedl (transmitere autozomal-recesivă) este caracterizat prin obezitate, degenerescenţă retiniană, polidactilie şi retard mental. Autorii prezintă demersul diagnostic la un sugar cu paratrofi e, polidactilie şi hipogenitalism.

Bardet-Biedl syndrome (autosomal-recessive inheritance) is characterized by obesity, retinal dystrophy, polydactyly and mental retardation. The authors emphasize the necessary steps in order to establish the diagnosis for an infant with overweight, polydactyly and hypogenitalism.

Smith-Lemli-Opitz syndrome (SLOS) is an autosomal-recessive inherited disease characterized by multiple anomalies secondary to cholesterol synthesis impairment. The authors present diagnosis peculiarities and limitation of treatment options in a 5-weeks old infant with ambiguous genitalia.

Sindromul Smith-Lemli-Opitz (SSLO) reprezintă o afecţiune cu transmitere autozomal-recesivă caracterizată prin multiple anomalii şi care se datorează anomaliilor în sinteza colesterolului. Autorii prezintă particularităţile diagnostice şi terapeutice la un sugar cu ambiguitate genitală.

Idiopathic ventral herniation of the spinal cord (SC) is not often encountered in daily practice. Its clinical prevalence, however, will increase through increasing awareness and more frequent use of MRI. A clear explanation of its pathophysiology has never been formulated. It was hypothesized that the findings during surgery might indicate the real causative mechanism. An extensive literature search was performed, using Embase, PubMed, and Google Scholar. Titles and abstracts were screened by two investigators, using strict inclusion and exclusion criteria. Reference lists of the full paper versions of each included article were checked. The following data were registered for the articles included: age, gender, level of herniation, relation to intervertebral disk, duration of symptoms, findings from surgery, and outcomes. Nine cases treated at our department were added. A total of 117 articles reporting on 259 patients were included. Including our cases, 268 patients were reviewed. Females outnumbered males (160/100). The mean age was 51.3 ± 12.0 years. In 236 patients, the duration of symptoms was reported: 55.5 ± 55.6 months. In 178 patients, the intraoperative findings for the herniated part of the SC were not mentioned. In 59 patients, a tumor-like extrusion was seen, without any alteration to the SC. Deformation of the SC itself was never observed. Biopsies of these structures were without clinical consequence. Based on the intraoperative findings reported in literature and the cases presented, acquired causes, such as trauma and erosion of the dura due to a herniated disk, were not plausible. We hypothesize that a non-functioning appendix to the SC can only develop during an early embryologic phase, in which several layers separate. We propose renaming this entity as congenital transdural appendix of the SC.

LEOPARD syndrome is a complex disorder characterized by multiple dysmorphogenetic features. Both syndromes LEOPARD and Noonan are caused by different mutations in the same gene (PTPN11). Authors emphasize diagnosis peculiarities in two related cases with facial dysmorphism. Index case is represented by a 10 year-old boy admitted for evaluation because of cephalofacial dysmorphism associated with mental disabilities. Family history: non-consanguineous parents; the father’s case and his sister with face dysmorphism. Clinical exam: short stature, impaired nutritional status, axillary freckles, widespread café-au-lait spots, face dysmorphism, webbed neck, skeletal anomalies and mental retardation. Blood investigations and cardiac ultrasonography: no anomalies. Differential diagnosis includes Noonan syndrome, Greig syndrome, type 1 neurofi bromatosis, Albright syndrome. Regarding patient genetic evaluation: normal karyotype; DNA sequencing revealed mutation in PTPN11 gene suggestive for LEOPARD syndrome. Authors also found same mutation for probant’s father. Conclusions. Authors described two cases with dysmorphic skull, skeletal anomalies, skin pigmentation, mental disabilities and short stature, justifying further genetic evaluation that revealed a very rare disorder.

Sindromul LEOPARD este o afecţiune ce include multiple anomalii dismorfogenetice. Sindromul LEOPARD, ca şi sindromul Noonan, este determinat de mutaţii ale genei PTPN11. Autorii menţionează particularităţile diagnostice la 2 cazuri înrudite cu dismorfi sm facial. Cazul index este reprezentat de băiat de 10 ani evaluat pentru dis morfi sm cranio-facial asociat cu retard mental. Antecedente heredo-colaterale: fără consangvinitate; tatăl pa cientului şi soră cu dismorfi sm facial. Examenul clinic: retard staturo-ponderal, pistrui axilari, pete caféau-lait diseminate, dismorfi sm facial, pterigium coli, anomalii scheletice, retard mental. Investigaţiile sangvine şi eco-cardiografi a: fără modifi cări. Pentru diagnosticul diferenţial s-au considerat sindroamele Noonan, Greig, neuro fi bromatoza tip 1, sindromul Mc Cune-Albright. Evaluarea genetică: cariotip normal; secvenţierea genei PTPN11 a relevat mutaţia ce confi rmă sindromul LEOPARD. Analiza genetică a relevat aceeaşi mutaţie la tatăl pacientului. Concluzii. Autorii au descris 2 cazuri familiale cu craniu dismorf, anomalii scheletice, pigmentaţia pielii, dizabilităţi mentale şi statură mică, justifi când evaluarea genetică care a identificat o afecţiune genetică foarte rară.

BACKGROUND: Reduced total brain volume is a consistent finding in children with Attention Deficit/Hyperactivity Disorder (ADHD). In order to get a better understanding of the neurobiology of ADHD, we take the first step in studying the dimensionality of current self-reported adult ADHD symptoms, by looking at its relation with total brain volume. METHODOLOGY/PRINCIPAL FINDINGS: In a sample of 652 highly educated adults, the association between total brain volume, assessed with magnetic resonance imaging, and current number of self-reported ADHD symptoms was studied. The results showed an association between these self-reported ADHD symptoms and total brain volume. Post-hoc analysis revealed that the symptom domain of inattention had the strongest association with total brain volume. In addition, the threshold for impairment coincides with the threshold for brain volume reduction. CONCLUSIONS/SIGNIFICANCE: This finding improves our understanding of the biological substrates of self-reported ADHD symptoms, and suggests total brain volume as a target intermediate phenotype for future gene-finding in ADHD.

Johanson-Blizzard syndrome (JBS; OMIM 243800) is an autosomal recessive disorder that includes congenital exocrine pancreatic insufficiency, facial dysmorphism with the characteristic nasal wing hypoplasia, multiple malformations, and frequent mental retardation. Our previous work has shown that JBS is caused by mutations in human UBR1, which encodes one of the E3 ubiquitin ligases of the N-end rule pathway. The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. One class of degradation signals (degrons) recognized by UBR1 are destabilizing N-terminal residues of protein substrates.Most JBS-causing alterations of UBR1 are nonsense, frameshift or splice-site mutations that abolish UBR1 activity. We report here missense mutations of human UBR1 in patients with milder variants of JBS. These single-residue changes, including a previously reported missense mutation, involve positions in the RING-H2 and UBR domains of UBR1 that are conserved among eukaryotes. Taking advantage of this conservation, we constructed alleles of the yeast Saccharomyces cerevisiae UBR1 that were counterparts of missense JBS-UBR1 alleles. Among these yeast Ubr1 mutants, one of them (H160R) was inactive in yeast-based activity assays, the other one (Q1224E) had a detectable but weak activity, and the third one (V146L) exhibited a decreased but significant activity, in agreement with manifestations of JBS in the corresponding JBS patients.These results, made possible by modeling defects of a human ubiquitin ligase in its yeast counterpart, verified and confirmed the relevance of specific missense UBR1 alleles to JBS, and suggested that a residual activity of a missense allele is causally associated with milder variants of JBS.

Genomics methodologies have significantly improved elucidation of Mendelian disorders. The combination with high-throughput functional-omics technologies potentiates the identification and confirmation of causative genetic variants, especially in singleton families of recessive inheritance. In a cohort of 99 individuals with abnormal Golgi glycosylation, 47 of which being unsolved, glycomics profiling was performed of total plasma glycoproteins. Combination with whole-exome sequencing in 31 cases revealed a known genetic defect in 15 individuals. To identify additional genetic factors, hierarchical clustering of the plasma glycomics data was done, which indicated a subgroup of four patients that shared a unique glycomics signature of hybrid type N-glycans. In two siblings, compound heterozygous mutations were found in SLC10A7, a gene of unknown function in human. These included a missense mutation that disrupted transmembrane domain 4 and a mutation in a splice acceptor site resulting in skipping of exon 9. The two other individuals showed a complete loss of SLC10A7 mRNA. The patients' phenotype consisted of amelogenesis imperfecta, skeletal dysplasia, and decreased bone mineral density compatible with osteoporosis. The patients' phenotype was mirrored in SLC10A7 deficient zebrafish. Furthermore, alizarin red staining of calcium deposits in zebrafish morphants showed a strong reduction in bone mineralization. Cell biology studies in fibroblasts of affected individuals showed intracellular mislocalization of glycoproteins and a defect in post-Golgi transport of glycoproteins to the cell membrane. In contrast to yeast, human SLC10A7 localized to the Golgi. Our combined data indicate an important role for SLC10A7 in bone mineralization and transport of glycoproteins to the extracellular matrix.