ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries.

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

Parents' perspectives and performance evaluation of facial analysis technologies for the diagnosis of congenital disorders

Dissertation (MSc (Genetics))--University of Pretoria, 2022.Congenital disorders are a major health care burden. Most congenital disorders that are due to genetic causes do not have a cure, but an early and accurate diagnosis may alleviate associated symptoms and contribute to the correct management of the disorder. However, there is a lack of medical geneticists and doctors who can make these diagnoses in developing countries. Thus, facial analysis technologies can provide a quick and objective way to initially diagnose individuals with a congenital disorder where resources are limited because almost half of all inherited disorders have a typical facial gestalt. Chapter 1 is a literature review, focusing on facial analysis technologies and how it is used to make an initial diagnosis based on the typical facial features of an individual, with a special focus on Face2Gene. I briefly reviewed the four disorders under investigation in this study, their prevalence, cause, and particularly the typical facial features associated with each disorder. We first aimed to better understand parents’ views on the collection, storage, use, and publication of their children’s facial images for research and diagnosis. Large datasets of facial photographs are required to train facial analysis algorithms, and we wanted to better understand the public’s views on this topic. This was achieved by conducting an online survey, found in Chapter 2, aimed at parents of children with and without a congenital disorder. The second aim of this study was to determine and compare the diagnostic accuracies of two- dimensional facial analyses of congenital disorders. Face2Gene is a popular phenotyping web tool and is free to use for healthcare professionals. The technology does not, however, classify an individual as “non-syndromic” and will suggest likely syndromes to all submitted facial images. Differentiation between syndromic and non-syndromic individuals is important for clinicians to determine if the child requires further testing or investigation into a potential diagnosis. Chapter 3 aimed to establish how well Face2Gene can differentiate between syndromic and non-syndromic facial images, and we compared that to our in-house analyses of the facial features of individuals. Previous research showed that Face2Gene did not perform well in African ethnic groups before training. This is likely due to the algorithm’s training data mostly consisting of European individuals. It is also important to establish a diagnosis as early as possible, to ensure the correct management strategies are put in place. In Chapter 4, we thus aimed to establish how well the Face2Gene algorithm can differentiate between syndromic and non-syndromic facial images in different syndrome, ethnic, and age groups. We again compared that to the results from our in-house analyses.University of PretoriaBiochemistry, Genetics and Microbiology (BGM)MSc (Genetics)Unrestricte

PhenoScore: AI-based phenomics to quantify rare disease and genetic variation

While both molecular and phenotypic data are essential when interpreting genetic variants, prediction scores (CADD, PolyPhen, and SIFT) have focused on molecular details to evaluate pathogenicity — omitting phenotypic features. To unlock the full potential of phenotypic data, we developed PhenoScore: an open source, artificial intelligence-based phenomics framework. PhenoScore combines facial recognition technology with Human Phenotype Ontology (HPO) data analysis to quantify phenotypic similarity at both the level of individual patients as well as of cohorts. We prove PhenoScore’s ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 25 out of 26 investigated genetic syndromes against clinical features observed in individuals with other neurodevelopmental disorders. Moreover, PhenoScore was able to provide objective clinical evidence for two distinct ADNP-related phenotypes, that had already been established functionally, but not yet phenotypically. Hence, PhenoScore will not only be of use to unbiasedly quantify phenotypes to assist genomic variant interpretation at the individual level, such as for reclassifying variants of unknown clinical significance, but is also of importance for detailed genotype-phenotype studies

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

Effect of 16P11.2 copy number variants on cognitive traits and brain structures

The 600kb 16p11.2 CNVs (breakpoints 4–5, 29.6-30.2 Mb-Hg19) are among the most frequent genetic risk factors for neurodevelopmental and psychiatric conditions: A 10-fold enrichment of deletions and duplications is observed in autism cohorts and a 10-fold enrichment of duplications in schizophrenia cohorts. Previous studies demonstrated “mirror” effects of both CNVs on body mass index and head circumference (deletion>control>duplication). However, the large global effect of brain size and the sample size of the two previous neuroimaging studies limited the interpretation of the analyses on regional brain structures, any estimate of the effect size, and the generalizability of the results across different ascertainments of the patients. In the first part of my Ph.D., I analyze structural magnetic resonance imaging (MRI) on 78 deletion carriers, 71 duplication carriers, and 212 controls. I show that both CNVs affect in a “mirror” way the volume and the cortical surface of the insula (Cohen’s d>1), whilst other brain regions are preferentially altered in either the deletion carriers (calcarine cortex and superior, middle, transverse temporal gyri, Cohen’s d>1) or the duplication carriers (caudate and hippocampus, Cohen’s d of 0.5 to 1). Results are generalizable across scanning sites, computational methods, age, sex, ascertainment for psychiatric disorders. They partially overlap with results of meta-analyses performed across psychiatric disorders. In the second part, I characterize the developmental trajectory of global brain metrics and regional brain structures in the 16p11.2 CNV carriers. I adapt a previously published longitudinal pipeline and normalizing method, derived from 339 typically developing individuals aged from 4.5 to 20 years old. From this population of reference, I Z-score our cross-sectional 16p11.2 dataset and show that all the brain alterations in the 16p11.2 carriers are already present at 4.5 years old and follow parallel trajectories to the controls. In summary, my results suggest that brain alterations, present in childhood and stable across adolescence and adulthood, are related to the risk conferred by the 16p11.2 CNVs, regardless of the carriers’ symptoms. Additional factors are therefore likely required for the development of psychiatric disorders. I highlight the relevance of studying genetic risk factors and mechanisms as a complement to groups defined by behavioral criteria. Further studies comparing multiple CNVs and monogenic conditions, from the earliest age, are required to understand the onset of neuroanatomical alterations and their overlap between different genetic risk factors for neurodevelopmental disorders. -- Les variations en nombre de copies (CNV), au locus 16p11.2 et d’une taille d’600kb (points de cassure 4–5, 29.6-30.2 Mb-Hg19) représentent un des facteurs de risque génétique les plus fréquents parmi les troubles psychiatriques : 10% d’enrichissement en délétion et duplication pour les troubles du spectre autistique, 10% d’enrichissement en duplication pour la schizophrénie. Les effets « miroirs » des deux CNVs sur l’indice de masse corporelle et le périmètre cranien ont déjà été démontrés (délétion>contrôle>duplication). Cependant, les différences en taille de cerveau et les échantillons des deux précédentes études de neuro- imagerie ont limité les analyses des régions cérébrales, l’estimation de la taille des effets, et la généralisation des résultats selon les modes de recrutement des patients. Dans cette thèse, j’analyse les images par résonance magnétique (IRM) de 78 porteurs de la délétion, 71 porteurs de la duplication et 212 participants contrôles. Je montre que les deux CNVs sont associées à des différences « en miroir » du volume et de la surface corticale de l’insula (Cohen’s d>1), tandis que le cortex calcarin, les gyri temporaux supérieur, moyen et transverse sont préférentiellement altérés par la délétion (Cohen’s d>1), les noyaux caudés et l’hippocampe sont préférentiellement altérés par la duplication (0.5<Cohen’s d<1). Les résultats sont généralisables à travers les differents sites d’IRM, les méthodes d’analyse computationnelle, les âges, les sexes et les divers diagnostiques psychiatriques des patients. Les résultats chevauchent partiellement ceux d’une méta-analyse sur plusieurs diagnostiques psychiatriques. Dans un second temps, je caractérise la trajectoire développementale de ces différences cérébrales. J’adapte un pipeline longitunal et une méthode de normalisation déjà publiés, construits à partir de 339 participants contrôles de 4.5 à 20 ans. Je calcule des Z-scores pour nos données transversales et montre que les différences cérébrales liées aux CNVs sont déjà présentes à 4.5 ans, avec les mêmes tailles d’effet et une trajectoire parallèle aux contrôles. En résumé, mes résultats suggèrent que les différences cérébrales, présentes dans la jeune enfance et stables à l’adolescence et l’âge adulte, sont liées au risque conféré par les CNVs en 16p11.2, quelque soient les symptômes. Des facteurs additionnels sont probablement nécessaires pour le développement de maladies psychiatriques. Je montre la pertinence d’étudier les facteurs de risque génétiques en complément des groupes de patients définis sur des critères comportementaux. Des études comparant diverses conditions génétiques, dès la naissance, sont nécessaires pour comprendre le début et le chevauchement des différences neuro-anatomiques observées pour différents facteurs de risque génétiques

Developmental malformation of the corpus callosum: a review of typical callosal development and examples of developmental disorders with callosal involvement

This review provides an overview of the involvement of the corpus callosum (CC) in a variety of developmental disorders that are currently defined exclusively by genetics, developmental insult, and/or behavior. I begin with a general review of CC development, connectivity, and function, followed by discussion of the research methods typically utilized to study the callosum. The bulk of the review concentrates on specific developmental disorders, beginning with agenesis of the corpus callosum (AgCC)—the only condition diagnosed exclusively by callosal anatomy. This is followed by a review of several genetic disorders that commonly result in social impairments and/or psychopathology similar to AgCC (neurofibromatosis-1, Turner syndrome, 22q11.2 deletion syndrome, Williams yndrome, and fragile X) and two forms of prenatal injury (premature birth, fetal alcohol syndrome) known to impact callosal development. Finally, I examine callosal involvement in several common developmental disorders defined exclusively by behavioral patterns (developmental language delay, dyslexia, attention-deficit hyperactive disorder, autism spectrum disorders, and Tourette syndrome)

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of big data (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA\u27s activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

Variations in Craniofacial and Velopharyngeal Structures Among Individuals with 22q11.2 Deletion Syndrome

22q11.2 deletion syndrome is the most common genetic cause of velopharyngeal dysfunction. Studies examining 22q11.2 deletion syndrome have thus far primarily focused on variations in the bony framework. Limited information exists regarding the velopharyngeal muscle variations for this clinically challenging population. However, with advances in MRI, muscle and soft tissue imaging is possible. A series of experiments were thus designed to explore and validate the use of our research methodology on normal control participants and a single participant with 22q11.2 deletion syndrome, before initiating the study on a larger sample of children with 22q11.2 deletion syndrome. The overarching aims of this investigation were to examine craniofacial and velopharyngeal characteristics among children with 22q11.2 deletion syndrome and to determine whether craniofacial measures can predict velopharyngeal structure and muscle configurations in this population. This investigation represents the first large scale attempt to image children with 22q11.2 DS without sedation. The aim of Study I was to validate the use of a supine MRI scanner over an upright scanner to obtain data of interest. Study II was focused on the application of a child-friendly MRI protocol to ensure data collection on young pediatric participants without the use of sedation. The aim of Study III was to translate our child-friendly MRI scanning protocol to a clinical population and assess feasibility in a single participant with 22q11.2 deletion syndrome. Study IV assessed craniofacial and velopharyngeal characteristics among children with 22q11.2 deletion syndrome using the imaging protocol detailed in studies one, two, and three. Results from this study suggest that children with 22q11.2 deletion syndrome have several craniofacial and velopharyngeal characteristics that are significantly different compared to children with normal velopharyngeal anatomy. This investigation describes a safe and effective method to obtain MRI data in a clinically complex population without the use of sedation. Individuals with 22q11.2 deletion syndrome present with unique velopharyngeal muscle variations that may contribute to the high rate of velopharyngeal dysfunction associated with this syndrome

Ethanol-Induced Face-Brain Dysmorphology Patterns Are Correlative and Exposure-Stage Dependent

Prenatal ethanol exposure is the leading preventable cause of congenital mental disability. Whereas a diagnosis of fetal alcohol syndrome (FAS) requires identification of a specific pattern of craniofacial dysmorphology, most individuals with behavioral and neurological sequelae of heavy prenatal ethanol exposure do not exhibit these defining facial characteristics. Here, a novel integration of MRI and dense surface modeling-based shape analysis was applied to characterize concurrent face-brain phenotypes in C57Bl/6J fetuses exposed to ethanol on gestational day (GD)7 or GD8.5. The facial phenotype resulting from ethanol exposure depended upon stage of insult and was predictive of unique patterns of corresponding brain abnormalities. Ethanol exposure on GD7 produced a constellation of dysmorphic facial features characteristic of human FAS, including severe midfacial hypoplasia, shortening of the palpebral fissures, an elongated upper lip, and deficient philtrum. In contrast, ethanol exposure on GD8.5 caused mild midfacial hypoplasia and palpebral fissure shortening, a shortened upper lip, and a preserved philtrum. These distinct, stage-specific facial phenotypes were associated with unique volumetric and shape abnormalities of the septal region, pituitary, and olfactory bulbs. By demonstrating that early prenatal ethanol exposure can cause more than one temporally-specific pattern of defects, these findings illustrate the need for an expansion of current diagnostic criteria to better capture the full range of facial and brain dysmorphology in fetal alcohol spectrum disorders

medical and dental considerations

Patients with an orofacial cleft (OFC) need complex treatment and require long-term and collective decisions from the multidisciplinary team. These patients may have an associated congenital malformation or syndrome. Some conditions like learning or psychiatric disorders or heart diseases can be diagnosed later in life. Therefore, the team members should examine the patients in different developmental stages to diagnose early an associated condition. Nevertheless, deep phenotyping of the dental and craniofacial affecting structures is only possible after 14 and 18 years of age, respectively, at the end of these structures’ development. Moreover, the genetic basis of OFC is multifactorial and, so far, not well understood. In our study, almost 25% of the examined patients with OFC had a positive family history (Bartzela et al., 2021). Patients with CPO have an associated anomaly or syndrome (66,7%) more often than patients with other cleft types. Skeletal (27,7%) and eye malformations (22,9%) were more common than malformations in other organs or systems. Sex predominance has been registered according to the cleft type. Males were more often observed in CL/P (71,4%) and females (59,7%) in CPO cleft types. Phenotyping CL/P pedigrees make understanding etiopathogenesis even more complicated (Bartzela et al., 2021). The increased prevalence of TA in these patients inside and outside the cleft region of the maxilla but also in the mandible suggests a common genetic pathway between OFC and TA. Patients with OFC require long-lasting, multidisciplinary orthodontic treatment with an MBA. Expansion and symmetry of the collapsed dental arches, followed by a secondary bone graft to correct the interrupted arch continuity, are required before the orthodontic tooth movement in the cleft region. The severe form of EARR related to orthodontic treatment is rare, and the most commonly affected teeth are the central incisors of the cleft side (Bartzela et al., 2020). Severe rotation of the central incisors on the cleft side, pre-existing EARR, atypical root form, specific bone anatomical aspects, oral habits (e.g., lip or tongue posture or dysfunction), and associated medical conditions have been considered as predisposing factors for EARR during the orthodontic treatment (Bartzela et al., 2020). Intercenter studies for evaluating treatment outcomes of patients with CLP can be carried out with e-mail transfer or CDs of images of the dental casts or digital models. The images could be protected by a password, allowing the participant raters from their computers to access and score the dental models. This method facilitates intercenter studies or remote clinical audits. Clinical trials, intercenter studies, and epidemiological data may help evaluate treatment results and identify the role of genetic variation bias and confounding factors on clinical phenotypes. Documentation and meticulous record collection of these patients for the quality assessment of the treatment outcome are mandatory. Early identification of associated syndromes or malformations is of vital importance, especially in life-threatening complications. The type and timing of orthodontic treatment and maxillofacial surgery are critical and often complicated by disrupting dental and craniofacial structures’ development. The team’s goal is to improve function and aesthetic outcomes and ascertain a better quality of life for these patients and their families. Patients’ and parents’ considerations, satisfaction, and psychosocial aspects need research evaluation. Further research is required for clinical recommendations and treatment consensus