GLI3 variants causing isolated polysyndactyly are not restricted to the protein's C-terminal third

Loss of function variants of GLI3 are associated with a variety of forms of polysyndactyly: Pallister-Hall syndrome (PHS), Greig-Cephalopolysyndactyly syndrome (GCPS), and isolated polysyndactyly (IPD). Variants affecting the N-terminal and C-terminal thirds of the GLI3 protein have been associated with GCPS, those within the central third with PHS. Cases of IPD have been attributed to variants affecting the C-terminal third of the GLI3 protein. In this study, we further investigate these genotype-phenotype correlations. Sequencing of GLI3 was performed in patients with clinical findings suggestive of a GLI3-associated syndrome. Additionally, we searched the literature for reported cases of either manifestation with mutations in the GLI3 gene. Here, we report 48 novel cases from 16 families with polysyndactyly in whom we found causative variants in GLI3 and a review on 314 previously reported GLI3 variants. No differences in location of variants causing either GCPS or IPD were found. Review of published data confirmed the association of PHS and variants affecting the GLI3 protein's central third. We conclude that the observed manifestations of GLI3 variants as GCPS or IPD display different phenotypic severities of the same disorder and propose a binary division of GLI3-associated disorders in either PHS or GCPS/polysyndactyly

Efficiency of Computer-Aided Facial Phenotyping (DeepGestalt) in Individuals With and Without a Genetic Syndrome: Diagnostic Accuracy Study

Background: Collectively, an estimated 5% of the population have a genetic disease. Many of them feature characteristics that can be detected by facial phenotyping. Face2Gene CLINIC is an online app for facial phenotyping of patients with genetic syndromes. DeepGestalt, the neural network driving Face2Gene, automatically prioritizes syndrome suggestions based on ordinary patient photographs, potentially improving the diagnostic process. Hitherto, studies on DeepGestalt’s quality highlighted its sensitivity in syndromic patients. However, determining the accuracy of a diagnostic methodology also requires testing of negative controls. Objective: The aim of this study was to evaluate DeepGestalt's accuracy with photos of individuals with and without a genetic syndrome. Moreover, we aimed to propose a machine learning–based framework for the automated differentiation of DeepGestalt’s output on such images. Methods: Frontal facial images of individuals with a diagnosis of a genetic syndrome (established clinically or molecularly) from a convenience sample were reanalyzed. Each photo was matched by age, sex, and ethnicity to a picture featuring an individual without a genetic syndrome. Absence of a facial gestalt suggestive of a genetic syndrome was determined by physicians working in medical genetics. Photos were selected from online reports or were taken by us for the purpose of this study. Facial phenotype was analyzed by DeepGestalt version 19.1.7, accessed via Face2Gene CLINIC. Furthermore, we designed linear support vector machines (SVMs) using Python 3.7 to automatically differentiate between the 2 classes of photographs based on DeepGestalt's result lists. Results: We included photos of 323 patients diagnosed with 17 different genetic syndromes and matched those with an equal number of facial images without a genetic syndrome, analyzing a total of 646 pictures. We confirm DeepGestalt’s high sensitivity (top 10 sensitivity: 295/323, 91%). DeepGestalt’s syndrome suggestions in individuals without a craniofacially dysmorphic syndrome followed a nonrandom distribution. A total of 17 syndromes appeared in the top 30 suggestions of more than 50% of nondysmorphic images. DeepGestalt’s top scores differed between the syndromic and control images (area under the receiver operating characteristic [AUROC] curve 0.72, 95% CI 0.68-0.76; P<.001). A linear SVM running on DeepGestalt’s result vectors showed stronger differences (AUROC 0.89, 95% CI 0.87-0.92; P<.001). Conclusions: DeepGestalt fairly separates images of individuals with and without a genetic syndrome. This separation can be significantly improved by SVMs running on top of DeepGestalt, thus supporting the diagnostic process of patients with a genetic syndrome. Our findings facilitate the critical interpretation of DeepGestalt’s results and may help enhance it and similar computer-aided facial phenotyping tools

Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus

During human organogenesis, lung development is a timely and tightly regulated developmental process under the control of a large number of signaling molecules. Understanding how genetic variants can disturb normal lung development causing different lung malformations is a major goal for dissecting molecular mechanisms during embryogenesis. Here, through exome sequencing (ES), array CGH, genome sequencing (GS) and Hi-C, we aimed at elucidating the molecular basis of bilateral isolated lung agenesis in three fetuses born to a non-consanguineous family. We detected a complex genomic rearrangement containing duplicated, triplicated and deleted fragments involving the SHH locus in fetuses presenting complete agenesis of both lungs and near-complete agenesis of the trachea, diagnosed by ultrasound screening and confirmed at autopsy following termination. The rearrangement did not include SHH itself, but several regulatory elements for lung development, such as MACS1, a major SHH lung enhancer, and the neighboring genes MNX1 and NOM1. The rearrangement incorporated parts of two topologically associating domains (TADs) including their boundaries. Hi-C of cells from one of the affected fetuses showed the formation of two novel TADs each containing SHH enhancers and the MNX1 and NOM1 genes. Hi-C together with GS indicate that the new 3D conformation is likely causative for this condition by an inappropriate activation of MNX1 included in the neo-TADs by MACS1 enhancer, further highlighting the importance of the 3D chromatin conformation in human disease

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Background: Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. // Methods: We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung's disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. // Findings: We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung's disease) from 264 hospitals (89 in high-income countries, 166 in middle-income countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in low-income countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. // Interpretation: Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between low-income, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

The global burden of cancer attributable to risk factors, 2010-19 : a systematic analysis for the Global Burden of Disease Study 2019

Background Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. Methods The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk-outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. Findings Globally, in 2019, the risk factors included in this analysis accounted for 4.45 million (95% uncertainty interval 4.01-4.94) deaths and 105 million (95.0-116) DALYs for both sexes combined, representing 44.4% (41.3-48.4) of all cancer deaths and 42.0% (39.1-45.6) of all DALYs. There were 2.88 million (2.60-3.18) risk-attributable cancer deaths in males (50.6% [47.8-54.1] of all male cancer deaths) and 1.58 million (1.36-1.84) risk-attributable cancer deaths in females (36.3% [32.5-41.3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20.4% (12.6-28.4) and DALYs by 16.8% (8.8-25.0), with the greatest percentage increase in metabolic risks (34.7% [27.9-42.8] and 33.3% [25.8-42.0]). Interpretation The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.Peer reviewe

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Längenpolymorphismus der pseudoautosomalen Region 1 in der menschlichen Population

Introduction: At each of their ends, the two human sex chromosomes feature a region of identical sequence. These two pseudoautosomal regions (PAR) enable a proper paring and subsequent segregation of the apart from that different sex chromosomes during male meiosis. The border between pseudoautosomal region 1 (PAR1) and the specificly gonosomal sequences originated during the divergence of the great apes. After having lost genetic material from its proximal end, the pseudoautosomal region is considered to be henceforth stable. Doing a copy number variation screening, we detected a duplication immediately proximal of PAR1 in 15 independent families. Although comprising X specific sequence, this duplication was exclusively inherited from father to son. This suggested the duplicon to be positioned on the Y chromosome. Is this duplicon an evolutionarily older version of PAR1 in the manner of a “non-deletion”? Methods: The following methods were used to tackle this issue: aCGH, FISH, PCR with gelelectrophoresis, BAC mediated targeted paired-end sequencing, Sanger sequencing, single molecule sequencing (PacBio) and Y-chr haplogroup and Y-STR typing. Results: This genetic analysis demonstrated that the duplicon featured not an older but a so far unknown younger variant of PAR1. This polymorphism elongating PAR1 by 105kb was generated by a non-allelic homoulogous recombination between the X and the Y chromosome, which was mediated by the 548 bp long repeat LTR6B. The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population. Conclusion: There is a pseudoautosomal length polymorphism in the human population. Pseudoautosomal regions do not only lose genetic material from their proximal ends but can also gain it there. This new mechanism shaping the sex chromosomal evolution could spare pseudoautosomal regions and thus Y-chromosomes from a progressive degradation.Einleitung: An ihren beiden Enden verfügen die menschlichen Geschlechtschromosomen über je einen identischen Sequenzabschnitt. Diese beiden pseudoautosomalen Regionen (PAR) ermöglichen den ansonsten unterschiedlichen Geschlechtschromosomen eine korrekte Paarung und nachfolgende Aufteilung während der Meiose des Mannes. Die Grenze zwischen pseudoautosomaler Region 1 (PAR1) und den spezifischen gonosomalen Sequenzen entstand während der Aufspaltung der Menschenaffen. Nachdem die pseudoautosomale Region an ihrem proximalen Ende Material eingebüßt hatte, gilt sie als fortan stabil. Bei einem Screening auf Kopiezahlpolymorphismen haben wir in 15 voneinander unabhängigen Familien eine Duplikation unmittelbar proximal von PAR1 entdeckt. Obwohl diese Duplikation eine X- spezifische Sequenz beinhaltete, wurde sie ausschließlich von Vater zu Sohn vererbt. Dies ließ vermuten, dass das Duplikon auf dem Y-Chromosom positioniert ist. Handelt es sich bei der Duplikation um eine evolutionär ältere Variante von PAR1 im Sinne einer „Non-Deletion“? Methodik: Um diese Fragestellung anzugehen, wurden folgende Verfahren durchgeführt: aCGH, FISH, PCR mit Gelelektrophorese, BAC- vermittelte gezielte paired-end Hochdurchsatzsequenzierung, Sequenzierung nach Sanger, Einzelmolekülsequenzierung (PacBio) und Y-chromosomale Haplogruppenbestimmung mittels Y-STR Typisierung. Ergebnisse: Diese genomische Analyse zeigte, dass es sich nicht um eine ältere, sondern um eine jüngere bisher unbekannte Variante der PAR1 handelt. Dieser die PAR1 um 105 kbp verlängernde Polymorphismus entstand durch eine nicht-allelische homologe Rekombination zwischen dem X- und dem Y-Chromosom, welche durch den nur 548 bp langen Repeat LTR6B vermittelt wurde. Die Identifikation der reziproken Deletion auf dem X-Chromosom einer Familie und das Vorkommen der Variante in verschiedenen Y-chromosomalen Haplogruppen zeigen, dass es sich dabei um ein wiederkehrendes genomisches Rearrangement in der menschlichen Population handelt. Schlussfolgerung: Es gibt einen Längenpolymorphismus von PAR1 in der menschlichen Population. Pseudoautosomale Regionen verlieren an ihren proximalen Enden nicht nur genetisches Material, sondern können dort auch welches hinzugewinnen. Dieser neue, die gonosomale Evolution gestaltende Mechanismus könnte pseudoautosomale Regionen und folglich auch Y-Chromosomen vor einer voranschreitenden Degradation bewahren

Variable pulmonary manifestations in Chitayat syndrome: Six additional affected individuals

Hand hyperphalangism leading to shortened index fingers with ulnar deviation, hallux valgus, mild facial dysmorphism and respiratory compromise requiring assisted ventilation are the key features of Chitayat syndrome. This condition results from the recurrent heterozygous missense variant NM_006494.2:c.266A>G; p.(Tyr89Cys) in ERF on chromosome 19q13.2, encoding the ETS2 repressor factor (ERF) protein. The pathomechanism of Chitayat syndrome is unknown. To date, seven individuals with Chitayat syndrome and the recurrent pathogenic ERF variant have been reported in the literature. Here, we describe six additional individuals, among them only one presenting with a history of assisted ventilation, and the remaining presenting with variable pulmonary phenotypes, including one individual without any obvious pulmonary manifestations. Our findings widen the phenotype spectrum caused by the recurrent pathogenic variant in ERF, underline Chitayat syndrome as a cause of isolated skeletal malformations and therefore contribute to the improvement of diagnostic strategies in individuals with hand hyperphalangism