Structural Birth Defects Research Articles

Sequence variants in HECTD1 result in a variable neurodevelopmental disorder.

Dysregulation of genes encoding the homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases has been linked to cancer and structural birth defects. One member of this family, the HECT-domain-containing protein 1 (HECTD1), mediates developmental pathways, including cell signaling, gene expression, and embryogenesis. Through GeneMatcher, we identified 14 unrelated individuals with 15 different variants in HECTD1 (10 missense, 3 frameshift, 1 nonsense, and 1 splicing variant) with neurodevelopmental disorders (NDDs), including autism, attention-deficit/hyperactivity disorder, and epilepsy. Of these 15 HECTD1 variants, 10 occurred de novo, 3 had unknown inheritance, and 2 were compound heterozygous. While all individuals in this cohort displayed NDDs, no genotype-phenotype correlation was apparent. Conditional knockout of Hectd1 in the neural lineage in mice resulted in microcephaly, severe hippocampal malformations, and complete agenesis of the corpus callosum, supporting a role for Hectd1 in embryonic brain development. Functional studies of select variants in C. elegans revealed dominant effects, including either change-of-function or loss-of-function/haploinsufficient mechanisms, which may explain phenotypic heterogeneity. Significant enrichment of de novo variants in HECTD1 was also shown in an independent cohort of 53,305 published trios with NDDs or congenital heart disease. Thus, our clinical and functional data support a critical requirement of HECTD1 for human brain development.

Gene-by-environment interactions involving maternal exposures with orofacial cleft risk in Filipinos.

Maternal exposures are known to influence the risk of isolated cleft lip with or without cleft palate (CL/P) - a common and highly heritable birth defect with a multifactorial etiology. To identify new CL/P risk loci, we conducted a genome-wide gene-environment interaction (GEI) analysis of CL/P on a sample of 540 cases and 260 controls recruited from the Philippines, incorporating the interaction effects of genetic variants with maternal smoking and vitamin use. As GEI analyses are typically low in power and the results can be difficult to interpret, we used multiple testing frameworks to evaluate potential GEI effects: 1 degree-of-freedom (1df) GxE test, the 3df joint test, and the two-step EDGE approach. While we did not detect any genome-wide significant interactions, we detected 12 suggestive GEI with smoking and 25 suggestive GEI with vitamin use between all testing frameworks. Several of these loci showed biological plausibility. Notable interactions with smoking include loci near FEZF1 , TWIST2, and NET1. While FEZF1 is involved in early neuronal development, TWIST2 and NET1 regulate epithelial-mesenchymal transition which is required for proper lip and palate fusion. Interactions with vitamins encompass CECR2 - a chromatin remodeling protein required for neural tube closure-and FURIN, a critical protease during early embryogenesis that activates various growth factor and extracellular-matrix protein. The activity of both proteins is influenced by folic acid. Our findings highlight the critical role of maternal exposures in identifying genes associated with structural birth defects such as CL/P and provide new paths to explore for CL/P genetics.

Left Ventricular False Tendons: A Morphological Study by Echocardiography.

This is a prospective study aimed to investigate the morphology of left ventricular false tendons (LVFTs) using echocardiography and explore its associations with age, sex, body mass index (BMI), congenital heart structural abnormalities, and premature ventricular contractions (PVCs). We analyzed data from 889 individuals who underwent consecutive echocardiograms at our ultrasound department between December 2023 and February 2024. Routine echocardiograms were performed to detect congenital structural abnormalities, with a focus on identifying LVFT. We examined the prevalence, number, and distribution of LVFTs, as well as their correlation with age, sex, BMI, and congenital heart structural abnormalities. LVFTs were detected in 460 of 889 cases (51.74%), totaling 672 LVFTs. LVFT prevalence significantly differed not only between sexes but also between ages. LVFT prevalence was higher in individuals with lower BMI. There was no significant difference in congenital heart structural abnormalities between the groups, but the composition of distinct types of structural abnormalities differed between the groups. The incidence of PVCs in the LVFT-positive group was significantly higher than in the LVFT-negative group. The prevalence of LVFTs is notably higher in males than females and tends to decrease with advancing age and increasing BMI. LVFTs display diverse morphological features and may interact synergistically with certain congenital heart structural abnormalities. LVFTs can easily lead to PVCs in healthy people, but the risk of leading to malignant PVCs does not seem to be high. Correctly recognizing the morphological characteristics of LVFTs helps to distinguish similar ultrasonic images of different diseases, thus avoiding missed diagnoses and misdiagnoses in ultrasound work and clinical practice.

3D printed sodium alginate/gelatin/tannic acid/calcium chloride scaffolds laden bone marrow mesenchymal stem cells to repair defective thyroid cartilage plate.

Due to the absence of blood vessels, cartilage exhibits extremely limited self-repair capacity. Currently, repairing laryngeal cartilage defects, resulting from conditions such as laryngeal tumors, injury, and congenital structural abnormalities, remains a significant challenge in the Department of Otolaryngology, Head and Neck Surgery. Previous research has often focused on enhancing the mechanical properties of synthetic materials. However, their low biological activity and weak cell adhesion necessitate compensatory measures. This study aims to capitalize on the advantages of natural materials in cartilage tissue engineering. Sodium alginate, gelatin, tannic acid, and calcium chloride were utilized to prepare bioinks through cross-linking for application in 3D printing cartilage scaffolds. Bone marrow mesenchymal stem cells with multidirectional differentiation potential were chosen as seed cells, with appropriate growth factors incorporated to promote their differentiation into cartilage during in vitro culture. The scaffold laden cells was subsequently implanted into rabbit thyroid cartilage plate defects at the appropriate time. HE staining, toluidine blue staining, Masson staining, and collagen type II staining were employed to assess cartilage defect repair at 4, 8, and 12 weeks, respectively. Results demonstrated that scaffolds made from natural materials could emulate the mechanical properties of fresh cartilage with commendable biocompatibility. Stained sections further confirmed the efficacy of the composite hydrogel scaffolds identified in this study in promoting rabbit thyroid cartilage plate restoration. In summary, this study successfully fabricated a natural material scaffold for rabbit laryngeal cartilage tissue engineering, thereby furnishing a new idea and experience for the clinical application of laryngeal cartilage defect reconstruction.

Congenital pulmonary airway malformation in a cat.

Congenital structural anomalies of the lower airways of the respiratory tract are uncommon in cats. We describe here a case of cystic pulmonary lesions in a 6-wk-old domestic shorthair cat consistent with congenital pulmonary airway malformation (CPAM; formerly referred to as cystic adenomatoid malformation of the lung, or congenital pulmonary adenomatoid malformation; Stocker type II). CPAM is rarely reported in veterinary species and, to our knowledge, has not been reported in cats. In humans and veterinary species, individuals with CPAM (Stocker types I-IV) can be asymptomatic at birth but are predisposed to developing respiratory abnormalities that typically manifest clinically in the early years of life. We review the pathologic features of CPAM.

Major structural congenital anomalies and causal pathways in people with cerebral palsy.

https://onlinelibrary.wiley.com/doi/10.1111/dmcn.16073

Intramuscular vascular malformations in pediatric patients: a retrospective study in a vascular anomalies clinic.

Intramuscular vascular malformations (IVMs) are rare developmental congenital structural abnormalities. Their clinical diagnosis is difficult, and imaging studies are essential to determine the type and extent of vessels involved. Treatment can be challenging and must be managed by a multidisciplinary team. A descriptive, observational, retrospective, longitudinal study of clinical records of patients diagnosed with IVMs who were evaluated at the vascular anomalies clinic from January 2011 to December 2021 was performed. Demographic, clinical, imaging, diagnosis, treatment, and response data were collected. Seven patients (five females and two males) with a mean age of 13.66 years (standard deviation 5.82 years) were included in the study. In all cases, the clinical diagnosis was venous and lymphatic malformation. The radiological findings were dilated and tortuous vascular structures or multilobulated lesions with septa inside, with or without vascular flow; these findings allowed diagnosis in all cases. Treatment modalities included sclerotherapy in five patients, surgical resection in two, medical treatment with sirolimus in three, and surveillance in one. Subsequent clinical evolution was favorable in all patients, with decreased pain in six (partial in four and total in two) and size reduction in one patient. IVMs in our pediatric population most frequently affect the lower extremities. The main symptoms and signs were pain on exertion and volume increase. Treatment can be challenging given the extension and depth of the malformations, so a combination of therapeutic modalities may be necessary to obtain the best outcome.

Genome-wide study of gene-by-sex interactions identifies risks for cleft palate.

Structural birth defects affect 3-4% of all live births and, depending on the type, tend to manifest in a sex-biased manner. Orofacial clefts (OFCs) are the most common craniofacial structural birth defects and are often divided into cleft lip with or without cleft palate (CL/P) and cleft palate only (CP). Previous studies have found sex-specific risks for CL/P, but these risks have yet to be evaluated in CP. CL/P is more common in males and CP is more frequently observed in females, so we hypothesized there would also be sex-specific differences for CP. Using a trio-based cohort, we performed sex-stratified genome-wide association studies (GWAS) based on proband sex followed by a genome-wide gene-by-sex (G × S) interaction testing. There were 13 loci significant for G × S interactions, with the top finding in LTBP1 (RR = 3.37 [2.04-5.56], p = 1.93 × 10-6). LTBP1 plays a role in regulating TGF-β bioavailability, and knockdown in both mice and zebrafish lead to craniofacial anomalies. Further, there is evidence for differential expression of LTBP1 between males and females in both mice and humans. Therefore, we tested the association between the imputed genetically regulated gene expression of genes with significant G × S interactions and the CP phenotype. We found significant association for LTBP1 in cell cultured fibroblasts in female probands (p = 0.0013) but not in males. Taken altogether, we show there are sex-specific risks for CP that are otherwise undetectable in a combined sex cohort, and LTBP1 is a candidate risk gene, particularly in females.

Diabetes and Early Development: Epigenetics, Biological Stress, and Aging.

Pregestational diabetes, either type 1 or type 2 diabetes, induces structural birth defects including neural tube defects and congenital heart defects in human fetuses. Rodent models of type 1 and type 2 diabetic embryopathy have been established and faithfully mimic human conditions. Hyperglycemia of maternal diabetes triggers oxidative stress in the developing neuroepithelium and the embryonic heart leading to the activation of proapoptotic kinases and excessive cell death. Oxidative stress also activates the unfolded protein response and endoplasmic reticulum stress. Hyperglycemia alters epigenetic landscapes by suppressing histone deacetylation, perturbing microRNA (miRNA) expression, and increasing DNA methylation. At cellular levels, besides the induction of cell apoptosis, hyperglycemia suppresses cell proliferation and induces premature senescence. Stress signaling elicited by maternal diabetes disrupts cellular organelle homeostasis leading to mitochondrial dysfunction, mitochondrial dynamic alteration, and autophagy impairment. Blocking oxidative stress, kinase activation, and cellular senescence ameliorates diabetic embryopathy. Deleting the mir200c gene or restoring mir322 expression abolishes maternal diabetes hyperglycemia-induced senescence and cellular stress, respectively. Both the autophagy activator trehalose and the senomorphic rapamycin can alleviate diabetic embryopathy. Thus, targeting cellular stress, miRNAs, senescence, or restoring autophagy or mitochondrial fusion is a promising approach to prevent poorly controlled maternal diabetes-induced structural birth defects. In this review, we summarize the causal events in diabetic embryopathy and propose preventions for this pathological condition. KEY POINTS: · Maternal diabetes induces structural birth defects.. · Kinase signaling and cellular organelle stress are critically involved in neural tube defects.. · Maternal diabetes increases DNA methylation and suppresses developmental gene expression.. · Cellular apoptosis and senescence are induced by maternal diabetes in the neuroepithelium.. · microRNAs disrupt mitochondrial fusion leading to congenital heart diseases in diabetic pregnancy..

Myotube Guidance: Shaping up the Musculoskeletal System.

Myofibers are highly specialized contractile cells of skeletal muscles, and dysregulation of myofiber morphogenesis is emerging as a contributing cause of myopathies and structural birth defects. Myotubes are the myofiber precursors and undergo a dramatic morphological transition into long bipolar myofibers that are attached to tendons on two ends. Similar to axon growth cones, myotube leading edges navigate toward target cells and form cell-cell connections. The process of myotube guidance connects myotubes with the correct tendons, orients myofiber morphology with the overall body plan, and generates a functional musculoskeletal system. Navigational signaling, addition of mass and volume, and identification of target cells are common events in myotube guidance and axon guidance, but surprisingly, the mechanisms regulating these events are not completely overlapping in myotubes and axons. This review summarizes the strategies that have evolved to direct myotube leading edges to predetermined tendon cells and highlights key differences between myotube guidance and axon guidance. The association of myotube guidance pathways with developmental disorders is also discussed.

Genome-wide association studies of Down syndrome associated congenital heart defects.

Congenital heart defects (CHDs) are the most common structural birth defect and are present in 40-50% of children born with Down syndrome (DS). To characterize the genetic architecture of DS-associated CHD, we sequenced genomes of a multiethnic group of children with DS and a CHD (n=886: atrioventricular septal defects (AVSD), n=438; atrial septal defects (ASD), n=122; ventricular septal defects (VSD), n=170; other types of CHD, n=156) and DS with a structurally normal heart (DS+NH, n=572). We performed four GWAS for common variants (MAF>0.05) comparing DS with CHD, stratified by CHD-subtype, to DS+NH controls. Although no SNP achieved genome-wide significance, multiple loci in each analysis achieved suggestive significance (p<2×10-6). Of these, the 1p35.1 locus (near RBBP4) was specifically associated with ASD risk and the 5q35.2 locus (near MSX2) was associated with any type of CHD. Each of the suggestive loci contained one or more plausible candidate genes expressed in the developing heart. While no SNP replicated (p<2×10-6) in an independent cohort of DS+CHD (DS+CHD: n=229; DS+NH: n=197), most SNPs that were suggestive in our GWASs remained suggestive when meta-analyzed with the GWASs from the replication cohort. These results build on previous work to identify genetic modifiers of DS-associated CHD.

MFRP variations cause nanophthalmos in five Chinese families with distinct phenotypic diversity.

Nanophthalmos is a congenital ocular structural anomaly that can cause significant visual loss in children. The early diagnosis and then taking appropriate clinical and surgical treatment remains a challenge for many ophthalmologists because of genetic and phenotypic heterogeneity. The objective of this study is to identify the genetic cause of nanophthalmos in the affected families and analyze the clinical phenotype of nanophthalmos with MFRP gene variation (Microphthalmia, isolated; OMIM#611040 and Nanophthalmos 2; OMIM#609549, respectively). Comprehensive ophthalmic examinations were performed on participants to confirm the phenotype. The genotype was identified using whole exome sequencing, and further verified the results among other family members by Sanger sequencing. The normal protein structure was constructed using Alphafold. Mutant proteins were visualized using pymol software. Pathogenicity of identified variant was determined by in silico analysis and the guidelines of American College of Medical Genetics and Genomics (ACMG). The relationship between genetic variants and clinical features was analyzed. Five nanophthalmos families were autosomal recessive, of which four families carried homozygous variants and one family had compound heterozygous variants in the MFRP gene. Both family one and family three carried the homozygous missense variant c.1486G>A (p.Glu496Lys) in the MFRP gene (Clinvar:SCV005060845), which is a novel variant and evaluated as likely pathogenic according to the ACMG guidelines and in silico analysis. The proband of family one presented papilloedema in both eyes, irregular borders, thickened retinas at the posterior pole, tortuous and dilated retinal vessels, and indistinguishable arteries and veins, while the proband of family three presented uveal effusion syndrome-like changes in the right eye. In families one and 3, despite carrying the same gene variant, the probands had completely different clinical phenotypes. The homozygous nonsense variant c.271C>T (p.Gln91Ter) (Clinvar:SCV005060846) of the MFRP gene was detected in family 2, presenting shallow anterior chamber in both eyes, pigmentation of peripheral retina 360° from the equator to the serrated rim showing a clear demarcation from the normal retina in the form of strips. Family four proband carried the homozygous missense variant c.1411G>A (p.Val471Met) in the MFRP gene (Clinvar:SCV005060847), family five proband carried compound heterozygous missense variants c.1486G>A (p.Glu496Lys) and c.602G>T (p.Arg201Leu) in the MFRP gene (Clinvar:SCV005060848), which is a novel variant and evaluated as likely pathogenic according to the ACMG guidelines and in silico analysis, and they all presented clinically with binocular angle-closure glaucoma, family four also had retinal vein occlusion in the right eye during the follow-up. In this study, pathogenic variants of the MFRP gene were detected in five nanophthalmos families, including two novel variants. It also revealed a distinct phenotypic diversity among five probands harboring variants in the MFRP gene. Our findings extend the phenotype associated with MFRP variants and is helpful for ophthalmologists in early diagnosis and making effective treatment and rehabilitation strategies.

Identification of congenital aortic valve malformations in juvenile natriuretic peptide receptor 2-deficient mice using high-frequency ultrasound.

Mouse models of congenital aortic valve malformations are useful for studying disease pathobiology, but most models have incomplete penetrance [e.g., ∼2 to 77% prevalence of bicuspid aortic valves (BAVs) across multiple models]. For longitudinal studies of pathologies associated with BAVs and other congenital valve malformations, which manifest over months in mice, it is operationally inefficient, economically burdensome, and ethically challenging to enroll large numbers of mice in studies without first identifying those with valvular abnormalities. To address this need, we established and validated a novel in vivo high-frequency (30 MHz) ultrasound imaging protocol capable of detecting aortic valvular malformations in juvenile mice. Fifty natriuretic peptide receptor 2 heterozygous mice on a low-density lipoprotein receptor-deficient background (Npr2+/-;Ldlr-/-; 32 males and 18 females) were imaged at 4 and 8 wk of age. Fourteen percent of the Npr2+/-;Ldlr-/- mice exhibited features associated with aortic valve malformations, including 1) abnormal transaortic flow patterns on color Doppler (recirculation and regurgitation), 2) peak systolic flow velocities distal to the aortic valves reaching or surpassing ∼1,250 mm/s by pulsed-wave Doppler, and 3) putative fusion of cusps along commissures and abnormal movement elucidated by two-dimensional (2-D) imaging with ultrahigh temporal resolution. Valves with these features were confirmed by ex vivo gross anatomy and histological visualization to have thickened cusps, partial fusions, or Sievers type-0 bicuspid valves. This ultrasound imaging protocol will enable efficient, cost effective, and humane implementation of studies of congenital aortic valvular abnormalities and associated pathologies in a wide range of mouse models.NEW & NOTEWORTHY We developed a high-frequency ultrasound imaging protocol for diagnosing congenital aortic valve structural abnormalities in 4-wk-old mice. Our protocol defines specific criteria to distinguish mice with abnormal aortic valves from those with normal tricuspid valves using color Doppler, pulsed-wave Doppler, and two-dimensional (2-D) imaging with ultrahigh temporal resolution. This approach enables early identification of valvular abnormalities for efficient and ethical experimental design of longitudinal studies of congenital valve diseases and associated pathologies in mice.

COVID-19 Vaccination in the First Trimester and Major Structural Birth Defects Among Live Births

COVID-19 vaccination is recommended throughout pregnancy to prevent pregnancy complications and adverse birth outcomes associated with COVID-19 disease. To date, data on birth defects after first-trimester vaccination are limited. To evaluate the associated risks for selected major structural birth defects among live-born infants after first-trimester receipt of a messenger RNA (mRNA) COVID-19 vaccine. This was a retrospective cohort study of singleton pregnancies with estimated last menstrual period (LMP) between September 13, 2020, and April 3, 2021, and ending in live birth from March 5, 2021, to January 25, 2022. Included were data from 8 health systems in California, Oregon, Washington, Colorado, Minnesota, and Wisconsin in the Vaccine Safety Datalink. Receipt of 1 or 2 mRNA COVID-19 vaccine doses in the first trimester, as part of the primary series. Selected major structural birth defects among live-born infants, identified from electronic health data using validated algorithms, with neural tube defects confirmed via medical record review. Among 42 156 eligible pregnancies (mean [SD] maternal age, 30.9 [5.0] years) 7632 (18.1%) received an mRNA COVID-19 vaccine in the first trimester. Of 34 524 pregnancies without a first-trimester COVID-19 vaccination, 2045 (5.9%) were vaccinated before pregnancy, 13 494 (39.1%) during the second or third trimester, and 18 985 (55.0%) were unvaccinated before or during pregnancy. Compared with pregnant people unvaccinated in the first trimester, those vaccinated in the first trimester were older (mean [SD] age, 32.3 [4.5] years vs 30.6 [5.1] years) and differed by LMP date. After applying stabilized inverse probability weighting, differences in baseline characteristics between vaccinated and unvaccinated pregnant persons in the first trimester were negligible (standardized mean difference <0.20). Selected major structural birth defects occurred in 113 infants (1.48%) after first-trimester mRNA COVID-19 vaccination and in 488 infants (1.41%) without first-trimester vaccine exposure; the adjusted prevalence ratio was 1.02 (95% CI, 0.78-1.33). In secondary analyses, with major structural birth defect outcomes grouped by organ system, no significant differences between infants vaccinated or unvaccinated in the first trimester were identified. In this multisite cohort study, among live-born infants, first-trimester mRNA COVID-19 vaccine exposure was not associated with an increased risk for selected major structural birth defects.

Ash1l loss-of-function results in structural birth defects and altered cortical development.

The histone methyltransferase ASH1L plays a crucial role in regulating gene expression across various organ systems during development, yet its role in brain development remains largely unexplored. Over 130 individuals with autism harbour heterozygous loss-of-function ASH1L variants, and population studies confirm it as a high-risk autism gene. Previous studies on Ash1l deficient mice have reported autistic-like behaviours and provided insights into the underlying neuropathophysiology. In this study, we used mice with a cre-inducible deletion of Ash1l exon 4, which results in a frame shift and premature stop codon (p.V1693Afs*2). Our investigation evaluated the impact of Ash1l loss-of-function on survival and craniofacial skeletal development. Using a tamoxifen-inducible cre strain, we targeted Ash1l knockout early in cortical development [Emx1-Cre-ERT2; embryonic Day (e) 10.5]. Immunohistochemistry was utilized to assess cortical lamination, while EdU incorporation aided in birthdating cortical neurons. Additionally, single-cell RNA sequencing was employed to compare cortical cell populations and identify genes with differential expression. At e18.5, the proportion of homozygous Ash1l germline knockout embryos appeared normal; however, no live Ash1l null pups were present at birth (e18.5: n = 77, P = 0.90; p0: n = 41, P = 0.00095). Notably, Ash1l-/- exhibited shortened nasal bones (n = 31, P = 0.017). In the cortical-specific knockout model, SATB2 neurons showed increased numbers (n = 6/genotype, P = 0.0001) and were distributed through the cortical plate. Birthdating revealed generation of ectopically placed deep layer neurons that express SATB2 (e13.5 injection: n = 4/genotype, P = 0.0126). Single cell RNA sequencing revealed significant differences in gene expression between control and mutant upper layer neurons, leading to distinct clustering. Pseudotime analysis indicated that the mutant cluster followed an altered cell differentiation trajectory. This study underscores the essential role of Ash1l in postnatal survival and normal craniofacial development. In the cortex, ASH1L exerts broad effects on gene expression and is indispensable for determining the fate of upper layer cortical neurons. These findings provide valuable insights into the potential mechanisms of ASH1L neuropathology, shedding light on its significance in neurodevelopmental disorders like autism.

Exploring the clinical utility of exome sequencing/Mono, Duo, Trio in prenatal testing: a retrospective study in a tertiary care centre in South India.

With the availability of Next Generation Sequencing (NGS) diagnosis of genetic disorders has improved significantly. Its use is also applicable to ascertain diagnosis and management in a perinatal setting. The study aims to detect the genetic aetiology of various congenital structural and functional defects using NGS technology in the reproductive cohort at a tertiary centre. The secondary objective is to address challenges in the interpretation of variants. This was a retrospective study of couples who underwent exome sequencing (Mono-testing proband only or Duo-testing parents only or Trio-testing proband and parents) for suspected single gene disorders between years 2020-2022 at a tertiary care perinatal center in the South India. American College of Medical Genetics (ACMG) guidelines were followed to classify the pathogenicity of the variants identified by exome sequencing. The overall diagnostic yield as defined by pathogenic/likely pathogenic variants obtained was (23/43) 53.4 %. The individual subsets have the following diagnostic yield viz., Mono 5/6 (83 %); Carrier 16/32 (50 %); Trio 2/5 (40 %). Diagnostic yield was significantly higher in consanguineous couples. However, miscarriage history, and organ system involvement did not have a significant effect on the diagnostic yield. Prenatal diagnosis was offered for seven patients based on the exome result. One fetus was confirmed with a compound heterozygous pathogenic variant. Diagnostic yield of exome sequencing in our cohort was 53 %. The detection of pathogenic variants was maximum in those cases undergoing Mono exome sequencing. In places where there is a high prevalence of consanguinity and endogamy, NGS may be offered as first line test in the context of prenatal diagnosis.

METB-09. VARIANT WORKBENCH IN THE KIDS FIRST PROGRAM FACILITATES GENOMIC DISCOVERIES IN PEDIATRIC NEURO-ONCOLOGY RESEARCH

Abstract The Gabriella Miller Kids First Pediatric Research Program (Kids First) aims at facilitating researchers to uncover new insights into the biology of childhood cancer and structural birth defects, including the discovery of shared genetic pathways between these disorders. Kids First Data Resource Center developed the Kids First Data Resource Portal (KFDRP), which is a centralized data platform for both Kids First and collaborative cohorts. Currently, KFDRP facilitates data access for 40 studies with over 35,500 participants. To assist researchers and clinicians in identifying potential disease-causing germline variants in the human genome, KFDRP released the Variant WorkBench (VWB), which facilitates variant querying, manipulation, analysis, and visualization. Cavatica is a widely used bioinformatics analysis platform developed by Velsera. Compared to a previous version, the Cavatica-based VWB has better support for data import/export, more convenient sharing of notebooks and data, and easier billing details, with the same level of scalable, cloud-based computing. Additionally, Cavatica-based VWB has incorporated multiple public reference databases, including Cancer Hotspots, ClinVar, COSMIC, dbNSFP, gnomAD, TOPMed, as well as gene-phenotype links provided by OMIM, HPO, Orphanet, and the Deciphering Developmental Disorders Project. These databases have been converted to parquet files, reducing process time and memory usage compared to regular text files, thus speeding up data retrieval and querying. Furthermore, Cavatica empowers users to create and share custom analysis workflows tailored to specific research questions and datasets, enhancing data utility and analysis accuracy. Here we present a gene-based variant filtering workflow that aggregates information from dbNSFP, HGMD, TOPMed, gnomAD, and ClinVar. We identified 1202 pathogenic/likely pathogenic variants in NF1, a gene that helps regulate cell growth, across 582 pediatric brain tumor samples within 6 mins. Among the variants, there are 21 protein-altering variants. Overall, the upgraded VWB is more powerful, user-friendly, and adaptable.

Expert consensus on the test development and preliminary implementation of whole genome sequencing for fetal structural abnormalities

Fetal structural anomalies and birth defects are primarily caused by genetic variants such as chromosomal number abnormalities, copy number variations (CNV), single nucleotide variants (SNV), and small insertions and deletions (indel). Whole-genome sequencing (WGS) based on next-generation sequencing (NGS) as an emerging technology for genetic disease diagnosis can detect the aforementioned types of variants. In recent years, high-depth WGS (> 30×) for prenatal diagnosis has also become available, and proved to be practical for unraveling the genetic etiology of fetal developmental abnormalities. To facilitate clinical practice, test development and preliminary implementation of WGS for diagnosing fetal structural anomalies, we have formulated a consensus over the application of WGS in prenatal diagnosis by compiling previously published consensuses, guidelines, and research findings to provide a guidance on data analysis, reporting recommendations, and consultation of prenatal WGS results.

Unraveling Patterns of Congenital Structural Malformations in Infants: A Hospital-Based Descriptive Study.

Introduction Congenital malformation studies serve several purposes, including establishing baseline rates, monitoring changes over time, exploring the origins of these defects, and helping in planning health services. Increasing public awareness about pediatric surgical interventions is another goal of these studies. However, the impact of congenital malformations is often underestimated in developing countries due to insufficient healthcare data and diagnostic facilities, particularly in rural areas. Families affected by the birth of a child with congenital malformations face significant stress and hardship. Methods The main aims of this study were to evaluate the clinical pattern of congenital structural malformations in our region (Uttarakhand, India), identify possibly associated factors of congenital malformations, and find out the immediate outcome of congenital malformations in enrolled participants. Results Among a total of 150 cases, 73 (48.7%) cases were inborn, whereas 77 (51.3%) cases were outborn. Investigation of congenital malformation revealed cleft lip or palate in 37 (24.7%) cases, congenital heart disease (CHD) in 33 (22%) cases, meningomyelocele (MMC) in 18 (12.0%) cases, anorectal malformation (ARM) in 11 (7.3%) cases, hypospadias in 10 (6.7%) cases, congenital talipes equinovarus (CTEV) in nine (6.0%) cases, tracheoesophageal fistula (TEF) in nine (6.0%) cases, polydactyly in seven (4.7%) cases, pelviureteric junction obstruction (PUJO) in four (2.7%) cases, duodenal atresia in three (2.0%) cases, midgut volvulus in three (2.0%) cases, umbilical sinus in two (1.3%) cases, sacrococcygeal teratoma (SCT) in one (0.7%) case, phimosis in one (0.7%) case, microtia in one (0.7%) case, and micrognathia in one (0.7%) case. Mortality was observed in 11 (7.3%) cases, whereas 105 (70%) cases were successfully discharged. Among 11 mortality cases, the cause of death was CHD in seven (63.2%) cases, TEF+CHD in two (18.1%) cases, MMC in one (9%) case, and duodenal atresia in one (9%) case. Conclusion Contrary to the common belief that advanced maternal age of greater than 35 years is a major cause, 86.6% of the congenital structural anomalies in our hospital-based study in Uttarakhand occurred in babies of mothers belonging to the age group of 18-30 years. Also, consanguineous marriage was observed in only 3.3% of cases, indicating that it may not be a major contributing factor causing congenital structural malformations in our region.External congenital anomalies are most commonly observed (60.7%), with cleft lip and cleft palate being the most common.The most frequently observed internal congenital anomaly is CHD (22%) followed by gastrointestinal (GI) (18.6%) and urinary anomalies (10.1%).Death and referral are commonly seen in CHD.

Risk of meningomyelocele mediated by the common 22q11.2 deletion.

Meningomyelocele is one of the most severe forms of neural tube defects (NTDs) and the most frequent structural birth defect of the central nervous system. We assembled the Spina Bifida Sequencing Consortium to identify causes. Exome and genome sequencing of 715 parent-offspring trios identified six patients with chromosomal 22q11.2 deletions, suggesting a 23-fold increased risk compared with the general population. Furthermore, analysis of a separate 22q11.2 deletion cohort suggested a 12- to 15-fold increased NTD risk of meningomyelocele. The loss of Crkl, one of several neural tube-expressed genes within the minimal deletion interval, was sufficient to replicate NTDs in mice, where both penetrance and expressivity were exacerbated by maternal folate deficiency. Thus, the common 22q11.2 deletion confers substantial meningomyelocele risk, which is partially alleviated by folate supplementation.