American Journal of Medical Genetics Part A

BackgroundApproximately 30-40% of genetic and rare disorders manifest with distinct facial patterns. Traditionally, clinical geneticists have qualitatively assessed facial morphology to support preliminary diagnosis and guide confirmatory genetic testing. However, enhancing early diagnostic accuracy through facial biomarkers demands advanced 3D technologies for analyzing facial dysmorphologies, a deeper understanding of condition-specific disruptions in facial development, and a broader inclusion of diverse human populations. To bridge this gap, we analyzed the 3D phenotypes associated with four genetic syndromes in an admixed Latin American population from Colombia. The sample comprised 47 individuals diagnosed with Down (DS), Morquio (MS), Noonan (NS), and Neurofibromatosis type 1 (NF1) syndromes along with 49 controls within the same age range. For each participant, we generated a 3D facial model using a multi-camera photogrammetric system and registered the 3D coordinates of 21 anatomical facial landmarks. Geometric morphometrics methods were employed to characterize syndrome-specific 3D facial dysmorphologies and to assess their variation compared to controls. We also examined whether these syndromes alter the ontogenetic trajectory of facial growth. ResultsFacial shape differed significantly in all syndromes except NF1. Consistently with previous 2D studies, we identified population-specific facial features in Colombian patients that are not reported in individuals of European descent. Pooled 3D analyses revealed a continuous spectrum of facial dysmorphology, with MS displaying the most distinct morphology and an altered ontogenic pattern. Facial size, sex and age were all significant factors modulating facial shape, with diagnosis explaining 14% of variation in facial morphology. ConclusionsOverall, these findings highlight the importance of accounting for interpopulation, sex and ontogenic variation in facial phenotypes to improve the diagnostic utility and of facial biomarkers. Such approaches may contribute to shortening the diagnostic odyssey for individuals with syndromic and rare genetic conditions.

Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting 80% of cytosolic proteins in humans. The human essential gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex, also including the accessory protein, NAA15. The full spectrum of human genetic variation in this pathway is currently unknown. Here we reveal the genetic landscape of variation in NAA10 and NAA15 in humans. Through a genotype-first approach, one clinician interviewed the parents of 56 individuals with NAA10 variants and 19 individuals with NAA15 variants, which were added to all known cases (N=106 for NAA10 and N=66 for NAA15). Although there is clinical overlap between the two syndromes, functional assessment demonstrates that the overall level of functioning for the probands with NAA10 variants is significantly lower than the probands with NAA15 variants. The phenotypic spectrum includes variable levels of intellectual disability, delayed milestones, autism spectrum disorder, craniofacial dysmorphology, cardiac anomalies, seizures, and visual abnormalities (including cortical visual impairment and microphthalmia). One female with the p.Arg83Cys variant and one female with an NAA15 frameshift variant both have microphthalmia. The frameshift variants located toward the C-terminal end of NAA10 have much less impact on overall functioning, whereas the females with the p.Arg83Cys missense in NAA10 have substantial impairment. The overall data are consistent with a phenotypic spectrum for these alleles, involving multiple organ systems, thus revealing the widespread effect of alterations of the NTA pathway in humans.

Up to 40% of genetic and rare disorders (RD) present facial dysmorphologies. Visual assessment of facial gestalt is commonly used for clinical diagnosis, health management and treatment monitoring. Quantitative approaches to facial phenotypes are more objective and provide first diagnoses of RD with relatively high accuracy, but are mainly based on populations of European descent, disregarding the influence of population ancestry. Here we assessed the facial phenotypes associated to four genetic disorders in a Latino-American population from Colombia. We recorded the coordinates of 18 facial landmarks in 2D images from 79 controls 51 pediatric individuals diagnosed with Down (DS), Morquio (MS), Noonan (NS) and Neurofibromatosis type 1 (NF1) syndromes. We quantified facial differences using Euclidean Distance Matrix Analysis (EDMA) and assessed the diagnostic accuracy of Face2gene, an automatic deep learning algorithm with widespread use in the clinical practice. Quantitative comparisons indicated that individuals diagnosed with DS and MS were associated with the most severe phenotypes, with 58.2% and 65.4% of facial traits significantly different as compared to controls. The percentage decreased to 47.7% in NS and to 11.4% in NF1. Each syndrome presented a characteristic pattern of facial dysmorphology, supporting the potential of facial biomarkers for disorder diagnosis. However, our results detected population-specific traits in the Colombian population as compared to the facial gestalt described in literature for DS, NS and NF1. When clinical diagnosis based on genetic testing was used to verify the diagnosis based on 2D facial pictures, our results showed that Face2Gene accuracy was very high in DS, moderate in NS and NF1, and very low in MS, with low gestalt similarity scores in highly admixed individuals. Our study underscores the added value of precise quantitative comparison of facial dysmorphologies in genetic and rare disorders and the need to incorporate populations with diverse contributions of Amerindian, African and European ancestry components to further improve automatic diagnostic methods.

NAA15 is a member of the NatA N-terminal acetyltransferase complex, which also includes the NAA10 enzymatic sub-unit. Individuals with variants in the NAA15 coding region develop NAA15-related neurodevelopmental syndrome, which presents with a wide array of manifestations that affect the heart, brain, musculoskeletal system, and behavioral and cognitive development. We tracked a cohort of 27 participants (9 females and 18 males) over time, each with a pathogenic NAA15 variant, and administered the Vineland-3 assessment to assess their adaptive functioning. We found that the cohort performed significantly worse compared to the normalized Vineland values. On average, females performed better than males, and they performed significantly better on the Motor Domain and Fine Motor Sub-Domain portions of the assessment. Over time, females showed a decrease in adaptive functioning, with the decline being especially correlated at the Coping, Domestic, and Fine motor sub-domains. Males (after excluding one outlier) showed a moderate positive correlation between age and ABC standard score. Ultimately, additional longitudinal data should be collected to determine the validity of the between sex-differences and to better understand the change in adaptive behavioral outcomes of individuals with NAA15-neurodevelopmental disorder as they age.

CHAMP1 disorder is a genetic neurodevelopmental condition caused by mutations in the CHAMP1 gene that result in premature termination codons. The disorder is associated with intellectual disability, medical comorbidities, and dysmorphic features. Deletions of the CHAMP1 gene, as part of 13q3 deletion syndrome, have been briefly described with the suggestion of a milder clinical phenotype. To date, no studies have directly assessed differences between individuals with mutations in CHAMP1 to those with deletions of the gene. We completed prospective clinical evaluations of 16 individuals with mutations and eight with deletions in CHAMP1. Analyses revealed significantly lower adaptive functioning across all domains assessed (i.e., communication, daily living skills, socialization, and motor skills) in the mutation group. Developmental milestones and medical features further showed difference between groups. The phenotypes associated with mutations, as compared to deletions, indicate likely difference in pathogenesis between groups, where deletions are acting through CHAMP1 haploinsufficiency and mutations are acting through dominant negative or gain of function mechanisms, leading to a more severe clinical phenotype. Understanding this pathogenesis is important to the future of novel therapies for CHAMP1 disorder and illustrates that mechanistic understanding of mutations must be carefully considered prior to treatment development.

CTNNB1 syndrome is a rare neurodevelopmental disorder caused by pathogenic variants in the CTNNB1 gene. Although its core clinical manifestations have been increasingly recognised, longitudinal data on cognitive, behavioural and motor trajectories remain limited, and the craniofacial phenotype has not previously been quantitatively characterised. This study provides longitudinal evidence on the cognitive, clinical and psychological profile of individuals with CTNNB1 syndrome, together with a detailed three-dimensional morphometric analysis of facial morphology. Cognitive, clinical, psychological and neuropsychological data were collected at two time points (T0 and T1), separated by a one-year interval, using a comprehensive and standardised assessment protocol. Longitudinal analyses indicated stability across most domains, with no evidence of systematic regression. A significant improvement in gross motor functioning was observed, particularly among younger participants. Linear mixed-effects models showed that age moderated developmental change, with younger individuals exhibiting greater gains over time in gross motor skills and adaptive behaviour compared to older participants. Three-dimensional facial morphometric analyses revealed a distinctive and statistically significant craniofacial pattern associated with CTNNB1 syndrome, independent of age and facial size. This phenotype was characterised by midfacial narrowing, reduced midface projection and mandibular retrusion. Importantly, facial shape variation was significantly associated with externalising behavioural problems and clinically relevant behavioural difficulties, suggesting a link between craniofacial morphology and behavioural severity. This study represents the first integrated longitudinal characterisation of CTNNB1 syndrome combining neurodevelopmental follow-up with quantitative craniofacial phenotyping. The findings indicate slow but progressive improvement in specific clinical domains during childhood and adolescence, alongside relative stability in global adaptive functioning, and highlight three-dimensional facial morphology as a sensitive structural biomarker for phenotypic stratification and clinical monitoring in CTNNB1 syndrome. Lay summaryThis study is the first to describe how children with CTNNB1 syndrome, a rare genetic condition that leads to global developmental delays, develop over time. We also performed advanced facial analysis to look for common facial features among patients.

Genetic variants in the gene Ankyrin Repeat Domain 11 (ANKRD11) and deletions in 16q24.3 are known to cause KBG syndrome, a rare syndrome associated with craniofacial, intellectual, and neurobehavioral anomalies. We report 25 unpublished individuals from 22 families, all with molecularly confirmed diagnoses of KBG syndrome. Twenty-one individuals have de novo variants, three have inherited variants, and one is inherited from a parent exhibiting low-level mosaicism. Of the variants, 20 are truncating (frameshift or nonsense), and the remaining five individuals have missense variants (with one of these in three family members). One of the missense variants has been found in at least two other affected individuals. We created a novel protocol for collection and reporting of data, including prospectively interviewing these individuals and their families throughout eight countries via videoconferencing by a single clinician. Participants medical records, including imaging, were reviewed, and data was uploaded to the Human Disease Gene website using Human Phenotype Ontology (HPO) terms. Photos of the participants were submitted to GestaltMatcher and Face2Gene (FDNA Inc, USA) for facial analysis, and we found similar facial phenotypes among the participants. Within our cohort, common traits included short stature, macrodontia, anteverted nares, wide nasal bridge, wide nasal base, thick eyebrows, synophrys and hypertelorism. Seventy-two percent of participants had gastrointestinal complaints and 80% had hearing loss. Three participants were started on growth hormone with positive results. Behavioral issues and global developmental delays were found in most participants. Neurologic abnormalities including seizures and/or EEG abnormalities were also very common (44%), suggesting that early detection and seizure prophylaxis could be an important point of intervention. Twenty-four percent were diagnosed with attention deficit hyperactivity disorder (ADHD) and 28% were diagnosed with autism spectrum disorder (ASD). Additionally, we have identified minimally reported symptoms, including recurrent sinus infections (16%) and previously unreported migraines (20%). Based on the videoconferencing and these data, we provide a set of recommendations regarding diagnostic and treatment approaches for KBG syndrome.

Background: Recurrent constellations of embryonic malformations (RCEMs) comprise multiple malformation conditions with largely unexplained etiologies and no established molecular biomarkers. A shared DNA methylation episignature was recently identified in VACTERL association and oculoauriculovertebral spectrum (OAVS). We sought to validate this episignature in an independent, deeply phenotyped cohort and evaluate its detection across related RCEMs. Methods: Genome-wide DNA methylation profiling was performed on peripheral blood from 38 participants with clinically diagnosed RCEMs, including VACTERL (n=21), partial VACTERL (n=3), OAVS (n=3), and other RCEM-related conditions (n=11). Results: The Episign V5 RCEM episignature demonstrated robust sensitivity for VACTERL (18/21, 85.7% positive), while the remaining three participants showed intermediate positivity. Of three participants with partial VACTERL, one with tracheoesophageal fistula demonstrated intermediate positivity, whereas the other two were negative. Episignature positivity was also identified in oculoauriculofrontonasal dysplasia (1/1, robust) and rhomboencephalosynapsis (1/2, robust) but was limited in OAVS (1/3, intermediate) and absent in frontonasal dysplasia (0/4). Conclusions: Independent validation establishes the Episign V5 RCEM episignature as a reproducible molecular biomarker for VACTERL, a condition that remains a diagnosis of exclusion. Variable detection across related malformation conditions suggests etiologic heterogeneity, whereas overlap among selected phenotypes supports epigenomic convergence across the RCEM spectrum.

BHLHE22 encodes a Class II basic helix-loop-helix transcription factor (bHLH). It is expressed exclusively in the retina and central nervous system (CNS), and functions as an important regulator of retinogenesis and neuronal differentiation. Mice lacking bhlhe22 show nearly complete loss of three brain comminsure, including the corpus callosum. Here we report eleven individuals from nine unrelated families with BHLHE22 variants, with a neurodevelopmental disorder presenting with absent or limited speech, severely impaired motor abilities, intellectual disability (ID), involuntary movements, autistic traits with stereotypies, abnormal muscle tone. The majority of individuals have partial or complete agenesis of the corpus callosum (ACC). Additional symptoms comprised of epilepsy, variable dysmorphic features, and eye anomalies. One additional individual had spastic paraplegia without delayed development and ACC, expanding the phenotype to milder and later onset forms. Four individuals carry de novo missense variants within the highly conserved helix-loop-helix domain while seven individuals from five unrelated families carry a recurrent homozygous frameshift variant, p.(Gly74Alafs*18). Our findings implicate BHLHE22 variants in causing a previously unidentified autosomal dominant and recessive neurodevelopmental disorder associated with ACC, severe motor, language, and cognitive delays, abnormal tone, and involuntary movements. To our knowledge, this is the first report of Class II bHLH variants in humans shown to significantly disrupt brain development, cognition, and movement.

ObjectiveTo identify rare and common CNVs associated with strabismus and amblyopia and to determine whether these variants reveal overlapping genetic mechanisms between the two disorders. DesignCase-control association study using structural variant calls from short-read whole- genome sequencing. Subject, participants and controls1,141 adults with strabismus, 566 with amblyopia (157 with both), and controls (95,806 for strabismus; 96,381 for amblyopia) enrolled in the All of Us Research Program and with available structural variant calls. MethodsCNVs were called using the GATK-SV pipeline from short-read whole genome sequencing (srWGS). After instituting a variety of quality control measures, including requiring two types of evidence and being identified by two different calling algorithms, CNVs present in 20 or more affected individuals were divided into rare (<1% population frequency) and common (>1% population frequency). The rates of each CNV were compared between affected individuals and controls. Significant CNVs were manually verified in IGV. Functional effects were annotated using Varient Effect Predictor from Ensembl. Main Outcome MeasuresOdds ratios for CNV carrier status in cases versus controls, adjusted for multiple testing (Benjamini-Hochberg FDR < 0.05); functional annotation, dosage sensitivity, regulatory element overlap, and pathway enrichment. ResultsFourteen rare and 29 common CNVs were significantly associated with strabismus; 1 rare and 2 common CNVs were associated with amblyopia (45 unique CNVs total). The rare CNV associated with amblyopia is an intronic deletion in MDGA2. Two common intronic deletions (GRIN2B; CACNA1B) were associated with both conditions and highly predictive of comorbid strabismus and amblyopia (47% comorbidity when both present, p < .001). Implicated genes predominantly affect synapse formation and function (e.g., CSMD1, GRIN2B, CACNA1B, RIMS1), neuronal migration (e.g., TUBB, EML1), and neurodevelopment; 64% have known neurodevelopmental phenotypes and 27% have been linked to mental health disorders. ConclusionsCNVs highlight synaptic and neurodevelopmental pathways as central to strabismus and amblyopia etiology and provide the first evidence of shared genetic risk. The combination of GRIN2B and CACNA1B deletions identify strabismus patients at high risk for amblyopia.

A wide range of behavioral phenotypes has been described in PWS patients including autism spectrum disorder (ASD). The prevalence of behavioral disorders was studied in 292 participants over 3 years with genetically confirmed PWS (N=164 females and N=128 males) with deletion (N=182) and UPD (N=99). The prevalence of ASD, and other behavioral disorders was tested for association with gender, genetic subtypes, and growth hormone (GH) treatment. The prevalence of ASD in PWS individuals was 19.5%, in concordance with previous studies at 25%. The frequency of ADHD was 10.7%. The mean age at diagnosis for ASD, ADHD, and disruptive behavior was 14.9{+/-}10.5, 9.3{+/-}5.9, and 19.6{+/-}14 years, respectively. There was no statistically significant difference in the prevalence of ASD and ADHD between deletion and UPD subjects, and between GH-treated and non-treated subjects. Patients with deletions had higher frequencies of anxiety than those with UPD(p=0.006). GH-treated participants had a lower frequency of depression and a higher frequency of anxiety than non-treated participants (p=0.04, p=0.02, respectively). This is the largest study to evaluate an association between genetically confirmed PWS and ASD. We found no significant difference in the frequency of ASD and other behavioral disorders across the genetic groups and GH treatment.

Colour agnosia is a disorder that impairs colour knowledge (naming, recognition) despite intact colour perception. Previously, we have identified the first and only-known family with hereditary developmental colour agnosia. The aim of the current study was to explore genomic regions and candidate genes that potentially cause this trait in this family. For three family members with developmental colour agnosia and three unaffected family members CGH-array analysis and exome sequencing was performed, and linkage analysis was carried out using DominantMapper, resulting in the identification of 19 cosegregating chromosomal regions. Whole exome sequencing resulted in 11 rare coding variants present in all affected family members with developmental colour agnosia and absent in unaffected members. These variants affected genes that have been implicated in neural processes and functions (CACNA2D4, DDX25, GRINA, MYO15A), that have a indirect link to brain function or development (MAML2, STAU1, TMED3), and a remaining group lacking brain expression or involved in non-neural traits (DEPDC7, OR1J1, OR8D4, RABEPK). Although this is an explorative study, the small set of candidate genes that could serve as a starting point for unravelling mechanisms of higher level cognitive functions and cortical specialization, and disorders therein such as developmental colour agnosia.

Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 220 individuals from 75 F-SMI families and 60 unrelated controls. Within pedigree prioritization employed criteria of rarity, functional consequence, and sharing by [&ge;]3 affected members. Across the sample, gene and gene-set-wide case-control association analysis was performed with Sequence Kernel Association Test, accounting for kinship. In 14/16 families with [&ge;]3 affected individuals, we identified a total of 79 rare predicted deleterious variants in 79 unique genes shared by [&ge;]3 members with SMI and absent in 60 unrelated controls. Twenty (25%) genes were implicated in monogenic neurodevelopmental syndromes in OMIM, a fraction that is a significant overrepresentation (Fishers Exact test OR = 2.47, p = 0.001). In gene-set wise SKAT, statistically significant association was noted for genes related to synaptic function (SKAT-p = 0.014). In this WES study in F-SMI, we identify private, rare, protein altering variants in genes previously implicated in Mendelian neuropsychiatric syndromes; suggesting pleiotropic influences in neurodevelopment between complex and Mendelian syndromes.

IntroductionAlstrom syndrome (ALMS, #203800) is an ultra-rare monogenic recessive disease. This the syndrome is associated with mutations in the ALMS1 gene, which codes for a centrosome structural protein responsible for centrosome cohesion. The type of mutation associated with ALMS is mostly cLOF (97%) and they are mainly located in exons 8, 10 and 16 of the gene. Other studies in the literature have tried to establish a genotype-phenotype correlation in this syndrome with little success. The difficulty in recruiting a large cohort in rare diseases is the main barrier to conducting this type of study. MethodsIn this study we have collected all cases published to date for ALMS. We have created a database with those patients who had a genetic diagnosis and an individualised clinical history. Finally, we have attempted to establish a genotype-phenotype correlation using the truncation site of the patients longest allele as a grouping criterion. ResultsWe collected a total of 357 patients of which 227 had complete clinical information, complete genetic diagnosis and meta information regarding sex and age. We have seen that there are 5 variants in high frequency with p.(Arg2722Ter) being the most common variant with 28 alleles. There are no gender differences in disease progression. Finally, truncating mutations in exon 10 seem to be correlated with a higher prevalence of liver disorders in patients with ALMS. ConclusionThe location of the mutation in the ALMS1 gene does not have a major impact on the phenotype developed by the patient. Only mutations in exon 10 of the ALMS1 gene were associated with a higher prevalence of liver disease.

PurposeThe integration of genome-wide sequencing (GWS), including whole-exome and whole-genome sequencing, has transformed pediatric diagnostics, yet the needs of parents and caregivers during this process remain insufficiently explored. This scoping review aims to synthesize current knowledge on parental and caregiver needs across the GWS process in pediatric settings to inform better clinical practices and support systems. MethodsA scoping review was conducted following PRISMA guidelines. Electronic databases including PubMed, PsycINFO, CINAHL, Embase, and Web of Science were searched, yielding 574 studies, with 47 meeting the inclusion criteria. Data extraction focused on study characteristics, clinical settings, and identified parental needs categorized into pre-test, interim, and post-test periods. Conventional content analysis was used to inductively code and identify themes. ResultsParental needs were categorized into two main themes: (1) Informational needs, encompassing tailored communication, understanding prognosis, logistics, and evolving information, and (2) Emotional support, emphasizing the importance of initial provider interactions and support from healthcare providers and peer groups. Informational and emotional needs were interrelated, impacting parents overall experiences. The review highlighted significant gaps during the interim waiting period, with needs largely focused on pre- and post-test periods. ConclusionParents navigating the pediatric GWS process require comprehensive informational and emotional support. Effective communication before testing and empathetic follow-up contribute to positive experiences. Addressing gaps at different time throughout the process and fostering continuous provider and peer support can enhance the integration of GWS in pediatric care, improving family-centered outcomes.

BackgroundTerminal 6p deletions are rare, and information on their clinical consequences is scarce, which impedes optimal management and follow-up by clinicians. The parent-driven Chromosome 6 Project collaborates with families of affected children worldwide to better understand the clinical effects of chromosome 6 aberrations and to support clinical guidance. A microarray report is required for participation, and detailed phenotype information is collected directly from parents through a multilingual web-based questionnaire. Information collected from parents is then combined with case data from literature reports. Here, we present our findings on 13 newly identified patients and 46 literature cases with genotypically well-characterised terminal and subterminal 6p deletions. We provide phenotype descriptions for both the whole group and for subgroups based on deletion size. ResultsThe total group shared a common phenotype characterised by ocular anterior segment dysgenesis, vision problems, brain malformations, congenital defects of the cardiac septa and valves, mild to moderate hearing impairment, eye movement abnormalities, hypotonia, mild developmental delay and dysmorphic features. These characteristics were observed in all subgroups, confirming a dominant role for FOXC1, one of the most distally deleted genes. Additional characteristics were seen in individuals with terminal deletions exceeding 4.02 Mb, namely complex heart defects, corpus callosum abnormalities, kidney abnormalities and orofacial clefting. Some of these additional features may be related to the loss of other genes in the terminal 6p region, such as RREB1 for the cardiac phenotypes and TUBB2A and TUBB2B for the cerebral phenotypes. In the newly identified patients, we observed previously unreported features including gastrointestinal problems, neurological abnormalities, balance problems and sleep disturbances. ConclusionsWe present an overview of the phenotypic characteristics observed in terminal and subterminal 6p deletions. This reveals a common phenotype that can be highly attributable to haploinsufficiency of FOXC1, with a possible additional effect of other genes in the 6p25 region. We also delineate the developmental abilities of affected individuals and report on previously unrecognised features, showing the added benefit of collecting information directly from parents. Based on our overview, we provide recommendations for clinical surveillance to support clinicians, patients and families.

The diagnostic yield of genetic testing for pediatric sensorineural hearing loss (SNHL) has remained at around 40% for over a decade despite newly discovered causative genes and the expanded use of exome sequencing (ES). This stagnation may be due to (1) a focus on coding regions of the genome and (2) an inability to resolve variants in complex genomic regions due to reliance on short-read sequencing technologies. Short-read genome sequencing (srGS) and long-read genome sequencing (lrGS) both provide exonic single nucleotide variant (SNV) and small indel detection at the same sensitivity as ES, but also evaluate intronic regions. lrGS provides improved resolution for structural variants (SV) and repetitive genomic regions. We sought to investigate the potential utility of lrGS in the diagnostic evaluation of a small cohort of patients with SNHL of unknown etiology after ES and srGS. 19 pediatric patients with SNHL underwent lrGS via PacBio SMRT sequencing. Sequencing data were processed using the PacBio WGS variant pipeline. The diagnostic yield for this lrGS cohort was 4/19 (21%). Relevant variants detected only with lrGS included a hemizygous deletion in trans with a missense variant in an area of high genomic homology (OTOA) and two single nucleotide loss-of-function variants in trans to a known copy-number-loss for a gene with a highly homologous pseudogene (STRC). A complex inversion was identified in the MITF gene which was also identified on post-hoc analysis by srGS. LrGS provides improved resolution for complex genomic structural variation which may increase diagnostic yield for genetic pediatric SNHL, and, potentially, rare disease more broadly.

Background and Objectives: Leukodystrophies are rare genetic diseases affecting the central nervous system white matter, leading to progressive disabilities and death. Although early diagnosis is critical for therapies, the penetrance and phenotypic spectrum of many leukodystrophies remain poorly defined. Here, we integrate sequencing population screening with longitudinal electronic health record (EHR) data. Our goals were to assess the prevalence of undiagnosed leukodystrophy, characterize phenotypic variability among genotype-positive individuals, and estimate penetrance across multiple leukodystrophies. Methods: We analyzed 19 genes associated with 13 leukodystrophies in pediatric and adult individuals recruited via the HerediGene Population Study, a 5-year study conducted primarily of healthy individuals in the U.S. intermountain west. Sequencing was performed on 210,983 individuals, consisting of genome sequencing for 34,033 and SNP panel imputation for 176,950. Variant results were cross-referenced to comprehensive and longitudinal (20+ years) clinical data in the Intermountain Health Enterprise Data Warehouse and to the Utah Leukodystrophy Program. Results: Pathogenic variants were identified in 4 genes (CSF1R, PLP1, POLR3A, SNORD118) in 9 individuals, none of whom had a clinical leukodystrophy diagnosis or characteristic MRI findings. These findings suggest that missed clinical diagnoses of most leukodystrophies are uncommon in a centralized healthcare system, but also demonstrate that for some leukodystrophies there may be variable or reduced penetrance, or broader phenotypic spectra than recognized. We used published incidence estimates and the observed leukodystrophy-associated genotypes to infer penetrance ranges that varied from wide for ultra-rare leukodystrophies, to tightly bounded for more prevalent conditions. Discussion: In this predominantly healthy population, we did not find any patients with leukodystrophy who had been genetically undiagnosed but then identified by sequencing. However, we identified 9 individuals with genotypes previously reported to result in leukodystrophy, but none of whom had clinical symptoms or MRI features associated with the specific leukodystrophy. Our results support a revised model in which leukodystrophies exist along a continuum of penetrance and expressivity, with implications for newborn screening, variant interpretation, and risk stratification.

Localized somatic overgrowth disorders that occur during development can be debilitating, and most often require surgical intervention. Although underlying genetic changes associated with overgrowth have been identified in the majority of cases, the cause of the dysregulated growth and its presentation is unknown. Here we detail current work on a specific overgrowth disorder, macrodactyly, in which overgrowth is localized and shows integration with developmental patterning of the limb, providing coordination of the resulting overgrowth structure. We provide clinical analysis of presentation of macrodactyly in a cohort of patients and provide experimental evidence for nerve and vascular-biased regulation of growth. We provide the first animal model that recapitulates macrodactyly and provide evidence that genetic modifiers may underlie the development of this disorder. The unique presentation of macrodactyly provides a framework to identify the causes and regulatory activities that shape hyperplastic signals that lead to integrated patterning in overgrowth. Use of our experimental model suggests potential for genetic modifiers as important for the particular presentation of this disorder over other PIK3CA-related growth disorders.

Sex chromosome aneuploidies (SCAs) are a family of genetic disorders that result from an atypical number of X and/or Y chromosomes. SCAs are the most common chromosomal abnormality, affecting [~]1/400 live births, yet are often underdiagnosed, leading to over-representation of more severely impacted individuals in many clinical studies. In addition to this ascertainment bias, existing work in SCAs has also been limited by low geographic and demographic diversity. To address these limitations, we have created the Generating Advancements with Longitudinal Analysis in X and Y variations (GALAXY) Registry. To date, GALAXY has accrued 295 verified SCA participants. Next steps include targeted recruitment of minoritized individuals regarding race, ethnicity, and socioeconomic status, and continuing engagement with the SCA community.