Recurrent Rare Copy Number Variants Increase Risk for Esotropia

Strabismus in Genetic Syndromes: A Review

Strabismus is a feature of many genetic syndromes, with highly variable penetrance. The congenital cranial dysinnervation disorders (CCDDs) result in paralytic strabismus, with limited eye movements. CCDDs result from either deficits in differentiation of the cranial motor neuron precursors or from abnormal axon guidance of the cranial nerves. Although most individuals with comitant strabismus are otherwise healthy, strabismus is a variable feature of many genetic syndromes, most commonly those associated with intellectual disability. We review 255 genetic syndromes in which strabismus has been described and discuss the variable penetrance. The association with intellectual disability and neurological disorders underscores the likely neurological basis of strabismus, but the variable penetrance emphasises the complexity of strabismus pathophysiology. The syndromes described here mostly result from loss of function or change in function of the responsible genes; one hypothesis is that nonsyndromic strabismus may result from altered expression or regulation of the same genes.

Chromosome 4 Duplication Associated with Strabismus Leads to Gene Expression Changes in iPSC-Derived Cortical Neurons

BACKGROUND/OBJECTIVES

Strabismus is the most common ocular disorder of childhood. Three rare, recurrent genetic duplications have been associated with both esotropia and exotropia, but the mechanisms by which they contribute to strabismus are unknown. This work aims to investigate the mechanisms of the smallest of the three, a 23 kb duplication on chromosome 4 (hg38|4:25,554,985-25,578,843).

METHODS

Using CRISPR and bridging oligos, we introduced the duplication into the Kolf2.1J iPSC line. We differentiated the parent line and the line with the duplication into cortical neurons using a three-dimensional differentiation protocol, and performed bulk RNASeq on neural progenitors (day 14) and differentiated neurons (day 63).

RESULTS

We successfully introduced the duplication into Kolf2.1J iPSCs by nucleofecting a bridging oligo for the newly formed junction along with cas9 ribonucleoparticles. We confirmed that the cells had a tandem duplication without inversion or deletion. The parent line and the line with the duplication both differentiated into neurons reliably. There were a total of 37 differentially expressed genes (DEGs) at day 63, 25 downregulated and 12 upregulated. There were 55 DEGs at day 14, 18 of which were also DEGs at day 63. The DEGs included a number of protocadherins, several genes involved in neuronal development, including SLITRK2, CSMD1, and VGF, and several genes of unknown function.

CONCLUSIONS

A copy number variant (CNV) that confers risk for strabismus affects gene expression of several genes involved in neural development, highlighting that strabismus most likely results from abnormal neural development, and identifying several new genes and pathways for further research into the pathophysiology of strabismus.

eNSMBL-PASD: Spearheading early autism spectrum disorder detection through advanced genomic computational frameworks utilizing ensemble learning models

Objective

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition influenced by various genetic and environmental factors. Currently, there is no definitive clinical test, such as a blood analysis or brain scan, for early diagnosis. The objective of this study is to develop a computational model that predicts ASD driver genes in the early stages using genomic data, aiming to enhance early diagnosis and intervention.

Methods

This study utilized a benchmark genomic dataset, which was processed using feature extraction techniques to identify relevant genetic patterns. Several ensemble classification methods, including Extreme Gradient Boosting, Random Forest, Light Gradient Boosting Machine, ExtraTrees, and a stacked ensemble of classifiers, were applied to assess the predictive power of the genomic features. TheEnsemble Model Predictor for Autism Spectrum Disorder (eNSMBL-PASD) model was rigorously validated using multiple performance metrics such as accuracy, sensitivity, specificity, and Mathew's correlation coefficient.

Results

The proposed model demonstrated superior performance across various validation techniques. The self-consistency test achieved 100% accuracy, while the independent set and cross-validation tests yielded 91% and 87% accuracy, respectively. These results highlight the model's robustness and reliability in predicting ASD-related genes.

Conclusion

The eNSMBL-PASD model provides a promising tool for the early detection of ASD by identifying genetic markers associated with the disorder. In the future, this model has the potential to assist healthcare professionals, particularly doctors and psychologists, in diagnosing and formulating treatment plans for ASD at its earliest stages.

Mental Health Conditions Associated With Strabismus in a Diverse Cohort of US Adults

Importance

Greater understanding of the association between strabismus and mental health conditions across sociodemographic backgrounds may inform strategies to improve mental well-being in this population.

Objective

To describe the association of strabismus with mental health conditions in a diverse cohort of US adults.

Design, Setting, and Participants

This cross-sectional study used data from the National Institutes of Health's All of Us Research Program, an ongoing program launched in 2015. The study included 3646 adults (aged ≥18 years) with strabismus and 3646 propensity score-matched controls. Statistical analysis was conducted from September 12, 2023, to January 29, 2024.

Main Outcomes and Measures

Adults with strabismus were propensity score matched on age, gender, race and ethnicity, income, educational level, and insurance status in a 1:1 ratio with adults without strabismus. The prevalences of anxiety, depression, substance use and addiction, bipolar disorder, and schizophrenia spectrum disorder among adults with strabismus were compared with controls. Logistic regression was used to evaluate the association of mental health conditions with sociodemographic factors in each group.

Results

This study included 3646 adults with strabismus (median age, 67 years [IQR, 53-76 years]; 2017 women [55%]) and 3646 propensity score-matched controls (median age, 67 years [IQR, 53-76 years]; 2017 women [55%]). Individuals with strabismus had higher prevalences of anxiety (1153 [32%] vs 519 [14%]; difference, 17%; 95% CI, 15%-19%; P < .001), depression (1189 [33%] vs 514 [14%]; difference, 19%; 95% CI, 17%-20%; P < .001), substance use and addiction (116 [3%] vs 51 [1%]; difference, 2%; 95% CI, 1%-3%; P < .001), bipolar disorder (253 [7%] vs 101 [3%]; difference, 4%; 95% CI, 3%-5%; P < .001), and schizophrenia spectrum disorder (103 [3%] vs 36 [1%]; difference, 2%; 95% CI, 1%-3%; P < .001) compared with individuals without strabismus. Among adults with strabismus, higher odds of mental health conditions were associated with younger age (odds ratio [OR], 1.11 per 10-year decrease; 95% CI, 1.06-1.16 per 10-year decrease), female gender (OR, 1.62; 95% CI, 1.41-1.85), Black or African American race and ethnicity (OR, 1.22; 95% CI, 1.01-1.48), low income (OR, 3.06; 95% CI, 2.56-3.67), and high school education or less (OR, 1.58; 95% CI, 1.34-1.85).

Conclusions and Relevance

In a diverse and nationwide cohort, adults with strabismus were more likely to have mental health conditions compared with adults without strabismus. Further investigation into the risk factors for poor mental health among adults with strabismus across sociodemographic backgrounds may offer novel opportunities for interventions to improve mental well-being in this population.

Presence of Copy Number Variants Associated With Esotropia in Patients With Exotropia

Importance

Strabismus is a common ocular disorder of childhood. There is a clear genetic component to strabismus, but it is not known if esotropia and exotropia share genetic risk factors.

Objective

To determine whether genetic duplications associated with esotropia are also associated with exotropia.

Design, Setting, and Participants

This was a cross-sectional study conducted from November 2005 to December 2023. Individuals with constant or intermittent exotropia of any magnitude or a history of surgery for exotropia were recruited from pediatric ophthalmic practices. Data were analyzed from March to December 2023.

Exposure

Genetic duplication.

Main Outcomes and Measures

Presence of genetic duplications at 2p11.2, 4p15.2, and 10q11.22 assessed by digital droplet polymerase chain reaction. Orthoptic measurements and history of strabismus surgery were performed.

Results

A total of 234 individuals (mean [SD] age, 19.5 [19.0] years; 127 female [54.3%]) were included in this study. The chromosome 2 duplication was present in 1.7% of patients with exotropia (4 of 234; P = .40), a similar proportion to the 1.4% of patients with esotropia (23 of 1614) in whom it was previously reported and higher than the 0.1% of controls (4 of 3922) previously reported (difference, 1.6%; 95% CI, 0%-3.3%; P < .001). The chromosome 4 duplication was present in 3.0% of patients with exotropia (7 of 234; P = .10), a similar proportion to the 1.7% of patients with esotropia (27 of 1614) and higher than the 0.2% of controls (6 of 3922) in whom it was previously reported (difference, 2.8%; 95% CI, 0.6%-5.0%; P < .001). The chromosome 10 duplication was present in 6.0% of patients with exotropia (14 of 234; P = .08), a similar proportion to the 4% of patients with esotropia (64 of 1614) and higher than the 0.4% of controls (18 of 3922) in whom it was previously reported (difference, 5.6%; 95% CI, 2.5%-8.6%; P < .001). Individuals with a duplication had higher mean (SD) magnitude of deviation (31 [13] vs 22 [14] prism diopters [PD]; difference, 9 PD; 95% CI, 1-16 PD; P = .03), were more likely to have constant (vs intermittent) exotropia (70% vs 29%; difference, 41%; 95% CI, 20.8%-61.2%; P < .001), and had a higher rate of exotropia surgery than those without a duplication (58% vs 34%; difference, 24%; 95% CI, 3%-44%; P = .02).

Conclusions and Relevance

In this cross-sectional study, results suggest that the genetic duplications on chromosomes 2, 4, and 10 were risk factors for exotropia as well as esotropia. These findings support the possibility that esotropia and exotropia have shared genetic risk factors. Whether esotropia or exotropia develops in the presence of these duplications may be influenced by other shared or independent genetic variants or by environmental factors.

Genetics of strabismus

Strabismus, or misalignment of the eyes, is the most common ocular disorder in the pediatric population, affecting approximately 2%-4% of children. Strabismus leads to the disruption of binocular vision, amblyopia, social and occupational discrimination, and decreased quality of life. Although it has been recognized since ancient times that strabismus runs in families, its inheritance patterns are complex, and its precise genetic mechanisms have not yet been defined. Family, population, and twin studies all support a role of genetics in the development of strabismus. There are multiple forms of strabismus, and it is not known if they have shared genetic mechanisms or are distinct genetic disorders, which complicates studies of strabismus. Studies assuming that strabismus is a Mendelian disorder have found areas of linkage and candidate genes in particular families, but no definitive causal genes. Genome-wide association studies searching for common variation that contributes to strabismus risk have identified two risk loci and three copy number variants in white populations. Causative genes have been identified in congenital cranial dysinnervation disorders, syndromes in which eye movement is limited or paralyzed. The causative genes lead to either improper differentiation of cranial motor neurons or abnormal axon guidance. This article reviews the evidence for a genetic contribution to strabismus and the recent advances that have been made in the genetics of comitant strabismus, the most common form of strabismus.

Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure

Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.

Commonly occurring genetic polymorphisms with a major impact on the risk of nonsyndromic strabismus: replication in a sample from Finland

PURPOSE

To replicate associations between polymorphisms in the WRB and TSPAN10 genes and strabismus in an independent Finnish cohort and to calculate their population attributable risk.

METHODS

Polymorphisms in the WRB (rs2244352) and TSPAN10 (rs6420484) genes were investigated in individuals from the FinnGen study group who had one of three categories of strabismus, with clinical diagnoses of (1) "strabismus-all subtypes" (3,515 cases and 173,384 controls), (2) "convergent concomitant strabismus" (ICD-10 code H50.0; 737 cases and 170,976 controls), and (3) "divergent concomitant strabismus" (ICD-10 code H50.1; 1,059 cases and 170,976 controls).

RESULTS

The WRB polymorphism was associated with "all subtypes" of strabismus (OR = 1.08; P = 0.008) and divergent strabismus (OR = 1.11; P = 0.046) but not with convergent strabismus (P = 0.41). The WRB polymorphism had a population attributable risk of 3.4% for all strabismus subtypes and 4.7% for divergent strabismus. The TSPAN10 polymorphism was associated with all three strabismus phenotypes: "all subtypes" (OR = 1.08; P = 0.002), convergent strabismus (OR = 1.19; P = 0.001) and divergent strabismus (OR = 1.20; P =7.21E-05). The population attributable risk for the TSPAN10 polymorphism was 6.0% for any strabismus, 13.3% for convergent strabismus, and 13.9% for divergent strabismus.

CONCLUSIONS

Genetic association with strabismus was replicated in a Finnish cohort for two common polymorphisms. Under the assumption that these polymorphisms are independent of other risk factors, they are responsible for up to 20% of isolated cases of strabismus in Finland, similar to estimates in other European populations.

Five novel copy number variations detected in patients with familial exudative vitreoretinopathy

Purpose

Familial exudative vitreoretinopathy (FEVR) is an inherited retinal vascular disease genetically heterogeneous with multiple causative genes. The aim of this study is to report five novel copy number variation (CNV) regions in FEVR patients and to investigate the possible contributions of novel CNVs to FEVR.

Methods

In this study, 824 FEVR families were collected. All cases were performed using the targeted next generation sequencing (NGS) assay, and families with no definite pathogenic mutations in FEVR genes were screened for CNVs according to the NGS results. Droplet digital polymerase chain reaction (ddPCR) testing was introduced to validate the screened CNV regions. We also reviewed the clinical presentations of the probands and affected family members associated with the novel CNVs and conducted segregation analysis.

Results

Five CNVs in five patients were detected in this study: heterozygous deletions of kinesin family member 11 (KIF11) exons 2-4, KIF11 exon 11, KIF11 exons 1-10, tetraspanin-12 (TSPAN12) exons 1-3, and low-density lipoprotein receptor-related protein 5 (LRP5) exons 19-21. Among the five affected families, TSPAN12 exons 1-3 heterozygous deletion and LRP5 exons 19-21 heterozygous deletion originate from the mother and the father of the proband, respectively. No other family members manifested as FEVR except for the probands. The correlation between disease severity and CNV loci seems uncertain.

Conclusions

Five novel CNV loci in FEVR patients were uncovered in this study, including one maternally-inherited and one paternally-inherited CNV region. Though there is no evidence of co-segregation between these CNVs and FEVR, our findings suggest novel genetic risk factors for FEVR.