Abstract
OBJECTIVE: To identify rare and common CNVs associated with strabismus and amblyopia and to determine whether these variants reveal overlapping genetic mechanisms between the two disorders. DESIGN: Case-control association study using structural variant calls from short-read whole- genome sequencing. SUBJECT PARTICIPANTS AND CONTROLS: 1,141 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. METHODS: CNVs 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 MEASURES: Odds 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. RESULTS: Fourteen 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. CONCLUSIONS: CNVs 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.