Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia

Background: Classical aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and an adult-onset progressive opacification of the cornea¬¬. >90% of classical aniridia is caused by heterozygous, loss of function variants affecting the PAX6 locus. Methods: Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. Results: Likely causative mutations were identified in 22/37 (59%) families. In 19/22 families the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. 1/19 has a novel heterozygous PAX6 frameshift variant missed on previous screens. 4/19 ¬have single nucleotide variants (one novel) affecting essential splice sites of PAX6 5’ non-coding exons. 2/19 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12/19 the causative variants are large-scale structural variants (SV); 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3/22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one co-segregated with familial aniridia. We were unable to establish inheritance status in remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. Conclusion: Whole genome sequencing proves an effective diagnostic test in most individuals with previously-unexplained aniridia