Fig. 1

Identification and validation of a balanced paracentric inversion involving PAX6 in patient ANI-1. a–b. Representation of long reads, breakpoints, and genomic elements involved in a 4.9 Mb paracentric inversion on chromosome 11. Nanopore long-read genome sequencing from high molecular weight DNA revealed a cryptic heterozygous inversion disrupting PAX6. The IGV and Ribbon tools were used to visualize read alignments from vcf and BAM files. Genes and regulatory elements most relevant to phenotypic expression of congenital aniridia, including PAX6 and downstream regulatory regions (DRR) and WT1 and adjacent genes next to the breakpoints, are depicted. BKP1 and BKP2: distal and proximal breakpoints. c. Validation of the distal breakpoint of the inverted allele fragment junctions (JX1 and JX2) on both sides by PCR and Sanger sequencing. d. Electrophoresis of the amplified-fragment junctions in the proband showed unique bands corresponding to the inverted allele in JX1 and JX2, while amplicons for the wild-type allele were also present in both parents. NTC: no template control. e. Schematic representation of the inversion and FISH findings. Centromeric D11Z1 and PAX6 probes are labeled in cyan blue and red, respectively. FISH analysis showed a well-defined red-associated PAX6 signal on wild-type chromosome 11 and spread and separated red-associated PAX6 signals on the inverted chromosome