Whole-Genome Sequencing in Diagnostics of Unsolved Cases of Inherited Retinal Diseases

Second variant missed by targeted sequencing: CNVs, non-coding variants, structural rearrangements (including delINV) and deep intronic variants creating a pseudoexon

One hundred and seven unrelated Russian patients with inherited retinal disease, each carrying a single pathogenic variant in one of nine common recessive genes (ABCA4, USH2A, EYS, CRB1, RPE65, CNGB3, CNGA3, CEP290, GUCY2D), underwent genome sequencing. Total diagnostic yield was 40.2% (43/107): a second variant was found in 27 cases (25.2%), mostly in EYS (9), USH2A (8) and ABCA4 (5), and the diagnosis was reassigned to another gene in 16 cases (15.0%). Second variants were mostly CNVs (55.5%), followed by non-coding variants (26.0%), structural rearrangements (14.8%, mostly delINV) and a single exonic point variant. Two recurrent CNVs stand out, a deletion of USH2A exons 22-24 and a deletion partially affecting EYS exon 19 (4 patients each). Minigene assays confirm the splicing effect of three novel deep intronic variants (CHM, EYS, CEP290) and of a non-canonical USH2A splice-acceptor variant.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

A telling result for inherited retinal disease: in a patient with a single variant in a recessive gene, the second allele is mostly a CNV, a non-coding variant or a rearrangement that targeted sequencing misses, making genome sequencing the logical test in this situation. The two recurrent USH2A and EYS deletions deserve particular attention at interpretation. A single-population cohort selected on a first variant, hence a high yield that is hard to extrapolate.

Analysis by Dr Thibaut Benquey