Inherited retinal disease diagnosis
Whole genome sequencing can help determine the cause of unexplained disease
Whole genome sequence can reveal hidden variants of genes associated with inherited retinal disease that will not be detected by conventional exon-based gene (exome) sequencing, said Susanne Roosing PhD, Radboud University Medical Center, Nijmegen, The Netherlands.
“The ultimate goal is to use this knowledge for gene therapy, often gene variant specific gene therapy,” said Dr Roosing told at Retina 19, a meeting held in Dublin, Ireland, by Fighting Blindness, a patient-led charity.
She noted that inherited retinal diseases (IRDs) have a high degree of heterogeneity. An estimated 60% of retinitis pigmentosa cases have a genetic cause of disease that can be found using exome sequencing, which is currently the most widely applied method for disease gene variant identification. Among those cases solved by exome sequencing, about 15% are caused by canonical splice site variants that are always conserved so always linked to exon skipping or noncanonical splice site variants that may also have an effect on splicing.
However, exome sequencing – the sequencing of those parts of the gene that are included in the final RNA product –has the inherent limitation that it will not detect the non-coding intronic variants of the genes. Whole genome sequencing, on the other hand, enables identification of causative deep intronic variants and can also detect variants in genes not previously associated with inheritable retinal disease.
Dr Roosing and her associates performed whole genome sequencing on 40 Irish cases and 60 Dutch or Israeli cases of unexplained IRD. In this way they were thus far able to determine the genetic cause in 12 cases, and candidate variants in 41 cases. In 26 cases they found no variants and in 21 their analysis is ongoing.
Among those cases where they found a genetic cause were 13 previously undetected variants in coding regions of known IRD genes. They included homozygous variants in known IRD genes (which were not included in the Target5000 panel) and a very large deletion in gene PDE6B.
The candidate variants in non-coding variants included deep intronic variants in the Bietti and Oguchi retinitis pigmentosa phenotypes associated with known IRD genes. They also found a very large inversion spanning numerous exons in a gene called EYS.
“Our next steps are to perform segregation analysis for candidate genes and variants where applicable, perform midigene assays for selected candidate variants based on different criteria to provide proof-of-pathogenecity and continue analysis of remaining cases. Unsolved cases will be further investigated for causative intronic variants (which aren’t yet identified as such), splice enhancers, splice silencers. Much knowledge remains to be gained,” Dr Roosing concluded.
Susanne Roosing: Susanne.Roosing@radboudumc.nl