Whole Genome Sequencing identifies a structural variant in the EYS gene in retinitis pigmentosa patients.

摘要

Purpose : To study the genetic basis of autosomal recessive Retinitis Pigmentosa (arRP) in a Spanish family negative for mutations, as investigated by Whole Exome Sequencing (WES), and to highlight the advantages of Whole Genome Sequencing (WGS) versus WES. Methods : WES was performed on the DNA of two siblings suffering from arRP, born from healthy and unrelated parents. Subsequently, one of the affected individuals was subjected to WGS analyses using the Complete Genomics platform. The generated genome data were processed using an expert in-house in silico pipeline. Results : Following our analytical pipeline, the nearly 4 million DNA variants that were generated by WGS of the proband were reduced to 677 potential pathogenic mutations. Among those, we identified no biallelic single nucleotide variations that could be deemed responsible for a recessive disease among the coding regions of the genome. Thus, we focused on the analysis of structural variations. Adopting this strategy, we identified a ~56 kb heterozygous deletion in the EYS gene, a known cause of arRP. This deletion is depriving the transcript of two exons and is predicted to have a deleterious impact on the protein. In addition, we also identified a novel missense variant, p.Y2971D, affecting an evolutionarily conserved amino acid. Interestingly, this missense change was previously missed by WES analysis due to the low-depth coverage of the region in question. Both variants, segregating with the disease within the family, were further validated by Sanger sequencing and MLPA analysis. Conclusions : With our study we emphasize the benefits of the use of WGS in unsolved cases of hereditary retinal disorders. Our work not only demonstrates that WGS enables the detection of structural events (e.g. deletions) that otherwise would have been unnoticed, but it also underscores that WGS performance is more reliable and uniform in terms of sequencing coverage. Furthermore, we also demonstrate that our analytic pipeline does reveal clinically relevant mutations, exploiting the full potential of WGS data. To date, the major focus of studies on Mendelian diseases, including RP, has been limited to exonic regions. However, non-coding variants in known or novel genes can also affect disease pathophysiology. WGS can indeed shed more light in the so called genomic 'dark matter' of the human genome and, and in particular of retinal degenerations. This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.