Whole exome sequencing may not be the best approach for identifying mutations in hotspot regions of the RPGR gene
Leila Javanparast Sheykhani1 , Fatemeh Suri1 *, Hamid Ahmadieh1 , Hamideh Sabbaghi2
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- 2 Ophthalmic Epidemiology Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
Abstract: Inherited retinal dystrophies (IRDs) are a prominent cause of blindness among children and active populations in developed nations. Among IRDs, retinitis pigmentosa (RP) emerges as a prevalent form, encompassing a diverse group of retinal diseases marked by the progressive degeneration of cone and rod photoreceptor cells. RP's estimated prevalence is approximately 1 in 3000-4000 individuals. Various inheritance patterns, such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), and mitochondrial inheritance, have been identified for RP. X-linked inheritance (XLRP) notably presents the most severe form of the disease, accounting for 10 to 15% of cases of RP. RPGR and RP2 genes are the most common causes of XLRP, which account for 70–90% and 7–18% of the cases, respectively. In this study, we aimed to investigate the disease-causing mutations underlying Iranian X-linked RP-affected patients.
Methods: We selected 23 unrelated RP families displaying the most likely inheritance pattern compatible with recessive X-linked inheritance from the pedigrees registered in Iran's national IRDs registry. Whole exome sequencing was carried out to find the causative genes of the patients.
Results: This exploration unveiled disease-causing mutations in seven families in the RPGR gene (30%). No mutations were detected in the remaining 16 families with X-linked inheritance patterns. Mutation in RP2 was not found in the investigated families.
Conclusion: The preferred and plausible protocol for molecular testing in IRD patients typically involves next-generation sequencing (NGS), encompassing targeted gene panels and whole exome sequencing. Previous studies have shown that around 60% of RPGR mutations occur in the ORF15 region of the gene, which contains a highly purine-rich sequence. However, due to this genomic region's technical challenges, molecular research faces obstacles in its sequencing. However, as the hot spot regions of the RPGR gene can be challenging to sequence fully using NGS methods, WES may not capture RPGR mutations in the ORF15. Consequently, as our mutation detection rate in X-linked RP was much lower than expected, we intend to screen additional families displaying potential X-linked inheritance for mutations in this gene using a direct sequencing protocol. The RP2 gene seems not to be a prevalent cause of the disease in Iranian X-linked RP patients.
