Abstract
RPGR exon ORF15 variants are one of the most frequent causes for inherited retinal disorders (IRDs), in particular retinitis pigmentosa. The low sequence complexity of this mutation hotspot makes it prone to indels and challenging for sequence data analysis. Whole-exome sequencing generally fails to provide adequate coverage in this region. Therefore, complementary methods are needed to avoid false positives as well as negative results. In this study, next-generation sequencing (NGS) was used to sequence long-range PCR amplicons for an IRD cohort of African ancestry. By developing a novel secondary analysis pipeline based on de novo assembly, we were able to avoid the miscalling of variants generated by standard NGS analysis tools. We identified pathogenic variants in 11 patients (13% of the cohort), two of which have not been reported previously. We provide a novel and alternative end-to-end secondary analysis pipeline for targeted NGS of ORF15 that is less prone to false positive and negative variant calls.
Highlights
Retinitis pigmentosa (RP) is an inherited retinal disorder (IRD) that is characterised by the loss of retinal rod photoreceptor cells [1]
Samples from the registry have been investigated over the years in various research projects, and only genetically unresolved indigenous African IRD cases were included in the present study
Amplification of the open reading frame 15 (ORF15) region of RPGR was possible for 82 of the 97 samples included in this study (85%)
Summary
Retinitis pigmentosa (RP) is an inherited retinal disorder (IRD) that is characterised by the loss of retinal rod photoreceptor cells [1]. Cone photoreceptor cells are inevitably affected, which can result in total blindness. RP is the most common IRD, with an estimated prevalence of about 1 in 3500–4000 individuals [1,3], and it can be inherited as an autosomal dominant (ad, 15–25%), autosomal recessive (ar, 35–50%) or an. A genetic diagnosis for IRD patients can confirm a clinical diagnosis, provide a clearer prognosis, form the basis of genetic counselling for families, and allow participation in gene-based therapy trials [5]. It is impossible to predict the causative RP gene based solely on phenotype and
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