Translational Vision Science & Technology January 2022, Vol.11, 6. doi:https://doi.org/10.1167/tvst.11.1.6

Abstract

Purpose: Comprehensive genetic testing for inherited retinal dystrophy (IRD) is challenged by difficult-to-sequence genomic regions, which are often mutational hotspots, such as RPGR ORF15. The purpose of this study was to evaluate the diagnostic contribution of RPGR variants in an unselected IRD patient cohort referred for testing in a clinical diagnostic laboratory.

Methods: A total of 5201 consecutive patients were analyzed with a clinically validated next-generation sequencing (NGS)–based assay, including the difficult-to-sequence RPGR ORF15 region. Copy number variant (CNV) detection from NGS data was included. Variant interpretation was performed per the American College of Medical Genetics and Genomics guidelines.

Results: A confirmed molecular diagnosis in RPGR was found in 4.5% of patients, 24.0% of whom were females. Variants in ORF15 accounted for 74% of the diagnoses; 29% of the diagnostic variants were in the most difficult-to-sequence central region of ORF15 (c.2470-3230). Truncating variants made up the majority (91%) of the diagnostic variants. CNVs explained 2% of the diagnostic cases, of which 80% were one- or two-exon deletions outside of ORF15.

Conclusions: Our findings indicate that high-throughput, clinically validated NGS-based testing covering the difficult-to-sequence region of ORF15, in combination with high-resolution CNV detection, can help to maximize the diagnostic yield for patients with IRD.

Translational Relevance: These results demonstrate an accurate and scalable method for the detection of RPGR-related variants, including the difficult-to-sequence ORF15 hotspot, which is relevant given current and emerging therapeutic opportunities.

Sari Tuupanen; Kimberly Gall; Johanna Sistonen; Inka Saarinen; Kati Kämpjärvi; Kirsty Wells; Katja Merkkiniemi; Pernilla von Nandelstadh; Laura Sarantaus; Johanna Känsäkoski; Emma Mårtenson; Hanna Västinsalo; Jennifer Schleit; Eeva-Marja Sankila; Annakarin Kere; Heidi Junnila; Pauli Siivonen; Margarita Andreevskaya; Ville Kytölä; Mikko Muona; Pertteli Salmenperä; Samuel Myllykangas; Juha Koskenvuo; Tero-Pekka Alastalo

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