Copy number variant detection using next-generation sequencing in EYS-associated retinitis pigmentosa

Area of Science:

• Genetics
• Ophthalmology
• Molecular Biology

Background:

• Retinitis pigmentosa (RP) is a leading inherited cause of blindness.
• Genetic diagnosis is crucial for RP patient management and prognosis.
• Next-generation sequencing (NGS) is widely used but has limitations in detecting copy number variations (CNVs).

Purpose of the Study:

• To re-evaluate copy number variations (CNVs) in the EYS gene, a primary cause of RP.
• To assess the utility of NGS in detecting CNVs in EYS-related RP cases.
• To compare NGS-based CNV detection with multiplex ligation-dependent probe amplification (MLPA).

Main Methods:

• NGS was used to screen for CNVs in EYS gene samples.
• Multiplex ligation-dependent probe amplification (MLPA) was employed to confirm NGS-identified CNVs.
• MLPA was also performed on a cohort of RP patients undiagnosed by NGS.

Main Results:

• NGS identified suspected CNVs in eight patients, all confirmed by MLPA.
• CNVs were detected in 2 out of 42 RP patients previously undiagnosed by NGS.
• Approximately 8.3% of patients with EYS-RP (10 out of 121) harbored CNVs.

Conclusions:

• NGS, with specific criteria, can be a valuable tool for detecting CNVs in EYS-related RP.
• While NGS missed CNVs in two cases, it showed no false positives.
• Combining NGS with confirmatory methods like MLPA enhances diagnostic accuracy for RP.