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Ophthalmology. 2010 Nov;117(11):2169-77.e3. doi: 10.1016/j.ophtha.2010.02.029. Epub 2010 Jun 29.

Development of a diagnostic genetic test for simplex and autosomal recessive retinitis pigmentosa.

Author information

1
Centre for Vision and Vascular Science, Queen's University, Belfast, Northern Ireland.

Abstract

PURPOSE:

Retinitis pigmentosa (RP) causes hereditary blindness in adults (prevalence, approximately 1 in 4000). Each of the more than 30 causative genes identified to date are responsible for only a small percentage of cases. Genetic diagnosis via traditional methods is problematic, and a single test with a higher probability of detecting the causative mutation would be very beneficial for the clinician. The goal of this study therefore was to develop a high-throughput screen capable of detecting both known mutations and novel mutations within all genes implicated in autosomal recessive or simplex RP.

DESIGN:

Evaluation of diagnostic technology.

PARTICIPANTS AND CONTROLS:

Participants were 56 simplex and autosomal recessive RP patients, with 360 population controls unscreened for ophthalmic disease.

METHODS:

A custom genechip capable of resequencing all exons containing known mutations in 19 disease-associated genes was developed (RP genechip). A second, commercially available arrayed primer extension (APEX) system was used to screen 501 individual previously reported variants. The ability of these high-throughput approaches to identify pathogenic variants was assessed in a cohort of simplex and autosomal recessive RP patients.

MAIN OUTCOME MEASURES:

Number of mutations and potentially pathogenic variants identified.

RESULTS:

The RP genechip identified 44 sequence variants: 5 previously reported mutations; 22 known single nucleotide polymorphisms (SNPs); 11 novel, potentially pathogenic variants; and 6 novel SNPs. There was strong concordance with the APEX array, but only the RP genechip detected novel variants. For example, identification of a novel mutation in CRB1 revealed a patient, who also had a single previously known CRB1 mutation, to be a compound heterozygote. In some individuals, potentially pathogenic variants were discovered in more than one gene, consistent with the existence of disease modifier effects resulting from mutations at a second locus.

CONCLUSIONS:

The RP genechip provides the significant advantage of detecting novel variants and could be expected to detect at least one pathogenic variant in more than 50% of patients. The APEX array provides a reliable method to detect known pathogenic variants in autosomal recessive RP and simplex RP patients and is commercially available. High-throughput genotyping for RP is evolving into a clinically useful genetic diagnostic tool.

FINANCIAL DISCLOSURE(S):

The author(s) have no proprietary or commercial interest in any materials discussed in this article.

PMID:
20591486
DOI:
10.1016/j.ophtha.2010.02.029
[Indexed for MEDLINE]
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