A new chip enables rapid detection of retinal disease genes defects

Researchers at the Netherlands Institute for Neuroscience have designed a custom resequencing chip that can detect known and new sequence changes in about 90 retinal disease genes using a new high-throughput strategy with a high sensitivity and specificity for one tenth of the cost of conventional direct sequencing, as reported in the recent issue of Ophthalmology journal.

The developed amplification strategy allows for the pooling of multiple patients with non-overlapping phenotypes, enabling many patients to be analyzed simultaneously in a fast and cost-effective manner.
This chip accurately and efficiently identified novel and known mutations in retinal disease genes in the study that included 60 patients.

The chip offers rapid analysis with high sensitivity and specificity, at about one-tenth the cost of conventional direct sequencing. The developed amplification strategy allows for the multiple patients to be pooled together with non-overlapping phenotypes, enabling many patients to be analyzed simultaneously in a fast and cost-effective manner.

The investigators designed a custom 300-kb Affymetrix resequencing chip that affords direct sequencing of 265,000 double-stranded bases of retinal disease genes. The study included patients with retinal disorders such as Leber's congenital amaurosis, ocular albinism, optic atrophy, glaucoma, pseudoxanthoma elasticum, retinitis pigmentosa and Stargardt's disease.

Direct sequencing of forward and reverse strands in relevant disease genes was performed to verify the presence of mutations in the DNA of the pooled patient sample. The investigators identified 87 known pathogenic and polymorphic sequence changes from 25 retinal disease genes. They developed primer sets for 1,445 amplicons representing genes tested on the chip.

Study results showed a detection rate of 99% and reproducibility rate of 100%, with no false positives. But the chip is not able to detect deletions of genetic material, and hence, it can be used to prescreen patients to improve the efficiency of subsequent formal DNA testing.

Source: Ophthalmology