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Genotyping Microarray (Disease Chip) for Leber Congenital Amaurosis: Detection of Modifier Alleles

¹From the Departments of Ophthalmology and ¹⁰Pathology, Columbia University, New York, New York; ³Asper Biotech, Ltd., Tartu, Estonia; ⁴Department of Pediatric Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts; the ⁵Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands; ⁶Hôpital Des Enfants Malades, Paris, France; the ⁷Department of Pediatric Ophthalmology, Strabismology and Ophthalmogenetics, Klinikum, University of Regensburg, Regensburg, Germany; the ⁸Johns Hopkins University, Baltimore, Maryland; and the ⁹Montreal Children’s Hospital, McGill University Health Center, Montreal, Quebec, Canada.

PURPOSE. Leber congenital amaurosis (LCA) is an early-onset inherited disorder of childhood blindness characterized by visual impairment noted soon after birth. Variants in at least six genes (AIPL1, CRB1, CRX, GUCY2D, RPE65, and RPGRIP1) have been associated with a diagnosis consistent with LCA or early-onset retinitis pigmentosa (RP). Genetically heterogeneous inheritance complicates the analyses of LCA cases, especially in patients without a family history of the disorder, and conventional methods are of limited value.

METHODS. To overcome these limitations, arrayed primer extension (APEX) technology was used to design a genotyping microarray for early-onset, severe retinal degenerations that includes all of the >300 disease-associated variants currently described in eight genes (in addition to the six just listed, the early-onset RP genes LRAT and MERTK were added). The resultant LCA array allows simultaneous detection of all known disease-associated alleles in any patient with early-onset RP. The array was validated by screening 93 confirmed patients with LCA who had known mutations. Subsequently, 205 novel LCA cases were screened on the array, followed by segregation analyses in families, if applicable.

RESULTS. The microarray was >99% effective in determining the existing genetic variation and yielded at least one disease-associated allele in approximately one third of the novel patients. More than two (expected) variants were discovered in a substantial fraction (22/300) of the patients, suggesting a modifier effect from more than one gene. In support of the latter hypothesis, the third allele segregated with a more severe disease phenotype in at least five families.

CONCLUSIONS. The LCA genotyping microarray is a robust and cost-effective screening tool, representing the prototype of a disease chip for genotyping patients with a genetically heterogeneous condition. Simultaneous screening for all known LCA-associated variants in large LCA cohorts allows systematic detection and analysis of genetic variation, facilitating prospective diagnosis and ultimately predicting disease progression.

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