MULTIALLELIC INHERITANCE AND/OR MODIFIER ALLELES IN LEBER CONGENITAL AMAUROSIS: ANALYSIS WITH THE LCA DISEASE CHIP

Abstract

Abstract: : Purpose: Variants in at least six genes (RPE65, GUCY2D, CRB1, RPGRIP1, CRX, and AIPL1) have been associated with a diagnosis consistent with Leber congenital amaurosis (LCA) or early–onset retinitis pigmentosa. Genetically heterogeneous inheritance complicates the analyses of LCA cases, especially sporadic, where conventional methods are of limited or no value. Previously, we had designed a genotyping microarray (disease chip) for LCA, which includes all >260 variants currently described in the six genes, allowing for the detection of all known LCA–associated variants (mutations) in any DNA sample in one simple reaction. We tested the array on a large cohort of LCA patients to determine the genotyping efficiency and to test if alleles from more than one gene are responsible for the LCA phenotype. Methods: The LCA genotyping microarray includes every known disease–associated sequence change described in LCA genes and a selection of common polymorphisms (for haplotype analysis). Over 200 LCA cases were screened on the array and followed by segregation analyses in families, if applicable. Results: The microarray was >98% effective in determining the existing genetic variation, and yielded at least one disease–associated allele in >30% of patients. More than two (expected) variants were discovered in a substantial fraction of patients, suggesting a multi–allelic inheritance or a modifier effect from more than one gene. In support of this hypothesis, the third allele segregated with a more severe disease phenotype in several families. Conclusions: The LCA genotyping microarray offers the most comprehensive and cost–effective tool for molecular diagnostics and basic science, representing the first instance where a "disease chip" is made available 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 causal genetic variation, facilitating prospective diagnosis and, ultimately, predicting the disease progression.

Keywords: retinal degenerations: hereditary • gene microarray • gene modifiers