A novel locus for autosomal dominant retinitis pigmentosa (adRP) on chromosome 19q13

Abstract

Purpose: The purpose of this study was to determine the cause of disease in a large, five-generation, African American family with autosomal dominant retinitis pigmentosa (adRP) but without detectable mutations in known adRP genes.

Methods: A total of 13 affected and 15 unaffected family members were enrolled in the study and clinical status was confirmed at the Retina Foundation of the Southwest, Dallas. DNAs from key affected family members were first screened by Sanger sequencing of genes known to cause dominant retinitis pigmentosa. Linkage mapping was conducted using Affymetrix 6.0 SNP/CNV arrays. Genomic regions with positive LOD scores were further characterized using short-tandem repeat polymorphisms. DNAs from several affected and inter-linking, unaffected individuals were then sequenced using retinal-capture next-generation sequencing (NGS), whole-genome NGS, and whole-exome NGS, using the Illumina platform. Rare variants tracking with disease in the family were evaluated by bioinformatic analysis and screening in a large cohort of unrelated adRP patients.

Results: No disease-causing mutations were detected in known adRP genes, and most known RP loci were excluded by linkage. Linkage mapping identified a disease-causing locus on chromosome 19q13.31-q13.33 flanked by markers D19S420 and D19S553, with a maximum LOD score of 4.0; other suggestive linkage regions were excluded by fine-structure mapping. The 19q region is 7.5 mb in length and contains 356 genes of which 267 are retinal-expressed. High-priority candidate genes in the region, including CRX, were investigated by multiple methods. No apparent disease-causing mutations were detected. Combining results from whole-exome and whole-genome NGS, 63 rare variants are tracking with disease in the family, however, none of these variants is an obvious cause of disease. These variants are currently under investigation.

Conclusions: A combination of linkage mapping and next-generation sequencing identified a novel adRP locus on 19q13. No mutations were detected in high-priority genes in the region but numerous rare variants are tracking with disease. Linkage mapping and NGS are powerful tools for localizing disease-causing genes causing dominant diseases. However, the extensive background variation in humans, including many rare, potentially-pathogenic variants, often confounds easy identification of true, disease-causing mutations.

Keywords: 696 retinal degenerations: hereditary • 604 mutations • 537 gene screening