Disease-causing mutations in a cohort of autosomal dominant RP (adRP) families without detectable mutations in known adRP genes

Abstract

Purpose: To determine the cause of disease in a cohort of 64 families with a diagnosis of adRP but without disease-causing mutations detected using panel-based Sanger sequencing and retinal-capture next-generation sequencing (NGS).

Methods: Unrelated probands in a cohort of 266 families with a diagnosis of adRP were tested by Sanger sequencing for mutations in known adRP genes and RPGR and RP2; probands without mutations were tested with retinal-capture NGS. Pathogenic mutations were identified in 76% of families. The remaining 64 families without detectable mutations were analyzed by a variety of methods including linkage mapping in suitably-large families, and whole-exome and whole-genome NGS. Potential disease-causing variants were tested in a panel of 200 adRP families not part of the original cohort.

Results: Linkage mapping localized the disease gene in 6 families to one or a few chromosomal sites, largely non-overlapping sites across families. Known retinal-disease genes in or contiguous to each linkage region were excluded by high-resolution linkage testing and/or sequencing. Whole-exome NGS was conducted in 10 or more affected members of the 6 families and in fewer members of 12 other families. Whole-genome NGS was conducted in 2 families. Rare variants tracking with disease were evaluated by bioinformatic methods and lists of potentially-pathogenic variants, and variants of unknown significance, were shared with other laboratories. A novel, dominant-acting mutation in RPE65 was identified in one family and a disease-causing mutation in a new adRP gene, HK1, was found in a second large family. From 10 to 100 rare variants were detected in the linkage regions of the remaining mapped families and numerous potentially-deleterious variants are tracking with disease in the smaller families. None of the rare variants detected are clearly pathogenic.

Conclusions: Mutations in at least 21 genes are known to cause adRP; linkage mapping in families without mutations in known genes indicates that several adRP genes remain to be found. Whole-exome and whole-genome NGS are powerful tools for finding disease-causing mutations in retinal disease genes but establishing pathogenicity of rare variants in families without mutations in known genes is a difficult problem. Data sharing between laboratories with similar research interests is a helpful adjunct to genetics research.