Variant prioritization and linkage mapping using whole-exome sequencing data for families with autosomal dominant retinitis pigmentosa (adRP)

Abstract

Purpose: To facilitate the identification of novel retinitis pigmentosa (RP) genes by family-based exome sequencing of adRP families. Novel approaches to linkage analysis, coupled with a comprehensive variant scoring strategy, narrow the search space and prioritize the most likely disease-causing variants.

Methods: A scoring algorithm was implemented to prioritize potential causal variants within a family according to segregation with the phenotype, population frequency, predicted effect, and retinal gene expression data. The search can be further refined in families with multiple affected individuals using two complementary approaches to exome-based linkage analysis: (1) Shared IBD analysis of common variants identifies segments of maximum identity-by-descent among affected individuals, and (2) Rare heterozygote rule out nominates regions based on shared rare variants and the absence of homozygous differences between affected individuals.

Results: Twenty-four families with probable adRP but lacking common disease-causing mutations were included in the study. We performed exome capture and sequencing on 75 total samples (2-7 affecteds, 0-2 unaffected controls per family), followed by variant prioritization and linkage analysis. A subset of these families also had regions from traditional linkage mapping of extended pedigrees, the results of which were highly concordant with our linkage analyses. Seven of 24 families (29%) were revealed to have unrecognized mutations in known RP genes that were both high-scoring by our algorithm and deemed likely pathogenic by clinical assessment. Analysis of the remaining 17 families has identified candidate variants in a number of interesting genes, some of which have already undergone further segregation testing in extended pedigrees.

Conclusions: Family-based exome sequencing is a powerful strategy for the identification of novel RP genes, yet these studies often identify thousands of potential causative variants. Here, we demonstrate that comprehensive scoring of individual variants coupled with two genetic linkage approaches can substantially refine the search for disease-causing mutations.

Keywords: 539 genetics • 534 gene mapping • 696 retinal degenerations: hereditary