Genomics approaches to identify an elusive defect at chromosome 17q22 in an autosomal dominant retinitis pigmentosa family

Abstract

Purpose : The gene defect in a large Dutch autosomal dominant retinitis pigmentosa (adRP) family was previously mapped to chromosome 17q. Linkage analysis on DNA samples of three generations, based on the analysis of affected persons, defined a critical region of 17.6 Mb on 17q22. This region contained the CA4 gene, known to be associated with adRP. To identify the elusive genetic defect, we expanded the linkage study by involving persons from the fourth generation and performed exome and genome sequencing.

Methods : Using a genome-wide SNP array containing 240,000 highly informative SNPs, DNAs of 35 affected and 28 healthy individuals were analyzed and employed for fine mapping of the adRP locus. Whole exome sequencing (WES) was performed for three affected family members and whole genome sequencing (WGS) was done in one of these patients. We searched for rare variants shared by the three affected persons and for structural variations in our in-house variant and CNV databases. The publically available ‘control’ databases dbSNP, Kaviar, GoNL, Wellderly were used to prioritize unique variants.

Results : Genome-wide linkage analysis confirmed the 17q22 region as the only region implicated in this Dutch adRP family. Haplotype analysis in 63 family members enabled us to refine the critical region. This region spans 16.0 Mb considering recombinations in affected persons and 5.1 Mb considering recombinations in affected and unaffected persons. The 5.1-Mb region contains 60 genes, among which CA4. No coding variants in CA4 were found. WGS data revealed a 226-kb tandem-duplication spanning GDPD1 and YPEL1, as well as the last exons of SMG8 and LINC01476. Although the duplication segregates with the phenotype in the family, its significance remains unknown. All adRP locus variants in the WGS data were verified using publically available control datasets in view of the autosomal dominant inheritance of the genetic defect and uniqueness of the locus and phenotype, leaving 615 variants of which two are coding variants.

Conclusions : We fine mapped an elusive adRP locus on chromosome 17q22 by expanding a linkage study in a large Dutch RP family and identified a novel tandem-duplication in the 5.1 Mb critical region. Additional studies are required to pinpoint the underlying genetic defect.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.