Comprehensive molecular diagnosis of a large cohort of 240 autosomal dominant retinitis pigmentosa families by Sanger and targeted next generation sequencing

Abstract

Purpose: To screen a cohort of 240 families with ascertained autosomal dominant retinitis pigmentosa (adRP) condition for mutations in genes known to cause adRP.

Methods: Two hundred and forty well-characterized adRP families were recruited mostly originating from France. The ten most frequently mutated adRP genes (RHO and PRPH2 in all exons, PRPF31, RP1, PRPF8, IMPDH1, NRL, PRPF3, NR2E3 and SNRNP200 in hot spots regions) were screened for mutations by Sanger sequencing of the probands. Patients without identified mutations were then sequenced using a targeted exon capture panel, which includes 123 retinal disease genes containing the 69 known adRP, autosomal recessive (arRP) and X-linked RP genes and several other retinal dystrophy genes.

Results: Disease-causing mutations were identified in 152 probands (62.5%), among which 43% had novel mutations. Four major genes, RHO (17.5%), PRPH2 (10.5%), RP1 (7.1%) and PRPF31 (6.3%) accounted for 41.5% of the cohort. Some genes revealed unexpectedly high prevalence of mutations: NR2E3 (4.6%), SNRNP200 (3.3%) and TOPORS (2.1%). No mutations were identified in nine adRP (CA4, FSCN2, GUCA1B, NRL, PRPF6, RDH12, ROM1, RP9/PAP1 and SEMA4A) and in arRP genes. Phenotype analysis showed moderate RP in many patients, with remarkable incomplete penetrance in PRPF31, SNRNP200 and RP1, and highly variable phenotype in PRPH2 including pericentral RP, diffuse RP and pseudovitelliform macular dystrophy in RP families.

Conclusions: Almost 2/3 of the families (62.5%) carry a mutation in a known adRP gene, implying that more than 1/3 (37.5%) of the families either have deep intronic mutations in a known gene, large chromosomal rearrangement not detected by techniques applied or are mutated in an unknown RP gene. Full exome sequencing is currently ongoing for 21 negative families.