Combining Homozygosity Mapping With Exome Capture To Identify The Causal Gene For Pericentral Retinitis Pigmentosa

Abstract

Purpose: : Pericentral retinitis pigmentosa (PCRP) is a rare subtype of RP with concentric retinal circles of photoreceptor death and viability. The biological reason and causal genes behind PCRP are not known. PCRP gene discovery will advance our understanding of retinal patterning, photoreceptor biology and retinal genetics. Our goal is to identify the PCRP gene using a combination of homozygosity mapping and exome capture.

Methods: : We phenotyped 2 consanguineous families with PCRP, a Lebanese family with 3 sibs and a Sardinian family with 3 sibs. We measured projected Snellen acuities, ERGs, retinal photography, in vivo microscopy, fundus autofluorescence (FAF) (Spectralis, Heidelberg Engineering) and kinetic perimetry (GVF). DNA was collected after informed consents. Known ARRP mutations (18 genes, 585 mutations) were excluded using APEX technology (Asper Ophthalmics). We performed SNP genotyping with 660 K SNP arrays. Regions of interest (overlap of sibs and overlap of two families) were further analyzed using the Illumina Genome Viewer and P-link software. Positional candidate genes were identified using the UCSC human genome browser (Feb 2009). We then performed exome capture by Roche Nimblegen Sequence Capture Arrays.

Results: : Affected members had the diagnostic pericentral scotomas from 2-20 degrees on GVF. Fundal exam showed concentric rings of normal/abnormal tissue. OCT identified a deposit of hyperfluorescent material between the photoreceptors and RPE. FAF showed rings of grainy hyperfluorescence. Our whole genome SNP genotyping of the first family identified four large homozygous regions on chr 4(8.6Mb), chr 12(6.1Mb), chr 12(1.4Mb) and chr 15(1Mb). In the second family we found significant homozygous regions on chr 6(6Mb), chr 11(5Mb) and chr 12(2 mb). We found significant overlap between the 2 families at chr 12 (1.3Mb, containing 17 genes). NGS identified 50 homozygous amino acid changing; splice site or frameshift mutations in the homozygous regions.

Conclusions: : Our analyses have identified a novel PCRP interval on chr 12, which does not overlap with known genes for other forms of RP. Phenotype analyses suggest that the causal protein for PCRP is possibly involved in phagocytosis in the subretinal space.

Keywords: gene screening • photoreceptors • retinal degenerations: hereditary