Fig. 2

Homozygosity mapping of SNP markers to define the critical region. SNP markers surrounding the most associated SNP from the GWAS (SNP BICF2G630247609; text highlighted in red) in LA PRA cases (PRA-affected LA) (A1–15) and controls (PRA-unaffected LA controls) (C1–27) are shown. The yellow coloured boxes represent the reference alleles, the pink coloured boxes highlight the alternate alleles and grey boxes represent missing data. The 1.3 Mb critical region was homozygous in 12 of the 15 cases used in GWAS analysis, as shown by the shaded region between positions CANFA33: 7,465,076- 8,738,020. One LA control (C10) is heterozygous for this region, in addition to two of the affected LA that are not homozygous for the critical region, as marked by asterisks (*). Locations of the four variants later followed up after subsequent WGS analysis (LINE-1 insertion, the top associated GWAS SNP (BICF2G630247609), and intronic SNVs in IMPG2 and CEP97) are indicated to show where these variants lie within the critical region