Exploring the Genetic Landscape of Retinal Diseases in North-Western Pakistan Reveals a High Degree of Autozygosity and a Prevalent Founder Mutation in ABCA4

Abstract

Variants in more than 271 different genes have been linked to hereditary retinal diseases, making comprehensive genomic approaches mandatory for accurate diagnosis. We explored the genetic landscape of retinal disorders in consanguineous families from North-Western Pakistan, harboring a population of approximately 35 million inhabitants that remains relatively isolated and highly inbred (~50% consanguinity). We leveraged on the high degree of consanguinity by applying genome-wide high-density single-nucleotide polymorphism (SNP) genotyping followed by targeted Sanger sequencing of candidate gene(s) lying inside autozygous intervals. In addition, we performed whole-exome sequencing (WES) on at least one proband per family. We identified 7 known and 4 novel variants in a total of 10 genes (ABCA4, BBS2, CNGA1, CNGA3, CNGB3, MKKS, NMNAT1, PDE6B, RPE65, and TULP1) previously known to cause inherited retinal diseases. In spite of all families being consanguineous, compound heterozygosity was detected in one family. All homozygous pathogenic variants resided in autozygous intervals ≥2.0 Mb in size. Putative founder variants were observed in the ABCA4 (NM_000350.2:c.214G>A; p.Gly72Arg; ten families) and NMNAT1 genes (NM_022787.3:c.25G>A; p.Val9Met; two families). We conclude that geographic isolation and sociocultural tradition of intrafamilial mating in North-Western Pakistan favor both the clinical manifestation of rare “generic” variants and the prevalence of founder mutations.

Next-Generation Sequencing Applications for Inherited Retinal Diseases

“…Similarly, EYS gene variants were found to be causative in 51% of a RP cohort from Japan [ 36 ]. This discovery is not unique, as several other parallel studies have revealed similar founder mutations in their target populations, for example, Belgium, RAX2 [ 37 ]; Costa Rica, RPE65 [ 38 ]; Finland, CERKL [ 39 ]; Japan, EYS [ 36 ]; Spain, RP1 [ 40 ] and ABCA4 [ 41 ]; Jewish community in Caucasia, PDE6B [ 42 ]; Pakistan, ABCA4 and NMNAT1 [ 43 ]; Guyana, BBS9 [ 44 ]; and Faroe Islands, MERTK [ 45 ]. The enrichment of these variants, several of which are large structural variants, emphasises the value of population-specific TS panels to target and detect mutations and mutational breakpoints that may be missed by commercial generic gene panel sequencing or even WES.…”

AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data

“…The same was true for the two other studies, where the presence of false-positive heterozygous genotypes was combined with the relatively short size of ROHs and/or the presence of a limited number of identifiable genotypes. In addition, AutoMap enabled the detection of new variants in a number of genes that were already associated with Mendelian conditions [35][36][37] . In conclusion, AutoMap is a reliable tool that can predict ROHs with high specificity and sensitivity, in less than a minute, even from VCF files derived from noisy exome sequencing data.…”

Whole exome sequencing and homozygosity mapping reveals genetic defects in consanguineous Iranian families with inherited retinal dystrophies

“…The rationale for this method is that unaffected parents who have some degree of kinship, belong to an ethnic group with high endogamy or are from a geographical isolate, could be heterozygotes for the same recessive mutation from a common ancestor. This mutation, which at the population level possibly will even be infrequent, can be brought to homozygosity since consanguinity can cause disease in these parents' children 23,24 . This feature makes the Iranian gene pool one of the richest resources for genetic investigations.…”