Homozygosity Mapping and Targeted Sanger Sequencing Reveal Genetic Defects Underlying Inherited Retinal Disease in Families from Pakistan

Abstract

BackgroundHomozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD).MethodsWe genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), congenital stationary night blindness (CSNB), or cone dystrophy (CD). We employed genome-wide single nucleotide polymorphism (SNP) array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS) of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families.ResultsHomozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1.ConclusionsHomozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.

Clinical Characterization of CNGB1-Related Autosomal Recessive Retinitis Pigmentosa

“…13,14 Variants in CNGB1 are an uncommon cause of RP, accounting for approximately 4% of arRP cases; there are limited reports describing the associated phenotypes. 10,[15][16][17][18][19][20] The present report describes the detailed clinical features of ten affected patients harboring likely pathogenic variants in CNGB1.…”

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

“…In this country, marriages of first cousins are highly favored, and families from Pakistan are considered a valuable resource for medical genetics research, which has led to significant scientific findings in the recent past [13,43]. Several studies on IRDs have been conducted in Pakistan during the last few years, but the majority of them were based on pedigrees from the Punjab and Sindh provinces [17][18][19][20]. Khan et al.…”

“…All variants were validated by Sanger sequencing and confirmed to co-segregate with the disease in all affected family members (Figure 2). While variants identified in the TULP1 (NM_001289395.1:c.1307A>G:p.Lys436Arg) and in the CNGA1 (NM_001142564.1: c.1298G>A:p.Gly433Asp) genes were formerly known to cause RP [18,31], DNA changes in PDE6B and in RPE65 have never been reported in any public databases. Since they are both loss-of-function variants (nonsense and frame-shift variants), they can be assumed to represent bona fide mutations.…”

“…Unsurprisingly, more than half of the patients from this study were born to consanguineous parents [16]. Recently, a few studies on IRDs have been published in Pakistan [17][18][19][20]. However, the majority of these reports were based on pedigrees from the Punjab and Sindh provinces, thus leaving North-Western Pakistan largely unexplored.…”

Prenatal and Postnatal Genetic Testing: Why, How, and When?

“…This can unmask uniparental disomy (in which both copies or portions of both chromosomes come from one parent), autosomal recessive conditions, consanguinity, and incest. 19,20 Results include pathogenic or likely pathogenic variants, variants of unknown significance (VUS), and benign or likely benign variants. Deletions can vary in size and small CNVs can be pathogenic harboring single gene or exon deletions.…”