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Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous Pakistani families.

Khan SY, Ali S, Naeem MA, Khan SN, Husnain T, Butt NH, Qazi ZA, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA - Mol. Vis. (2015)

Bottom Line: An ophthalmic clinical examination consisting of fundus photography and electroretinography confirmed the diagnosis of RP.Haplotype analyses identified the region; however, the region did not segregate with the disease phenotype in the family.Taken together with our previously published work, our data suggest that mutations in PDE6A account for about 2% of the total genetic load of RP in our cohort and possibly in the Pakistani population as well.

View Article: PubMed Central - PubMed

Affiliation: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore MD.

ABSTRACT

Purpose: This study was conducted to localize and identify causal mutations associated with autosomal recessive retinitis pigmentosa (RP) in consanguineous familial cases of Pakistani origin.

Methods: Ophthalmic examinations that included funduscopy and electroretinography (ERG) were performed to confirm the affectation status. Blood samples were collected from all participating individuals, and genomic DNA was extracted. A genome-wide scan was performed, and two-point logarithm of odds (LOD) scores were calculated. Sanger sequencing was performed to identify the causative variants. Subsequently, we performed whole exome sequencing to rule out the possibility of a second causal variant within the linkage interval. Sequence conservation was performed with alignment analyses of PDE6A orthologs, and in silico splicing analysis was completed with Human Splicing Finder version 2.4.1.

Results: A large multigenerational consanguineous family diagnosed with early-onset RP was ascertained. An ophthalmic clinical examination consisting of fundus photography and electroretinography confirmed the diagnosis of RP. A genome-wide scan was performed, and suggestive two-point LOD scores were observed with markers on chromosome 5q. Haplotype analyses identified the region; however, the region did not segregate with the disease phenotype in the family. Subsequently, we performed a second genome-wide scan that excluded the entire genome except the chromosome 5q region harboring PDE6A. Next-generation whole exome sequencing identified a splice acceptor site mutation in intron 16: c.2028-1G>A, which was completely conserved in PDE6A orthologs and was absent in ethnically matched 350 control chromosomes, the 1000 Genomes database, and the NHLBI Exome Sequencing Project. Subsequently, we investigated our entire cohort of RP familial cases and identified a second family who harbored a splice acceptor site mutation in intron 10: c.1408-2A>G. In silico analysis suggested that these mutations will result in the elimination of wild-type splice acceptor sites that would result in either skipping of the respective exon or the creation of a new cryptic splice acceptor site; both possibilities would result in retinal photoreceptor cells that lack PDE6A wild-type protein.

Conclusions: we report two splice acceptor site variations in PDE6A in consanguineous Pakistani families who manifested cardinal symptoms of RP. Taken together with our previously published work, our data suggest that mutations in PDE6A account for about 2% of the total genetic load of RP in our cohort and possibly in the Pakistani population as well.

No MeSH data available.


Related in: MedlinePlus

Sequence alignment illustrating the conservations of PDE6A splice acceptor sites. c.2028–1G and c.1408–2A are fully conserved in the PDE6A orthologs. The organisms in brown and blue are primates and placental mammals, respectively, and the c.2028–1G and c.1408–2A variations are in red.
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f5: Sequence alignment illustrating the conservations of PDE6A splice acceptor sites. c.2028–1G and c.1408–2A are fully conserved in the PDE6A orthologs. The organisms in brown and blue are primates and placental mammals, respectively, and the c.2028–1G and c.1408–2A variations are in red.

Mentions: Next, we interrogated our entire cohort of RP familial cases by genotyping STR markers that span the PDE6A followed by bidirectional sequencing of the coding exons and exon–intron boundaries. We identified an additional familial case, PKRP140 (Figure 4D), who harbored a splice acceptor site mutation in intron 10: c.1408–2A>G (Figure 4E-G). We recruited a total of 15 individuals of PKRP140; ten of these participating individuals manifested symptoms of RP. The splice acceptor mutation segregated with the disease phenotype (RP) in the family (Figure 4D-G) and was not found in 350 ethnically matched control chromosomes and the 1000 Genomes and NHLBI Exome Sequencing Project databases. We further evaluated the conservation of c.1408–2A and c.2028–1G in other PDE6A orthologs. As shown in Figure 5, c.1408–2A and c.2028–1G are fully conserved in primates, placental mammals, and vertebrate PDE6A orthologs.


Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous Pakistani families.

Khan SY, Ali S, Naeem MA, Khan SN, Husnain T, Butt NH, Qazi ZA, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA - Mol. Vis. (2015)

Sequence alignment illustrating the conservations of PDE6A splice acceptor sites. c.2028–1G and c.1408–2A are fully conserved in the PDE6A orthologs. The organisms in brown and blue are primates and placental mammals, respectively, and the c.2028–1G and c.1408–2A variations are in red.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4539017&req=5

f5: Sequence alignment illustrating the conservations of PDE6A splice acceptor sites. c.2028–1G and c.1408–2A are fully conserved in the PDE6A orthologs. The organisms in brown and blue are primates and placental mammals, respectively, and the c.2028–1G and c.1408–2A variations are in red.
Mentions: Next, we interrogated our entire cohort of RP familial cases by genotyping STR markers that span the PDE6A followed by bidirectional sequencing of the coding exons and exon–intron boundaries. We identified an additional familial case, PKRP140 (Figure 4D), who harbored a splice acceptor site mutation in intron 10: c.1408–2A>G (Figure 4E-G). We recruited a total of 15 individuals of PKRP140; ten of these participating individuals manifested symptoms of RP. The splice acceptor mutation segregated with the disease phenotype (RP) in the family (Figure 4D-G) and was not found in 350 ethnically matched control chromosomes and the 1000 Genomes and NHLBI Exome Sequencing Project databases. We further evaluated the conservation of c.1408–2A and c.2028–1G in other PDE6A orthologs. As shown in Figure 5, c.1408–2A and c.2028–1G are fully conserved in primates, placental mammals, and vertebrate PDE6A orthologs.

Bottom Line: An ophthalmic clinical examination consisting of fundus photography and electroretinography confirmed the diagnosis of RP.Haplotype analyses identified the region; however, the region did not segregate with the disease phenotype in the family.Taken together with our previously published work, our data suggest that mutations in PDE6A account for about 2% of the total genetic load of RP in our cohort and possibly in the Pakistani population as well.

View Article: PubMed Central - PubMed

Affiliation: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore MD.

ABSTRACT

Purpose: This study was conducted to localize and identify causal mutations associated with autosomal recessive retinitis pigmentosa (RP) in consanguineous familial cases of Pakistani origin.

Methods: Ophthalmic examinations that included funduscopy and electroretinography (ERG) were performed to confirm the affectation status. Blood samples were collected from all participating individuals, and genomic DNA was extracted. A genome-wide scan was performed, and two-point logarithm of odds (LOD) scores were calculated. Sanger sequencing was performed to identify the causative variants. Subsequently, we performed whole exome sequencing to rule out the possibility of a second causal variant within the linkage interval. Sequence conservation was performed with alignment analyses of PDE6A orthologs, and in silico splicing analysis was completed with Human Splicing Finder version 2.4.1.

Results: A large multigenerational consanguineous family diagnosed with early-onset RP was ascertained. An ophthalmic clinical examination consisting of fundus photography and electroretinography confirmed the diagnosis of RP. A genome-wide scan was performed, and suggestive two-point LOD scores were observed with markers on chromosome 5q. Haplotype analyses identified the region; however, the region did not segregate with the disease phenotype in the family. Subsequently, we performed a second genome-wide scan that excluded the entire genome except the chromosome 5q region harboring PDE6A. Next-generation whole exome sequencing identified a splice acceptor site mutation in intron 16: c.2028-1G>A, which was completely conserved in PDE6A orthologs and was absent in ethnically matched 350 control chromosomes, the 1000 Genomes database, and the NHLBI Exome Sequencing Project. Subsequently, we investigated our entire cohort of RP familial cases and identified a second family who harbored a splice acceptor site mutation in intron 10: c.1408-2A>G. In silico analysis suggested that these mutations will result in the elimination of wild-type splice acceptor sites that would result in either skipping of the respective exon or the creation of a new cryptic splice acceptor site; both possibilities would result in retinal photoreceptor cells that lack PDE6A wild-type protein.

Conclusions: we report two splice acceptor site variations in PDE6A in consanguineous Pakistani families who manifested cardinal symptoms of RP. Taken together with our previously published work, our data suggest that mutations in PDE6A account for about 2% of the total genetic load of RP in our cohort and possibly in the Pakistani population as well.

No MeSH data available.


Related in: MedlinePlus