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

Shahid Khan, Shahbaz Ali, Muhammad Asif Naeem, Shaheen N. Khan, Tayyab Husnain, Nadeem H. Butt, Zaheeruddin A. Qazi, Javed Akram, Sheikh Riazuddin, Radha Ayyagari, J. Fielding Hejtmancik, Sheikh Amer Riazuddin

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)871-882
Number of pages12
JournalMolecular Vision
Volume21
StatePublished - Aug 18 2015

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RNA Splice Sites
Retinitis Pigmentosa
Exome
Mutation
Genome
Electroretinography
Computer Simulation
Introns
Genetic Load
Chromosomes
National Heart, Lung, and Blood Institute (U.S.)
Vertebrate Photoreceptor Cells
Photography
Genetic Markers
Haplotypes
Exons
Databases
Phenotype
DNA
Population

ASJC Scopus subject areas

  • Ophthalmology

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Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous pakistani families. / Khan, Shahid; Ali, Shahbaz; Naeem, Muhammad Asif; Khan, Shaheen N.; Husnain, Tayyab; Butt, Nadeem H.; Qazi, Zaheeruddin A.; Akram, Javed; Riazuddin, Sheikh; Ayyagari, Radha; Hejtmancik, J. Fielding; Riazuddin, Sheikh Amer.

In: Molecular Vision, Vol. 21, 18.08.2015, p. 871-882.

Research output: Contribution to journalArticle

Khan, S, Ali, S, Naeem, MA, Khan, SN, Husnain, T, Butt, NH, Qazi, ZA, Akram, J, Riazuddin, S, Ayyagari, R, Hejtmancik, JF & Riazuddin, SA 2015, 'Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous pakistani families', Molecular Vision, vol. 21, pp. 871-882.
Khan, Shahid ; Ali, Shahbaz ; Naeem, Muhammad Asif ; Khan, Shaheen N. ; Husnain, Tayyab ; Butt, Nadeem H. ; Qazi, Zaheeruddin A. ; Akram, Javed ; Riazuddin, Sheikh ; Ayyagari, Radha ; Hejtmancik, J. Fielding ; Riazuddin, Sheikh Amer. / Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous pakistani families. In: Molecular Vision. 2015 ; Vol. 21. pp. 871-882.
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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.",
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AU - Khan, Shahid

AU - Ali, Shahbaz

AU - Naeem, Muhammad Asif

AU - Khan, Shaheen N.

AU - Husnain, Tayyab

AU - Butt, Nadeem H.

AU - Qazi, Zaheeruddin A.

AU - Akram, Javed

AU - Riazuddin, Sheikh

AU - Ayyagari, Radha

AU - Hejtmancik, J. Fielding

AU - Riazuddin, Sheikh Amer

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N2 - 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.

AB - 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.

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