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Homozygosity Mapping in Leber Congenital Amaurosis and Autosomal Recessive Retinitis Pigmentosa in South Indian Families.

Srilekha S, Arokiasamy T, Srikrupa NN, Umashankar V, Meenakshi S, Sen P, Kapur S, Soumittra N - PLoS ONE (2015)

Bottom Line: Homozygosity mapping using Affymetrix 10K HMA GeneChip on the arRP family identified a novel nonsense mutation in MERTK.In one of the eleven LCA families, the causative gene/mutation was not identified but many homozygous blocks were noted indicating that a possible novel locus/gene might be involved.The genotype and phenotype features, especially the fundus changes for AIPL1, RPE65, CRB1, RDH12 genes were as reported earlier.

View Article: PubMed Central - PubMed

Affiliation: SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India; Ph.D Scholar, Birla Institute of Technology & Science (BITS), Hyderabad, India.

ABSTRACT
Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP) are retinal degenerative diseases which cause severe retinal dystrophy affecting the photoreceptors. LCA is predominantly inherited as an autosomal recessive trait and contributes to 5% of all retinal dystrophies; whereas RP is inherited by all the Mendelian pattern of inheritance and both are leading causes of visual impairment in children and young adults. Homozygosity mapping is an efficient strategy for mapping both known and novel disease loci in recessive conditions, especially in a consanguineous mating, exploiting the fact that the regions adjacent to the disease locus will also be homozygous by descent in such inbred children. Here we have studied eleven consanguineous LCA and one autosomal recessive RP (arRP) south Indian families to know the prevalence of mutations in known genes and also to know the involvement of novel loci, if any. Complete ophthalmic examination was done for all the affected individuals including electroretinogram, fundus photograph, fundus autofluorescence, and optical coherence tomography. Homozygosity mapping using Affymetrix 250K HMA GeneChip on eleven LCA families followed by screening of candidate gene(s) in the homozygous block identified mutations in ten families; AIPL1 - 3 families, RPE65- 2 families, GUCY2D, CRB1, RDH12, IQCB1 and SPATA7 in one family each, respectively. Six of the ten (60%) mutations identified are novel. Homozygosity mapping using Affymetrix 10K HMA GeneChip on the arRP family identified a novel nonsense mutation in MERTK. The mutations segregated within the family and was absent in 200 control chromosomes screened. In one of the eleven LCA families, the causative gene/mutation was not identified but many homozygous blocks were noted indicating that a possible novel locus/gene might be involved. The genotype and phenotype features, especially the fundus changes for AIPL1, RPE65, CRB1, RDH12 genes were as reported earlier.

No MeSH data available.


Related in: MedlinePlus

2% Agarose gel electrophoresis showing cDNA amplification of exon 11–13 of IQCB1.Lane 1-100bp ladder, Lane 3- Affected index case, Lane 5 & 7—Carrier parents, Lane 9—Control, Lane 2, 4, 6, 8—empty wells Fig 2b Eletrophoretogram trace showing the amplified cDNA of control and proband. In proband exon 11 is followed by exon 13 and exon 12 is completely deleted, whereas in control, exon 11, 12 and 13 is continuous. The end of exon 11 is marked in both the phoretograms.
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pone.0131679.g002: 2% Agarose gel electrophoresis showing cDNA amplification of exon 11–13 of IQCB1.Lane 1-100bp ladder, Lane 3- Affected index case, Lane 5 & 7—Carrier parents, Lane 9—Control, Lane 2, 4, 6, 8—empty wells Fig 2b Eletrophoretogram trace showing the amplified cDNA of control and proband. In proband exon 11 is followed by exon 13 and exon 12 is completely deleted, whereas in control, exon 11, 12 and 13 is continuous. The end of exon 11 is marked in both the phoretograms.

Mentions: The four intronic mutations; RPE65 c.858+1G>T, SPATA7 c.913-2A>G, IQCB1 c.1278+6T>A, RDH12 c.344-8C>T, are present either in the conserved splice acceptor or donor site or within ten bases of the intron following the exon. Analysis of cDNA prepared from lymphocytes of LCA-4 family members using specific primers encompassing IQCB1 exons 11–13, revealed a single transcript of 338bp in the affected and two transcripts of 338 and 487bp, respectively in the heretozygous carrier parents (Fig 2a). Direct sequencing revealed that in the proband, exon 12 has been completely deleted (338bp amplicon) whereas both the parents were heterozygous carriers (338bp deleted and 478 wild type amplicons, respectively; Fig 2b). This skipping of exon 12 in the affected is predicted to result in a truncated protein, p.(Gln378Alafs*2). The consequence of c.344-8C>T mutation on the splicing of the retinal-specific RDH12 gene could not been determined but the change was predicted to alter splicing. The two missense mutations, CRB1 c.3307G>A p.(Gly1103Arg) and AIPL1 c.247G>A p.(Glu83Lys) analysed with PolyPhen 2 [44] and SIFT [45] were both predicted to be probably damaging and deleterious (Table 4 details the results of the in-silico analysis).


Homozygosity Mapping in Leber Congenital Amaurosis and Autosomal Recessive Retinitis Pigmentosa in South Indian Families.

Srilekha S, Arokiasamy T, Srikrupa NN, Umashankar V, Meenakshi S, Sen P, Kapur S, Soumittra N - PLoS ONE (2015)

2% Agarose gel electrophoresis showing cDNA amplification of exon 11–13 of IQCB1.Lane 1-100bp ladder, Lane 3- Affected index case, Lane 5 & 7—Carrier parents, Lane 9—Control, Lane 2, 4, 6, 8—empty wells Fig 2b Eletrophoretogram trace showing the amplified cDNA of control and proband. In proband exon 11 is followed by exon 13 and exon 12 is completely deleted, whereas in control, exon 11, 12 and 13 is continuous. The end of exon 11 is marked in both the phoretograms.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493089&req=5

pone.0131679.g002: 2% Agarose gel electrophoresis showing cDNA amplification of exon 11–13 of IQCB1.Lane 1-100bp ladder, Lane 3- Affected index case, Lane 5 & 7—Carrier parents, Lane 9—Control, Lane 2, 4, 6, 8—empty wells Fig 2b Eletrophoretogram trace showing the amplified cDNA of control and proband. In proband exon 11 is followed by exon 13 and exon 12 is completely deleted, whereas in control, exon 11, 12 and 13 is continuous. The end of exon 11 is marked in both the phoretograms.
Mentions: The four intronic mutations; RPE65 c.858+1G>T, SPATA7 c.913-2A>G, IQCB1 c.1278+6T>A, RDH12 c.344-8C>T, are present either in the conserved splice acceptor or donor site or within ten bases of the intron following the exon. Analysis of cDNA prepared from lymphocytes of LCA-4 family members using specific primers encompassing IQCB1 exons 11–13, revealed a single transcript of 338bp in the affected and two transcripts of 338 and 487bp, respectively in the heretozygous carrier parents (Fig 2a). Direct sequencing revealed that in the proband, exon 12 has been completely deleted (338bp amplicon) whereas both the parents were heterozygous carriers (338bp deleted and 478 wild type amplicons, respectively; Fig 2b). This skipping of exon 12 in the affected is predicted to result in a truncated protein, p.(Gln378Alafs*2). The consequence of c.344-8C>T mutation on the splicing of the retinal-specific RDH12 gene could not been determined but the change was predicted to alter splicing. The two missense mutations, CRB1 c.3307G>A p.(Gly1103Arg) and AIPL1 c.247G>A p.(Glu83Lys) analysed with PolyPhen 2 [44] and SIFT [45] were both predicted to be probably damaging and deleterious (Table 4 details the results of the in-silico analysis).

Bottom Line: Homozygosity mapping using Affymetrix 10K HMA GeneChip on the arRP family identified a novel nonsense mutation in MERTK.In one of the eleven LCA families, the causative gene/mutation was not identified but many homozygous blocks were noted indicating that a possible novel locus/gene might be involved.The genotype and phenotype features, especially the fundus changes for AIPL1, RPE65, CRB1, RDH12 genes were as reported earlier.

View Article: PubMed Central - PubMed

Affiliation: SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India; Ph.D Scholar, Birla Institute of Technology & Science (BITS), Hyderabad, India.

ABSTRACT
Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP) are retinal degenerative diseases which cause severe retinal dystrophy affecting the photoreceptors. LCA is predominantly inherited as an autosomal recessive trait and contributes to 5% of all retinal dystrophies; whereas RP is inherited by all the Mendelian pattern of inheritance and both are leading causes of visual impairment in children and young adults. Homozygosity mapping is an efficient strategy for mapping both known and novel disease loci in recessive conditions, especially in a consanguineous mating, exploiting the fact that the regions adjacent to the disease locus will also be homozygous by descent in such inbred children. Here we have studied eleven consanguineous LCA and one autosomal recessive RP (arRP) south Indian families to know the prevalence of mutations in known genes and also to know the involvement of novel loci, if any. Complete ophthalmic examination was done for all the affected individuals including electroretinogram, fundus photograph, fundus autofluorescence, and optical coherence tomography. Homozygosity mapping using Affymetrix 250K HMA GeneChip on eleven LCA families followed by screening of candidate gene(s) in the homozygous block identified mutations in ten families; AIPL1 - 3 families, RPE65- 2 families, GUCY2D, CRB1, RDH12, IQCB1 and SPATA7 in one family each, respectively. Six of the ten (60%) mutations identified are novel. Homozygosity mapping using Affymetrix 10K HMA GeneChip on the arRP family identified a novel nonsense mutation in MERTK. The mutations segregated within the family and was absent in 200 control chromosomes screened. In one of the eleven LCA families, the causative gene/mutation was not identified but many homozygous blocks were noted indicating that a possible novel locus/gene might be involved. The genotype and phenotype features, especially the fundus changes for AIPL1, RPE65, CRB1, RDH12 genes were as reported earlier.

No MeSH data available.


Related in: MedlinePlus