title: Homozygosity mapping guided next generation sequencing to identify the causative genetic variation in inherited retinal degenerative diseases.
abstract: Inherited retinal degeneration (IRD) are a group of genetically heterogeneous disease of which retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are the most common and severe type. In our study we had taken three unrelated South Indian consanguineous IRD families. Homozygosity mapping was done using Affymetrix 250K Nsp1 GeneChip in each of LCA, Cone-Rod dystrophy (CRD) and autosomal recessive RP (arRP) families followed by targeted re-sequencing by next generation sequencing (NGS) on Illumina MiSeq. Known candidate genes ranging from 1-8 in numbers within the homozygous blocks were identified by homozygosity mapping and targeted NGS revealed the causative mutations; RDH12 c.832A>C, ABCA4 c.1462G>T, CDHR1c.1384_1392delCTCCTGGACinsG, in the LCA, CRD and arRP families, respectively. The identified mutations were validated by Sanger sequencing, segregation in the families and their absence in 200 control chromosomes. Homozygosity mapping guided targeted NGS, especially when more numbers of known candidate genes within the homozygous blocks are observed is a comprehensive method for mutation identification. Molecular data from a larger retinal degenerative disease cohort would reveal the spectrum and prevalence of mutations and genes in Indian population. Molecular diagnosis also aids in genetic counseling, offering carrier and prenatal testing to family members.
authors.affiliation: SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.|PhD Scholar, Birla Institute of Technology & Science (BITS), Hyderabad, India.
authors.forename: Srilekha
authors.initials: S
authors.lastname: Sundaramurthy
authors.affiliation: Departments of Paediatric Ophthalmology and Strabismus, Chennai, India.
authors.forename: Meenakshi
authors.initials: M
authors.lastname: Swaminathan
authors.affiliation: Vitreo-Retinal Services, Medical Research Foundation, Chennai, India.
authors.forename: Parveen
authors.initials: P
authors.lastname: Sen
authors.affiliation: SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.
authors.forename: Tharigopala
authors.initials: T
authors.lastname: Arokiasamy
authors.affiliation: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, India.
authors.forename: Swati
authors.initials: S
authors.lastname: Deshpande
authors.affiliation: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, India.
authors.forename: Neetha
authors.initials: N
authors.lastname: John
authors.affiliation: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, India.
authors.forename: Rupali A
authors.initials: RA
authors.lastname: Gadkari
authors.affiliation: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, India.
authors.forename: Ashraf U
authors.initials: AU
authors.lastname: Mannan
authors.affiliation: SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.
authors.forename: Nagasamy
authors.initials: N
authors.lastname: Soumittra
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002874:Chromosome Mapping; D003241:Consanguinity; D004252:DNA Mutational Analysis; D005260:Female; D005451:Fluorescein Angiography; D056726:Genetic Association Studies; D014644:Genetic Variation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D006801:Humans; D057130:Leber Congenital Amaurosis / Q000175:diagnosis* / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D009154:Mutation; D010375:Pedigree; D010641:Phenotype; D055815:Young Adult