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Background  Leber congenital amaurosis (LCA) is the most severe form of inherited retinal visual impairment in children. So far, mutations in more than 20 genes have been known to cause LCA and among them,  RPE65  is a suitable candidate for gene therapy. The mutational screenings of  RPE65  and other LCA genes are requisite in support of emerging gene specific therapy for LCA. Therefore, we have carried out a comprehensive LCA genes screening using a combined approach of direct sequencing and DNA microarray based Asper chip analysis.    Methodology/Principal Findings  Thirty clinically diagnosed index LCA cases from Southern India were screened for coding and flanking intronic regions of  RPE65  through direct sequencing. Among thirty, 25 cases excluded from  RPE65  mutations were subjected to Asper chip analysis, testing 784 known pathogenic variations in 15 major LCA genes. In  RPE65  screening, four different pathogenic variations including two novel (c.361insT & c.939T>A) and two known (c.394G>A & c.361delT) mutations were identified in five index cases. In the chip analysis, seven known pathogenic mutations were identified in six index cases, involving genes  GUCY2D, RPGRIP1, AIPL1, CRX and IQCB1 . Overall, 11 out of 30 LCA cases (36.6%) revealed pathogenic variations with the involvement of  RPE65  (16.6%),  GUCY2D  (10%),  RPGRIP1  (3.3%),  AIPL1  (3.3%) and  CRX  &  IQCB1  (3.3%).    Conclusions/Significance  Our study suggests that such combined screening approach is productive and cost-effective for mutation detection and can be applied in Indian LCA cohort for molecular diagnosis and genetic counselling.

Mutational Screening of LCA Genes Emphasizing RPE65 in South Indian Cohort of Patients