Genetic profile and mutation spectrum of Leber congenital amaurosis in a larger Indian cohort using high throughput targeted re-sequencing.

To provide a comprehensive data on the prevalence of mutations in Leber congenital amaurosis (LCA) candidate genes from a larger Indian cohort. Ninety-two unrelated subjects were recruited after complete ophthalmic examination and informed consent. Targeted re-sequencing of 20 candidate genes was performed using Agilent HaloPlex target enrichment assay and sequenced on Illumina MiSeq platform. The data were analyzed using standard bioinformatics pipeline, variants annotated, validated and segregated. Genotype-phenotype correlation was performed for the mutation-positive cases. Targeted next generation sequencing (NGS) for the 20 candidate genes generated data with an average sequence coverage and depth of 99.03% and 134X, respectively. Mutations were identified in 61% (56/92) of the cases, which were validated, segregated in the families and absent in 200 control chromosomes. These mutations were observed in 14/20 candidate genes and 39% (21/53) were novel. Distinct phenotypes were observed with respect to genotypes. To our knowledge, this study presents the first comprehensive mutation spectrum of LCA in a large Indian cohort. The mutation-negative cases indicate scope for finding novel candidate gene(s) although mutations in deep intronic and regulatory regions cannot be ruled out.

Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness.

Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disorder which represents rod photoreceptor dysfunction or signal transmission defect from photoreceptors to adjacent bipolar cells. Patients displaying photoreceptor dysfunction show a Riggs-electroretinogram (ERG) while patients with a signal transmission defect show a Schubert-Bornschein ERG. The latter group is subdivided into complete or incomplete (ic) CSNB. Only few CSNB cases with Riggs-ERG and only one family with a disease-causing variant in SLC24A1 have been reported. Whole-exome sequencing (WES) in a previously diagnosed icCSNB patient identified a homozygous nonsense variant in SLC24A1. Indeed, re-investigation of the clinical data corrected the diagnosis to Riggs-form of CSNB. Targeted next-generation sequencing (NGS) identified compound heterozygous deletions and a homozygous missense variant in SLC24A1 in two other patients, respectively. ERG abnormalities varied in these three cases but all patients had normal visual acuity, no myopia or nystagmus, unlike in Schubert-Bornschein-type of CSNB. This confirms that SLC24A1 defects lead to CSNB and outlines phenotype/genotype correlations in CSNB subtypes. In case of unclear clinical characteristics, NGS techniques are helpful to clarify the diagnosis.

Consanguinity and ocular genetic diseases in South India: analysis of a five-year study.

OBJECTIVE: Consanguineous marriage is a widely practised social custom in Asia and northern Africa. In south India, Dravidian Hindus have contracted consanguineous marriages for over 2,000 years. In the present study, the influence of consanguinity on the prevalence of visual disorders was examined in patients attending a specialist genetic eye clinic. SUBJECTS AND METHODS: A total of 2,335 patients attending Sankara Nethralaya, Chennai, India, were screened for genetic eye disorders over a five-year period. The patients were drawn from all parts of India and from neighbouring countries in south Asia. RESULTS AND DISCUSSION: Six hundred and seventy-three (28.8%) of the patients tested for ophthalmic genetic disorders reported a family history of consanguinity. The majority (n = 574) of these families were from south India. In the patient group as a whole, the most common form of consanguineous union was between first cousins (n = 367), followed by uncle/niece marriage (n = 177), equivalent to a mean coefficient of inbreeding alpha = 0.0202. Among the consanguineous families, 430 of 673 (63.9%) had retinitis pigmentosa, 167 of these cases were autosomal recessive and 199 were isolated cases. The public in regions such as south India should be made aware of the merits and demerits of consanguineous marriages.

Tumor necrosis factor allelic polymorphism with diabetic retinopathy in India.

The association of tumor necrosis factor (TNF) with diabetic retinopathy (DR) has been described previously. A total of 207 Asian Indian patients of 15-year duration of type 2 diabetes were identified. This group included (i) 100 patients with DR and (ii) 107 patients without retinopathy (DNR). In this study, we correlated the length of the (GT)n microsatellite di-nucleotide repeat upstream to the promoter region of TNF gene with susceptibility for the development of retinopathy. The microsatellite was polymerase chain reaction amplified and electrophoresed on polyacrylamide gel and silver stained. In our study population, there were 18 alleles ranging from 97 to 131 base pairs (bp). Allele 4 (103 bp) had a higher prevalence (9.81%) in the DNR group compared to that (2.5%) in the DR group (P=0.002). Patients with retinopathy and allele 8 (111 bp) had a tendency to develop proliferative diabetic retinopathy (PDR). In this study of Indian subjects, it is suggested that allele 4 is a low risk allele for developing retinopathy and allele 8 (111 bp) shows an association with PDR.