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Hazra, A.

Publications and source records attributed to Hazra, A..

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A study of Mutation in ATP7B gene and its correlation with clinical phenotype and radiological features in Wilson Disease patients

IntroductionWilson Disease (WD) is an autosomal recessive disease caused by mutations in the ATP7B gene. Clinical manifestations of WD are variable. Identification of prevalent mutations in a given population is necessary to provide mutation-based molecular diagnosis. Previous studies have detected common mutations in this part of the world and our study aimed to correlate genotype with clinical and radiological features. MethodsA descriptive cross-sectional observational study was conducted over a period of two years in a tertiary care hospital and neurology referral unit of Kolkata, India. All WD patients within the study period and meeting the inclusion criteria were included. Demographic data collection, clinical examination and relevant laboratory investigations were done. Magnetic resonance imaging of brain and cognitive assessment by Mini Mental Score Exam (MMSE) were also performed. Blood was collected for genetic analyses. PCR-Sanger sequencing of exons 2,4,6,8,10,14,16,18 of ATP7B gene was done based on previous reports of mutation hotspots of ATP7B gene for WD in Eastern India. Genotype phenotype correlation was attempted using two supervised machine learning methods, viz. logistic regression with an elastic-net penalty and the random forest. ResultsOf 52 WD patients were included in the study, 57.7% were males. The mean age at diagnosis was 13.96 years. Majority (61.8%) of the patients had dystonia on presentation, followed by dysarthria (41.2%), tremor (17.6%) and ataxia (11.8%). The mean MMSE and Frontal Assessment Battery score were 23.74 and 10.63 respectively and both were lower than the normal baseline values.Out of the total cohort of 52 patients,15(28.8%) harbored previously reported common mutations from this part of the country. Of the 15, 12 had the same mutation of c.813C>A(p.cys271Ter).The presence of common mutationswas associated with several distinct clinical phenotypes in the mathematical models but larger sample sizes are needed to corroborate the correlation. ConclusionsWD patients in eastern India have significant genotypic and phenotypic diversity. Further studies with larger samples and screening of remaining exons are warranted.

neuroscience

Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. In the scope of present work, elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from [~]10.4 GB sequence data, encompassing 15 chromosomes of reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. High percent of heterozygous loci in the majority of the cultivars reflect their hybrid ancestry as reported earlier. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants, most of them are involved in signal transduction, biosynthesis of secondary metabolite, transcriptional and translational regulation. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001). The selection of significant marker-trait associations with the Bonferroni correction threshold retained a set of 57 SNPs distributed across 14 chromosomes to be linked with eight phenotypic traits. High impact and trait-associated nucleotide polymorphisms perceived in this study can be exploited in worldwide germplasm of contrasting origin to depict their heritability and to unlock their potentiality in marker-assisted breeding.

genomics