Exploration of Genetic Association Studies with Collagen Variants in Clinically Diagnosed Primary Knee Osteoarthritis in South Indian Population: A Non-replication Study

CYP2C19 is a polymorphic enzyme involved in the metabolism of clinically important drugs. Genotype-phenotype association studies of CYP2C19 have reported wide ranges in the metabolic ratios of its substrates. These discrepancies could be attributed to the variations in the promoter region and this aspect has been reported recently. The observations in the recent reports on the influence of promoter region variants on the metabolism of CYP2C19 substrates might also have been influenced by the copy number variations of CYP2C19. In this paper, we describe copy number variations of CYP2C19 using real-time polymerase chain reaction by comparative Ct method. No copy number variations were observed in the south Indian population indicating the observed discrepancies in genotype-phenotype association studies might be due to the regulatory region polymorphisms as reported earlier.

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Impact of type 2 diabetes variants identified through genome-wide association studies in early-onset type 2 diabetes from South Indian population

Genomics & Informatics ◽

10.5808/gi.2020.18.3.e27 ◽

2020 ◽

Vol 18 (3) ◽

pp. e27

Author(s):

Samuel Liju ◽

Manickam Chidambaram ◽

Viswanathan Mohan ◽

Venkatesan Radha

Keyword(s):

Type 2 Diabetes ◽

Early Onset ◽

Indian Population ◽

Association Studies ◽

Genome Wide Association ◽

South Indian Population ◽

Genome Wide Association Studies ◽

South Indian ◽

Genome Wide

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COVID-19 and Indian population: a comparative genetic analysis

10.1101/2021.12.15.21267816 ◽

2021 ◽

Author(s):

Saurabh Patil ◽

Sandhya Kiran Pemmasani ◽

Neelima Chitturi ◽

Ishita Bhatnagar ◽

Anuradha Acharya ◽

...

Keyword(s):

Immune Response ◽

Allele Frequency ◽

Genetic Association ◽

South Asian ◽

Indian Population ◽

Association Studies ◽

East Asian ◽

Genetic Association Studies ◽

Allele Frequencies ◽

Indian Origin

Background Major risk factors of COVID-19 include older age, male gender, and comorbidities. In addition, host genetic makeup is also known to play a major role in COVID-19 susceptibility and severity. To assess the genetic predisposition of the Indian population to COVID-19, a comparative analysis of the frequencies of polymorphisms directly or potentially associated with COVID-19 susceptibility, severity, immune response, and fatal outcomes was done between the Indian population and other major populations (European, African, East Asian, South Asian, and American). Materials and methods Polymorphisms directly or potentially associated with COVID-19 susceptibility, severity, immune response, and mortality were mined from genetic association studies, comparative genetic studies, expression quantitative trait loci studies among others. Genotype data of these polymorphisms were either sourced from the GenomegaDB database of Mapmygenome India Ltd. (sample size = 3054; Indian origin) or were imputed. Polymorphisms with minor allele frequency >= 0.05 and that are in Hardy-Weinberg equilibrium in the Indian population were considered for allele frequency comparison between the Indian population and 1000 Genome population groups. Results Allele frequencies of 421 polymorphisms were found to be significantly different in the Indian population compared to European, African, East Asian, South Asian, and American populations. 128 polymorphisms were shortlisted based on linkage disequilibrium and were analyzed in detail. Apart from well-studied genes, like ACE2, TMPRSS2, ADAM17, and FURIN, variants from AHSG, IFITM3, PTPN2, CD209, CCL5, HEATR9, SELENBP9, AGO1, HLA-G, MX1, ICAM3, MUC5B, CRP, C1GALT1, and other genes were also found to be significantly different in Indian population. These variants might be implicated in COVID-19 susceptibility and progression. Conclusion Our comparative study unraveled multiple genetic variants whose allele frequencies were significantly different in the Indian population and might have a potential role in COVID-19 susceptibility, its severity, and fatal outcomes. This study can be very useful for selecting candidate genes/variants for future COVID-19 related genetic association studies.

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Genetic association of ADIPOQ gene variants with type 2 diabetes, obesity and serum adiponectin levels in south Indian population

Gene ◽

10.1016/j.gene.2013.09.012 ◽

2013 ◽

Vol 532 (2) ◽

pp. 253-262 ◽

Cited By ~ 61

Author(s):

Kandaswamy Ramya ◽

Kuppuswamy Ashok Ayyappa ◽

Saurabh Ghosh ◽

Viswanathan Mohan ◽

Venkatesan Radha

Keyword(s):

Type 2 Diabetes ◽

Genetic Association ◽

Indian Population ◽

Serum Adiponectin ◽

South Indian Population ◽

Gene Variants ◽

Adipoq Gene ◽

South Indian

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The genetic susceptibility profile of type 2 diabetes and reflection of its possible role related to reproductive dysfunctions in the southern Indian population of Hyderabad

BMC Medical Genomics ◽

10.1186/s12920-021-01129-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kumuda Irgam ◽

Battini Sriteja Reddy ◽

Sai Gayathri Hari ◽

Swathi Banapuram ◽

Battini Mohan Reddy

Keyword(s):

Type 2 Diabetes ◽

Genetic Association ◽

Large Scale ◽

Indian Population ◽

Association Studies ◽

Genetic Association Studies ◽

Significant Snps ◽

Allelic Association ◽

Gender Specific

Abstract Background The genetic association studies of type 2 diabetes mellitus (T2DM) hitherto undertaken among the Indian populations are grossly inadequate representation of the ethnic and geographic heterogeneity of the country. In view of this and due to the inconsistent nature of the results of genetic association studies, it would be prudent to undertake large scale studies in different regions of India considering wide spectrum of variants from the relevant pathophysiological pathways. Given the reproductive dysfunctions associated with T2DM, it would be also interesting to explore if some of the reproductive pathway genes are associated with T2DM. The present study is an attempt to examine these aspects in the southern Indian population of Hyderabad. Methods A prioritized panel of 92 SNPs from a large number of metabolic and reproductive pathway genes was genotyped on 500 cases and 500 controls, matched for ethnicity, age and BMI, using AGENA MassARRAYiPLEX™ platform. Results The allelic association results suggested 14 SNPs to be significantly associated with T2DM at P ≤ 0.05 and seven of those—rs2241766-G (ADIPOQ), rs6494730-T (FEM1B), rs1799817-A and rs2059806-T (INSR), rs11745088-C (FST), rs9939609-A and rs9940128-A (FTO)—remained highly significant even after correction for multiple testing. A great majority of the significant SNPs were risk in nature. The ROC analysis of the risk scores of the significant SNPs yielded an area under curve of 0.787, suggesting substantial power of our study to confer these genetic variants as predictors of risk for T2DM. Conclusions The associated SNPs of this study are known to be specifically related to insulin signaling, fatty acid metabolism and reproductive pathway genes and possibly suggesting the role of overlapping phenotypic features of insulin resistance, obesity and reproductive dysfunctions inherent in the development of diabetes. Large scale studies involving gender specific approach may be required in order to identify the precise nature of population and gender specific risk profiles for different populations, which might be somewhat distinct.

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