Unity in diversity: An overview of the genomic anthropology of India

Context: India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses. Objective and methods: Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications. Results: The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country. Conclusion: This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations. © 2014 Informa UK Ltd

Genetics of coronary heart disease with reference to ApoAI-CIII-AIV gene region.

Cardiovascular diseases are affected by multiple factors like genetic as well as environmental hence they reveal factorial nature. The evidences that genetic factors are susceptible for developing cardiovascular diseases come from twin studies and familial aggregation. Different ethnic populations reveal differences in the prevalence coronary artery disease (CAD) pointing towards the genetic susceptibility. With progression in molecular techniques different developments have been made to comprehend the disease physiology. Molecular markers have also assisted to recognize genes that may provide evidences to evaluate the role of genetic factors in causation of susceptibility towards CAD. Numerous studies suggest the contribution of specific "candidate genes", which correlate with various roles/pathways that are involved in the coronary heart disease. Different studies have revealed that there are large numbers of genes which are involved towards the predisposition of CAD. However, these reports are not consistent. One of the reasons could be weak contribution of genetic susceptibility of these genes. Genome wide associations show different chromosomal locations which dock, earlier unknown, genes which may attribute to CAD. In the present review different ApoAI-CIII-AIV gene clusters have been discussed

Epigenetics and Epigenomics: the future of nutritional interventions?

Epigenetics and Epigenomics: the future of nutritional interventions

Distribution of ApoE Variants in Four Northeast Indian Populations

Polymorphisms in the human apolipoprotein E gene (ApoE) have been extensively studied for associations with various complex diseases. Numerous population genetic studies have reported the distribution of ApoE alleles in global populations. In this study, we present new data on the distribution of ApoE polymorphisms among four Northeast Indian populations, namely, Kachari, Rabha, Ahom, and an Indo-European caste group. Allele frequencies, Hardy-Weinberg equilibrium, genotype and phenotype probabilities were based on the two SNPs, rs7412 and rs429358. Of the APOE genotypes, derived from rs429358 and rs7412 SNPs, 3/3 and 3/4 genotypes were the most frequent in all groups and only Rabha showed higher frequency of 2/3 genotype. The Kachari population showed the highest frequency of CT genotype for SNP rs429358 and the highest frequency of allele *E4 in the Indian subcontinent, which was much higher than other study populations of eastern India

Omega 3 fatty acids, inflammation and DNA methylation: an overview

Omega-3 polyunsaturated fatty acids (n-3 PUFAs) are known to be anti-inflammatory and to alter gene expression within the cells. Emerging evidence indicates that one of the mechanisms for this process involves the alteration of epigenetic markers, such as DNA methylation. The focus of this overview is to document the current evidence for n-3 PUFA effects on DNA methylation and how these may impact on the inflammatory processes

Distribution of ApoE Variants in Four Northeast Indian Populations

Polymorphisms in the human apolipoprotein E gene (ApoE) have been extensively studied for associations with various complex diseases. Numerous population genetic studies have reported the distribution of ApoE alleles in global populations. In this study, we present new data on the distribution of ApoE polymorphisms among four Northeast Indian populations, namely, Kachari, Rabha, Ahom, and an Indo-European caste group. Allele frequencies, Hardy-Weinberg equilibrium, genotype and phenotype probabilities were based on the two SNPs, rs7412 and rs429358. Of the APOE genotypes, derived from rs429358 and rs7412 SNPs, 3/3 and 3/4 genotypes were the most frequent in all groups and only Rabha showed higher frequency of 2/3 genotype. The Kachari population showed the highest frequency of CT genotype for SNP rs429358 and the highest frequency of allele *E4 in the Indian subcontinent, which was much higher than other study populations of eastern India

A time efficient adaptation of GC-FID method for the analysis of PBMC lipid composition

Peripheral Blood Mononuclear Cells (PBMC) comprise of lymphocytes and monocytes which are involved in the pathogenesis of chronic inflammatory diseases. A method for estimation of PBMC lipid composition was modified from an existing method for plasma to support our fish oil intervention study in mild-moderate asthmatics. This modification involved an hour long direct transesterification reaction using methanol and acetyl chloride followed by a modified GC-FID method. The identification of PBMC fatty acid composition was achieved by relative comparison with a 37 Fatty Acid component standard. The method was found to be reproducible and accurate with a within batch and between batch Coefficient of variation (CV) of <10%. The modified method was adapted for PBMC total lipid estimation and was considered suitable to detect changes in PBMC composition following fish oil supplementation. This method is quick, scalable, and cost effective for large scale population and intervention studies. Keywords: Fatty acids, PBMC, fish oil, Gas chromatography Introduction Fish oils comprise of two major omega 3 polyunsaturated fatty acids (PUFAs) namely Eicosapentaenoic Acid (EPA, 20:5) and Docosahexaenoic Acid (DHA, 22:6), these PUFAs are important structural components of cell membranes. In fish oil supplementation studies, an incorporation of EPA and DHA in total cell lipids and phospholipids, which occurs mostly at the expense of omega 6 PUFAs (primarily Arachidonic Acid, AA, 20:4), is expected. The extraction of fatty acids from cells and tissues is generally based on the original methods of Folch (1957) or Bligh & Dyer (1959), which have been widely applied and used on different types of cells (Damsgaard et al. 2008; Garcia-Larsen 2011; Grindel et al. 2013). Similarly, there are standard methods for derivatisation of lipids (acid-catalysed) (Lepage and Roy 1986; Morrison and Smith 1964, Matsumot et al. 2013) in a quantitative manner (Blau and Halket 1993; Christie 2003). Masood et al. (2005) proposed a method for measurement of fatty acids in plasma samples which is principally derived from Lepage & Roy (1986) with advantages of speed, reproducibility, lower toxicity and cost. While previous investigations have concentrated upon the use of plasma samples for the analysis of fatty acid composition of cells, the focus of this paper is the use of PBMC

N-3 fatty acids and asthma

Copyright © 2016 The Authors. Asthma is one of the most common and prevalent problems worldwide affecting over 300 million individuals. There is some evidence from observational and intervention studies to suggest a beneficial effect of n-3 PUFA in inflammatory diseases, specifically asthma. Marine-based n-3 PUFA have therefore been proposed as a possible complementary/alternative therapy for asthma. The proposed anti-inflammatory effects of n-3 fatty acids may be linked to a change in cell membrane composition. This altered membrane composition following n-3 fatty acid supplementation (primarily EPA and DHA) can modify lipid mediator generation via the production of eicosanoids with a reduced inflammatory potential/impact. A recently identified group of lipid mediators derived from EPA including E-series resolvins are proposed to be important in the resolution of inflammation. Reduced inflammation attenuates the severity of asthma including symptoms (dyspnoea) and exerts a bronchodilatory effect. There have been no major health side effects reported with the dietary supplementation of n-3 fatty acids or their mediators; consequently supplementing with n-3 fatty acids is an attractive non-pharmacological intervention which may benefit asthma

Genetic analysis of novel Alu insertion polymorphisms in selected Indian populations.

Indian subpopulations (Chenchu, Koya, and Lobana Sikh) were analyzed at the genetic level for 12 Alu polymorphisms. These markers were then utilized to establish levels of genetic identity between the Indian populations and more widely between the Indian populations and a European population.Previously collected blood samples were extracted using the phenol-chloroform method. The samples were utilized as templates for PCR using Alu specific primers and then analyzed by agarose gel electrophoresis for the presence and absence of the approximately 300 bp insertions. Allele frequencies were calculated by the gene counting method and were tested for Hardy-Weinberg equilibrium, heterozygosities, inbreeding coefficient, and GST to assess the level of genetic differentiation.All of the Alu loci were polymorphic in the three Indian populations studied and their average observed heterozygosity ranged from 0.294 (Lobana Sikh) to 0.357 (Koya). Allele and genotype frequency variation at the 2b, 9a, and ACE loci led to statistically significant pairwise differences among the three study populations. Overall population heterogeneity was observed for 7 out of 12 Alu polymorphisms.The overall results show that these Indian samples, though displaying significant genetic variation and differences among themselves, form an Indian cluster, which as expected, is distinct from the European sample (Russian). As Alus are easily analyzed and quantified by standard and cost-effective methodologies, this finding further reinforces their utility as effective population genetic markers. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc

Distribution of APOE variants in four Northeast Indian populations

Polymorphisms in the human apolipoprotein E gene (ApoE) have been extensively studied for associations with various complex diseases. Numerous population genetic studies have reported the distribution of ApoE alleles in global populations. In this study, we present new data on the distribution of ApoE polymorphisms among four Northeast Indian populations, namely, Kachari, Rabha, Ahom, and an Indo-European caste group. Allele frequencies, Hardy-Weinberg equilibrium, genotype and phenotype probabilities were based on the two SNPs, rs7412 and rs429358. Of the APOE genotypes, derived from rs429358 and rs7412 SNPs, 3/3 and 3/4 genotypes were the most frequent in all groups and only Rabha showed higher frequency of 2/3 genotype. The Kachari population showed the highest frequency of CT genotype for SNP rs429358 and the highest frequency of allele *E4 in the Indian subcontinent, which was much higher than other study populations of eastern India