CYP11B2 gene polymorphisms and hypertension in highlanders accustomed to high salt intake

Mean population salt consumption in India: a systematic review

BACKGROUND

Member states of the WHO, including India, have adopted a target 30% reduction in mean population salt consumption by 2025 to prevent noncommunicable diseases. Our aim was to support this initiative by summarizing existing data that describe mean salt consumption in India.

METHOD

Electronic databases - MEDLINE via Ovid, EMBASE, CINAHL and the Cochrane Database of Systematic Reviews - were searched up to November 2015 for studies that reported mean or median dietary salt intake in Indian adults aged 19 years and older. Random effects meta-analysis was used to obtain summary estimates of salt intake.

RESULTS

Of 1201 abstracts identified, 90 were reviewed in full text and 21 were included: 18 cross-sectional surveys (n = 225 024), two randomized trials (n = 255) and one case-control study (n = 270). Data were collected between 1986 and 2014, and reported mean salt consumption levels were between 5.22 and 42.30 g/day. With an extreme outlier excluded, overall mean weighted salt intake was 10.98 g/day (95% confidence interval 8.57-13.40). There was significant heterogeneity between the estimates for contributing studies (I = 99.97%) (P homogeneity ≤0.001), which was likely attributable to the different measurement methods used and the different populations studied. There was no evidence of a change in intake over time (P trend = 0.08).

CONCLUSION

The available data leave some uncertainty about exact mean salt consumption in India but there is little doubt that population salt consumption far exceeds the WHO-recommended maximum of 5 g per person per day.

The impacts of the interaction of genetic variation, CYP11β2 and NEDD4L, with sodium intake on pediatric obesity with gender difference: a 3-year panel study

Backgrounds/Objectives:This panel study was to predict the incidences of pediatric obesity by the interaction of sodium (Na) intake and nine single-nucleotide polymorphisms (SNPs) of salt-sensitive genes (SSGs), ACE(angiotensin-converting enzyme), ADD1 G460W,AGT M235T,CYP11β2 (cytochrome P450 family 11-subfamily β-2, -aldosterone synthase),GNB3 C285T,GRK4(A142V)(G-protein-coupled receptor kinases type 4),GRK4 (A486V),NEDD4L (neural precursor cell expressed developmentally downregulated 4 like; rs2288774) and SLC12A3 (solute carrier family 12 (Na/Cl transporters)-member 3), selected from genome-wide association study.

SUBJECTS/METHODS

Non-obese (non-OB) Korean children of 9 years old were recruited from eight elementary schools in Seoul in 2007 and 2009, each. Follow-up subjects (total=798) in 2010 and 2012 were final participants. Participants were classified as OB group for those whose body mass index were over the 85th percentile using the 'Korean National Growth Charts', and others were classified as non-OB. With nine SNPs typing, the genetic interaction with the variation of Na intake for 3 years was evaluated as an obesity risk.

RESULTS

The obesity incidence rate for non-OB children at baseline after 3 years was 10.31%. Na intake in non-OB after 3 years was significantly decreased compared with the baseline, whereas Na intake reduction was undetectable in OB. We found gender differences on association between the changes of Na intake and the obesity incidence for 3 years by the SSG variation. Odds ratio for the obesity risk was 5.75 times higher in girls having hetero/mutant types of NEDD4L with higher Na intakes (Q2+Q3+Q4 in quartiles) compared with that in the wild type with the lowest Na intake (Q1). Girls with hetero/mutant of CYP11β2 tended to increase the obesity incidence as Na intake increased (Q1<Q2<Q3<Q4, P-value trend=0.047). The other seven SNPs of SSGs had no significance over Na intake.

CONCLUSIONS

From this panel study and the previous cross-sectional study, we found CYP11β2 as the common gene, powerful to explain the interaction between obesity incidence and Na intake, in particular, among girls. Girls with hetero/mutant allele of this gene should reduce their daily Na intake to prevent obesity.

Lungs at high-altitude: genomic insights into hypoxic responses

Hypobaric hypoxia at high altitude (HA) results in reduced blood arterial oxygen saturation, perfusion of organs with hypoxemic blood, and direct hypoxia of lung tissues. The pulmonary complications in the cells of the pulmonary arterioles due to hypobaric hypoxia are the basis of the pathophysiological mechanisms of high-altitude pulmonary edema (HAPE). Some populations that have dwelled at HA for thousands of years have evolutionarily adapted to this environmental stress; unadapted populations may react with excessive physiological responses that impair health. Individual variations in response to hypoxia and the mechanisms of HA adaptation provide insight into physiological responses. Adaptive and maladaptive responses include alterations in pathways such as oxygen sensing, hypoxia signaling, K+- and Ca2+-gated channels, redox balance, and the renin-angiotensin-aldosterone system. Physiological imbalances are linked with genetic susceptibilities, and nonhomeostatic responses in gene regulation that occur by small RNAs, histone modification, and DNA methylation predispose susceptible humans to these HA illnesses. Elucidation of the interaction of these factors will lead to a more comprehensive understanding of HA adaptations and maladaptations and will lead to new therapeutics for HA disorders related to hypoxic lungs.

Association of the human CYP11B2 gene and essential hypertension in southwest Han Chinese population: a haplotype-based case-control study

Aldosterone synthase produces aldosterone, which regulates electrolytes and thereby blood pressure (BP). The aldosterone-synthase gene (CYP11B2) has been regarded as a candidate gene for essential hypertension. To address this issue, we carried out a haplotype-based, case-control study to explore the association between a human CYP11B2 gene and essential hypertension (EH) in the southwest Han population of China (n = 1020 individuals). Four tag single-nucleotide polymorphisms (SNPs) (rs4536, rs4545, rs3097, and rs3802230) and the C-344T polymorphism, as well as the K173R polymorphism in the CYP11B2 gene, were genotyped using the PCR-RFLP method. Single-locus analysis showed that the C allele of rs3802230 was significantly more prevalent in the EH subjects as compared to control subjects, adjusted for covariates. Haplotype analysis showed that the haplotype AAGC constructed by the tag SNPs (rs4536, rs4545, rs3097, and rs3802230), which carried the susceptible rs3802230 C allele, significantly increased the risk of essential hypertension with an odds ratios equal to 3.56 (P = 0.0001). The present results indicated that the rs3802230 C allele might be a risk marker for essential hypertension and haplotype AAGC might confer high genetic susceptibility to essential hypertension in a southwest Han Chinese population.

Haplotype-based case-control study of the human CYP11B2 gene and essential hypertension in Yi and Hani minorities of China

This haplotype-based case-control study investigated whether the aldosterone synthase gene (CYP11B2) might be implicated in the pathogenesis of essential hypertension in Yi (226 individuals) and Hani (296 individuals) minorities of China. Four tag SNPs (rs4536, rs4545, rs3097, and rs3802230) and the K173R polymorphism were genotyped using the PCR-RFLP method. In the Hani minority, rs4536 was significantly associated with hypertension, after Bonferroni correction. H9 AGGC constructed by tag SNPs was significantly higher in hypertensives than in controls (P = 0.001). Further, we observed that haplotype AGGC remained significantly associated with male hypertension after adjustment for covariates (OR = 3.76, P = 0.002). In the Yi minority, it was found that the CYP11B2 gene was not significantly associated with hypertension. These results indicated that haplotype AGGC conferred an increased risk for hypertension in the Hani minority male. In addition, CYP11B2 may not be associated with hypertension in the Yi minority of China.

CYP11B2 gene haplotypes independently and in concurrence with aldosterone and aldosterone to renin ratio increase the risk of hypertension

OBJECTIVES

Aldosterone synthase produces aldosterone, which regulates electrolytes and thereby blood pressure. Polymorphisms in aldosterone-synthase gene (CYP11B2) may associate with heterogeneous aldosterone production and hypertension. Hence, we investigated -344T/C, Iw/Ic polymorphisms of CYP11B2, plasma renin activity (PRA) and aldosterone concentration (PAC).

DESIGN AND METHODS

Consecutive ethnically-matched 450 hypertensive patients and 360 controls were screened by PCR-RFLP for genotypes and haplotypes; PRA and PAC were measured.

RESULTS

The Iw/Ic polymorphism distribution differed significantly between the two groups (LRT chi(2)=15.8, df=2, P=0.000). The mutant allele-Ic and genotype-Ic/Ic were overrepresented in patients (35% versus 27% and 13% versus 7%). Overrepresentation of T-Ic haplotype in patients was identified as risk haplotype (P=0.000). Patients had significantly higher PAC and aldosterone-to-renin ratio (ARR; P=0.000), which was Ic-allele dependent.

CONCLUSIONS

The haplotype T-Ic associated with hypertension susceptibility. Correlation between Ic-allele and raised ARR likely serve in hypertension management.

Potential roles of high salt intake and maternal malnutrition in the development of hypertension in disadvantaged populations

1. It has been argued that all major risk factors for cardiovascular disease have been identified. Yet, epidemiological studies undertaken to identify risk factors have largely focused on populations in developed nations or on the urban or relatively affluent rural populations of developing countries. Poor rural populations are seldom studied. 2. Somewhat different risk factors may operate in poor rural populations. Evidence for this is provided by the finding that, in disadvantaged rural India, the prevalence of hypertension is greater than would be expected based on established risk factors in these populations. One risk factor to be considered is a poor intrauterine environment. 3. In animals, maternal macro- and micronutrient malnutrition can lead to reduced nephron endowment. Nephron deficiency, in turn, can render blood pressure salt sensitive. The combination of nephron deficiency and excessive salt intake will predispose to hypertension. 4. Human malnutrition may have similar effects, particularly in regions of the world where malnutrition is endemic and where women are disadvantaged by existing social practices. 5. Moreover, high salt intake is endemic in many parts of Asia, including India. Therefore, we propose that maternal malnutrition (leading to reduced nephron endowment), when combined with excessive salt intake postnatally, will account, at least in part, for the unexpectedly high prevalence of hypertension in disadvantaged rural communities in India and elsewhere.

Significance of angiotensinogen gene haplotypes and genotypes combinations in hypertension

OBJECTIVE

Renin-angiotensin system gene polymorphisms are associated with essential hypertension; angiotensinogen gene variants are considered potential genetic risk factors. The aim of this study was to investigate the contribution of the G-6A, T174M, M235T polymorphisms, genotypic interactions, and haplotypes toward essential hypertension.

METHODS

In a case-control design, 810 consecutive ethnically matched unrelated individuals comprising 450 hypertensive patients and 360 controls were recruited. Genotyping by polymerase chain reaction-restriction fragment length polymorphism, genotypes combinations, and haplotypes analyses were performed. Plasma renin activity and plasma aldosterone concentration were measured.

RESULTS

The G-6A and M235T polymorphisms differed significantly (P = 0.007, odds ratio = 1.9, 95% confidence interval = 1.2-2.9; P < 0.0001, odds ratio = 3.7, 95% confidence interval = 2.3-5.7, respectively), wherein the -6A and 235T mutant alleles were over-represented in hypertensive patients (P < 0.0001, each). Genotypes combinations of six wild-type alleles versus the remaining resulted in odds ratio of 2.4 (P < 0.0001), further mutant alleles based combinations linearly correlated with systolic, diastolic, and mean blood pressure. Over-representation of the haplotypes, namely, A/174T, 174T/235T, A/235T, and A/174T/235T in hypertensive patients and G/174T, 174T/235M, G/235M, and G/174T/235M in controls, was identified as risk and protective haplotypes (P < 0.0001, each), respectively. The patients had significantly higher plasma aldosterone concentration and lower plasma renin activity (P < 0.0001), the former correlated with -6A and 235T alleles (P < 0.0001).

CONCLUSION

The interaction among G-6A, M235T and T174M polymorphisms in combinations or haplotypes emerged significant. These findings, conjoint with significant high plasma aldosterone concentration and low plasma renin activity, suggest low-renin hypertension in our study population.

Skinfold thickness and blood pressure across C-344T polymorphism of CYP11B2 gene

OBJECTIVE

To ascertain whether body adiposity is associated with the C-344T polymorphism of the CYP11B2 gene codifying for aldosterone synthase.

DESIGN

A cross-sectional epidemiological evaluation of a highly homogeneous unselected general population of Caucasians.

METHODS

Lifestyle, medical history, anthropometrics, subscapular, triceps and suprailiac skinfold thickness, lying blood pressure and biochemical measures were recorded in a population-based study among 1386 unselected subjects (56.5% women) living in a secluded valley. All were genotyped for C-344T allele status. Continuous variables were compared across genotypes with analysis of covariance and correlations evaluated using the Pearson method. Odds ratios (OR) were calculated for the TT and CT genotype versus the CC homozygotes and compared with the T-carriers with a logistic model.

RESULTS

The C-344T genotypic frequency did not deviate from Hardy-Weinberg equilibrium. In women, higher values of triceps and subscapular skinfold thickness were found in the CC homozygotes than in the T-carriers. In this sex, skinfold thickness also directly correlated with both systolic and diastolic blood pressure in the T-carriers only. The logistic regression for the dependent variable arterial hypertension showed an influence of triceps [OR 1.07, 95% confidence interval (CI) 1.02-1.12, P=0.006], subscapular (OR 1.13, 95% CI 1.06-1.20, P<0.0001) and suprailiac (OR 1.08, 95% CI 1.01-1.15, P=0.03) skinfold in T-carrier women only. These relationships were not detectable in men. The aldosterone-to-renin ratios were comparable across genotypes and sexes.

CONCLUSION

The C-344T polymorphism of the CYP11B2 gene seems to exert a sex-specific influence on body adiposity, independent of adrenal aldosterone.

Genetics of salt-sensitive hypertension

Excess dietary salt intake represents a predominant cause of hypertension. However, individual blood pressure response to salt is heterogeneous, possibly due to different inherited susceptibility. The early identification of rare monogenic forms of hypertension associated with abnormalities of renal tubular sodium handling and response to diuretics highlighted the important role of renal alterations in salt-sensitive hypertension. Thereafter, interest has concentrated on the identification of more common allelic variants of candidate genes for hypertension in relation to the salt-sensitivity phenotype. By now, relatively large numbers of such variants have been described, and the pathogenic role of gene-gene interaction has received increasing attention. The alternative approach, consisting of the search for quantitative trait loci in the human genome linked to the transmission of salt-sensitive hypertension, has so far been less successful and cost-effective. This review summarizes consolidated knowledge and discusses the most recent novel findings on the impact of genetic variance on salt-sensitivity of blood pressure.

Association of the C−344T aldosterone synthase gene variant with essential hypertension: a meta-analysis

BACKGROUND

The CYP11B2 gene (CYP11B2) encoding aldosterone synthase has been associated with essential hypertension and some, but not all, studies have reported that the C-344T variant may influence the risk of the disease.

OBJECTIVE

We performed a systematic review of the literature by means of a meta-analysis to evaluate the influence of the C-344T CYP11B2 polymorphism on arterial hypertension and intermediate phenotypes.

METHODS

From 485 reports, we included 42 observational studies, case-control and cohort at baseline. Fixed and random effect models were used to pool data from individual studies.

RESULTS

From 19 heterogeneous studies including 5343 essential hypertensive and 5882 control subjects, we found a significant association between hypertension and the C-344T variant in fixed but not in random effect models [for homozygous CC: odds ratio (OR), 0.834; 95% confidence interval (CI), 0.760-0.914; P < 0.0001, n = 11 225]. Besides, homozygous CC subjects had lower plasma renin activity (D, -0.161; 95% CI, -0.279 to -0.043; P < 0.01, n = 1428) but no difference in plasma aldosterone levels (D, -0.006; 95% CI, -0.081 to 0.07; P = 0.88, n = 2872). Limiting the quantitative analysis of blood pressure to 13 studies including only untreated individuals, no significant association was found for systolic arterial blood pressure (D, 0.042; 95% CI, -0.057 to 0.141; P = 0.41, n = 1775) and diastolic arterial blood pressure (D, 0.026; 95% CI, -0.073 to 0.125; P = 0.61, n = 1775).

CONCLUSION

Homozygous individuals for the -344C CYP11B2 allele are at 17% lower risk of hypertension with respect to homozygous TT subjects.

Aldosterone Synthase Gene T-344C Polymorphism, Sodium and Blood Pressure in a Free-Living Population: A Community-Based Study

There have been few epidemiological studies on the gene-environmental interaction between the aldosterone synthase gene (CYP11B2) T-344C polymorphism and sodium in relation to blood pressure in a free-living general population. We hypothesized a priori that persons with the T allele of CYP11B2 would have elevated blood pressure levels in response to a higher sodium intake, and thus the association between the T-344C polymorphism and blood pressure would be more evident among persons with a high sodium intake than among those with a low sodium intake. Study subjects were 2,823 men and women aged 30-74 in a Japanese community. We examined the associations between the T-344C polymorphism and blood pressure levels, stratified by sodium variables estimated by 24-h urinary sodium excretion and a dietary questionnaire. There was no significant difference in blood pressure levels among the CC, TC and TT groups for either or both sexes. However, among persons with higher sodium excretion, mean systolic blood pressure levels tended to be higher in those with the TC (+3.0 mmHg, p=0.06) and TT (+2.9 mmHg, p=0.07) genotypes than in those with the CC genotype, but this tendency was not seen among those with lower sodium excretion (-4.0 mmHg, p=0.03 for TC vs. CC; -3.0 mmHg, p=0.11 for TT vs. CC; p for interaction =0.006). In conclusion, we found no association between CYP11B2 and blood pressure for total subjects or for persons with a higher sodium intake. However, a possible gene-blood pressure association among persons with higher sodium intake needs to be explored further.

Disturbed Homeostasis in Sodium-Restricted Mice Heterozygous and Homozygous for Aldosterone Synthase Gene Disruption

We have determined that differences in expression of aldosterone synthase (AS) affect responses to a low-salt diet. In AS-null mice (AS(-/-)), but not in wild-type, low salt significantly decreased plasma sodium and increased potassium. The increased urine volume (1.5xwild-type) and decreased urine osmolality (0.7xwild-type), present in AS(-/-) mice on normal salt, became more severe (2.3xwild-type and 0.5xwild-type) on low salt, but neither changed in wild-type. In both genotypes, plasma vasopressin was similar on normal and low salt, and desmopressin injection significantly increased urine osmolality. Renal mRNA levels for aquaporin 1 and 3 were unchanged by genotype or diet and epithelial sodium channel and Na(+)-K(+)-2Cl(-)-cotransporter by genotype. In AS(-/-) mice, aquaporin 2 mRNA increased on normal salt, whereas Na(+)Cl(-)-cotransporter and cortex K(+) channel mRNAs decreased on both diets. The low blood pressure of AS(-/-) mice was decreased further by low salt, despite additional increases in renin, intrarenal arterial wall thickness, and macula densa cyclogenase-2 mRNA. In AS(+/-) mice on normal salt, adrenal AS mRNA was slightly decreased (0.7xwild-type), but blood pressure was normal. On low salt, their blood pressure was less than wild-type (101+/-2 mm Hg versus 106+/-2 mm Hg), even though renin mRNA increased to 2xwild-type. We conclude that aldosterone is critical for urine concentration and maintenance of blood pressure and even a mild reduction of AS expression makes blood pressure sensitive to low salt, suggesting that genetic differences of AS levels in humans may influence how blood pressure responds to dietary salt.

Heterozygotes of NOS3 Polymorphisms Contribute to Reduced Nitrogen Oxides in High-Altitude Pulmonary Edema

STUDY OBJECTIVES

High-altitude pulmonary edema (HAPE), which develops on exertion under hypoxic conditions, aggravates due to endothelial dysfunction. Repeat events of the disorder suggests of genetic susceptibility. Endothelial nitric oxide synthase gene (NOS3), a regulator of vasodilation, has emerged as a strong candidate marker. In the present study, we investigated G894T, 27-base-pair 4b/4a (variable number of tandem repeat), -922A/G, and -786T/C polymorphisms of NOS3, individually or in combination, for an association with HAPE.

DESIGN

A cross-sectional case control study.

SETTINGS

Blood samples of HAPE-resistant lowlanders (HAPE-r) were obtained at sea level, and blood samples of patients with HAPE (HAPE-p) were obtained at Sonam Norboo Memorial Hospital, Leh, at 3,500 m.

PARTICIPANTS

The study groups consisted of 60 HAPE-r inducted two to three times to altitudes > 3,600 m; and 72 HAPE-p, who had HAPE on their first visit to high altitude.

RESULTS

Nitrogen oxides (NOx) at 77.9 +/- 28.6 micromol/L were significantly elevated in HAPE-r as compared to 42.39 +/- 12.93 micromol/L in HAPE-p (p < 0.0001). Genotype distribution of G894T and 4b/4a polymorphisms was significantly different in the two groups (p = 0.001 and 0.009, respectively). Haplotype analysis revealed -922A/G and -786T/C polymorphisms in complete linkage disequilibrium. The wild-type haplotypes G-b (G894T, 4b/4a), G-A (G894T, -922A/G), and G-b-A (G894T, 4b/4a, -922A/G) were significantly overrepresented in HAPE-r (p < 0.0001, p = 0.03, and p = 0.02, respectively). The heterozygote genotype combination GTba as compared to wild-type combination GGbb was significantly higher in HAPE-p (chi2 = 18.62, p = 0.00009; odds ratio, 7.20; 95% confidence interval, 2.82 to 18.38). The combination of four heterozygotes GTbaAGTC was overrepresented in HAPE-p (p = 0.04), whereas the wild-type genotype combination GGbbAATT was overrepresented in HAPE-r (p = 0.002). Furthermore, the GGbb combination correlated with significantly elevated NOx as compared to remaining combinations as a whole in both HAPE-r and HAPE-p (p = 0.01 and 0.004, respectively).

CONCLUSIONS

Reduced NOx and combination of heterozygotes associate with the susceptibility to HAPE. The study impels another step toward application of NOx as a diagnostic marker for HAPE. The NOS3 GTba and GTbaAGTC genotype combinations may find application as genetic markers for predicting the risk for HAPE.

Predominance of interaction among wild-type alleles of CYP11B2 in Himalayan natives associates with high-altitude adaptation

Sojourners visiting high-altitude (HA) (>2500 m) are susceptible to HA disorders; on the contrary, HA natives are well adapted to the extreme hypoxic environment. High aldosterone levels are believed to be involved in HA disorders, we, therefore, envisaged role of CYP11B2 gene variants in HA adaptation and therefore investigated the -344T/C, intron-2 conversion (Iw/Ic), K173R, and A5160C polymorphisms. In addition, polymorphisms in AGT, AT1R, ATP1A1, ADRB2, and GSTP1 genes were also investigated. The study comprised of 662 subjects, comprising of 426 Himalayan highlanders (HLs) and 236 lowlanders (LLs). The -344T/C and K173R polymorphisms were found to be in complete linkage disequilibrium. The wild-type allele -344T and combination of wild-type homozygous genotypes between -344T/C, Iw/Ic, and A5160C polymorphisms, containing all the six wild-type alleles were over-represented in the HLs (p < 0.0001, and p = 0.008, respectively). The wild-type haplotypes -344T-Iw, -344T-5160A, and -344T-Iw-5160A also showed over-representation in the HLs (p < 0.0001). Furthermore, greater the number of wild-type alleles, lower was the ARR (p < 0.05). The genotype distribution in remaining genes did not differ. To conclude, the over-representation of wild-type -344T allele, genotype combinations and haplotypes of CYP11B2, and their correlation with lower aldosterone levels associate with HA adaptation in the HLs. Such an allelic presentation in sojourners may help them cope with adverse HA environment.

The human obesity gene map: the 2005 update

This paper presents the 12th update of the human obesity gene map, which incorporates published results up to the end of October 2005. Evidence from single-gene mutation obesity cases, Mendelian disorders exhibiting obesity as a clinical feature, transgenic and knockout murine models relevant to obesity, quantitative trait loci (QTL) from animal cross-breeding experiments, association studies with candidate genes, and linkages from genome scans is reviewed. As of October 2005, 176 human obesity cases due to single-gene mutations in 11 different genes have been reported, 50 loci related to Mendelian syndromes relevant to human obesity have been mapped to a genomic region, and causal genes or strong candidates have been identified for most of these syndromes. There are 244 genes that, when mutated or expressed as transgenes in the mouse, result in phenotypes that affect body weight and adiposity. The number of QTLs reported from animal models currently reaches 408. The number of human obesity QTLs derived from genome scans continues to grow, and we now have 253 QTLs for obesity-related phenotypes from 61 genome-wide scans. A total of 52 genomic regions harbor QTLs supported by two or more studies. The number of studies reporting associations between DNA sequence variation in specific genes and obesity phenotypes has also increased considerably, with 426 findings of positive associations with 127 candidate genes. A promising observation is that 22 genes are each supported by at least five positive studies. The obesity gene map shows putative loci on all chromosomes except Y. The electronic version of the map with links to useful publications and relevant sites can be found at http://obesitygene.pbrc.edu.

The Indian Genome Variation database (IGVdb): a project overview

Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy.