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Walia GK, Panniyammakal J, Agarwal T, Jalal R, Gupta R, Ramakrishnan L, Tandon N, Roy A, Krishnan A, Prabhakaran D. Evaluation of genetic variants related to lipid levels among the North Indian population. Front Genet 2024; 14:1234693. [PMID: 38348409 PMCID: PMC10859749 DOI: 10.3389/fgene.2023.1234693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/31/2023] [Indexed: 02/15/2024] Open
Abstract
Background: A heavy burden of cardiometabolic conditions on low- and middle-income countries like India that are rapidly undergoing urbanization remains unaddressed. Indians are known to have high levels of triglycerides and low levels of HDL-C along with moderately higher levels of LDL-C. The genome-wide findings from Western populations need to be validated in an Indian context for a better understanding of the underlying etiology of dyslipidemia in India. Objective: We aim to validate 12 genetic variants associated with lipid levels among rural and urban Indian populations and derive unweighted and weighted genetic risk scores (uGRS and wGRS) for lipid levels among the Indian population. Methods: Assuming an additive model of inheritance, linear regression models adjusted for all the possible covariates were run to examine the association between 12 genetic variants and total cholesterol, triglycerides, HDL-C, LDL-C, and VLDL-C among 2,117 rural and urban Indian participants. The combined effect of validated loci was estimated by allelic risk scores, unweighted and weighted by their effect sizes. Results: The wGRS for triglycerides and VLDL-C was derived based on five associated variants (rs174546 at FADS1, rs17482753 at LPL, rs2293889 at TRPS1, rs4148005 at ABCA8, and rs4420638 at APOC1), which was associated with 36.31 mg/dL of elevated triglyceride and VLDL-C levels (β = 0.95, SE = 0.16, p < 0.001). Similarly, every unit of combined risk score (rs2293889 at TRPS1 and rs4147536 at ADH1B) was associated with 40.62 mg/dL of higher total cholesterol (β = 1.01, SE = 0.23, p < 0.001) and 33.97 mg/dL of higher LDL-C (β = 1.03, SE = 0.19, p < 0.001) based on its wGRS (rs2293889 at TRPS1, rs4147536 at ADH1B, rs4420638 at APOC1, and rs660240 at CELSR2). The wGRS derived from five associated variants (rs174546 at FADS1, rs17482753 at LPL, rs4148005 at ABCA8, rs4420638 at APOC1, and rs7832643 at PLEC) was associated with 10.64 mg/dL of lower HDL-C (β = -0.87, SE = 0.14, p < 0.001). Conclusion: We confirm the role of eight genome-wide association study (GWAS) loci related to different lipid levels in the Indian population and demonstrate the combined effect of variants for lipid traits among Indians by deriving the polygenic risk scores. Similar studies among different populations are required to validate the GWAS loci and effect modification of these loci by lifestyle and environmental factors related to urbanization.
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Affiliation(s)
- Gagandeep Kaur Walia
- Public Health Foundation of India, New Delhi, India
- Centre for Chronic Disease Control, New Delhi, India
| | - Jeemon Panniyammakal
- Centre for Chronic Disease Control, New Delhi, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Tripti Agarwal
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Ruchita Jalal
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Ruby Gupta
- Centre for Chronic Disease Control, New Delhi, India
| | | | - Nikhil Tandon
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Ambuj Roy
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Anand Krishnan
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Dorairaj Prabhakaran
- Public Health Foundation of India, New Delhi, India
- Centre for Chronic Disease Control, New Delhi, India
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Agarwal T, Lyngdoh T, Dudbridge F, Chandak GR, Kinra S, Prabhakaran D, Reddy KS, Relton CL, Davey Smith G, Ebrahim S, Gupta V, Walia GK. Causal relationships between lipid and glycemic levels in an Indian population: A bidirectional Mendelian randomization approach. PLoS One 2020; 15:e0228269. [PMID: 31995593 PMCID: PMC6988960 DOI: 10.1371/journal.pone.0228269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/12/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Dyslipidemia and abnormal glycemic traits are leading causes of morbidity and mortality. Although the association between the two traits is well established, there still exists a gap in the evidence for the direction of causality. OBJECTIVE This study aimed to examine the direction of the causal relationship between lipids and glycemic traits in an Indian population using bidirectional Mendelian randomization (BMR). METHODS The BMR analysis was conducted on 4900 individuals (2450 sib-pairs) from the Indian Migration Study. Instrument variables were generated for each lipid and glycemic trait (fasting insulin, fasting glucose, HOMA-IR, HOMA-β, LDL-cholesterol, HDL-cholesterol, total cholesterol and triglycerides) to examine the causal relationship by applying two-stage least squares (2SLS) regression in both directions. RESULTS Lipid and glycemic traits were found to be associated observationally, however, results from 2SLS showed that only triglycerides, defined by weighted genetic risk score (wGRS) of 3 SNPs (rs662799 at APOAV, rs780094 at GCKR and rs4420638 at APOE/C1/C4), were observed to be causally effecting 1.15% variation in HOMA-IR (SE = 0.22, P = 0.010), 1.53% in HOMA- β (SE = 0.21, P = 0.001) and 1.18% in fasting insulin (SE = 0.23, P = 0.009). No evidence for a causal effect was observed in the reverse direction or between any other lipid and glycemic traits. CONCLUSION The study findings suggest that triglycerides may causally impact various glycemic traits. However, the findings need to be replicated in larger studies.
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Affiliation(s)
- Tripti Agarwal
- Indian Institute of Public Health-Delhi, Public Health Foundation of India, Gurgaon, India
| | - Tanica Lyngdoh
- Indian Institute of Public Health-Delhi, Public Health Foundation of India, Gurgaon, India
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Sanjay Kinra
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Shah Ebrahim
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vipin Gupta
- Department of Anthropology, University of Delhi, Delhi, India
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Sung Y, Feng Z, Subedi S. A genome-wide association study of multiple longitudinal traits with related subjects. Stat (Int Stat Inst) 2016; 5:22-44. [PMID: 27134745 DOI: 10.1002/sta4.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pleiotropy is a phenomenon that a single gene inflicts multiple correlated phenotypic effects, often characterized as traits, involving multiple biological systems. We propose a two-stage method to identify pleiotropic effects on multiple longitudinal traits from a family-based data set. The first stage analyzes each longitudinal trait via a three-level mixed-effects model. Random effects at the subject-level and at the family-level measure the subject-specific genetic effects and between-subjects intraclass correlations within families, respectively. The second stage performs a simultaneous association test between a single nucleotide polymorphism and all subject-specific effects for multiple longitudinal traits. This is performed using a quasi-likelihood scoring method in which the correlation structure among related subjects is adjusted. Two simulation studies for the proposed method are undertaken to assess both the type I error control and the power. Furthermore, we demonstrate the utility of the two-stage method in identifying pleiotropic genes or loci by analyzing the Genetic Analysis Workshop 16 Problem 2 cohort data drawn from the Framingham Heart Study and illustrate an example of the kind of complexity in data that can be handled by the proposed approach. We establish that our two-stage method can identify pleiotropic effects whilst accommodating varying data types in the model.
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Affiliation(s)
- Yubin Sung
- Department of Mathematics & Statistics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Zeny Feng
- Department of Mathematics & Statistics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Sanjeena Subedi
- Department of Mathematics & Statistics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Ye H, Zhou A, Hong Q, Tang L, Xu X, Xin Y, Jiang D, Dai D, Li Y, Wang DW, Duan S. Positive Association between APOA5 rs662799 Polymorphism and Coronary Heart Disease: A Case-Control Study and Meta-Analysis. PLoS One 2015; 10:e0135683. [PMID: 26309253 PMCID: PMC4550406 DOI: 10.1371/journal.pone.0135683] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 07/26/2015] [Indexed: 01/08/2023] Open
Abstract
Objective Apolipoprotein A5 (APOA5) is associated with plasma triglyceride (TG) levels, a risk factor for coronary heart disease (CHD). This study explored the association between CHD and the APOA5 rs662799 polymorphism. Methods We collected 1,521 samples (783 CHD patients and 738 controls) for this case-control study. Meta-analysis was performed using Review Manager Software and Stata Software. Results Significant differences were observed between CHD cases and controls at the level of both genotype (χ2 = 8.964, df = 2, P = 0.011) and allele (χ2 = 9.180, df = 1, P = 0.002, OR = 1.275, 95% CI = 1.089–1.492). A breakdown analysis by gender showed a significant association of APOA5 rs662799 with CHD in males (χ2 = 7.770, df = 1, P = 0.005; OR = 1.331, 95% CI = 1.088–1.628). An additional meta-analysis using 21378 cases and 28428 controls established that rs662799 is significantly associated with CHD (P < 0.00001). Conclusion Both our case-control study and meta-analysis confirm a significant association between APOA5 rs662799 and CHD. In addition, our results suggest a male-specific association between the APOA5 rs662799 polymorphism and CHD.
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Affiliation(s)
- Huadan Ye
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Annan Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Qiangxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Linlin Tang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xuting Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yanfei Xin
- Center of Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Danjie Jiang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongjun Dai
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yirun Li
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dao Wen Wang
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (SWD); (DWW)
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
- * E-mail: (SWD); (DWW)
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Sumegi K, Jaromi L, Magyari L, Kovesdi E, Duga B, Szalai R, Maasz A, Matyas P, Janicsek I, Melegh B. Functional variants of lipid level modifier MLXIPL, GCKR, GALNT2, CILP2, ANGPTL3 and TRIB1 genes in healthy Roma and Hungarian populations. Pathol Oncol Res 2015; 21:743-9. [PMID: 25573592 DOI: 10.1007/s12253-014-9884-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 12/22/2014] [Indexed: 01/15/2023]
Abstract
The role of triglyceride metabolism in different diseases, such as cardiovascular or cerebrovascular diseases is still under extensive investigations. In genome-wide studies several polymorphisms have been reported, which are highly associated with plasma lipid level changes. Our goal was to examine eight variants: rs12130333 at the ANGPTL3, rs16996148 at the CILP2, rs17321515 at the TRIB1, rs17145738 and rs3812316 of the MLXIPL, rs4846914 at GALNT2, rs1260326 and rs780094 residing at the GCKR loci. A total of 399 Roma (Gypsy) and 404 Hungarian population samples were genotyped using PCR-RFLP method. Significant differences were found between Roma and Hungarian population samples in both MLXIPL variants (C allele frequency of rs17145738: 94.1% vs. 85.6%, C allele frequency of rs3812316: 94.2% vs. 86.8% in Romas vs. in Hungarians, p < 0.05), in ANGPTL3 (T allele frequency of rs1213033: 12.2% vs. 18.5% in Romas vs. Hungarians, p < 0.05) and GALNT2 (G allele frequency of rs4846914: 46.6% vs. 54.5% Romas vs. in Hungarians, p < 0.05), while no differences over SNPs could be verified and the known minor alleles showed no correlation with triglyceride levels in any population samples. The current study revealed fundamental differences of known triglyceride modifying SNPs in Roma population. Failure of finding evidence for affected triglyceride metabolism shows that these susceptibility genes are much less effective compared for example to the apolipoprotein A5 gene.
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Affiliation(s)
- Katalin Sumegi
- Department of Medical Genetics, Clinical Centre, University of Pecs, Szigeti u. 12, Pecs, H-7624, Hungary,
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Kuper H, Taylor A, Krishna KVR, Ben-Shlomo Y, Gupta R, Kulkarni B, Prabhakaran D, Davey Smith G, Wells J, Ebrahim S, Kinra S. Is vulnerability to cardiometabolic disease in Indians mediated by abdominal adiposity or higher body adiposity. BMC Public Health 2014; 14:1239. [PMID: 25438835 PMCID: PMC4289237 DOI: 10.1186/1471-2458-14-1239] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/18/2014] [Indexed: 11/10/2022] Open
Abstract
Background Indians may be particularly vulnerable to cardiometabolic disease, potentially due to higher body fat for a given BMI, or a tendency towards depositing abdominal adiposity. The aim of the study is to assess whether different measures of the distribution of adiposity (abdominal versus whole body) or amount of adiposity (DXA versus traditional anthropometric) are better at predicting prevalent cardiometabolic risk markers in an Indian population. Methods Participants were recruited from the Indian Migration Study (IMS) and the Andhra Pradesh Children and Parent Study (APCAPS). Participants attended a clinic in Hyderabad, India, January 2009-December 2010. Adiposity was measured by conventional anthropometry (including weight, height, waist) and DXA scanning (whole body and abdominal). Blood samples were taken and assessed for fasting plasma glucose, insulin, cholesterol, and triglycerides and blood pressure was measured. Lifestyle data were collected by questionnaire. Results We invited 4 617 participants to the clinic (1 995 IMS; 2 622 APCAPS) and examined 918 from IMS (46%) and 1 451 from APCAPS (55%). There were strong and consistent relationships between adiposity and cardiometabolic risk factors. Cardiometabolic risk factors did not appear to be more strongly associated with DXA measures as opposed to BMI, or skinfold measures of body fat. There was some evidence that WHR was more closely related to diabetes than total body adiposity, but this was not apparent for the other measures of abdominal adiposity (DXA measures, waist circumference) or other cardiometablic risk factors. Conclusions No strong evidence supports that DXA measures or abdominal measures of adiposity are better at predicting the prevalence of cardiometabolic risk factors in comparison to BMI. Electronic supplementary material The online version of this article (doi:10.1186/1471-2458-14-1239) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hannah Kuper
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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Sharma M, Ganguly N. Burden of cardiovascular diseases in Indians: Estimating trends of coronary artery disease and using low cost risk screening tools. APOLLO MEDICINE 2014. [DOI: 10.1016/j.apme.2014.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Walia GK, Gupta V, Aggarwal A, Asghar M, Dudbridge F, Timpson N, Singh NS, Kumar MR, Kinra S, Prabhakaran D, Reddy KS, Chandak GR, Smith GD, Ebrahim S. Association of common genetic variants with lipid traits in the Indian population. PLoS One 2014; 9:e101688. [PMID: 24991929 PMCID: PMC4081649 DOI: 10.1371/journal.pone.0101688] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 06/10/2014] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies (GWAS) have been instrumental in identifying novel genetic variants associated with altered plasma lipid levels. However, these quantitative trait loci have not been tested in the Indian population, where there is a poorly understood and growing burden of cardiometabolic disorders. We present the association of six single nucleotide polymorphisms in 1671 sib pairs (3342 subjects) with four lipid traits: total cholesterol, triglycerides, high density lipoprotein cholesterol (HDL-C) and low density lipoprotein cholesterol (LDL-C). We also investigated the interaction effects of gender, location, fat intake and physical activity. Each copy of the risk allele of rs964184 at APOA1 was associated with 1.06 mmol/l increase in triglycerides (SE = 0.049; p = 0.006), rs3764261 at CETP with 1.02 mmol/l increase in both total cholesterol (SE = 0.042; p = 0.017) and HDL-C (SE = 0.041; p = 0.008), rs646776 at CELSR2-PSRC1-SORT1 with 0.96 mmol/l decrease in cholesterol (SE = 0.043; p = 0.0003) and 0.15 mmol/l decrease in LDL-C levels (SE = 0.043; p = 0.0003) and rs2954029 at TRIB1 with 1.02 mmol/l increase in HDL-C (SE = 0.039; p = 0.047). A combined risk score of APOA1 and CETP loci predicted an increase of 1.25 mmol/l in HDL-C level (SE = 0.312; p = 0.0007). Urban location and sex had strong interaction effects on the genetic association of most of the studied loci with lipid traits. To conclude, we validated four genetic variants (identified by GWAS in western populations) associated with lipid traits in the Indian population. The interaction effects found here may explain the sex-specific differences in lipid levels and their heritability. Urbanization appears to influence the nature of the association with GWAS lipid loci in this population. However, these findings will require replication in other Indian populations.
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Affiliation(s)
- Gagandeep Kaur Walia
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
- * E-mail: (GKW); (VG)
| | - Vipin Gupta
- Department of Anthropology, University of Delhi, Delhi, India
- * E-mail: (GKW); (VG)
| | - Aastha Aggarwal
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
| | - Mohammad Asghar
- Department of Anthropology, Rajiv Gandhi University, Itanagar, Arunachal Pradesh, India
| | - Frank Dudbridge
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nicholas Timpson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | | | - M. Ravi Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Sanjay Kinra
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dorairaj Prabhakaran
- Centre for Chronic Disease Control, New Delhi, India
- Public Health Foundation of India, New Delhi, India
| | | | | | - George Davey Smith
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Shah Ebrahim
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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