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Miranda JP, Pereira A, Corvalán C, Miquel JF, Alberti G, Gana JC, Santos JL. Genetic determinants of serum bilirubin using inferred native American gene variants in Chilean adolescents. Front Genet 2024; 15:1382103. [PMID: 38826804 PMCID: PMC11140026 DOI: 10.3389/fgene.2024.1382103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 06/04/2024] Open
Abstract
Gene variants in the UGT1A1 gene are strongly associated with circulating bilirubin levels in several populations, as well as other variants of modest effect across the genome. However, the effects of such variants are unknown regarding the Native American ancestry of the admixed Latino population. Our objective was to assess the Native American genetic determinants of serum bilirubin in Chilean admixed adolescents using the local ancestry deconvolution approach. We measured total serum bilirubin levels in 707 adolescents of the Chilean Growth and Obesity Cohort Study (GOCS) and performed high-density genotyping using the Illumina-MEGA array (>1.7 million genotypes). We constructed a local ancestry reference panel with participants from the 1000 Genomes Project, the Human Genome Diversity Project, and our GOCS cohort. Then, we inferred and isolated haplotype tracts of Native American, European, or African origin to perform genome-wide association studies. In the whole cohort, the rs887829 variant and others near UGT1A1 were the unique signals achieving genome-wide statistical significance (b = 0.30; p = 3.34 × 10-57). After applying deconvolution methods, we found that significance is also maintained in Native American (b = 0.35; p = 3.29 × 10-17) and European (b = 0.28; p = 1.14 × 10-23) ancestry components. The rs887829 variant explained a higher percentage of the variance of bilirubin in the Native American (37.6%) compared to European ancestry (28.4%). In Native American ancestry, carriers of the TT genotype of this variant averaged 4-fold higher bilirubinemia compared to the CC genotype (p = 2.82 × 10-12). We showed for the first time that UGT1A1 variants are the primary determinant of bilirubin levels in Native American ancestry, confirming its pan-ethnic relevance. Our study illustrates the general value of the local ancestry deconvolution approach to assessing isolated ancestry effects in admixed populations.
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Affiliation(s)
- José P. Miranda
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Medicine, PhD in Epidemiology Program, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile and Universidad de Chile, Santiago, Chile
| | - Ana Pereira
- Instituto de Nutrición y Tecnología de los Alimentos INTA, Universidad de Chile, Santiago, Chile
| | - Camila Corvalán
- Instituto de Nutrición y Tecnología de los Alimentos INTA, Universidad de Chile, Santiago, Chile
| | - Juan F. Miquel
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gigliola Alberti
- Pediatrics Division, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology and Pediatric Nutrition, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan C. Gana
- Pediatrics Division, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology and Pediatric Nutrition, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José L. Santos
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Medicine, PhD in Epidemiology Program, Pontificia Universidad Católica de Chile, Santiago, Chile
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Benton MC, Lea RA, Macartney-Coxson D, Bellis C, Carless MA, Curran JE, Hanna M, Eccles D, Chambers GK, Blangero J, Griffiths LR. Serum bilirubin concentration is modified by UGT1A1 haplotypes and influences risk of type-2 diabetes in the Norfolk Island genetic isolate. BMC Genet 2015; 16:136. [PMID: 26628212 PMCID: PMC4667444 DOI: 10.1186/s12863-015-0291-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/02/2015] [Indexed: 02/06/2023] Open
Abstract
Background Located in the Pacific Ocean between Australia and New Zealand, the unique population isolate of Norfolk Island has been shown to exhibit increased prevalence of metabolic disorders (type-2 diabetes, cardiovascular disease) compared to mainland Australia. We investigated this well-established genetic isolate, utilising its unique genomic structure to increase the ability to detect related genetic markers. A pedigree-based genome-wide association study of 16 routinely collected blood-based clinical traits in 382 Norfolk Island individuals was performed. Results A striking association peak was located at chromosome 2q37.1 for both total bilirubin and direct bilirubin, with 29 SNPs reaching statistical significance (P < 1.84 × 10−7). Strong linkage disequilibrium was observed across a 200 kb region spanning the UDP-glucuronosyltransferase family, including UGT1A1, an enzyme known to metabolise bilirubin. Given the epidemiological literature suggesting negative association between CVD-risk and serum bilirubin we further explored potential associations using stepwise multivariate regression, revealing significant association between direct bilirubin concentration and type-2 diabetes risk. In the Norfolk Island cohort increased direct bilirubin was associated with a 28 % reduction in type-2 diabetes risk (OR: 0.72, 95 % CI: 0.57-0.91, P = 0.005). When adjusted for genotypic effects the overall model was validated, with the adjusted model predicting a 30 % reduction in type-2 diabetes risk with increasing direct bilirubin concentrations (OR: 0.70, 95 % CI: 0.53-0.89, P = 0.0001). Conclusions In summary, a pedigree-based GWAS of blood-based clinical traits in the Norfolk Island population has identified variants within the UDPGT family directly associated with serum bilirubin levels, which is in turn implicated with reduced risk of developing type-2 diabetes within this population. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0291-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - R A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - D Macartney-Coxson
- Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, 5240, New Zealand.
| | - C Bellis
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia. .,Texas Biomedical Research Institute, San Antonio, TX, 78227-5301, USA.
| | - M A Carless
- Texas Biomedical Research Institute, San Antonio, TX, 78227-5301, USA.
| | - J E Curran
- Texas Biomedical Research Institute, San Antonio, TX, 78227-5301, USA.
| | - M Hanna
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - D Eccles
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - G K Chambers
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - J Blangero
- South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA.
| | - L R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
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Dai X, Wu C, He Y, Gui L, Zhou L, Guo H, Yuan J, Yang B, Li J, Deng Q, Huang S, Guan L, Hu D, Zhu J, Min X, Lang M, Li D, Yang H, Hu FB, Lin D, Wu T, He M. A genome-wide association study for serum bilirubin levels and gene-environment interaction in a Chinese population. Genet Epidemiol 2013; 37:293-300. [PMID: 23371916 DOI: 10.1002/gepi.21711] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/27/2012] [Accepted: 12/27/2012] [Indexed: 11/07/2022]
Abstract
Bilirubin is an effective antioxidant and is influenced by both genetic and environmental factors. Recent genome-wide association studies (GWAS) have identified multiple loci affecting serum total bilirubin levels. However, most of the studies were conducted in European populations and little attention has been devoted either to genetic variants associated with direct and indirect bilirubin levels or to the gene-environment interactions on bilirubin levels. In this study, a two-stage GWAS was performed to identify genetic variants associated with all types of bilirubin levels in 10,282 Han Chinese individuals. Gene-environment interactions were further examined. Briefly, two previously reported loci, UGT1A1 on 2q37 (rs6742078 and rs4148323, combined P = 1.44 × 10(-89) and P = 5.05 × 10(-69) , respectively) and SLCO1B3 on 12p12 (rs2417940, combined P = 6.93 × 10(-19) ) were successfully replicated. The two loci explained 9.2% and 0.9% of the total variations of total bilirubin levels, respectively. Ethnic genetic differences were observed between Chinese and European populations. More importantly, a significant interaction was found between rs2417940 in SLCO1B3 gene and smoking on total bilirubin levels (P = 1.99 × 10(-3) ). Single nucleotide polymorphism (SNP) rs2417940 had stronger effects on total bilirubin levels in nonsmokers than in smokers, suggesting that the effects of SLCO1B3 genotype on bilirubin levels were partly dependent on smoking status. Consistent associations and interactions were observed for serum direct and indirect bilirubin levels.
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Affiliation(s)
- Xiayun Dai
- MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei, China
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Kolder ICRM, Tanck MWT, Bezzina CR. Common genetic variation modulating cardiac ECG parameters and susceptibility to sudden cardiac death. J Mol Cell Cardiol 2012; 52:620-9. [PMID: 22248531 DOI: 10.1016/j.yjmcc.2011.12.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/23/2011] [Accepted: 12/31/2011] [Indexed: 01/19/2023]
Abstract
Sudden cardiac death (SCD) is a prevalent cause of death in Western societies. Genome-wide association studies (GWAS) conducted over the last few years have uncovered common genetic variants modulating risk of SCD. Furthermore, GWAS studies uncovered several loci impacting on heart rate and ECG indices of conduction and repolarization, as measures of cardiac electrophysiological function and likely intermediate phenotypes of SCD risk. We here review these recent developments and their implications for the identification of novel molecular pathways underlying normal electrophysiological function and susceptibility to SCD.
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Affiliation(s)
- Iris C R M Kolder
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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Abstract
Total serum bilirubin is associated with several clinical outcomes, including cardiovascular disease, diabetes and drug metabolism. We conducted a genome-wide association study in 619 healthy unrelated African Americans in an attempt to replicate reported findings in Europeans and Asians and to identify novel loci influencing total serum bilirubin levels. We analyzed a dense panel of over two million genotyped and imputed SNPs in additive genetic models adjusting for age, sex, and the first two significant principal components from the sample covariance matrix of genotypes. Thirty-nine SNPs spanning a 78 kb region within the UGT1A1 displayed P-values <5 × 10−8. The lowest P-value was 1.7 × 10−22 for SNP rs887829. None of SNPs in the UGT1A1 remained statistically significant in conditional association analyses that adjusted for rs887829. In addition, SNP rs10929302 located in phenobarbital response enhancer module was significantly associated with bilirubin level with a P-value of 1.37 × 10−11; this enhancer module is believed to have a critical role in phenobarbital treatment of hyperbilirubinemia. Interestingly, the lead SNP, rs887829, is in strong linkage disequilibrium (LD) (r2≥0.74) with rs10929302. Taking advantage of the lower LD and shorter haplotypes in African-ancestry populations, we identified rs887829 as a more refined proxy for the causative variant influencing bilirubin levels. Also, we replicated the reported association between variants in SEMA3C and bilirubin levels. In summary, UGT1A1 is a major locus influencing bilirubin levels and the results of this study promise to contribute to understanding of the etiology and treatment of hyperbilirubinaemia in African-ancestry populations.
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Bielinski SJ, Chai HS, Pathak J, Talwalkar JA, Limburg PJ, Gullerud RE, Sicotte H, Klee EW, Ross JL, Kocher JPA, Kullo IJ, Heit JA, Petersen GM, de Andrade M, Chute CG. Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels. Mayo Clin Proc 2011; 86:606-14. [PMID: 21646302 PMCID: PMC3127556 DOI: 10.4065/mcp.2011.0178] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To create a cohort for cost-effective genetic research, the Mayo Genome Consortia (MayoGC) has been assembled with participants from research studies across Mayo Clinic with high-throughput genetic data and electronic medical record (EMR) data for phenotype extraction. PARTICIPANTS AND METHODS Eligible participants include those who gave general research consent in the contributing studies to share high-throughput genotyping data with other investigators. Herein, we describe the design of the MayoGC, including the current participating cohorts, expansion efforts, data processing, and study management and organization. A genome-wide association study to identify genetic variants associated with total bilirubin levels was conducted to test the genetic research capability of the MayoGC. RESULTS Genome-wide significant results were observed on 2q37 (top single nucleotide polymorphism, rs4148325; P=5.0 × 10(-62)) and 12p12 (top single nucleotide polymorphism, rs4363657; P=5.1 × 10(-8)) corresponding to a gene cluster of uridine 5'-diphospho-glucuronosyltransferases (the UGT1A cluster) and solute carrier organic anion transporter family, member 1B1 (SLCO1B1), respectively. CONCLUSION Genome-wide association studies have identified genetic variants associated with numerous phenotypes but have been historically limited by inadequate sample size due to costly genotyping and phenotyping. Large consortia with harmonized genotype data have been assembled to attain sufficient statistical power, but phenotyping remains a rate-limiting factor in gene discovery research efforts. The EMR consists of an abundance of phenotype data that can be extracted in a relatively quick and systematic manner. The MayoGC provides a model of a unique collaborative effort in the environment of a common EMR for the investigation of genetic determinants of diseases.
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Affiliation(s)
- Suzette J Bielinski
- Division of Epidemiology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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