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Yang S, Yin RX, Miao L, Zhang QH, Zhou YG, Wu J. Association between the LIPG polymorphisms and serum lipid levels in the Maonan and Han populations. J Gene Med 2019; 21:e3071. [PMID: 30657227 PMCID: PMC6590183 DOI: 10.1002/jgm.3071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 01/19/2023] Open
Abstract
Introduction The Maonan population is a relatively isolated minority in China. Little is known about endothelial lipase gene (LIPG) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. The present study aimed to detect the association of several LIPG SNPs and environmental factors with serum lipid levels in the Chinese Maonan and Han populations. Methods In total, 773 subjects of Maonan ethnicity and 710 participants of Han ethnicity were randomly selected from our previous stratified randomized samples. Genotypes of the LIPG rs2156552, rs4939883 and rs7241918 SNPs were determined by polymerase chain reaction‐restriction fragment length polymorphism, and then confirmed by direct sequencing. Results The allelic (rs2156552, rs4939883 and rs7241918) and genotypic (rs2156552 and rs4939883) frequencies were different between the two ethnic groups (p < 0.05–0.01). The minor allele carriers had lower apolipoprotein (Apo)A1/ApoB ratio (rs2156552 and rs7241918), high‐density lipoprotein cholesterol (HDL‐C) and apolipoprotein (Apo)A1 (rs2156552) levels and higher ApoB levels (rs4939883) in the Han population, and lower HDL‐C (rs2156552, rs4939883 and rs7241918) levels in the Maonan minority than the minor allele non‐carriers (p < 0.0167 after Bonferroni correction). Subgroup analyses according to sex showed that the minor allele carriers had a lower ApoA1/ApoB ratio (rs2156552 and rs7241918) and higher ApoB levels (rs7241918) in Han males, and lower ApoA1 and HDL‐C levels in Maonan females than the minor allele non‐carriers (p < 0.0167–0.001). Conclusions The present study demonstrates the association between the LIPG polymorphsims and serum lipid levels in the two ethnic groups. These associations might have an ethnic‐ and or/sex‐specificity.
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Affiliation(s)
- Shuo Yang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Liu Miao
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Qing-Hui Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Yong-Gang Zhou
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Jie Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
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Yang S, Yin RX, Miao L, Zhou YG, Wu J, Zhang QH. LIPG SNPs, their haplotypes and gene-environment interactions on serum lipid levels. Lipids Health Dis 2019; 18:10. [PMID: 30621702 PMCID: PMC6325827 DOI: 10.1186/s12944-018-0942-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/04/2018] [Indexed: 02/06/2023] Open
Abstract
Background Maonan nationality is a relatively conservative and isolated minority in the Southwest of China. Little is known about the association of endothelial lipase gene (LIPG) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. Methods A total of 1280 subjects of Maonan nationality and 1218 participants of Han nationality were randomly selected from our previous stratified randomized samples. Genotypes of the four LIPG SNPs were determined by polymerase chain reaction-restriction fragment length polymorphism, and then confirmed by direct sequencing. Results Several SNPs were associated with high-density lipoprotein cholesterol (rs3813082, rs2000813 and rs2097055) in the both ethnic groups; total cholesterol and apolipoprotein (Apo) A1 (rs2000813) in Han nationality; and low-density lipoprotein cholesterol, ApoB, triglyceride (rs2097055) and ApoA1 (rs3819166) in Maonan minority (P < 0.0125 for all after Bonferroni correction). The commonest haplotype was rs3813082T-rs2000813C-rs2097055T-rs3819166A (Han, 44.2% and Maonan, 48.7%). The frequencies of the T-C-T-A, T-C-T-G, T-T-C-G and G-T-C-G haplotypes were different between the Maonan and Han populations (P < 0.05–0.001). The associations between haplotypes and dyslipidemia were also different in the Han and/or Maonan populations (P < 0.05–0.001). Conclusions The differences in serum lipid profiles between the two ethnic groups might partly be attributed to these LIPG SNPs, their haplotypes and gene-environmental interactions. Trial registration Retrospectively registered.
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Affiliation(s)
- Shuo Yang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China.
| | - Liu Miao
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Yong-Gang Zhou
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Jie Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Qing-Hui Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
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Khounphinith E, Yin RX, Cao XL, Huang F, Wu JZ, Li H. TIMD4 rs6882076 SNP Is Associated with Decreased Levels of Triglycerides and the Risk of Coronary Heart Disease and Ischemic Stroke. Int J Med Sci 2019; 16:864-871. [PMID: 31337960 PMCID: PMC6643107 DOI: 10.7150/ijms.31729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/03/2019] [Indexed: 12/24/2022] Open
Abstract
Background: The T-cell immunoglobulin and mucin domain 4 gene (TIMD4) rs6882076 single nucleotide polymorphism (SNP) has been associated with serum total cholesterol, low-density lipoprotein cholesterol and triglycerides (TG) levels, but the results are inconsistent. Moreover, little is known about such association in Chinese populations. The aim of this study was to detect the association of the TIMD4 rs6882076 SNP and serum lipid levels and the risk of coronary heart disease (CHD) and ischemic stroke (IS) in a Southern Chinese Han population. Methods: Genotypes of the TIMD4 rs6882076 SNP in 1765 unrelated subjects (CHD, 581; IS, 559 and healthy controls, 625) were determined by the Snapshot Technology. Results: The genotypic and allelic frequencies of the TIMD4 rs6882076 SNP were different between the CHD/IS patients and controls (P < 0.05 for all). The subjects with CT/TT genotypes were associated with decreased risk of CHD (P = 0.014 for CT/TT vs. CC genotypes, P = 0.010 for T vs. C alleles) and IS (P = 0.003 for CT/TT vs. CC genotypes; P = 0.016 for T vs. C alleles). The T allele carriers in healthy controls were also associated with decreased levels of serum TG. Conclusions: The results of the present study suggest that the TIMD4 rs6882076 SNP is associated with decreased risk of CHD and IS in our study population. It is likely to decrease the CHD and IS risk by reducing serum TG levels.
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Affiliation(s)
- Eksavang Khounphinith
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning 530021, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Xiao-Li Cao
- Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning 530021, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning 530021, Guangxi, China.,Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning 530021, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Jin-Zhen Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Hui Li
- Clinical Laboratory of the Affiliated Cancer Hospital, Guangxi Medical University, 71 Hedi Road, Nanning 530021, Guangxi, China
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Wang DS, Yin RX, Li KG, Lu L, Su Y, Yan RQ. Association between the MVK rs2287218 SNP and the risk of coronary heart disease and ischemic stroke: A case-control study. Biosci Trends 2018; 12:403-411. [PMID: 30101835 DOI: 10.5582/bst.2018.01146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Duo-Shun Wang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University
| | - Kai-Guang Li
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University
| | - Li Lu
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University
| | - Yuan Su
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University
| | - Rong-Qin Yan
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University
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Qiu L, Yin RX, Khounphinith E, Zhang FH, Yang DZ, Pan SL. Association of the APOA1 rs964184 SNP and serum lipid traits in the Chinese Maonan and Han populations. Lipids Health Dis 2018; 17:105. [PMID: 29747660 PMCID: PMC5944063 DOI: 10.1186/s12944-018-0759-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/24/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Maonan nationality belongs to a mountain ethnic minority in China. Little is known about the association of apolipoprotein A1 gene (APOA1) rs964184 single nucleotide polymorphism (SNP) and serum lipid levels in this population. The aim of this study was to detect the association of the APOA1 rs964184 SNP and several environmental factors with serum lipid profiles in the Chinese Maonan and Han populations. METHODS Genotypes of the APOA1 rs964184 SNP in 867 individuals of Maonan nationality and 820 participants of Han nationality were determined by polymerase chain reaction and restriction fragment length polymorphism, combined with gel electrophoresis, and confirmed by direct sequencing. RESULTS The frequencies of CC, CG and GG genotypes of the APOA1 rs964184 SNP were 68.86, 29.18 and 1.96% in the Maonan population, and 63.78, 30.85 and 5.37% in the Han population (P < 0.001). The frequency of the G allele was 16.55% in Maonan and 20.79% in Han (P < 0.001). The G allele carriers had lower high-density lipoprotein cholesterol (HDL-C) levels in Maonan and higher triglyceride (TG) levels in Han peoples than the G allele non-carriers. Subgroup analyses showed that the G allele carriers had lower HDL-C levels in both Maonan males and females; and lower apolipoprotein (Apo) A1 levels and the ApoA1/ApoB ratio in Han males than the G allele non-carriers. Serum lipid parameters in the two ethnic groups were also associated with several environmental factors. CONCLUSIONS The present study reveals that there may be a racial/ethnic- and/or gender-specific association between the APOA1 rs964184 SNP and serum lipid parameters in our study populations. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
- Ling Qiu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China.
| | - Eksavang Khounphinith
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Fen-Han Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - De-Zhai Yang
- Department of Molecular Genetics, Medical Scientific Research Center, Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China
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Yang S, Yin RX, Miao L, Zhang QH, Zhou YG, Wu J. Association of CPS1 rs1047891 SNP and serum lipid levels in two Chinese ethnic groups. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:2887-2900. [PMID: 31938413 PMCID: PMC6958253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/08/2018] [Indexed: 06/10/2023]
Abstract
Carbamoyl-phosphate synthase 1 gene (CPS1) rs1047891 single nucleotide polymorphism (SNP) has been associated with a number of metabolic disorders including obesity, insulin resistance, and hyperhomocysteine (HCY). Studies on association between this SNP and prevalence of dyslipidemia have been few, with no report from Chinese subjects. This study was to investigate association of rs1047891 SNP and several environment factors with serum lipid levels in Chinese Han and Maonan populations. Genotypes of rs1047891 SNP in 810 individuals of Maonan and 795 participants of Han nationality were determined by polymerase chain reaction-restriction fragment length polymorphism and then confirmed by direct sequencing. Frequencies of CC, CA, and AA genotypes were 71.32%, 25.16%, and 3.52% in Han and 61.36%, 31.85%, and 6.79% in Maonan populations (P < 0.01), respectively. The frequency of A allele was 16.10% in Han and 22.72% in Maonan individuals (P < 0.001), respectively. Subjects with CA/AA genotypes had lower high-density lipoprotein cholesterol (HDL-C) and apolipoprotein (Apo) A1 levels in Han. They had higher low-density lipoprotein cholesterol (LDL-C) levels and lower HDL-C levels in Maonan than subjects with CC genotype (P < 0.05-0.01). Subgroup analyses revealed that subjects with CA/AA genotypes had lower HDL-C and ApoA1 levels in Han females, higher LDL-C levels in Maonan males, and lower HDL-C levels in both Maonan males and females than subjects with CC genotype (P < 0.05-0.01). Serum lipid parameters were also correlated with several environmental factors in both ethnic groups. The difference in serum lipid profiles between Han and Maonan populations may partly result from different polymorphisms of CPS1 rs1047891 and SNP-enviromental interactions.
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Affiliation(s)
- Shuo Yang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, Guangxi, China
| | - Liu Miao
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, Guangxi, China
| | - Qing-Hui Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, Guangxi, China
| | - Yong-Gang Zhou
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, Guangxi, China
| | - Jie Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, Guangxi, China
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Qiu L, Yin RX, Khounphinith E, Li KG, Wang DS, Wu JZ. Association of the CYP26A1 rs2068888 polymorphism and serum lipid traits in the Chinese Maonan and Han populations. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:11867-11879. [PMID: 31966551 PMCID: PMC6966032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/10/2017] [Indexed: 06/10/2023]
Abstract
The cytochrome P450 protein plays an important role in the synthesis of cholesterol and other lipid parameters. But little is known about the association of the single nucleotide polymorphism (SNP) of rs2068888 near cytochrome P450 26A1 gene (CYP26A1) and serum lipid profiles in the Chinese Maonan and Han populations. This study explored such association in the two populations. Genotyping of the CYP26A1 rs2068888 SNP was performed in 833 unrelated individuals of Maonan and 701 participants of Han by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and confirmed by direct sequencing. The genotypic and allelic frequencies of the CYP26A1 rs2068888 SNP were significantly different between the Maonan and Han. The frequencies of AA, AG and GG genotypes were 75.51%, 23.41% and 1.08% in the Maonan population, and 64.62%, 33.10% and 2.28% in the Han population (P < 0.001). The frequency of the G allele was 12.78% in Maonan and 18.83% in Han (P < 0.001). The level of serum total cholesterol (TC) was lower in Maonan than in Han. The G allele carriers had higher serum TC level in Maonan than the G allele non-carriers. Subgroup analyses indicated that the G allele carriers had higher serum TC level in Maonan females. Serum lipid parameters in the two ethnic groups were also associated with several environmental factors. These findings revealed that there may be a racial/ethnic- and/or sex-specific association between the CYP26A1 rs2068888 SNP and serum lipid parameters in some populations.
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Affiliation(s)
- Ling Qiu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, China
| | - Eksavang Khounphinith
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, China
| | - Kai-Guang Li
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, China
| | - Duo-Shun Wang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, China
| | - Jin-Zhen Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University Nanning 530021, China
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Zhang F, Xie D, Liang M, Xiong M. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits. PLoS Genet 2016; 12:e1005965. [PMID: 27104857 PMCID: PMC4841563 DOI: 10.1371/journal.pgen.1005965] [Citation(s) in RCA: 10] [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: 05/28/2015] [Accepted: 03/08/2016] [Indexed: 12/02/2022] Open
Abstract
To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. The widely used statistical methods test interaction for single phenotype. However, we often observe pleotropic genetic interaction effects. The simultaneous gene-gene (GxG) interaction analysis of multiple complementary traits will increase statistical power to detect GxG interactions. Although GxG interactions play an important role in uncovering the genetic structure of complex traits, the statistical methods for detecting GxG interactions in multiple phenotypes remains less developed owing to its potential complexity. Therefore, we extend functional regression model from single variate to multivariate for simultaneous GxG interaction analysis of multiple correlated phenotypes. Large-scale simulations are conducted to evaluate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare power with traditional multivariate pair-wise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for interaction analysis is applied to five phenotypes of exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) to detect pleiotropic GxG interactions. 267 pairs of genes that formed a genetic interaction network showed significant evidence of interactions influencing five traits.
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Affiliation(s)
- Futao Zhang
- Department of Computer Science, College of Internet of Things, Hohai University, Changzhou, China
| | - Dan Xie
- College of Information Engineering, Hubei University of Chinese Medicine, Hubei, China
| | - Meimei Liang
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Momiao Xiong
- Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
- * E-mail:
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Guo T, Yin RX, Lin WX, Wang W, Huang F, Pan SL. Association of the variants and haplotypes in the DOCK7, PCSK9 and GALNT2 genes and the risk of hyperlipidaemia. J Cell Mol Med 2016; 20:243-65. [PMID: 26493351 PMCID: PMC4727555 DOI: 10.1111/jcmm.12713] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 09/07/2015] [Indexed: 01/09/2023] Open
Abstract
Little is known about the association between the single nucleotide polymorphisms (SNPs) and haplotypes of the dedicator of cytokinesis 7 (DOCK7), pro-protein convertase subtilisin/kexin type 9 (PCSK9) and polypeptide N-acetylgalactosaminyltransferase 2 (GALNT2) and serum lipid traits in the Chinese populations. This study was to determine the association between nine SNPs in the three genes and their haplotypes and hypercholesterolaemia (HCH)/hypertriglyceridaemia (HTG), and to identify the possible gene-gene interactions among these SNPs. Genotyping was performed in 733 HCH and 540 HTG participants. The haplotype of C-C-G-C-T-G-C-C-G [in the order of DOCK7 rs1168013 (G>C), rs10889332 (C>T); PCSK9 rs615563 (G>A), rs7552841 (C>T), rs11206517 (T>G); and GALNT2 rs1997947 (G>A), rs2760537 (C>T), rs4846913 (C>A) and rs11122316 (G>A) SNPs] was associated with increased risk of HCH and HTG. The haplotypes of C-C-G-C-T-G-C-C-A and G-C-G-T-T-G-T-C-G were associated with a reduced risk of HCH and HTG. The haplotypes of G-C-G-C-T-G-C-C-A and G-C-G-C-T-G-T-C-G were associated with increased risk of HCH. The haplotypes of C-T-G-C-T-G-C-C-G, G-C-A-C-T-G-C-C-G and G-C-G-C-T-G-C-C-A were associated with an increased risk of HTG. The haplotypes of G-C-G-C-T-G-T-C-A and G-C-G-T-T-G-T-C-G were associated with a reduced risk of HTG. In addition, possible inter-locus interactions among the DOCK7, PCSK9 and GALNT2 SNPs were also noted. However, further functional studies of these genes are still required to clarify which SNPs are functional and how these genes actually affect the serum lipid levels.
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Affiliation(s)
- Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Wei-Xiong Lin
- Department of Molecular Genetics, Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Wang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning, Guangxi, China
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Guo T, Yin RX, Huang F, Yao LM, Lin WX, Pan SL. Association between the DOCK7, PCSK9 and GALNT2 Gene Polymorphisms and Serum Lipid levels. Sci Rep 2016; 6:19079. [PMID: 26744084 PMCID: PMC4705473 DOI: 10.1038/srep19079] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/04/2015] [Indexed: 01/02/2023] Open
Abstract
This study was to determine the association between several single nucleotide polymorphisms (SNPs) in the dedicator of cytokinesis 7 (DOCK7), proprotein convertase subtilisin/kexin type 9 (PCSK9) and polypeptide N-acetylgalactosaminyltransferase 2 (GALNT2) and serum lipid levels. Genotyping of 9 SNPs was performed in 881 Jing subjects and 988 Han participants. Allele and genotype frequencies of the detected SNPs were different between the two populations. Several SNPs were associated with triglyceride (TG, rs10889332, rs615563, rs7552841, rs1997947, rs2760537, rs4846913 and rs11122316), high-density lipoprotein (HDL) cholesterol (rs1997947), low-density lipoprotein (LDL) cholesterol (rs1168013 and rs7552841), apolipoprotein (Apo) A1 (rs1997947), ApoB (rs10889332 and rs7552841), and ApoA1/ApoB ratio (rs7552841) in Jing minority; and with TG (rs10889332, rs615563, rs7552841, rs11206517, rs1997947, rs4846913 and rs11122316), HDL cholesterol (rs11206517 and rs4846913), LDL cholesterol (rs1168013), ApoA1 (rs11206517 and rs4846913), ApoB (rs7552841), and ApoA1/ApoB ratio (rs4846913) in Han nationality. Strong linkage disequilibria were noted among the SNPs. The commonest haplotype was G-C-G-C-T-G-C-C-G (>10%). The frequencies of C-C-G-C-T-G-T-C-G, G-C-A-C-T-G-C-C-G, G-C-G-C-T-A-C-C-A, G-C-G-C-T-G-C-C-A, G-C-G-C-T-G-T-C-A haplotypes were different between the two populations. Haplotypes could explain much more serum lipid variation than any single SNP alone especially for TG. Differences in lipid profiles between the two populations might partially attribute to these SNPs and their haplotypes.
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Affiliation(s)
- Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Nanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Nanning 530021, Guangxi, China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Nanning 530021, Guangxi, China
| | - Li-Mei Yao
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Nanning 530021, Guangxi, China
| | - Wei-Xiong Lin
- Department of Molecular Genetics, Medical Scientific Research Center, Nanning 530021, Guangxi, China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning 530021, Guangxi, China
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Guo T, Yin RX, Bin Y, Nie RJ, Chen X, Pan SL. Association of the SPT2 chromatin protein domain containing 1 gene rs17579600 polymorphism and serum lipid traits. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:12995-13010. [PMID: 26722495 PMCID: PMC4680440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
SPT2 chromatin protein domain containing 1 gene (SPTY2D1) is a candidate gene for dyslipidemia. The single nucleotide polymorphism (SNP) of rs7934205 near SPTY2D1 locus was ethnic- and sex-specific associated with serum lipid levels in our previous study. Whether SPTY2D1 rs17579600 SNP and several environmental factors are associated with serum lipid profiles is unknown. A total of 712 participants of Han and 689 unrelated individuals of Mulao were included. The genotype and allele frequencies of SPTY2D1 rs17579600 SNP were different between the Han and Mulao populations (TT, 74.3% vs. 55.7%; TC, 17.6% vs. 31.2%, CC, 8.1% vs. 13.1%, P = 0.028; T, 83.1% vs. 71.3%; C, 16.9% vs. 28.7%, P = 0.044), and between males and females in the both ethnic groups. The levels of serum apolipoprotein (Apo) A1 in Han, triglyceride (TG) in Mulao, and total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), ApoA1 and ApoB in Mulao males were difference among the genotypes. The C allele carriers had higher ApoA1 in Han, lower TG in Mulao, and lower TC, LDL-C and ApoB and higher ApoA1 in Mulao males than the C allele non-carriers. Serum lipid parameters were also associated with several environmental factors in both ethnic groups. The differences suggesting there may be a racial/ethnic- and/or sex-specific association between the SPTY2D1 rs17579600 SNP and serum lipid parameters in some ethnic groups.
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Affiliation(s)
- Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Yuan Bin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Rong-Jun Nie
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Xia Chen
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical UniversityNanning 530021, Guangxi, People’s Republic of China
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Guo T, Yin RX, Li H, Wang YM, Wu JZ, Yang DZ. Association of the Trp316Ser variant (rs1801690) near the apolipoprotein H (β2-glycoprotein-I) gene and serum lipid levels. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:7291-7304. [PMID: 26261630 PMCID: PMC4525964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/22/2015] [Indexed: 06/04/2023]
Abstract
The objective of the present study was to detect the association of the Trp316Ser variant (rs1801690) near the apolipoprotein H (β2-glycoprotein-I) gene and serum lipid levels in the Mulao and Han populations. A total of 879 subjects of Mulao and 844 subjects of Han Chinese were included. The levels of serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and ApoA1 in Mulao, and triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), ApoA1 and the ratio of ApoA1/ApoB in Han were different among the three genotypes of the rs1801690 SNP (P < 0.05-0.01). Subgroup analyses showed that the levels of TC, TG, LDL-C, and ApoA1 in Mulao males; ApoA1 in Mulao females; TC, TG, HDL-C and ApoB and the ApoA1/ApoB ratio in Han males; and HDL-C, ApoA1 and the ApoA1/ApoB ratio in Han females were associated with the genotypes of rs1801690 (P < 0.05-0.001). Serum lipid parameters were also associated with several environmental factors (P < 0.05-0.001). The Trp316Ser variant (rs1801690) near the apolipoprotein H (β2-glycoprotein-I) gene was associated with some serum lipid parameters in the two ethnic groups, but the trends of association suggest that the Trp316Ser variant (rs1801690) near the apolipoprotein H (β2-glycoprotein-I) gene might have racial/ethnic-and/or gender-specificity.
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Affiliation(s)
- Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Hui Li
- Clinical Laboratory of The Affiliated Cancer Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, People’s Republic of China
| | - Yi-Ming Wang
- Department of Molecular Biology, Medical Scientific Research Center, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, People’s Republic of China
| | - Jin-Zhen Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - De-Zhai Yang
- Department of Molecular Biology, Medical Scientific Research Center, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, People’s Republic of China
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Guo T, Yin RX, Nie RJ, Chen X, Bin Y, Lin WX. Suppressor of cytokine signaling 3 A+930-->G (rs4969168) polymorphism is associated with apolipoprotein A1 and low-density lipoprotein cholesterol. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:7305-7317. [PMID: 26261631 PMCID: PMC4525965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/22/2015] [Indexed: 06/04/2023]
Abstract
This study aimed to detect the association of the suppressor of cytokine signaling 3 gene (SOCS3) A+930-->G (rs4969168) single nucleotide polymorphism (SNP) and environmental factors with serum lipid levels in the Han and Mulao populations. Genotyping of the SOCS3 A+930-->G (rs4969168) SNP was performed in 752 of Han and 690 of Mulao participants using polymerase chain reaction and restriction fragment length polymorphism. The genotype and allele frequencies were significantly different between the Han and Mulao populations (GG, 57.71% vs. 51.16%, GA, 36.97% vs. 41.16%, AA, 5.32% vs. 7.68%, P = 0.023; G, 76.20% vs. 71.74%, A, 23.80% vs. 28.26%; P = 0.006; respectively). Serum apolipoprotein (Apo) A1 levels in Han were different among the genotypes (P < 0.05). Subgroup analyses showed that the levels of ApoA1 in Han females, and ApoA1 and low-density lipoprotein cholesterol (LDL-C) in Mulao males were different among the genotypes (P < 0.05). Serum lipid parameters were also associated with several environmental factors in both ethnic groups (P < 0.05-0.001). These findings suggest that there may be a racial/ethnic- and/or sex-specific association between the SOCS3 A+930-->G (rs4969168) SNP and serum lipid parameters in some populations.
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Affiliation(s)
- Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Rong-Jun Nie
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Xia Chen
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Yuan Bin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, China
| | - Wei-Xiong Lin
- Department of Molecular Biology, Medical Scientific Research Center, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi, China
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Guo T, Yin RX, Chen X, Bin Y, Nie RJ, Li H. Sex-specific association of the SPTY2D1 rs7934205 polymorphism and serum lipid levels. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:665-681. [PMID: 25755761 PMCID: PMC4348833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
The objective of the present study was to detect the association of the rs7934205 single nucleotide polymorphism (SNP) near the Suppressor of Ty, domain containing 1 gene (SPTY2D1) and serum lipid levels between males and females in the Mulao and Han populations. Genotyping of SPTY2D1 rs7934205 SNP was performed in 933 of Mulao and 865 of Han participants using polymerase chain reaction and restriction fragment length polymorphism. The T allele frequency was different between Mulao males and females (23.2% vs. 27.9%, P = 0.018). The genotype and allele frequencies were also different between Han males and females (P = 0.020 and P = 0.004; respectively). Serum levels of apolipoprotein (Apo) A1 in Mulao males; and total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), ApoA1 and ApoB in Mulao females were different between the CC and CT/TT genotypes (P < 0.05). Serum TC, ApoB levels in Han males, and ApoB levels in Han females were different between the CC and CT/TT genotypes (P < 0.05). The subjects with CT/TT genotype in both Mulao and Han males and females have more favorable lipid profiles than those with CC genotype. These findings suggest that the association between the SPTY2D1 rs7934205 SNP and serum lipid levels might have ethnic- and/or sex-specificity.
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Affiliation(s)
- Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Xia Chen
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Yuan Bin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Rong-Jun Nie
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
| | - Hui Li
- Clinical Laboratory of The Affiliated Cancer Hospital, Guangxi Medical UniversityNanning 530021, Guangxi, China
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