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Lee YH, Chang YS, Hsieh CC, Wang RT, Chang JG, Chen CJ, Chang SJ. APOE and KLF14 genetic variants are sex-specific for low high-density lipoprotein cholesterol identified by a genome-wide association study. Genet Mol Biol 2022; 45:e20210280. [PMID: 35238325 PMCID: PMC8892272 DOI: 10.1590/1678-4685-gmb-2021-0280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/28/2021] [Indexed: 11/22/2022] Open
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Copy Number Variants in Four Italian Turkey Breeds. Animals (Basel) 2021; 11:ani11020391. [PMID: 33546454 PMCID: PMC7913726 DOI: 10.3390/ani11020391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Hybrid Turkey selection is focusing on meat production traits characterized by high genetic heritability; the strong directional selection is well known to produce a constant loss in genetic diversity. Genetic characterization is one of the essential activities in the management of populations at risk of extinction. In addition, the genetic structure at the population level and the relationships between individuals are nowadays analysable at the genomic level. In this paper, the genome of 4 different Italian turkey breeds included in the Autochthonous Italian Poultry Breeds Register are analysed in order to obtain a genome-wide Copy Number Variant scan to ameliorate the existing knowledge of the genomic structure of Italian local turkey breeds. Differences have been described at genomic level for physiological, reproductive, and behavioral traits. The analyzed breeds are clearly distinguishable at the genomic level, and their relationships are clearly linked to their geographical origin and to the history of the rural structure of their developing regions. Genome information based on Copy Number Variant (CNV) detection has generated important information in this study concerning the uniqueness of the Italian local turkey breeds. Abstract Heritage breeds can be considered a genetic reservoir of genetic variability to be conserved and valorized considering their historical, cultural, and adaptive characteristics and possibly for their high potential in commercial hybrid genetic improvement by gene introgression. The aim of the present research is to investigate via Copy Number Variant (CNVs) the genomic makeup of 4 Italian autochthonous turkey breeds (Bronzato Comune—BrCI, 24; Ermellinato di Rovigo—ErRo, 24; Parma e Piacenza—PrPc, 25; Romagnolo—RoMa, 29). CNVs detection was performed using two different software and an interbreed CNVs comparison was carried out. A total of 1077 CNVs were identified in 102 turkeys, summarized into 519 CNV regions (CNVRs), which resulted after merging in 101 and 18 breed and shared regions. Biodiversity was analyzed using the effective information supplied by CNVs analysis, and BrCI and ErRo were characterized by a low mapped CNV number. Differences were described at a genomic level related to physiological, reproductive, and behavioral traits. The comparison with other three Italian turkey breeds (Brianzolo, Colle Euganei, and Nero Italiano) using a CNV data set available in the literature showed high clustering properties at the genomic level, and their relationships are strictly linked to the geographical origin and to the history of the rural structure of their native regions.
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Cole J, Blackhurst DM, Solomon GAE, Ratanjee BD, Benjamin R, Marais AD. Atherosclerotic cardiovascular disease in hyperalphalipoproteinemia due to LIPG variants. J Clin Lipidol 2021; 15:142-150.e2. [PMID: 33414088 DOI: 10.1016/j.jacl.2020.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 01/28/2023]
Abstract
BACKGROUND High density lipoprotein cholesterol (HDL-C) concentration correlates inversely with atherosclerotic cardiovascular disease (ASCVD) risk and is included in risk calculations. Endothelial lipase (EL) is a phospholipase that remodels HDL. Deficiency of EL due to mutations in its gene, LIPG, is associated with hyperalphalipoproteinemia. The effects of EL on HDL function and ASCVD risk remain poorly understood. OBJECTIVES To determine whether hyperalphalipoproteinemia due to EL deficiency is protective against ASCVD. METHODS We identified LIPG variants amongst patients with severe hyperalphalipoproteinemia (HDL-C >2.5 mmol/L) attending a referral lipid clinic in the Western Cape Province of South Africa. We analysed the clinical and biochemical phenotypes amongst primary hyperalphalipoproteinemia cases (males HDL-C >1.6 mmol/L; females HDL-C >1.8 mmol/L) due to LIPG variants, and the distribution of variants in normal and hyperalphalipoproteinemia ranges of HDL-C. RESULTS 1007 patients with HDL-C concentration ranging from 1.2 to 4.5 mmol/L were included. Seventeen females had primary hyperalphalipoproteinemia. Vascular disease was prominent, but not associated with HDL-C concentration, LDL-C concentration or carotid artery intima media thickness. Two novel and three known LIPG variants were identified in severe hyperalphalipoproteinemia. Four additional variants were identified in the extended cohort. Two common variants appeared normally distributed across the HDL-C concentration range, while six less-common variants were found only at higher HDL-C concentrations. One rare variant had a moderate effect. CONCLUSION Hyperalphalipoproteinemia due to LIPG variants is commoner in females and may not protect against ASCVD. Use of current risk calculations may be inappropriate in patients with hyperalphalipoproteinemia due to EL deficiency. Our study cautions targeting EL to reduce risk.
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Affiliation(s)
- Justine Cole
- Division of Chemical Pathology, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa; Chemical Pathology, National Health Laboratory Service, C17 Groote Schuur Hospital, Main Road, Observatory, 7925, Cape Town, South Africa.
| | - Diane Mary Blackhurst
- Division of Chemical Pathology, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Gabriele Anna Eva Solomon
- Division of Chemical Pathology, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Bharati Dhanluxmi Ratanjee
- Division of Chemical Pathology, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Ryan Benjamin
- Division of Chemical Pathology, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa; Chemical Pathology, National Health Laboratory Service, C17 Groote Schuur Hospital, Main Road, Observatory, 7925, Cape Town, South Africa
| | - Adrian David Marais
- Division of Chemical Pathology, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa.
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Liu CX, Yin RX, Shi ZH, Deng GX, Zheng PF, Wei BL, Guan YZ. EHBP1 SNPs, Their Haplotypes, and Gene-Environment Interactive Effects on Serum Lipid Levels. ACS OMEGA 2020; 5:7158-7169. [PMID: 32280856 PMCID: PMC7143410 DOI: 10.1021/acsomega.9b03522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
The associations between single nucleotide polymorphisms (SNPs) rs2710642 and rs10496099 and their effect on the EH domain-binding protein 1 (EHBP1) gene and serum lipid profiles remain uncertain. This study was performed to investigate the two EHBP1 SNPs in Han and Maonan populations, including their association, haplotypes, and effects on serum lipid levels. Two EHBP1 SNPs in 564 Han and 796 Maonan participants were genotyped by high-throughput sequencing, and then the genotype and haplotype distributions of two EHBP1 SNPs were analyzed. Moreover, risk factors and their effects on serum lipid levels were analyzed using multivariable linear regression and logistic regression analyses. In Han and Maonan populations, a significant difference was found in the allelic and genotypic frequencies of the EHBP1 rs2710642 and rs10496099 SNPs and the alternate alleles of rs2710642A and rs10496099C might be potentially beneficial for healthy lipid levels. Medium linkage disequilibrium between the two SNPs was noted in each ethnic group, and four main haplotypes were detected. The rs2710642G-rs10496099C haplotype was associated with high triglycerides (TGs) and low high-density lipoprotein cholesterol, and the rs2710642A-rs10496099C haplotype was associated with low TGs and high apolipoprotein A1. The rs2710642G-rs10496099C haplotype was a high-risk factor for hyperlipidemia, and it interacted with smoking, fasting blood glucose, and hypertension to increase but with the female factor to decrease the prevalence of hyperlipidemia in Han individuals. The EHBP1 rs2710642 and rs10496099 SNPs and gene-environment interactions were associated with serum lipid profiles and hyperlipidemia, which is of ethnic specificity to our study populations.
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Affiliation(s)
- Chun-Xiao Liu
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, 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, Nanning 530021, Guangxi, People’s Republic
of China
- Guangxi
Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular
Disease Control and Prevention, Nanning 530021, Guangxi, People’s Republic of China
- Guangxi
Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning 530021, Guangxi, People’s Republic
of China
| | - Zong-Hu Shi
- Department
of Prevention and Health Care, The Fourth Affiliated Hospital, Guangxi Medical University, Liuzhou 545005, Guangxi, People’s Republic
of China
| | - Guo-Xiong Deng
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Peng-Fei Zheng
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Bi-Liu Wei
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Yao-Zong Guan
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
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Qiu L, Yin RX, Nie RJ, Hu XJ, Khounphinith E, Zhang FH. The CXCL12 SNPs and their haplotypes are associated with serum lipid traits. Sci Rep 2019; 9:19524. [PMID: 31862910 PMCID: PMC6925251 DOI: 10.1038/s41598-019-55725-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
The relationship among the single nucleotide polymorphisms (SNPs) of the C-X-C motif chemokine ligand 12 gene (CXCL12) and the serum lipid profiles in the Chinese population has rarely been described, especially in somewhat old-fashioned and isolated Maonan minority. The goal of the current study was to elucidate the connection among the CXCL12 rs501120 and rs1746048 SNPs, haplotypes, several environmental factors and serum lipid traits in the Maonan as well as Han populations. Genotyping of the two SNPs, gel electrophoresis and direct sequencing were accomplished in 1,494 distinct subjects (Maonan, 750 and Han, 744) using polymerase chain reaction and restriction fragment length polymorphism. The frequencies of genotypes as well as alleles of the two SNPs were not similar between the two ethnic groups. The rs501120 SNP was related with serum total cholesterol levels, while the rs1746048 SNP was related with serum apolipoprotein (Apo) B levels. Four haplotypes were identified, of which the rs501120A-rs1746048C haplotype was the most common. The haplotypes of rs501120A-rs1746048T increased and rs501120G-rs1746048C decreased the risk of hyperlipidemia (P < 0.001 for each), showing consistent association with the levels of serum triglyceride, ApoA1 and ApoB. These outcomes specify that the CXCL12 SNPs as well as their haplotypes are related to serum lipid levels. Different serum lipid levels between both populations may partially be related to the CXCL12 SNPs, their haplotypes along with several environmental factors.
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Affiliation(s)
- Ling Qiu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 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, Nanning, 530021, Guangxi, People's Republic of China. .,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, 530021, Guangxi, People's Republic of China. .,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, 530021, Guangxi, People's Republic of China.
| | - Rong-Jun Nie
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China
| | - Xi-Jiang Hu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China
| | - Eksavang Khounphinith
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 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, Nanning, 530021, Guangxi, People's Republic of China
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