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Apolipoprotein A1/C3/A5 haplotypes and serum lipid levels. Lipids Health Dis 2011; 10:140. [PMID: 21854571 PMCID: PMC3170230 DOI: 10.1186/1476-511x-10-140] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 08/19/2011] [Indexed: 01/08/2023] Open
Abstract
Background The association of single nucleotide polymorphisms (SNPs) in the apolipoprotein (Apo) A1/C3/A4/A5 gene cluster and serum lipid profiles is inconsistent. The present study was undertaken to detect the association between the ApoA1/C3/A5 gene polymorphisms and their haplotypes with serum lipid levels in the general Chinese population. Methods A total of 1030 unrelated subjects (492 males and 538 females) aged 15-89 were randomly selected from our previous stratified randomized cluster samples. Genotyping of the ApoA1 -75 bp G>A, ApoC3 3238C>G, ApoA5 -1131T>C, ApoA5 c.553G>T and ApoA5 c.457G>A was performed by polymerse chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. Pair-wise linkage disequilibria and haplotype analysis among the five SNPs were estimated. Results The levels of high-density lipoprotein cholesterol (HDL-C) and ApoA1 were lower in males than in femailes (P < 0.05 for each). The allelic and genotypic frequencies of the SNPs were no significant difference between males and females except ApoC3 3238C>G. There were 11 haplotypes with a frequency >1% identified in the cluster in our population. At the global level, the haplotypes comprised of all five SNPs were significantly associated with all seven lipid traits. In particular, haplotype G-G-C-C-A (6%; in the order of ApoA5 c.553G>T, ApoA5 c.457G>A, ApoA5 -1131T>C, ApoC3 3238C>G, and ApoA1 -75bp G>A) and G-A-T-C-G (4%) showed consistent association with total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), ApoA1, ApoB, and the ApoA1/ApoB ratio. In addition, carriers of haplotype G-G-T-C-G (26%) had increased serum concentration of HDL-C and ApoA1, whereas carriers of G-G-C-G-G (15%) had high concentrations of TC, triglyceride (TG) and ApoB. We also found that haplotypes with five SNPs explain much more serum lipid variation than any single SNP alone, especially for TG (4.4% for haplotype vs. 2.4% for -1131T>C max based on R-square) and HDL-C (5.1% for haplotype vs. 0.9% for c.553G>T based on R-square). Serum lipid parameters were also correlated with genotypes and several environment factors. Conclusions Several common SNPs and their haplotypes in the ApoA1/C3/A5 gene cluster are closely associated with modifications of serum lipid parameters in the general Chinese population.
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Chien KL, Fang WH, Wen HC, Lin HP, Lin YL, Lin SW, Wu JH, Kao JT. APOA1/C3/A5 haplotype and risk of hypertriglyceridemia in Taiwanese. Clin Chim Acta 2007; 390:56-62. [PMID: 18206649 DOI: 10.1016/j.cca.2007.12.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 12/19/2007] [Accepted: 12/19/2007] [Indexed: 11/17/2022]
Abstract
BACKGROUND Apolipoprotein A5 gene (APOA5) has been shown to modulate plasma triglyceride concentrations. We investigated 2 distinct APOA1/C3/A5 haplotypes roles for hypertriglyceridemia. METHODS We recruited 308 cases of hypertriglyceridemia and 281 normal controls from a hospital. Twelve single nucleotide polymorphisms (SNPs) across the APOA1/C3/A5 gene region were genotyped. RESULTS One haplotype containing the minor alleles of the APOA5 (-1131T>C, c.553G>T) and APOA1 (-3013C>T,-75G>A) was more prevalent in cases than in controls (11.3% vs. 1.1%, respectively) and was statistically significantly associated with high triglycerides (adjusted odds ratio: 12.83, 95% confidence interval [CI]: 5.1-32.4, P<0.001). Another haplotype that was associated with hypertriglyceridemia (adjusted odds ratio 2.13, 95% CI, 1.37-3.29, P=0.001). Participants carrying both minor alleles of APOA5-1131CC and c.553TT had a 116% higher triglyceride concentration compared with those carrying common allele. CONCLUSIONS The APOA1/C3/A5 haplotype represents an important locus for predicting risk of hypertriglyceridemia among Taiwanese.
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Affiliation(s)
- Kuo-Liong Chien
- Institute of Preventive Medicine, College of Public School, National Taiwan University, Taiwan
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Abstract
PURPOSE OF REVIEW To provide an overview of recent advances that have defined the first putative genes behind familial combined hyperlipidemia, the most common genetic dyslipidemia and a major risk factor for early coronary heart disease. RECENT FINDINGS The first locus for familial combined hyperlipidemia on 1q21-23 revealed a gene encoding a transcription factor critical in lipid and glucose metabolism, USF1. All the associated variants represent noncoding single nucleotide polymorphisms, one of which affects the binding site of nuclear proteins with a putative effect on transcript levels of USF1. Transcript analyses of fat biopsies have exposed risk-allele related changes in the downstream genes. Another recent clue to the molecular pathogenesis of familial combined hyperlipidemia is the association of the high triglyceride trait with the APOA5 gene, located on 11q. More familial combined hyperlipidemia genes are expected to be found, since linkage evidence exists for additional loci on 16q24 and 20q12-q13.1. SUMMARY Genetic research of familial combined hyperlipidemia families has revealed several linked loci guiding to susceptibility genes. The USF1 transcription factor is the major gene underlying the 1q21-23 linkage. Modifying genes, especially influencing the high triglyceride trait, include APOC3 and APOA5, the latter representing a downstream target of USF1 and implying a USF1-dependent pathway in the molecular pathogenesis of dyslipidemias.
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Affiliation(s)
- Jussi Naukkarinen
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
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Abstract
Familial combined hyperlipidemia (FCHL) constitutes a substantial risk factor for atherosclerosis since it is observed in about 20% of coronary heart disease (CHD) patients under 60 years. FCHL, characterized by elevated levels of total cholesterol (TC) and triglycerides (TGs), or both, is also one of the most common familial hyperlipidemias with a prevalence of 1%-6% in Western populations. Numerous studies have been performed to identify genes contributing to FCHL. The recent linkage and association studies and their replications are beginning to elucidate the genetic variations underlying the susceptibility to FCHL. Three chromosomal regions on 1q21-23, 11p and 16q22-24.1 have been replicated in different study samples, offering targets for gene hunting. In addition, several candidate gene studies have replicated the influence of the lipoprotein lipase (LPL) gene and apolipoprotein A1/C3/A4/A5 (APOA1/C3/A4/A5) gene cluster in FCHL. Recently, the linked region on chromosome 1q21 was successfully fine-mapped and the upstream transcription factor 1 (USF1) gene identified as the underlying gene for FCHL. This finding has now been replicated in independent FCHL samples. However, the total number of variants, the risk related to each variant and their relative contributions to the disease susceptibility are not known yet.
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Affiliation(s)
- Elina Suviolahti
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-7088, USA
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Zhang C, Lopez-Ridaura R, Rimm EB, Rifai N, Hunter DJ, Hu FB. Interactions between the -514C->T polymorphism of the hepatic lipase gene and lifestyle factors in relation to HDL concentrations among US diabetic men. Am J Clin Nutr 2005; 81:1429-35. [PMID: 15941898 DOI: 10.1093/ajcn/81.6.1429] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Low plasma HDL-cholesterol concentrations are a hallmark of diabetic dyslipidemia. A common polymorphism (-514C-->T) of the hepatic lipase gene (LIPC), which accounts for up to 30% of the variation in hepatic lipase activity, has been associated with low hepatic lipase activity and high HDL-cholesterol concentrations. OBJECTIVE We examined the association between this polymorphism and plasma HDL-cholesterol concentrations and evaluated whether this association was modified by adiposity and dietary fat intake. DESIGN We followed men aged 40-75 y who participated in the Health Professionals Follow-Up Study in 1986. Among 18 159 men who returned blood samples by 1994, 780 had confirmed type 2 diabetes at blood drawing or during follow-up to 1998 and were free of cardiovascular disease at blood drawing. RESULTS After adjustment for age, smoking, alcohol consumption, fasting status, glycated hemoglobin concentration, physical activity, and body mass index, HDL-cholesterol concentrations were significantly higher in men with the C/T or T/T genotype than in those with the C/C genotype (adjusted x: 40.9 and 38.8 mg/dL, respectively; P = 0.01). We observed significant LIPC -514 polymorphism x body mass index and LIPC -514 polymorphism x saturated fat intake interactions for HDL-cholesterol concentrations (P = 0.003 for both). The T allele was associated with higher HDL-cholesterol concentrations only in men who were not overweight or who had higher saturated fat intake. CONCLUSION Our study suggests that the effects of -514C-->T of the LIPC gene on HDL concentrations were modified by saturated fat intake and obesity.
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Affiliation(s)
- Cuilin Zhang
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA.
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Fullerton SM, Buchanan AV, Sonpar VA, Taylor SL, Smith JD, Carlson CS, Salomaa V, Stengård JH, Boerwinkle E, Clark AG, Nickerson DA, Weiss KM. The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster. Hum Genet 2004; 115:36-56. [PMID: 15108119 DOI: 10.1007/s00439-004-1106-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 02/16/2004] [Indexed: 01/08/2023]
Abstract
While there is considerable appeal to the idea of selecting a few SNPs to represent all, or much, of the DNA sequence variability in a local chromosomal region, it is also important to quantify what detail is lost in adopting such an approach. To address this issue, we compared high- and low-resolution depictions of sequence diversity for the same genomic region, the APOA1/C3/A4/A5 gene cluster on chromosome 11. First, extensive re-sequencing identified all nucleotide and sequence haplotype variation of the linked apolipoprotein genes in 72 individuals from three populations: African-Americans from Jackson, Miss., Europeans from North Karelia, Finland, and European-Americans from Rochester, Minn. We identified 124 SNPs in 17.7 kb and significant differences in variation among genes. APOC3 gene diversity was particularly distinctive at high resolution, showing large allele frequency differences ( F(ST) values >0.250) between Jackson and the other two samples, and divergent population-specific haplotype lineages. Next, we selected haplotype-tagging SNPs (htSNPs) for each gene, at a density of approximately one SNP per kb, using an algorithm suggested by Stram et al. (2003). The 17 htSNPs identified were then used to reconstruct low-resolution haplotypes, from which inferences about the structure of variation were also drawn. This comparison showed that while the htSNPs successfully tagged common haplotype variation, they also left much underlying sequence diversity undetected and failed, in some cases, to co-classify groups of closely related haplotypes. The implications of these findings for other haplotype-based descriptions of human variation are discussed.
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Affiliation(s)
- Stephanie M Fullerton
- Department of Anthropology, Penn State University, 409 Carpenter Bldg., University Park, PA 16802, USA.
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Eichenbaum-Voline S, Olivier M, Jones EL, Naoumova RP, Jones B, Gau B, Patel HN, Seed M, Betteridge DJ, Galton DJ, Rubin EM, Scott J, Shoulders CC, Pennacchio LA. Linkage and association between distinct variants of the APOA1/C3/A4/A5 gene cluster and familial combined hyperlipidemia. Arterioscler Thromb Vasc Biol 2003; 24:167-74. [PMID: 14551155 PMCID: PMC2773540 DOI: 10.1161/01.atv.0000099881.83261.d4] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Combined hyperlipidemia is a common disorder, characterized by a highly atherogenic lipoprotein profile and a substantially increased risk of coronary heart disease. The purpose of this study was to establish whether variations of apolipoprotein A5 (APOA5), a newly discovered gene of lipid metabolism located 30 kbp downstream of the APOA1/C3/A4 gene cluster, contributes to the transmission of familial combined hyperlipidemia (FCHL). METHODS AND RESULTS We performed linkage and association tests on 128 families. Two independent alleles, APOA5c.56G and APOC3c.386G, of the APOA1/C3/A4/A5 gene cluster were overtransmitted in FCHL (P=0.004 and 0.007, respectively). This was paired with reduced transmission of the common APOA1/C3/A4/A5 haplotype (frequency 0.4461) to affected subjects (P=0.012). The APOA5c.56G genotype accounted for 7.3% to 13.8% of the variance in plasma triglyceride levels in probands (P<0.004). The APOC3c.386G genotypes accounted for 4.4% to 5.1% of the variance in triglyceride levels in FCHL spouses (P<0.007), suggesting that this allele marks a FCHL quantitative trait as well as representing a susceptibility locus for the condition. CONCLUSIONS A combined linkage and association analysis establishes that variation at the APOA1/C3/A4/A5 gene cluster contributes to FCHL transmission in a substantial proportion of northern European families.
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Affiliation(s)
- Sophie Eichenbaum-Voline
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
| | - Michael Olivier
- Human and Molecular Genetics Centre, Medical College of Wisconsin, Milwaukee, Wisc
| | - Emma L. Jones
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
| | - Rossitza P. Naoumova
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
| | - Bethan Jones
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
| | - Brian Gau
- Human and Molecular Genetics Centre, Medical College of Wisconsin, Milwaukee, Wisc
| | - Hetal N. Patel
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
| | - Mary Seed
- Department of Cardiovascular Medicine, Charing Cross Hospital
| | - D. John Betteridge
- Department of Medicine, Royal Free and University College Medical School, University College London
| | - David J. Galton
- Department of Metabolism and Genetics, St Bartholomew’s Hospital, London, UK
| | - Edward M. Rubin
- Genome Sciences Department, Lawerence Berkeley National Laboratory, Berkeley, Calif
- Joint Genome Institute, Department of Energy, Walnut Creek, Calif
| | - James Scott
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
- Genetics and Genomics Research Institute, Imperial College London
| | - Carol C. Shoulders
- Genomic and Molecular Medicine Group, Medical Research Council Clinical Sciences Centre, Hammersmith Hospital
| | - Len A. Pennacchio
- Genome Sciences Department, Lawerence Berkeley National Laboratory, Berkeley, Calif
- Joint Genome Institute, Department of Energy, Walnut Creek, Calif
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Groenendijk M, Cantor RM, Funke H, Dallinga-Thie GM. Two newly identified SNPs in the APO AI-CIII intergenic region are strongly associated with familial combined hyperlipidaemia. Eur J Clin Invest 2001; 31:852-9. [PMID: 11737222 DOI: 10.1046/j.1365-2362.2001.00888.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND We previously reported linkage and association of the apoAI-CIII-AIV gene region on chromosome 11 with familial combined hyperlipidaemia (FCHL). However, the observed epistasis resulting in an increased susceptibility to FCHL still remains unexplained. We hypothesize that the region between the apo AI and apo CIII genes may harbour functional mutations that might be in linkage disequilibrium with the already identified SstI and MspI polymorphisms, and provide an alternative explanation for the observed relationship. METHODS Using sequence analysis, we identified four new single nucleotide polymorphisms (SNPs) in the apo AI-CIII intergenic region. These four variants, T(3213)C, A(3235)C, T(3287)C and A(5132)C, were studied in 30 FCHL probands, 159 hyperlipidaemic relatives, 327 normolipidaemic relatives, and 218 spouses from the same families in which the original results were obtained. RESULTS The allele frequencies were significantly different between probands and spouses (P < 0.05). Transmission/disequilibrium test (TDT) analyses revealed more frequent transmission of the minor alleles to the affected offspring. The minor genotype was associated with elevated plasma cholesterol and triglyceride levels. The T(3213)C and MspI, and the A(3235)C and SstI SNPs were in complete linkage disequilibrium, resulting in two different major haplotypes 2-2-1-2-2-1 and 1-1-2-2-2-2 (MspI-T(3213)C-A(3235)C-T(3287)C-A(5132)C-SstI). Both haplotypes appear to predispose to FCHL independently, and account, together with the wild-type, for almost 90% of those occurring in these FCHL families, extending the high-risk combination of haplotypes that were reported previously. CONCLUSION These newly identified additional intergenic SNPs therefore provide an alternative explanation for the observed association of the SstI and MspI polymorphisms to the increased susceptibility for FCHL.
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Affiliation(s)
- M Groenendijk
- Department of Internal Medicine, University Medical Center Utrecht, 3508 GA Utrecht, the Netherlands
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Breslow JL. Genetics of lipoprotein abnormalities associated with coronary artery disease susceptibility. Annu Rev Genet 2001; 34:233-254. [PMID: 11092828 DOI: 10.1146/annurev.genet.34.1.233] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coronary heart disease is a complex genetic disease with many genes involved, environmental influences, and important gene-environment interactions. This review discusses the genetic basis of the principal lipoprotein abnormalities associated with coronary heart disease susceptibility in the general population. Individual sections discuss genes regulating LDL cholesterol, HDL cholesterol, and triglyceride levels. A section is included on the effects of the common apo E genetic variation on lipoprotein levels, as well as sections on the genetic regulation of lipoprotein(a) levels, genes regulating the inverse relationship between triglyceride-rich lipoproteins and HDL cholesterol levels, and our current understanding of the genetic basis of familial combined hyperlipidemia. It is clear that the field has progressed, with early studies focused mainly on the association of candidate gene RFLPs with phenotypes, later studies of candidate genes in both parametric and nonparametric linkage studies, and now more and more studies combining linkage analysis with genome scans to identify new loci that influence lipoprotein phenotypes. The future should provide us with the capability to perform reasonable genetic profiling for lipoprotein abnormalities associated with coronary heart disease susceptibility.
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Affiliation(s)
- J L Breslow
- Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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Dallongeville J, Meirhaeghe A, Cottel D, Fruchart JC, Amouyel P, Helbecque N. Gender related association between genetic variations of APOC-III gene and lipid and lipoprotein variables in northern France. Atherosclerosis 2000; 150:149-57. [PMID: 10781646 DOI: 10.1016/s0021-9150(99)00362-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The goal of the present study was to assess the impact of variability at the APOC-III insulin response element (APOC-III IRE) genetic locus on lipid, lipoprotein and complex lipoprotein particle levels as well as on the risk of dyslipidemia, in the population of northern France. To this end, 590 men and 579 women were randomly selected in the urban community of Lille in the framework of the MONICA project. Three polymorphisms, -482, -455 in the APOC-III insulin response element (IRE) and SstI in the 3'-noncoding region of the APOC-III gene locus were assessed. Compared to the most common alleles, the rare alleles of -482 and -455 were associated with increased levels of apoB-containing particles (LDL-cholesterol, apoB) and of triglyceride-related markers (apoC-III and LpC-III:B) in women, but not in men, suggesting a gender-related impact of APOC-III polymorphisms on these variables. Similarly, triglycerides, LpC-III:B and apoB were higher in women bearing the rare allele of SstI than in those with the most common allele. There was no evidence for any significant association between any of the -482, -455, and SstI alleles and lipid disorders (mixed hyperlipidemia, hypertriglyceridemia and hypercholesterolemia) in this sample of randomly selected men and women from northern France. In contrast, the prevalence of the haplotype that combined the rare alleles of the -482 and -455 sites was increased only in women with hypertriglyceridemia. Therefore, although the individual risk of hypertriglyceridemia is increased in women with the haplotype T, C at -482, -455, it appears that the -482, -455 and SstI APOC-III gene polymorphisms are not major contributors to the risk of dyslipidemia in the population of northern France.
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Affiliation(s)
- J Dallongeville
- Service d'Epidémiologie et de Santé Publique-INSERM U-508, Institut Pasteur de Lille, 1 rue du Professeur Calmette, 59019, Lille, France
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Abstract
Complex disorders are caused by several environmental factors that interact with multiple genes. These diseases are common at the population level and constitute a major health problem in Western societies. Familial combined hyperlipidemia (FCHL) is characterized by elevated levels of serum total cholesterol, triglycerides, or both. This disorder is estimated to be common in Western populations with a prevalence of 1% to 2%. In addition, 14% of patients with premature coronary heart disease (CHD) have FCHL, making this disorder one of the most common genetic dyslipidemias underlying premature CHD. Both genetic and environmental factors are suggested to affect the complex FCHL phenotype, but no specific susceptibility genes to FCHL have been identified. It is hoped that further analysis of the first FCHL locus and other new loci obtained in genome-wide scans will guide us to genes predisposing to this complex disorder.
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Affiliation(s)
- P Pajukanta
- University of California, Los Angeles, Department of Human Genetics, Los Angeles, California, USA
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