1
|
Yang J, Liu F, Li Y, Wu D, Zhang Z, Chen S, Deng M, Yang C, Yang J. Forkhead box C2 is associated with insulin resistance in gestational diabetes mellitus. Gynecol Endocrinol 2022; 38:499-502. [PMID: 35532201 DOI: 10.1080/09513590.2022.2072485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE This study aimed to investigate serum levels of adiponectin, and the mRNA expression of forkhead box C2 (FOXC2) and glucose transporter-4 (GLUT4) in visceral adipose tissue obtained from patients with gestational diabetes mellitus (GDM) and healthy pregnant women. METHODS Venous blood samples were obtained from 60 pregnant women with gestational normal glucose tolerance (GNGT) and 21 patients with GDM. Visceral adipose tissues were obtained from 11 women with GDM and 30 with GNGT. Serum adiponectin levels were detected by enzyme-linked immunosorbent assay, and FOXC2 and GLUT4 mRNA expression were detected by quantitative polymerase chain reaction. RESULTS Serum adiponectin concentrations were lower in the women with GDM than in the controls (p < .05). FOXC2 and GLUT4 mRNA expression were decreased in visceral adipose tissue of GDM women than in the controls (p < .05). Correlation analyses showed that FOXC2 tended to have a positive correlation with GLUT4 in GDM patients' visceral adipose tissue (p =.0564). CONCLUSION Our results revealed that decreased adiponectin, FOXC2, and GLUT4 expression were associated with increased risk of GDM and the regulation mechanism of GLUT4 mediated by FOXC2 would be the focus of further studies.
Collapse
Affiliation(s)
- Jing Yang
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Fen Liu
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Yi Li
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Dongbo Wu
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Zhenhui Zhang
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Sicen Chen
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Mandan Deng
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Chengying Yang
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| | - Jing Yang
- Department of Obstetrics and Gynecology, The First hospital of Changsha, Changsha, China
| |
Collapse
|
2
|
Trinder M, Vikulova D, Pimstone S, Mancini GBJ, Brunham LR. Polygenic architecture and cardiovascular risk of familial combined hyperlipidemia. Atherosclerosis 2021; 340:35-43. [PMID: 34906840 DOI: 10.1016/j.atherosclerosis.2021.11.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/06/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND AIMS Familial combined hyperlipidemia (FCHL) is one of the most common inherited lipid phenotypes, characterized by elevated plasma concentrations of apolipoprotein B-100 and triglycerides. The genetic inheritance of FCHL remains poorly understood. The goals of this study were to investigate the polygenetic architecture and cardiovascular risk associated with FCHL. METHODS AND RESULTS We identified individuals with an FCHL phenotype among 349,222 unrelated participants of European ancestry in the UK Biobank using modified versions of 5 different diagnostic criteria. The prevalence of the FCHL phenotype was 11.44% (n = 39,961), 5.01% (n = 17,485), 1.48% (n = 5,153), 1.10% (n = 3,838), and 0.48% (n = 1,688) according to modified versions of the Consensus Conference, Dutch, Mexico, Brunzell, and Goldstein criteria, respectively. We performed discovery, case-control genome-wide association studies for these different FCHL criteria and identified 175 independent loci associated with FCHL at genome-wide significance. We investigated the association of genetic and clinical risk with FCHL and found that polygenic susceptibility to hypercholesterolemia or hypertriglyceridemia and features of metabolic syndrome were associated with greater prevalence of FCHL. Participants with an FCHL phenotype had a similar risk of incident coronary artery disease compared to participants with monogenic familial hypercholesterolemia (adjusted hazard ratio vs controls [95% confidence interval]: 2.72 [2.31-3.21] and 1.90 [1.30-2.78]). CONCLUSIONS These results suggest that, rather than being a single genetic entity, the FCHL phenotype represents a polygenic susceptibility to dyslipidemia in combination with metabolic abnormalities. The cardiovascular risk associated with an FCHL phenotype is similar to that of monogenic familial hypercholesterolemia, despite being ∼5x more common.
Collapse
Affiliation(s)
- Mark Trinder
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada; Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Diana Vikulova
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada; Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon Pimstone
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - G B John Mancini
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Liam R Brunham
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada; Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
3
|
Genetics of Familial Combined Hyperlipidemia (FCHL) Disorder: An Update. Biochem Genet 2021; 60:453-481. [PMID: 34478023 DOI: 10.1007/s10528-021-10130-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
Familial combined hyperlipidemia (FCHL) is one of the most common familial lipoprotein disorders of the lipoproteins, with a prevalence of 0.5% to 2% in different populations. About 10% of these patients suffer from cardiovascular disease and this number is increased by up to 11.3% in the young survivors of myocardial infarction and by 40% among all the survivors of myocardial infarction. Although initially thought to be that FCHL has an inheritance pattern of monogenic, the disease's etiology is still not fully understood and it appears that FCHL has a complex pattern related to genetic variants, environmental factors, and lifestyles. Two strategies have been used to identify its complex genetic background: candidate gene and the linkage approach, which have yielded an extensive list of genes associated with FCHL with a variable degree of scientific evidence. Until now, more than 30 different genetic variants have been identified related to FCHL. In this study, we aimed to review the individual genes that have been described in FCHL and how these genes and variants can be related to the current concept of metabolic pathways resulting in familial combined hyperlipidemia.
Collapse
|
4
|
Ganel L, Chen L, Christ R, Vangipurapu J, Young E, Das I, Kanchi K, Larson D, Regier A, Abel H, Kang CJ, Scott A, Havulinna A, Chiang CWK, Service S, Freimer N, Palotie A, Ripatti S, Kuusisto J, Boehnke M, Laakso M, Locke A, Stitziel NO, Hall IM. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences. Hum Genomics 2021; 15:34. [PMID: 34099068 PMCID: PMC8185936 DOI: 10.1186/s40246-021-00335-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/26/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a combination of the number of mitochondria per cell and cell-type composition. Here, we studied MT-CN variation in blood-derived DNA from 19184 Finnish individuals using a combination of genome (N = 4163) and exome sequencing (N = 19034) data as well as imputed genotypes (N = 17718). RESULTS We identified two loci significantly associated with MT-CN variation: a common variant at the MYB-HBS1L locus (P = 1.6 × 10-8), which has previously been associated with numerous hematological parameters; and a burden of rare variants in the TMBIM1 gene (P = 3.0 × 10-8), which has been reported to protect against non-alcoholic fatty liver disease. We also found that MT-CN is strongly associated with insulin levels (P = 2.0 × 10-21) and other metabolic syndrome (metS)-related traits. Using a Mendelian randomization framework, we show evidence that MT-CN measured in blood is causally related to insulin levels. We then applied an MT-CN polygenic risk score (PRS) derived from Finnish data to the UK Biobank, where the association between the PRS and metS traits was replicated. Adjusting for cell counts largely eliminated these signals, suggesting that MT-CN affects metS via cell-type composition. CONCLUSION These results suggest that measurements of MT-CN in blood-derived DNA partially reflect differences in cell-type composition and that these differences are causally linked to insulin and related traits.
Collapse
Affiliation(s)
- Liron Ganel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lei Chen
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan Christ
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Erica Young
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Indraniel Das
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Krishna Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - David Larson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Allison Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Haley Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandra Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aki Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Susan Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Adam Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
5
|
Farook VS, Coletta DK, Puppala S, Schneider J, Chittoor G, Hu SL, Winnier DA, Norton L, Dyer TD, Arya R, Cole SA, Carless M, Göring HH, Almasy L, Mahaney MC, Comuzzie AG, Curran JE, Blangero J, Duggirala R, Lehman DM, Jenkinson CP, Defronzo RA. Linkage of type 2 diabetes on chromosome 9p24 in Mexican Americans: additional evidence from the Veterans Administration Genetic Epidemiology Study (VAGES). Hum Hered 2013; 76:36-46. [PMID: 24060607 DOI: 10.1159/000354849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/02/2013] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Type 2 diabetes (T2DM) is a complex metabolic disease and is more prevalent in certain ethnic groups such as the Mexican Americans. The goal of our study was to perform a genome-wide linkage (GWL) analysis to localize T2DM susceptibility loci in Mexican Americans. METHODS We used the phenotypic and genotypic data from 1,122 Mexican-American individuals (307 families) who participated in the Veterans Administration Genetic Epidemiology Study (VAGES). GWL analysis was performed using the variance components approach. Data from 2 additional Mexican-American family studies, the San Antonio Family Heart Study (SAFHS) and the San Antonio Family Diabetes/Gallbladder Study (SAFDGS), were combined with the VAGES data to test for improved linkage evidence. RESULTS After adjusting for covariate effects, T2DM was found to be under significant genetic influences (h2 = 0.62, p = 2.7 × 10(-6)). The strongest evidence for linkage of T2DM occurred between markers D9S1871 and D9S2169 on chromosome 9p24.2-p24.1 (LOD = 1.8). Given that we previously reported suggestive evidence for linkage of T2DM at this region also in SAFDGS, we found the significant and increased linkage evidence (LOD = 4.3, empirical p = 1.0 × 10(-5), genome-wide p = 1.6 × 10(-3)) for T2DM at the same chromosomal region, when we performed a GWL analysis of the VAGES data combined with the SAFHS and SAFDGS data. CONCLUSION Significant T2DM linkage evidence was found on chromosome 9p24 in Mexican Americans. Importantly, the chromosomal region of interest in this study overlaps with several recent genome-wide association studies involving T2DM-related traits. Given its overlap with such findings and our own initial T2DM association findings in the 9p24 chromosomal region, high throughput sequencing of the linked chromosomal region could identify the potential causal T2DM genes.
Collapse
Affiliation(s)
- Vidya S Farook
- Southwest Foundation for Biomedical Research, San Antonio, Tex., USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Abstract
Key components of atherosclerotic plaque known to drive disease progression are macrophages and cholesterol. It has been widely understood, and bolstered by recent evidence, that the efflux of cholesterol from macrophage foam cells quells disease progression or even to promote regression. Following macrophage cholesterol efflux, cholesterol loaded onto HDL must be removed from the plaque environment. Here, we focus on recent evidence that the lymphatic vasculature is critical for the removal of cholesterol, likely as a component of HDL, from tissues including skin and the artery wall. We discuss the possibility that progression of atherosclerosis might in part be linked to sluggish removal of cholesterol from the plaque.
Collapse
Affiliation(s)
- Catherine Martel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | | |
Collapse
|
7
|
Wijsman EM. The role of large pedigrees in an era of high-throughput sequencing. Hum Genet 2012; 131:1555-63. [PMID: 22714655 PMCID: PMC3638020 DOI: 10.1007/s00439-012-1190-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/07/2012] [Indexed: 12/13/2022]
Abstract
Rare variation is the current frontier in human genetics. The large pedigree design is practical, efficient, and well-suited for investigating rare variation. In large pedigrees, specific rare variants that co-segregate with a trait will occur in sufficient numbers so that effects can be measured, and evidence for association can be evaluated, by making use of methods that fully use the pedigree information. Evidence from linkage analysis can focus investigation, both reducing the multiple testing burden and expanding the variants that can be evaluated and followed up, as recent studies have shown. The large pedigree design requires only a small fraction of the sample size needed to identify rare variants of interest in population-based designs, and many highly suitable, well-understood, and available statistical and computational tools already exist. Samples consisting of large pedigrees with existing rich phenotype and genome scan data should be prime candidates for high-throughput sequencing in the search of the determinants of complex traits.
Collapse
Affiliation(s)
- Ellen M Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA 98195-7720, USA.
| |
Collapse
|
8
|
Reddy MVPL, Iatan I, Weissglas-Volkov D, Nikkola E, Haas BE, Juvonen M, Ruel I, Ruel MJI, Sinsheimer JS, Genest J, Pajukanta P. Exome sequencing identifies 2 rare variants for low high-density lipoprotein cholesterol in an extended family. ACTA ACUST UNITED AC 2012; 5:538-46. [PMID: 22923419 DOI: 10.1161/circgenetics.112.963264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Exome sequencing is a recently implemented method to discover rare mutations for Mendelian disorders. Less is known about its feasibility to identify genes for complex traits. We used exome sequencing to search for rare variants responsible for a complex trait, low levels of serum high-density lipoprotein cholesterol (HDL-C). METHODS AND RESULTS We conducted exome sequencing in a large French-Canadian family with 75 subjects available for study, of which 27 had HDL-C values less than the fifth age-sex-specific population percentile. We captured ≈50 Mb of exonic and transcribed sequences of 3 closely related family members with HDL-C levels less than the fifth age-sex percentile and sequenced the captured DNA. Approximately 82,000 variants were detected in each individual, of which 41 rare nonsynonymous variants were shared by the sequenced affected individuals after filtering steps. Two rare nonsynonymous variants in the ATP-binding cassette, subfamily A (ABC1), member 1 (ABCA1), and lipoprotein lipase genes predicted to be damaging were investigated for cosegregation with the low HDL-C trait in the entire extended family. The carriers of either variant had low HDL-C levels, and the individuals carrying both variants had the lowest HDL-C values. Interestingly, the ABCA1 variant exhibited a sex effect which was first functionally identified, and, subsequently, statistically demonstrated using additional French-Canadian families with ABCA1 mutations. CONCLUSIONS This complex combination of 2 rare variants causing low HDL-C in the extended family would not have been identified using traditional linkage analysis, emphasizing the need for exome sequencing of complex lipid traits in unexplained familial cases.
Collapse
Affiliation(s)
- M V Prasad Linga Reddy
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Daneshpour MS, Rebai A, Houshmand M, Alfadhli S, Zeinali S, Hedayati M, Zarkesh M, Azizi F. 8q24.3 and 11q25 chromosomal loci association with low HDL-C in metabolic syndrome. Eur J Clin Invest 2011; 41:1105-12. [PMID: 21443751 DOI: 10.1111/j.1365-2362.2011.02516.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND High-density lipoprotein cholesterol (HDL-C) levels are low in Iranians. Low HDL-C is the most frequent phenotype in metabolic syndrome (MetS) among the Iranian population (32%). This has been claimed to be related to genetic factors. MATERIALS AND METHODS To investigate possible genes linked to this disorder, 12 microsatellite markers were selected. They were used in 107 families with MetS and low HDL-C to analyse relevant association and linkage signals. RESULT Family-based association tests under the biallelic mode gave many positive association signals. Higher association - after correction for multiple testing - was found to be linked with marker D8S1743 and D11S1304 (P < 0·003). The obtained results suggested evidence for association with regions on chromosome 8, 11 and to a lesser degree on chromosome 16. Nonparametric linkage analysis performed by Merlin software gave no significant correlation for any of the chromosomal regions. By considering only families with positive Nonparametric Logarithm of odds (LOD) scores, higher association can clearly be visible with D16S3096 and D11S934. CONCLUSIONS These results suggest that 8q22-24; 11q23-25 and 16q23-24 regions are very likely to contain genes that control HDL-C level in Iranian families with metabolic syndrome.
Collapse
Affiliation(s)
- Maryam Sadat Daneshpour
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti MC, Tehran, Iran
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Day-Williams AG, Blangero J, Dyer TD, Lange K, Sobel EM. Unifying ideas for non-parametric linkage analysis. Hum Hered 2011; 71:267-80. [PMID: 21822022 PMCID: PMC7077094 DOI: 10.1159/000323752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 12/21/2010] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Non-parametric linkage analysis (NPL) exploits marker allele sharing among affected relatives to map genes influencing complex traits. Computational barriers force approximate analysis on large pedigrees and the adoption of a questionable perfect data assumption (PDA) in assigning p values. To improve NPL significance testing on large pedigrees, we examine the adverse consequences of missing data and PDA. We also introduce a novel statistic, Q-NPL, appropriate for NPL analysis of quantitative traits. METHODS Using simulated and real data sets with qualitative traits, we compare NPL analysis results for four testing procedures and various degrees of missing data. The simulated data sets vary from all nuclear families, to all large pedigrees, to a mix of pedigrees of different sizes. We implemented the Kong and Cox linear adjustment of p values in the software packages Mendel and SimWalk. We perform similar analysis with Q-NPL on quantitative traits of various heritabilities. RESULTS The Kong and Cox extension for significance testing is robust to realistic missing data patterns, greatly improves p values in approximate analyses, and works equally well for qualitative and quantitative traits and small and large pedigrees. The Q-NPL statistic is robust to missing data and shows good power to detect linkage for quantitative traits with a wide spectrum of heritabilities. CONCLUSIONS The Kong and Cox extension should be a standard tool for calculating NPL p values. It allows the combination of exact and estimated analyses into a single significance score. Q-NPL should be a standard statistic for NPL analysis of quantitative traits. The new statistics are implemented in Mendel and SimWalk.
Collapse
Affiliation(s)
| | - John Blangero
- Department of Department of Genetics, Texas Biomedical Research Institute, San Antonio, Tex., USA
| | - Thomas D. Dyer
- Department of Department of Genetics, Texas Biomedical Research Institute, San Antonio, Tex., USA
| | - Kenneth Lange
- Department of Human Genetics
- Department of Biomathematics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, Calif
| | | |
Collapse
|
11
|
Dong C, Beecham A, Wang L, Slifer S, Wright CB, Blanton SH, Rundek T, Sacco RL. Genetic loci for blood lipid levels identified by linkage and association analyses in Caribbean Hispanics. J Lipid Res 2011; 52:1411-9. [PMID: 21558551 DOI: 10.1194/jlr.p013672] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To identify genetic loci influencing blood lipid levels in Caribbean Hispanics, we first conducted a genome-wide linkage scan in 1,211 subjects from 100 Dominican families on five lipid quantitative traits: total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), triglycerides (TG), and LDL-C/HDL-C ratio. We then investigated the association between blood lipid levels and 21,361 single nucleotide polymorphisms (SNP) under the 1-logarithm of odds (LOD) unit down regions of linkage peaks in an independent community-based subcohort (N = 814, 42% Dominican) from the Northern Manhattan Study (NOMAS). We found significant linkage evidence for LDL-C/HDL-C on 7p12 (multipoint LOD = 3.91) and for TC on 16q23 (LOD = 3.35). In addition, we identified suggestive linkage evidence of LOD > 2.0 on 15q23 for TG, 16q23 for LDL-C, 19q12 for TC and LDL-C, and 20p12 for LDL-C. In the association analysis of the linkage peaks, we found that seven SNPs near FLJ45974 were associated with LDL-C/HDL-C with a nominal P < 3.5 × 10(-5), in addition to associations (P < 0.0001) for other lipid traits with SNPs in or near CDH13, SUMF2, TLE3, FAH, ARNT2, TSHZ3, ZNF343, RPL7AL2, and TMC3. Further studies are warranted to perform in-depth investigations of functional genetic variants in these regions.
Collapse
Affiliation(s)
- Chuanhui Dong
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Leduc MS, Lyons M, Darvishi K, Walsh K, Sheehan S, Amend S, Cox A, Orho-Melander M, Kathiresan S, Paigen B, Korstanje R. The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol. J Lipid Res 2011; 52:1139-1149. [PMID: 21444760 DOI: 10.1194/jlr.m009175] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association (GWA) studies represent a powerful strategy for identifying susceptibility genes for complex diseases in human populations but results must be confirmed and replicated. Because of the close homology between mouse and human genomes, the mouse can be used to add evidence to genes suggested by human studies. We used the mouse quantitative trait loci (QTL) map to interpret results from a GWA study for genes associated with plasma HDL cholesterol levels. We first positioned single nucleotide polymorphisms (SNPs) from a human GWA study on the genomic map for mouse HDL QTL. We then used mouse bioinformatics, sequencing, and expression studies to add evidence for one well-known HDL gene (Abca1) and three newly identified genes (Galnt2, Wwox, and Cdh13), thus supporting the results of the human study. For GWA peaks that occur in human haplotype blocks with multiple genes, we examined the homologous regions in the mouse to prioritize the genes using expression, sequencing, and bioinformatics from the mouse model, showing that some genes were unlikely candidates and adding evidence for candidate genes Mvk and Mmab in one haplotype block and Fads1 and Fads2 in the second haplotype block. Our study highlights the value of mouse genetics for evaluating genes found in human GWA studies.
Collapse
|
13
|
Sáez ME, González-Pérez A, Martínez-Larrad MT, Gayán J, Real LM, Serrano-Ríos M, Ruiz A. WWOX gene is associated with HDL cholesterol and triglyceride levels. BMC MEDICAL GENETICS 2010; 11:148. [PMID: 20942981 PMCID: PMC2967537 DOI: 10.1186/1471-2350-11-148] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 10/14/2010] [Indexed: 01/22/2023]
Abstract
Background Altered lipid profile, and in particular low HDL and high triglyceride (TG) plasma levels, are within the major determinants of cardiovascular diseases. The identification of quantitative trait loci (QTL) affecting these lipid levels is a relevant issue for predictive purposes. The WWOX gene has been recently associated with HDL levels. This gene is located at chromosome 16q23, a region previously linked to familial combined hyperlipidemia (FCHL) and HDL. Our objective is to perform a genetic association analysis at the WWOX gene region with HDL, TG and TG/HDL ratio. Methods A quantitative association analysis performed in 801 individuals selected from the Spanish general population. Results For HDL levels, two regions of intron 8 display clustering of positive signals (p < 0.05) but none of them was associated in the haplotypic analysis (0.07 ≤ p ≤ 0.165). For TG levels not only intron 8 but also a 27 kb region spanning from the promoter region to intron 4 are associated in this study. For the TG/HDL genetic association analysis, positive signals are coincident with those of the isolated traits. Interestingly, haplotypic analysis at the 5' region showed that variation in this region modified both HDL and TG levels, especially the latter (p = 0.003). Conclusions Our results suggest that WWOX is a QTL for both TG and HDL.
Collapse
Affiliation(s)
- María E Sáez
- Departamento de Genómica Estructural, Neocodex, 41092 Sevilla, Spain.
| | | | | | | | | | | | | |
Collapse
|
14
|
Weissglas-Volkov D, Pajukanta P. Genetic causes of high and low serum HDL-cholesterol. J Lipid Res 2010; 51:2032-57. [PMID: 20421590 DOI: 10.1194/jlr.r004739] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Plasma levels of HDL cholesterol (HDL-C) have a strong inherited basis with heritability estimates of 40-60%. The well-established inverse relationship between plasma HDL-C levels and the risk of coronary artery disease (CAD) has led to an extensive search for genetic factors influencing HDL-C concentrations. Over the past 30 years, candidate gene, genome-wide linkage, and most recently genome-wide association (GWA) studies have identified several genetic variations for plasma HDL-C levels. However, the functional role of several of these variants remains unknown, and they do not always correlate with CAD. In this review, we will first summarize what is known about HDL metabolism, monogenic disorders associated with both low and high HDL-C levels, and candidate gene studies. Then we will focus this review on recent genetic findings from the GWA studies and future strategies to elucidate the remaining substantial proportion of HDL-C heritability. Comprehensive investigation of the genetic factors conferring to low and high HDL-C levels using integrative approaches is important to unravel novel pathways and their relations to CAD, so that more effective means of diagnosis, treatment, and prevention will be identified.
Collapse
|
15
|
Yang R, Li L, Seidelmann SB, Shen GQ, Sharma S, Rao S, Abdullah KG, Mackinlay KG, Elston RC, Chen Q, Topol EJ, Wang QK. A genome-wide linkage scan identifies multiple quantitative trait loci for HDL-cholesterol levels in families with premature CAD and MI. J Lipid Res 2010; 51:1442-51. [PMID: 20075193 DOI: 10.1194/jlr.m004325] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Plasma HDL cholesterol levels (HDL-C) are an independent predictor of coronary artery disease (CAD). We have completed a genome-wide linkage scan for HDL-C in a US cohort consisting of 388 multiplex families with premature CAD (GeneQuest). The heritability of HDL-C in GeneQuest was 0.37 with gender and age as covariates (P = 5.1 x 10(-4)). Two major quantitative trait loci (QTL) for log-transformed HDL-C adjusted for age and gender were identified onto chromosomes 7p22 and 15q25 with maximum multipoint logarithm of odds (LOD) scores of 3.76 and 6.69, respectively. Fine mapping decreased the 7p22 LOD score to a nonsignificant level of 3.09 and split the 15q25 QTL into two loci, one minor QTL on 15q22 (LOD = 2.73) that spanned the LIPC gene, and the other at 15q25 (LOD = 5.63). A family-based quantitative transmission disequilibrium test (QTDT) revealed significant association between variant rs1800588 in LIPC and HDL-C in the GeneQuest population (P = 0.0067), which may account for the minor QTL on 15q22. The 15q25 QTL is the most significant locus identified for HDL-C to date, and these results provide a framework for the ultimate identification of the underlying HDL-C variant and gene on chromosomes 15q25, which will provide insights into novel regulatory mechanisms of HDL-C metabolism.
Collapse
Affiliation(s)
- Rong Yang
- Department of Molecular Cardiology, Lerner Research Institute, The Cleveland Clinic Foundation, Center for Cardiovascular Genetics, Cleveland, OH 44195, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Weissglas-Volkov D, Plaisier CL, Huertas-Vazquez A, Cruz-Bautista I, Riaño-Barros D, Herrera-Hernandez M, Riba L, Cantor RM, Sinsheimer JS, Aguilar-Salinas CA, Tusie-Luna T, Pajukanta P. Identification of two common variants contributing to serum apolipoprotein B levels in Mexicans. Arterioscler Thromb Vasc Biol 2009; 30:353-9. [PMID: 19965785 DOI: 10.1161/atvbaha.109.196402] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND PURPOSE Although the Mexican population has a high predisposition to dyslipidemias and premature coronary artery disease, this population is underinvestigated for the genetic factors conferring the high susceptibility. This study attempted to determine these genetic factors. METHODS AND RESULTS First, we investigated apolipoprotein B (apoB) levels in Mexican extended families with familial combined hyperlipidemia using a two-step testing strategy. In the screening step, we screened 5721 single-nucleotide polymorphisms (SNPs) for linkage signals with apoB. In the test step, we analyzed the 130 SNPs residing in regions of suggestive linkage signals for association with apoB. We identified significant associations with two SNPs (ie, rs1424032 [P=6.07x10(-6)] and rs1349411 [P=2.72x10(-4)]) that surpassed the significance level for the number of tests performed in the test step (P<3.84x10(-4)). Second, these SNPs were tested for replication in Mexican hyperlipidemic case-control samples. The same risk alleles as in the families with familial combined hyperlipidemia were significantly associated (P<0.05) with apoB in the case-control samples. The rs1349411 resides near the apoB messenger RNA editing enzyme (APOBEC1) involved in the processing of APOB messenger RNA in the small intestine. The rs1424032 resides in a highly conserved noncoding region predicted to function as a regulatory element. CONCLUSIONS We identified two novel variants, rs1349411 and rs1424032, for serum apoB levels in Mexicans.
Collapse
Affiliation(s)
- Daphna Weissglas-Volkov
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, Calif 90095-7088, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Ruan X, Ma L, Wang S, Lindpaintner K, Liu X, Wang B, Peng Z, Ma X, Cheng M, Zhang J, Liu L, Wang X. Association of two CETP polymorphisms with HDL levels in the Chinese obese population. Obesity (Silver Spring) 2009; 17:2196-201. [PMID: 19444232 DOI: 10.1038/oby.2009.138] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The association of two cholesterol ester transfer protein (CETP) polymorphisms, D442G and TAQIB (B1-->B2), with high-density lipoprotein (HDL) levels in 932 Chinese obese individuals (BMI >or= 27) was investigated in comparison with normal controls (BMI <or= 24). Independent association was demonstrated for TAQIB minor allele B2 and CETP442 minor allele G with elevated HDL levels. The CETP D442G polymorphism was associated with a much greater increase in HDL levels in subjects with BMI exceeding 27 kg/m(2) (+5.42 mg/dl, P = 0.0007) compared to normal controls (+1.97 mg/dl, P = 0.275), and the increase in HDL reached the highest level among subjects with BMI exceeding 30 kg/m(2) (+6.80 mg/dl, P = 0.016). TAQIB showed significant association with HDL levels only in normal BMI subgroup (P = 0.0017). TAQIB significantly interacted with serum triglyceride (TG) on modulating HDL levels (P = 0.027). The TAQIB-TG interaction effect remained marginally significant after controlling for BMI (P = 0.057). We conclude that D442G polymorphism is associated with more HDL elevation in obesity. TAQIB interacts with serum TG on modulating HDL levels, and the interaction is partly independent of BMI.
Collapse
Affiliation(s)
- Xiaoyang Ruan
- Laboratory of Human Genetics, Beijing Hypertension League Institute, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Genome scan for loci regulating HDL cholesterol levels in Finnish extended pedigrees with early coronary heart disease. Eur J Hum Genet 2009; 18:604-13. [PMID: 19935834 DOI: 10.1038/ejhg.2009.202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Coronary heart disease (CHD) is the leading cause of mortality in Western societies. Its risk is inversely correlated with plasma high-density lipoprotein cholesterol (HDL-C) levels, and approximately 50% of the variability in these levels is genetically determined. In this study, the aim was to carry out a whole-genome scan for the loci regulating plasma HDL-C levels in 35 well-defined Finnish extended pedigrees (375 members genotyped) with probands having low HDL-C levels and premature CHD. The additive genetic heritability of HDL-C was 43%. A variance component analysis revealed four suggestive quantitative trait loci (QTLs) for HDL-C levels, with the highest LOD score, 3.1, at the chromosomal locus 4p12. Other suggestive LOD scores were 2.1 at 2q33, 2.1 at 6p24 and 2.0 at 17q25. Three suggestive loci for the qualitative low HDL-C trait were found, with a nonparametric multipoint score of 2.6 at the chromosomal locus 10p15.3, 2.5 at 22q11 and 2.1 at 6p12. After correction for statin use, the strongest evidence of linkage was shown on chromosomes 4p12, 6p24, 6p12, 15q22 and 22q11. To search for the underlying gene on chromosome 6, we analyzed two functional and positional candidate genes (peroxisome proliferator-activated receptor-delta (PPARD), and retinoid X receptor beta, (RXRB)), but found no significant evidence of association. In conclusion, we identified seven chromosomal regions for HDL-C regulation exceeding the level for suggestive evidence of linkage.
Collapse
|
19
|
Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. Eur J Hum Genet 2009; 18:342-7. [PMID: 19844255 DOI: 10.1038/ejhg.2009.157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Low levels of high-density lipoprotein cholesterol (HDL-C) are an independent risk factor for cardiovascular disease. To identify novel genetic variants that contribute to HDL-C, we performed genome-wide scans and quantitative association studies in two study samples: a Quebec-wide study consisting of 11 multigenerational families and a study of 61 families from the Saguenay-Lac St-Jean (SLSJ) region of Quebec. The heritability of HDL-C in these study samples was 0.73 and 0.49, respectively. Variance components linkage methods identified a LOD score of 2.61 at 98 cM near the marker D16S515 in Quebec-wide families and an LOD score of 2.96 at 86 cM near the marker D16S2624 in SLSJ families. In the Quebec-wide sample, four families showed segregation over a 25.5-cM (18 Mb) region, which was further reduced to 6.6 Mb with additional markers. The coding regions of all genes within this region were sequenced. A missense variant in CHST6 segregated in four families and, with additional families, we observed a P value of 0.015 for this variant. However, an association study of this single-nucleotide polymorphism (SNP) in unrelated Quebec-wide samples was not significant. We also identified an SNP (rs11646677) in the same region, which was significantly associated with a low HDL-C (P=0.016) in the SLSJ study sample. In addition, RT-PCR results from cultured cells showed a significant difference in the expression of CHST6 and KIAA1576, another gene in the region. Our data constitute additional evidence for a locus on chromosome 16q23-24 that affects HDL-C levels in two independent French-Canadian studies.
Collapse
|
20
|
Horra A, Salazar J, Ferré R, Vallvé JC, Guardiola M, Rosales R, Masana L, Ribalta J. Prox-1 and FOXC2 gene expression in adipose tissue: A potential contributory role of the lymphatic system to familial combined hyperlipidaemia. Atherosclerosis 2009; 206:343-5. [DOI: 10.1016/j.atherosclerosis.2009.02.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 02/17/2009] [Accepted: 02/18/2009] [Indexed: 11/25/2022]
|
21
|
Iatan I, Dastani Z, Do R, Weissglas-Volkov D, Ruel I, Lee JC, Huertas-Vazquez A, Taskinen MR, Prat A, Seidah NG, Pajukanta P, Engert JC, Genest J. Genetic variation at the proprotein convertase subtilisin/kexin type 5 gene modulates high-density lipoprotein cholesterol levels. ACTA ACUST UNITED AC 2009; 2:467-75. [PMID: 20031622 DOI: 10.1161/circgenetics.109.877811] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND A low level of plasma high-density lipoprotein cholesterol (HDL-C) is a risk factor for cardiovascular disease. HDL particles are modulated by a variety of lipases, including endothelial lipase, a phospholipase present on vascular endothelial cells. The proprotein convertase subtilisin/kexin type 5 (PCSK5) gene product is known to directly inactivate endothelial lipase and indirectly cleave and activate angiopoetin-like protein 3, a natural inhibitor of endothelial lipase. We therefore investigated the effect of human PCSK5 genetic variants on plasma HDL-C levels. METHODS AND RESULTS Haplotypes at the PCSK5 locus were examined in 9 multigenerational families that included 60 individuals with HDL-C <10th percentile. Segregation with low HDL-C in 1 family was found. Sequencing of the PCSK5 gene in 12 probands with HDL-C <5th percentile identified 7 novel variants. Using a 2-stage design, we first genotyped these single-nucleotide polymorphisms (SNPs) along with 163 tagSNPs and 12 additional SNPs (n=182 total) in 457 individuals with documented coronary artery disease. We identified 9 SNPs associated with HDL-C (P<0.05), with the strongest results for rs11144782 and rs11144766 (P=0.002 and P=0.005, respectively). The SNP rs11144782 was also associated with very low-density lipoprotein (P=0.039), triglycerides (P=0.049), and total apolipoprotein levels (P=0.022). In stage 2, we replicated the association of rs11144766 with HDL-C (P=0.014) in an independent sample of Finnish low HDL-C families. In a combined analysis of both stages (n=883), region-wide significance of rs11144766 and low HDL-C was observed (unadjusted P=1.86x10(-4) and Bonferroni-adjusted P=0.031). CONCLUSIONS We conclude that variability at the PCSK5 locus influences HDL-C levels, possibly through the inactivation of endothelial lipase activity, and, consequently, atherosclerotic cardiovascular disease risk.
Collapse
Affiliation(s)
- Iulia Iatan
- Department of Biochemistry, Cardiovascular Research Laboratories, Cardiology Division, McGill University Health Centre/Royal Victoria Hospital, Montreal, Quebec, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Lee JC, Weissglas-Volkov D, Kyttälä M, Dastani Z, Cantor RM, Sobel EM, Plaisier CL, Engert JC, van Greevenbroek MM, Kane JP, Malloy MJ, Pullinger CR, Huertas-Vazquez A, Aguilar-Salinas CA, Tusie-Luna T, de Bruin TW, Aouizerat BE, van der Kallen CC, Croce CM, Aqeilan RI, Marcil M, Viikari JS, Lehtimäki T, Raitakari OT, Kuusisto J, Laakso M, Taskinen MR, Genest J, Pajukanta P. WW-domain-containing oxidoreductase is associated with low plasma HDL-C levels. Am J Hum Genet 2008; 83:180-92. [PMID: 18674750 DOI: 10.1016/j.ajhg.2008.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/27/2008] [Accepted: 07/02/2008] [Indexed: 10/21/2022] Open
Abstract
Low serum HDL-cholesterol (HDL-C) is a major risk factor for coronary artery disease. We performed targeted genotyping of a 12.4 Mb linked region on 16q to test for association with low HDL-C by using a regional-tag SNP strategy. We identified one SNP, rs2548861, in the WW-domain-containing oxidoreductase (WWOX) gene with region-wide significance for low HDL-C in dyslipidemic families of Mexican and European descent and in low-HDL-C cases and controls of European descent (p = 6.9 x 10(-7)). We extended our investigation to the population level by using two independent unascertained population-based Finnish cohorts, the cross-sectional METSIM cohort of 4,463 males and the prospective Young Finns cohort of 2,265 subjects. The combined analysis provided p = 4 x 10(-4) to 2 x 10(-5). Importantly, in the prospective cohort, we observed a significant longitudinal association of rs2548861 with HDL-C levels obtained at four different time points over 21 years (p = 0.003), and the T risk allele explained 1.5% of the variance in HDL-C levels. The rs2548861 resides in a highly conserved region in intron 8 of WWOX. Results from our in vitro reporter assay and electrophoretic mobility-shift assay demonstrate that this region functions as a cis-regulatory element whose associated rs2548861 SNP has a specific allelic effect and that the region forms an allele-specific DNA-nuclear-factor complex. In conclusion, analyses of 9,798 subjects show significant association between HDL-C and a WWOX variant with an allele-specific cis-regulatory function.
Collapse
|
23
|
Presson AP, Sobel EM, Pajukanta P, Plaisier C, Weeks DE, Aberg K, Papp JC. Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis. BMC Bioinformatics 2008; 9:317. [PMID: 18644149 PMCID: PMC2515855 DOI: 10.1186/1471-2105-9-317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 07/21/2008] [Indexed: 11/15/2022] Open
Abstract
Background Correctly merged data sets that have been independently genotyped can increase statistical power in linkage and association studies. However, alleles from microsatellite data sets genotyped with different experimental protocols or platforms cannot be accurately matched using base-pair size information alone. In a previous publication we introduced a statistical model for merging microsatellite data by matching allele frequencies between data sets. These methods are implemented in our software MicroMerge version 1 (v1). While MicroMerge v1 output can be analyzed by some genetic analysis programs, many programs can not analyze alignments that do not match alleles one-to-one between data sets. A consequence of such alignments is that codominant genotypes must often be analyzed as phenotypes. In this paper we describe several extensions that are implemented in MicroMerge version 2 (v2). Results Notably, MicroMerge v2 includes a new one-to-one alignment option that creates merged pedigree and locus files that can be handled by most genetic analysis software. Other features in MicroMerge v2 enhance the following aspects of control: 1) optimizing the algorithm for different merging scenarios, such as data sets with very different sample sizes or multiple data sets, 2) merging small data sets when a reliable set of allele frequencies are available, and 3) improving the quantity and 4) quality of merged data. We present results from simulated and real microsatellite genotype data sets, and conclude with an association analysis of three familial dyslipidemia (FD) study samples genotyped at different laboratories. Independent analysis of each FD data set did not yield consistent results, but analysis of the merged data sets identified strong association at locus D11S2002. Conclusion The MicroMerge v2 features will enable merging for a variety of genotype data sets, which in turn will facilitate meta-analyses for powering association analysis.
Collapse
Affiliation(s)
- Angela P Presson
- Department of Human Genetics, University of California, Los Angeles, CA 90095, USA.
| | | | | | | | | | | | | |
Collapse
|
24
|
FOXC2 controls Ang-2 expression and modulates angiogenesis, vascular patterning, remodeling, and functions in adipose tissue. Proc Natl Acad Sci U S A 2008; 105:10167-72. [PMID: 18621714 DOI: 10.1073/pnas.0802486105] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adipogenesis is spatiotemporally coupled to angiogenesis throughout adult life, and the interplay between these two processes is communicated by multiple factors. Here we show that in a transgenic mouse model, increased expression of forkhead box C2 (FOXC2) in the adipose tissue affects angiogenesis, vascular patterning, and functions. White and brown adipose tissues contain a considerably high density of microvessels appearing as vascular plexuses, which show redistribution of vascular smooth muscle cells and pericytes. Dysfunction of these primitive vessels is reflected by impairment of skin wound healing. We further provide a mechanistic insight of the vascular phenotype by showing that FOXC2 controls Ang-2 expression by direct activation of its promoter in adipocytes. Remarkably, an Ang-2-specific antagonist almost completely reverses this vascular phenotype. Thus, the FOXC2-Ang-2 signaling system is crucial for controlling adipose vascular function, which is part of an adaptation to increased adipose tissue metabolism.
Collapse
|
25
|
Kim TM, Yim SH, Chung YJ. Copy Number Variations in the Human Genome: Potential Source for Individual Diversity and Disease Association Studies. Genomics Inform 2008. [DOI: 10.5808/gi.2008.6.1.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
26
|
Park HS, Kim JI, Cho SI, Sung JH, Kim HL, Ju YS, Bayasgalan G, Lee MK, Seo JS. Genome-wide Linkage Study for Plasma HDL Cholesterol Level in an Isolated Population of Mongolia. Genomics Inform 2008. [DOI: 10.5808/gi.2008.6.1.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
27
|
Sung JH, Lee MK, Seo JS. Inbreeding Coefficients in Two Isolated Mongolian Populations - GENDISCAN Study. Genomics Inform 2008. [DOI: 10.5808/gi.2008.6.1.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
28
|
Vinson A, Mahaney MC, Cox LA, Rogers J, VandeBerg JL, Rainwater DL. A pleiotropic QTL on 2p influences serum Lp-PLA2 activity and LDL cholesterol concentration in a baboon model for the genetics of atherosclerosis risk factors. Atherosclerosis 2008; 196:667-73. [PMID: 17767937 PMCID: PMC2289511 DOI: 10.1016/j.atherosclerosis.2007.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 06/22/2007] [Accepted: 07/16/2007] [Indexed: 11/24/2022]
Abstract
Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)), the major portion of which is bound to low-density lipoprotein, is an independent biomarker of cardiovascular disease risk. To search for common genetic determinants of variation in both Lp-PLA(2) activity and LDL cholesterol (LDL-C) concentration, we assayed these substances in serum from 679 pedigreed baboons. Using a maximum likelihood-based variance components approach, we detected significant evidence for a QTL affecting Lp-PLA(2) activity (LOD=2.79, genome-wide P=0.039) and suggestive evidence for a QTL affecting LDL-C levels (LOD=2.16) at the same location on the baboon ortholog of human chromosome 2p. Because we also found a significant genetic correlation between the two traits (rho(G)=0.50, P<0.00001), we conducted bivariate linkage analyses of Lp-PLA(2) activity and LDL-C concentration. These bivariate analyses improved the evidence (LOD=3.19, genome-wide P=0.015) for a QTL at the same location on 2p, corresponding to the human cytogenetic region 2p24.3-p23.2. The QTL-specific correlation between the traits (rho(Q)=0.62) was significantly different from both zero and 1 (P[rho(Q)=0]=0.047; P[rho(Q)=1]=0.022), rejecting the hypothesis of co-incident linkage and consistent with incomplete pleiotropy at this locus. We conclude that polymorphisms at the QTL described in this study exert some genetic effects that are shared between Lp-PLA(2) activity and LDL-C concentration.
Collapse
Affiliation(s)
- A Vinson
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245, United States.
| | | | | | | | | | | |
Collapse
|
29
|
Lee JC, Weissglas-Volkov D, Kyttälä M, Sinsheimer JS, Jokiaho A, de Bruin TWA, Lusis AJ, Brennan ML, van Greevenbroek MMJ, van der Kallen CJH, Hazen SL, Pajukanta P. USF1 Contributes to High Serum Lipid Levels in Dutch FCHL Families and U.S. Whites With Coronary Artery Disease. Arterioscler Thromb Vasc Biol 2007; 27:2222-7. [PMID: 17673701 DOI: 10.1161/atvbaha.107.151530] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective—
Familial combined hyperlipidemia (FCHL) characterized by high serum total cholesterol and/or triglycerides (TGs) is a common dyslipidemia predisposing to coronary artery disease (CAD). Recently, the upstream transcription factor 1 (
USF1
) was linked and associated with FCHL and TGs in Finnish FCHL families. Here we examined the previously associated rs3737787 SNP in extended Dutch FCHL families (n=532) and in a cohort of US subjects who underwent diagnostic coronary angiography (n=1533).
Methods and Results—
In males of the Dutch FCHL families, we observed significant sex-dependent associations between the common allele of rs3737787 and FCHL, TGs, and related metabolic traits (
P
=0.02 to 0.006). In the U.S. Whites, sex-dependent associations with TGs and related metabolic traits were observed for the common allele of rs3737787 in males (
P
=0.04 to 0.02) and rare allele in females (
P
=0.05 to 0.002). This intriguing relationship was further supported by the highly significant genotype
x
sex interactions observed for TGs in the Dutch and TGs and body mass index (BMI) in U.S. White subjects with CAD (
P
=0.0005 to 0.00004).
Conclusion—
These data show that
USF1
influences several cardiovascular risk factors in a sex-dependent manner in Dutch FCHL families and U.S. Whites with CAD. A significant interaction between sex and genotype was shown to affect TGs and BMI.
Collapse
Affiliation(s)
- Jenny C Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Bella JN, Tang W, Kraja A, Rao DC, Hunt SC, Miller MB, Palmieri V, Roman MJ, Kitzman DW, Oberman A, Devereux RB, Arnett DK. Genome-wide linkage mapping for valve calcification susceptibility loci in hypertensive sibships: the Hypertension Genetic Epidemiology Network Study. Hypertension 2007; 49:453-60. [PMID: 17224468 DOI: 10.1161/01.hyp.0000256957.10242.75] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
It remains unclear whether genetic factors contribute to the susceptibility to valve calcification. Accordingly, echocardiograms and genotyping were performed in 1871 hypertensive siblings who participated in the Hypertension Genetic Epidemiology Network Study. Genome-wide affected sibpair nonparametric linkage analysis was conducted using the allele-sharing method implemented in the Merlin computer program. A total of 1014 sibships from 858 families were evaluated for aortic valve sclerosis or mitral annular calcification. Of these, 78 sibships from 68 families contained > or =2 affected siblings with > or =1 type of valve calcification (142 affected siblings). All 3 of the traits showed a modest degree of familial aggregation, with sibling recurrence risk (SD) and sibling recurrence risk ratio (95% CI) being 0.25 (0.035) and 2.31 (1.72 to 3.11) for aortic valve sclerosis, 0.25 (0.035) and 1.78 (1.36 to 2.33) for mitral annular calcification, and 0.31 (0.030) and 1.52 (1.24 to 1.85) for aortic valve sclerosis and mitral annular calcification, respectively. Affected sibpair linkage analysis revealed the highest logarithm of odds score (3.14) in chromosome 16 at 105.6 cM for aortic valve sclerosis. Other chromosomal regions with logarithm of odds score > or =1.9 were found in chromosomes 19 (2.88), 16 (2.63), 1 (2.12), and 2 (2.03) for aortic valve sclerosis and chromosome 13 (2.12) for any valve calcification. There was no logarithm of odds score > or =1.9 for mitral annular calcification. Our study shows strong linkage of aortic valve sclerosis to chromosome 16q22.1-q22.3 and suggestive linkage to chromosome 19p13.11-p11 and identifies several other promising genomic regions that may contain specific susceptibility loci for valve calcification.
Collapse
|
31
|
Abstract
PURPOSE OF REVIEW High-density lipoproteins have multi-factorial anti-atherosclerosis properties: they have potent anti-oxidant effects and prevent the oxidation of low-density lipoproteins; they have anti-inflammatory effects; they modulate vascular endothelial cell function and transport cholesterol back to the liver for excretion into the bile - a process called reverse cholesterol transport. The present review focuses on genetic aspects of high-density lipoprotein metabolism, with genomic approaches used to identify genes that regulate high-density lipoproteins in humans. RECENT FINDINGS Disorders of the many genes that code for proteins, including transporters, enzymes, receptors, transfer proteins and lipases, involved in high-density lipoprotein metabolism have been identified in humans as causing extremes of high-density lipoprotein cholesterol, and provide potential novel therapeutic avenues. These, however, explain fewer than 5% of the causes of low high-density lipoprotein cholesterol in the general population. SUMMARY Genome-wide linkage studies of large cohorts, with discrete as well as quantitative trait loci analyses, followed by association studies have enabled the identification of large chromosomal regions that may harbor genes that modulate high-density lipoprotein cholesterol levels in humans. Using mouse genetics, the results of the HapMap project and novel genetic approaches will allow the discovery of novel genes in high-density lipoprotein metabolism.
Collapse
Affiliation(s)
- Zari Dastani
- Cardiovascular Genetics Laboratory, Division of Cardiology, McGill University Health Centre/Royal Victoria Hospital, Montréal, Québec, Canada
| | | | | | | |
Collapse
|
32
|
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.
Collapse
Affiliation(s)
- Jussi Naukkarinen
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
| | | | | |
Collapse
|
33
|
Abstract
Longitudinal population studies have confirmed plasma levels of high-density lipoprotein (HDL) cholesterol to be an important inverse coronary risk factor. Although environmental influences are known to regulate HDL cholesterol levels, genetic factors are also known to be important, and over 25 candidate genes have been proposed to be associated with variation in HDL cholesterol levels. A variety of monogenic conditions of extremely low or high HDL cholesterol has helped to delineate the physiology of HDL cholesterol metabolism in humans, which has led to the development of new therapeutic approaches to HDL cholesterol. However, most causes of genetic variation in HDL cholesterol in the general population are likely oligogenic or polygenic. We review the monogenic disorders associated with both high and low HDL cholesterol and the relevance of mutations and polymorphisms in these genes to variation in HDL cholesterol levels in the general population.
Collapse
Affiliation(s)
- Atif Qasim
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | | |
Collapse
|
34
|
Arya R, Demerath E, Jenkinson CP, Göring HHH, Puppala S, Farook V, Fowler S, Schneider J, Granato R, Resendez RG, Dyer TD, Cole SA, Almasy L, Comuzzie AG, Siervogel RM, Bradshaw B, DeFronzo RA, MacCluer J, Stern MP, Towne B, Blangero J, Duggirala R. A quantitative trait locus (QTL) on chromosome 6q influences birth weight in two independent family studies. Hum Mol Genet 2006; 15:1569-79. [PMID: 16611675 DOI: 10.1093/hmg/ddl076] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Low birth weight is an important cause of infant mortality and morbidity worldwide. Birth weight has been shown to be inversely correlated with adult complex diseases such as obesity, type-2 diabetes and cardiovascular disease. However, little is known about the genetic factors influencing variation in birth weight and its association with diseases that occur in later life. We, therefore, have performed a genome-wide search to identify genes that influence birth weight in Mexican-Americans using the data from the San Antonio Family Birth Weight Study participants (n=840). Heritability of birth weight was estimated as 72.0+/-8.4% (P<0.0001) after adjusting for the effects of sex and term. Multipoint linkage analysis yielded the strongest evidence for linkage of birth weight (LOD=3.7) between the markers D6S1053 and D6S1031 on chromosome 6q. This finding has been replicated (LOD=2.3) in an independent European-American population. Together, these findings provide substantial evidence (LOD(adj)=4.3) for a major locus influencing variation in birth weight. This region harbors positional candidate genes such as chorionic gonadotropin, alpha chain; collagen, type XIX, alpha-1; and protein-tyrosine phosphatase, type 4A, 1 that may play a role in fetal growth and development. In addition, potential evidence for linkage (LOD>or=1.2) was found on chromosomes 1q, 2q, 3q, 4q, 9p, 19p and 19q with LODs ranging from 1.3 to 2.7. Thus, we have found strong evidence for a major gene on chromosome 6q that influences variation in birth weight in both Mexican- and European-Americans.
Collapse
Affiliation(s)
- Rector Arya
- Division of Clinical Epidemiology, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229-3900, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Abstract
PURPOSE OF REVIEW Familial combined hyperlipidemia is a common complex disease that accounts for up to 20% of premature coronary heart disease. The upstream transcription factor 1, located on 1q21, was recently shown to be linked and associated with familial combined hyperlipidemia in Finnish families. Upstream transcription factor 1 is the first gene identified by positional cloning for familial combined hyperlipidemia. Replication studies are critical to investigation of complex diseases because only they can verify the importance of the original findings. We review recent studies that examine the genetic contribution and functional consequence of upstream transcription factor 1 variants to familial combined hyperlipidemia and type 2 diabetes mellitus. Aiming beyond upstream transcription factor 1, we also evaluate novel strategies that have made it possible to globally examine the genome and the transcriptome. RECENT FINDINGS Three independent studies support the role of upstream transcription factor 1 in familial combined hyperlipidemia. The results for type 2 diabetes mellitus and the metabolic syndrome have been less conclusive highlight novel strategies for gene identification in familial combined hyperlipidemia. SUMMARY Currently, genetic and functional evidence is supportive of a role for upstream transcription factor 1 in the etiology of familial combined hyperlipidemia and its component traits, although the mechanism of causality still remains largely unknown.
Collapse
Affiliation(s)
- Jenny C Lee
- Department of Human Genetics bDepartment of Medicine/Division of Cardiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | | | | |
Collapse
|
36
|
Harrap SB, Wong ZYH, Scurrah KJ, Lamantia A. Genome-wide linkage analysis of population variation in high-density lipoprotein cholesterol. Hum Genet 2006; 119:541-6. [PMID: 16570200 DOI: 10.1007/s00439-006-0167-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2006] [Accepted: 03/05/2006] [Indexed: 10/24/2022]
Abstract
Lower plasma levels of high-density lipoprotein cholesterol (HDL-C) are associated with the metabolic syndrome (insulin resistance, obesity, hypertension) and higher cardiovascular risk. Recent association studies have suggested rare alleles responsible for very low HDL-C levels. However, for individual cardiovascular risk factors, the majority of population-attributable deaths are associated with average rather than extreme levels. Therefore, genetic factors that determine the population variation of HDL-C are particularly relevant. We undertook genome-wide and fine mapping to identify linkage to HDL-C in healthy adult nuclear families from the Victorian Family Heart Study. In 274 adult sibling pairs (average age 24 years, average plasma HDL-C 1.4 mmol/l), genome-wide mapping revealed suggestive evidence for linkage on chromosome 4 (Z score = 3.5, 170 cM) and nominal evidence for linkage on chromosomes 1 (Z = 2.1, 176 cM) and 6 (Z = 2.6, 29 cM). Using genotypes and phenotypes from 932 subjects (233 of the sibling pairs and their parents), finer mapping of the locus on chromosome 4 strengthened our findings with a peak probability (Z score = 3.9) at 169 cM. Our linkage data suggest that chromosome 4q32.3 is linked with normal population variation in HDL-C. This region coincides with previous reports of linkage to apolipoprotein AII (a major component of HDL) and encompasses the gene encoding the carboxypeptidase E, relevant to the metabolic syndrome and HDL-C. These findings are relevant for further understanding of the genetic determinants of cardiovascular risk at a population level.
Collapse
Affiliation(s)
- Stephen B Harrap
- Department of Physiology, The University of Melbourne, 3010 Parkville, VIC, Australia.
| | | | | | | |
Collapse
|
37
|
Ylisaukko-oja T, Alarcón M, Cantor RM, Auranen M, Vanhala R, Kempas E, von Wendt L, Järvelä I, Geschwind DH, Peltonen L. Search for autism loci by combined analysis of Autism Genetic Resource Exchange and Finnish families. Ann Neurol 2006; 59:145-55. [PMID: 16288458 DOI: 10.1002/ana.20722] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Several genome-wide screens have been performed in autism spectrum disorders resulting in the identification of numerous putative susceptibility loci. Analyses of pooled primary data should result in an increased sample size and the different study samples have a potential to strengthen the evidence for some earlier identified loci, reveal novel loci, and even to provide information of the general significance of the locus. The objective of this study was to search for potential susceptibility loci for autism, which are supported by two independent samples. METHODS We performed a combined analysis of the primary genome scan data of the Autism Genetic Resource Exchange (AGRE) and Finnish autism samples to reveal susceptibility loci potentially shared by these study samples. RESULTS In the initial combined data analysis, the best loci (p < 0.05) were observed at 1p12-q25, 3p24-26, 4q21-31, 5p15-q12, 6q14-21, 7q33-36, 8q22-24, 17p12-q21, and 19p13-q13. The combined analysis of Finnish and AGRE families showed the most promising shared locus on 3p24-26 with nonparametric logarithm of odds (NPL) score of 2.20 (p = 0.011). The combined data analysis did not provide increased linkage evidence for the earlier identified loci on 3q25-27 or 17p12-q21. However, the 17p12-q21 locus remained promising also in the combined sample (NPL(all) =2.38, p = 0.0076). INTERPRETATION Our study of 314 autism families highlights the importance of further analyses on 3p24-26 locus involving comprehensive molecular genetic analyses of oxytocin receptor gene (OXTR), a positional and functional candidate gene for autism.
Collapse
Affiliation(s)
- Tero Ylisaukko-oja
- Department of Molecular Medicine, National Public Health Institute, University of Helsinki, 00251 Helsinki, Finland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Feitosa MF, Province MA, Heiss G, Arnett DK, Myers RH, Pankow JS, Hopkins PN, Borecki IB. Evidence of QTL on 15q21 for high-density lipoprotein cholesterol: the National Heart, Lung, and Blood Institute Family Heart Study (NHLBI FHS). Atherosclerosis 2006; 190:232-7. [PMID: 16529751 DOI: 10.1016/j.atherosclerosis.2006.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 01/05/2006] [Accepted: 02/01/2006] [Indexed: 10/24/2022]
Abstract
A genome-wide linkage scan was conducted to identify regions potentially having quantitative trait loci (QTLs) influencing high-density lipoprotein (HDL) cholesterol. We found suggestive evidence of a QTL (lod score (LOD)=1.75, p=0.00224, and q=0.07649) influencing the variation of plasma levels of age- and sex-adjusted HDL-cholesterol on chromosome 15q21 at marker D15S659 in the NHLBI FHS data. Owing to the perturbations to lipid profiles associated with diabetes, the analysis was repeated excluding diabetic subjects from the sample. The lod score increased from 1.75 to 2.71 (p=0.00021, q=0.05392) at the same chromosome 15 location, despite the reduction in sample size. This finding indicates that the inclusion of diabetic subjects in the analysis may confound the presence of a QTL for HDL-cholesterol on 15q21. Because of the known effects of important covariates such as metabolic variables and lifestyle habits that may interact with a putative QTL, we also analyzed HDL-cholesterol with a progressive adjustment. When body mass index, smoking, and habitual alcohol intake were added to age- and sex-adjustment, we found strong evidence for linkage in the complete sample (LOD=4.77, p=0.0000013, and q=0.00016) as well as in the non-diabetic sub-sample (LOD=4.52, p=0.0000025, and q=0.00026) on chromosome 15q21 (between D15S659 and D15S195 markers). These results suggest that there are multiple pathways and factors involving genetic and environmental effects influencing HDL-cholesterol levels, and by taking some of these known factors into account, we obtained strong evidence of a QTL influencing HDL-cholesterol levels. While this putative QTL may also have an effect in diabetes, our data suggest a more pronounced role in non-diabetics. A prominent candidate gene residing within the linkage region on 15q21 is hepatic lipase (HL), which has a major role in lipoprotein metabolism.
Collapse
Affiliation(s)
- Mary F Feitosa
- Division of Statistical Genomics, Center for Genome Sciences, Washington University School of Medicine, 660 S. Euclid, Campus Box 8067, St. Louis, MO 63110-1093, USA.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Puppala S, Dodd GD, Fowler S, Arya R, Schneider J, Farook VS, Granato R, Dyer TD, Almasy L, Jenkinson CP, Diehl AK, Stern MP, Blangero J, Duggirala R. A genomewide search finds major susceptibility loci for gallbladder disease on chromosome 1 in Mexican Americans. Am J Hum Genet 2006; 78:377-92. [PMID: 16400619 PMCID: PMC1380282 DOI: 10.1086/500274] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 11/16/2005] [Indexed: 12/11/2022] Open
Abstract
Gallbladder disease (GBD) is one of the major digestive diseases. Its risk factors include age, sex, obesity, type 2 diabetes, and metabolic syndrome (MS). The prevalence of GBD is high in minority populations, such as Native and Mexican Americans. Ethnic differences, familial aggregation of GBD, and the identification of susceptibility loci for gallstone disease by use of animal models suggest genetic influences on GBD. However, the major susceptibility loci for GBD in human populations have not been identified. Using ultrasound-based information on GBD occurrence and a 10-cM gene map, we performed multipoint variance-components analysis to localize susceptibility loci for GBD. Phenotypic and genotypic data from 715 individuals in 39 low-income Mexican American families participating in the San Antonio Family Diabetes/Gallbladder Study were used. Two GBD phenotypes were defined for the analyses: (1) clinical or symptomatic GBD, the cases of cholecystectomies due to stones confirmed by ultrasound, and (2) total GBD, the clinical GBD cases plus the stone carriers newly diagnosed by ultrasound. With use of the National Cholesterol Education Program/Adult Treatment Panel III criteria, five MS risk factors were defined: increased waist circumference, hypertriglyceredemia, low high-density lipoprotein cholesterol, hypertension, and high fasting glucose. The MS risk-factor score (range 0-5) for a given individual was used as a single, composite covariate in the genetic analyses. After accounting for the effects of age, sex, and MS risk-factor score, we found stronger linkage signals for the symptomatic GBD phenotype. The highest LOD scores (3.7 and 3.5) occurred on chromosome 1p between markers D1S1597 and D1S407 (1p36.21) and near marker D1S255 (1p34.3), respectively. Other genetic locations (chromosomes 2p, 3q, 4p, 8p, 9p, 10p, and 16q) across the genome exhibited some evidence of linkage (LOD >or=1.2) to symptomatic GBD. Some of these chromosomal regions corresponded with the genetic locations of Lith loci, which influence gallstone formation in mouse models. In conclusion, we found significant evidence of major genetic determinants of symptomatic GBD on chromosome 1p in Mexican Americans.
Collapse
Affiliation(s)
- Sobha Puppala
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245-0549, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Elina Suviolahti
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-7088, USA
| | | | | |
Collapse
|
41
|
Dastani Z, Quiogue L, Plaisier C, Engert JC, Marcil M, Genest J, Pajukanta P. Evidence for a gene influencing high-density lipoprotein cholesterol on chromosome 4q31.21. Arterioscler Thromb Vasc Biol 2005; 26:392-7. [PMID: 16322534 DOI: 10.1161/01.atv.0000198243.83781.a3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE A low level of plasma high-density lipoprotein cholesterol (HDL-C) is a major risk factor for coronary atherosclerosis. To identify novel genes regulating plasma HDL-C levels, we investigated 13 multigenerational French Canadian families with an average of 12 affected individuals per family for genome-wide signals, which we subsequently fine mapped. METHODS AND RESULTS We genotyped a total of 362 individuals, including 151 affected subjects for 485 autosomal microsatellite markers. In parametric 2-point linkage analyses, the highest 2-point logarithm of odds (lod) score of 4.6 was observed with marker D4S424 on chromosome 4q31.21 (at approximately 142 Mb). The multipoint analysis of this region resulted in a lod score of 3.8 and a lod -1 region of 12.2 cM, containing 40 known genes. The results were obtained by allowing for genetic heterogeneity among these extended pedigrees, and approximately 50% of families were linked to this region with the highest single-pedigree lod score being 3.6. We further restricted the linked region from 12.2 to 2.9 cM (2.37 Mb) by genotyping 15 additional markers in the 3 families with the highest lod scores. We sequenced 4 genes with a likely role in lipid metabolism as well as 2 genes residing directly under the linkage peak but found no evidence for a causative variant. None of the genes residing in the significantly restricted 2.37-Mb region has been associated previously with HDL-C metabolism. CONCLUSIONS This study provides significant evidence for a gene influencing HDL-C on chromosome 4q31.21.
Collapse
Affiliation(s)
- Zari Dastani
- Department of Medicine, McGill University, Montreal, Canada
| | | | | | | | | | | | | |
Collapse
|
42
|
Malhotra A, Coon H, Feitosa MF, Li WD, North KE, Price RA, Bouchard C, Hunt SC, Wolford JK. Meta-analysis of genome-wide linkage studies for quantitative lipid traits in African Americans. Hum Mol Genet 2005; 14:3955-62. [PMID: 16301214 DOI: 10.1093/hmg/ddi419] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic influences on lipid traits have been suggested by numerous studies. In addition to heritability studies, over 50 genome scans have been performed to identify regions of linkage for quantitative lipid levels. Five of these scans have been performed in African Americans (four univariate and one bivariate linkage analysis), but with results that have been largely inconclusive. Linkage analyses are often limited by both sample size and heterogeneity, which may lead to nominal LOD scores or lack of evidence for linkage; the use of meta-analysis to combine linkage results from populations with similar ethnic backgrounds may help overcome some of these limitations. Thus, we performed a meta-analysis using data from four genome scans conducted in African American families to identify chromosomal regions showing evidence of linkage for total cholesterol (TC), triglycerides (TG), low density lipoprotein cholesterol (LDL) and high density lipoprotein cholesterol (HDL). Significant evidence (i.e. P<0.00042) for linkage was found for LDL on chromosome 1q32.1-q41 (Pweighted=0.00014 and Punweighted=0.00007) and 1q41-q44 (Pweighted=0.00017 and Punweighted=0.00014). We found suggestive evidence (i.e. P<0.00847) for TG on 16p12.1-q11.2 and for HDL on 4p15.1-p11. We also assessed heterogeneity between studies and found significant evidence for low heterogeneity for both regions on chromosome 1q (P=0.0300 and P=0.0279, respectively) for LDL and chromosome 16 (P=0.0429) for TG. Statistically significant evidence for linkage and low heterogeneity on chromosome 1q therefore suggest that this region may harbor a gene underlying the inheritance of LDL in African Americans.
Collapse
Affiliation(s)
- Alka Malhotra
- Diabetes and Obesity Research Unit, Translational Genomics Research Institute, Phoenix, AZ 85004, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Meex SJR, van der Kallen CJH, van Greevenbroek MMJ, Eurlings PMH, El Hasnaoui M, Evelo CTA, Lindsey PJ, Luiken JJFP, Glatz JFC, de Bruin TWA. Up-regulation of CD36/FAT in preadipocytes in familial combined hyperlipidemia. FASEB J 2005; 19:2063-5. [PMID: 16219805 DOI: 10.1096/fj.04-2403fje] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Familial combined hyperlipidemia (FCHL) shows many features of the metabolic syndrome. The strong genetic component makes it an excellent model to study the genetic background of metabolic syndrome and insulin resistance. Adipose tissue is believed to contribute to, or even underlie, the FCHL phenotype and is an interesting target tissue for gene expression studies. However, interpretation of adipose tissue gene expression experiments is complex since expression differences cannot only arise as a direct consequence of a genetic trait, but may also reflect an adaptation to metabolic influences at the cellular level. In the present study, we measured gene expression levels in cultured primary human preadipocytes from FCHL and control subjects. Since isolated preadipocytes were allowed to replicate for weeks under standardized conditions, the contribution of previous metabolic influences is rather small whereas genetic defects are preserved and expressed in vitro. The main finding was up-regulation of CD36/FAT in FCHL preadipocytes, confirmed in two independent groups of subjects, and a concomitant increase in CD36/FAT-mediated fatty acid uptake. CD36/FAT overexpression has previously been shown to be associated with other insulin-resistant states. The present data suggest that CD36/FAT overexpression in FCHL occurs very early in adipocyte differentiation and may be of genetic origin.
Collapse
Affiliation(s)
- Steven J R Meex
- Laboratory of Molecular Metabolism and Endocrinology, Department of Internal Medicine, Maastricht, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Coronary heart disease (CHD) is the leading cause of death among individuals with type 2 diabetes. Dyslipidemia contributes significantly to CHD in diabetic patients, in whom lipid abnormalities include hypertriglyceridemia, low HDL cholesterol, and increased levels of small, dense LDL particles. To identify genes for lipid-related traits, we performed genome-wide linkage analyses for levels of triglycerides and HDL, LDL, and total cholesterol in Caucasian, Hispanic, and African-American families from the Genetics of NIDDM (GENNID) study. Most lipid traits showed significant estimates of heritability (P < 0.001) with the exception of triglycerides and the triglyceride/HDL ratio in African Americans. Variance components analysis identified linkage on chromosome 3p12.1-3q13.31 for the triglyceride/HDL ratio (logarithm of odds [LOD] = 3.36) and triglyceride (LOD = 3.27) in Caucasian families. Statistically significant evidence for linkage was identified for the triglyceride/HDL ratio (LOD = 2.45) on 11p in Hispanic families in a region that showed suggestive evidence for linkage (LOD = 2.26) for triglycerides in this population. In African Americans, the strongest evidence for linkage (LOD = 2.26) was found on 19p13.2-19q13.42 for total cholesterol. Our findings provide strong support for previous reports of linkage for lipid-related traits, suggesting the presence of genes on 3p12.1-3q13.31, 11p15.4-11p11.3, and 19p13.2-19q13.42 that may influence traits underlying lipid abnormalities associated with type 2 diabetes.
Collapse
MESH Headings
- Adult
- Aged
- Black People/genetics
- Cholesterol/blood
- Cholesterol, HDL/blood
- Cholesterol, LDL/blood
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 3/genetics
- Coronary Disease/etiology
- Databases, Genetic
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/genetics
- Female
- Genetic Linkage
- Genetic Predisposition to Disease
- Hispanic or Latino/genetics
- Humans
- Hyperlipidemias/complications
- Hyperlipidemias/genetics
- Lod Score
- Male
- Middle Aged
- Phenotype
- Quantitative Trait, Heritable
- Registries
- Triglycerides/blood
- White People/genetics
- Black or African American
Collapse
Affiliation(s)
- Alka Malhotra
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | |
Collapse
|
45
|
Huertas-Vazquez A, Aguilar-Salinas C, Lusis AJ, Cantor RM, Canizales-Quinteros S, Lee JC, Mariana-Nuñez L, Riba-Ramirez RML, Jokiaho A, Tusie-Luna T, Pajukanta P. Familial Combined Hyperlipidemia in Mexicans. Arterioscler Thromb Vasc Biol 2005; 25:1985-91. [PMID: 15976322 DOI: 10.1161/01.atv.0000175297.37214.a0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To investigate the largely unknown genetic component of the common lipid disorder, familial combined hyperlipidemia (FCHL) in Mexicans, we analyzed the upstream transcription factor 1 (USF1) gene that was recently associated with FCHL and high triglycerides (TG) in Finns. We also analyzed the Mexican FCHL families for 26 microsatellite markers residing in the seven chromosomal regions on 2p25.1, 9p23, 10q11.23, 11q13, 16q24.1, 19q13, and 21q21, previously linked to FCHL in whites. METHODS AND RESULTS We genotyped 314 individuals in 24 Mexican families for 13 SNPs spanning an 88-kb region, including USF1. The FCHL and TG traits showed significant evidence for association with 3 SNPs, hCV1459766, rs3737787, and rs2073658, and haplotype analyses further supported these findings (probability values of 0.05 to 0.0009 for SNPs and their haplotypes). Of these SNPs, hCV1459766 is located in the F11 receptor (F11R) gene, located next to USF1, making it difficult to exclude. Importantly, the association was restricted to a considerably smaller region than in the Finns (14 kb versus 46 kb), possibly because of a different underlying linkage disequilibrium structure. In addition, 1 of the 7 regions, 16q24.1, showed suggestive evidence for linkage (a lod score of 2.6) for total cholesterol in Mexicans. CONCLUSIONS This study, the first to extensively investigate the genetic component of the common FCHL disorder in Mexicans, provides independent evidence for the role of USF1 in FCHL in an outbred population and links the 16q24.1 region to an FCHL-component trait in Mexicans.
Collapse
Affiliation(s)
- Adriana Huertas-Vazquez
- Molecular y Medicina Genómica del Instituto de Investigaciones Biomédicas, UNAM, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Söderlund S, Soro-Paavonen A, Ehnholm C, Jauhiainen M, Taskinen MR. Hypertriglyceridemia is associated with preβ-HDL concentrations in subjects with familial low HDL. J Lipid Res 2005; 46:1643-51. [PMID: 15897606 DOI: 10.1194/jlr.m400480-jlr200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prebeta-HDL particles act as the primary acceptors of cellular cholesterol in reverse cholesterol transport (RCT). An impairment of RCT may be the reason for the increased risk of coronary heart disease (CHD) in subjects with familial low HDL. We studied the levels of serum prebeta-HDL and the major regulating factors of HDL metabolism in 67 subjects with familial low HDL and in 64 normolipidemic subjects. We report that the subjects with familial low HDL had markedly reduced prebeta-HDL concentrations compared with the normolipidemic subjects (17.4 +/- 7.2 vs. 23.4 +/- 7.8 mg apolipoprotein A-I/dl; P < 0.001). A positive correlation was observed between prebeta-HDL concentration and serum triglyceride (TG) level (r = 0.334, P = 0.006). In addition, serum TG level was found to be the strongest predictor of prebeta-HDL concentration in subjects with familial low HDL. The activities of cholesteryl ester transfer protein and hepatic lipase were markedly increased in subjects with familial low HDL without a significant correlation to prebeta-HDL concentration. Our results support the hypothesis that impaired RCT is one mechanism behind the increased risk for CHD in subjects with familial low HDL.
Collapse
Affiliation(s)
- Sanni Söderlund
- Division of Cardiology, Department of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | | | |
Collapse
|
47
|
|
48
|
Turner ST, Peyser PA, Kardia SLR, Bielak LF, Sheedy PF, Boerwinkle E, de Andrade M. Genomic loci with pleiotropic effects on coronary artery calcification. Atherosclerosis 2005; 185:340-6. [PMID: 16054150 DOI: 10.1016/j.atherosclerosis.2005.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 06/03/2005] [Accepted: 06/07/2005] [Indexed: 11/26/2022]
Abstract
We measured 381 genomewide markers and performed genetic linkage analyses in search of loci influencing coronary artery calcification (CAC), a measure of atherosclerosis determined by electron beam computed tomography, in 948 non-Hispanic white siblings (mean age [+/-standard deviation] = 59.6 +/- 9.9 years; 73.7% hypertensive). Measured risk factors for atherosclerosis included body mass index, pulse pressure, and high-density lipoprotein (HDL)-cholesterol. After adjustment for sex and age, the logarithm transformed measure of CAC was heritable (0.40 +/- 0.08, P < 0.0001) and genetically correlated with body mass index (0.28, P < 0.001), pulse pressure (0.36, P < 0.001), and HDL-cholesterol (-0.19, P < 0.001). Univariate linkage analysis demonstrated evidence of linkage for CAC, defined by maximum LOD scores (MLS) >or= 1.30, on chromosomes 1p, 4p, 5q, 7p, 13q, and 14q. Bivariate linkage analyses of CAC with each risk factor provided evidence of two regions with pleiotropic effects on CAC and HDL-cholesterol on chromosomes 4p16 (MLS=3.03, P = 0.00084) and 9q12 (MLS = 3.21, P = 0.00056), and of a region with pleiotropic effects on CAC and body mass index on chromosome 17p11 (MLS = 3.04, P = 0.00082). Inasmuch as the chromosome 9 and 17 regions were not detected in the univariate linkage analysis for CAC, multivariate linkage analyses of CAC and genetically correlated risk factors may help localize genes for coronary atherosclerosis.
Collapse
Affiliation(s)
- Stephen T Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
| | | | | | | | | | | | | |
Collapse
|
49
|
Gagnon F, Jarvik GP, Badzioch MD, Motulsky AG, Brunzell JD, Wijsman EM. Genome scan for quantitative trait loci influencing HDL levels: evidence for multilocus inheritance in familial combined hyperlipidemia. Hum Genet 2005; 117:494-505. [PMID: 15959807 DOI: 10.1007/s00439-005-1338-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Accepted: 04/27/2005] [Indexed: 11/25/2022]
Abstract
Several genome scans in search of high-density lipoprotein (HDL) quantitative trait loci (QTLs) have been performed. However, to date the actual identification of genes implicated in the regulation of common forms of HDL abnormalities remains unsuccessful. This may be due, in part, to the oligogenic and multivariate nature of HDL regulation, and potentially, pleiotropy affecting HDL and other lipid-related traits. Using a Bayesian Markov Chain Monte Carlo (MCMC) approach, we recently provided evidence of linkage of HDL level variation to the APOA1-C3-A4-A5 gene complex, in familial combined hyperlipidemia pedigrees, with an estimated number of two to three large QTLs remaining to be identified. We also presented results consistent with pleiotropy affecting HDL and triglycerides at the APOA1-C3-A4-A5 gene complex. Here we use the same MCMC analytic strategy, which allows for oligogenic trait models, as well as simultaneous incorporation of covariates, in the context of multipoint analysis. We now present results from a genome scan in search for the additional HDL QTLs in these pedigrees. We provide evidence of linkage for additional HDL QTLs on chromosomes 3p14 and 13q32, with results on chromosome 3 further supported by maximum parametric and variance component LOD scores of 3.0 and 2.6, respectively. Weaker evidence of linkage was also obtained for 7q32, 12q12, 14q31-32 and 16q23-24.
Collapse
Affiliation(s)
- France Gagnon
- Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
50
|
Dong C, Li WD, Li D, Price RA. Interaction between obesity-susceptibility loci in chromosome regions 2p25-p24 and 13q13-q21. Eur J Hum Genet 2005; 13:102-8. [PMID: 15470360 DOI: 10.1038/sj.ejhg.5201292] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
One of the chief complexities of genetic influences on human obesity appears to be gene-gene interactions. Here, we employed model-free approaches to look for gene-gene interaction effects in human obesity using genome scan data from 260 European American families. We found consistent evidence for statistical interaction between 2p25-p24 (18-38 cM) and 13q13-q21 (26-47 cM). For discrete traits, the positive correlations were significant at P<0.0001 (P</=0.0023 after correction for multiple tests) in both IBD-based and NPL-based analyses for BMI>/=40 kg/m(2). Other analytic approaches gave consistent, supportive results. For quantitative traits, interaction effects were significant for BMI (P=0.0012), percent fat (P=0.0265) and waist circumference (P=0.0023) in a Haseman-Elston regression model, and for BMI (P=0.0043) in variance component analysis. Our findings suggest that obesity-susceptibility loci in chromosome regions 2p25-p24 and 13q13-21 may interact to influence extreme human obesity. The identification of gene-gene interactions may prove crucial to understanding the contributions of genes, which, by themselves, have relatively small effects on obesity susceptibility and resistance.
Collapse
Affiliation(s)
- Chuanhui Dong
- Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | |
Collapse
|