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Nikkola E, Ko A, Alvarez M, Cantor RM, Garske K, Kim E, Gee S, Rodriguez A, Muxel R, Matikainen N, Söderlund S, Motazacker MM, Borén J, Lamina C, Kronenberg F, Schneider WJ, Palotie A, Laakso M, Taskinen MR, Pajukanta P. Family-specific aggregation of lipid GWAS variants confers the susceptibility to familial hypercholesterolemia in a large Austrian family. Atherosclerosis 2017; 264:58-66. [PMID: 28772107 DOI: 10.1016/j.atherosclerosis.2017.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/27/2017] [Accepted: 07/21/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS Hypercholesterolemia confers susceptibility to cardiovascular disease (CVD). Both serum total cholesterol (TC) and LDL-cholesterol (LDL-C) exhibit a strong genetic component (heritability estimates 0.41-0.50). However, a large part of this heritability cannot be explained by the variants identified in recent extensive genome-wide association studies (GWAS) on lipids. Our aim was to find genetic causes leading to high LDL-C levels and ultimately CVD in a large Austrian family presenting with what appears to be autosomal dominant inheritance for familial hypercholesterolemia (FH). METHODS We utilized linkage analysis followed by whole-exome sequencing and genetic risk score analysis using an Austrian multi-generational family with various dyslipidemias, including elevated TC and LDL-C, and one family branch with elevated lipoprotein (a) (Lp(a)). RESULTS We did not find evidence for genome-wide significant linkage for LDL-C or apparent causative variants in the known FH genes rather, we discovered a particular family-specific combination of nine GWAS LDL-C SNPs (p = 0.02 by permutation), and putative less severe familial hypercholesterolemia mutations in the LDLR and APOB genes in a subset of the affected family members. Separately, high Lp(a) levels observed in one branch of the family were explained primarily by the LPA locus, including short (<23) Kringle IV repeats and rs3798220. CONCLUSIONS Taken together, some forms of FH may be explained by family-specific combinations of LDL-C GWAS SNPs.
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Affiliation(s)
- Elina Nikkola
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Arthur Ko
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA; Molecular Biology Institute at UCLA, Los Angeles, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Rita M Cantor
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Kristina Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Elliot Kim
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Stephanie Gee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Alejandra Rodriguez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | | | - Niina Matikainen
- Endocrinology, Abdominal Centre, Helsinki University Hospital, Finland; Heart and Lung Center, Helsinki University Hospital, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Finland
| | - Sanni Söderlund
- Heart and Lung Center, Helsinki University Hospital, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Finland
| | - Mahdi M Motazacker
- Department of Clinical Genetics, Academic Medical Center at the University of Amsterdam, The Netherlands
| | - Jan Borén
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, University of Gothenburg and Sahlgrenska University Hospital, Sweden
| | - Claudia Lamina
- Division of Genetic Epidemiology, Medical University of Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Medical University of Innsbruck, Austria
| | - Wolfgang J Schneider
- Department Medical Biochemistry, Medical University Vienna and Max F. Perutz Laboratories, Austria
| | - Aarno Palotie
- Institute for Molecular Medicine, University of Helsinki, Finland; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital, Boston, MA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Marja-Riitta Taskinen
- Heart and Lung Center, Helsinki University Hospital, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA; Molecular Biology Institute at UCLA, Los Angeles, USA; Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA.
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Brænne I, Kleinecke M, Reiz B, Graf E, Strom T, Wieland T, Fischer M, Kessler T, Hengstenberg C, Meitinger T, Erdmann J, Schunkert H. Systematic analysis of variants related to familial hypercholesterolemia in families with premature myocardial infarction. Eur J Hum Genet 2015; 24:191-7. [PMID: 26036859 DOI: 10.1038/ejhg.2015.100] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/02/2015] [Accepted: 04/17/2015] [Indexed: 01/16/2023] Open
Abstract
Familial hypercholesterolemia (FH) is an oligogenic disorder characterized by markedly elevated low-density lipoprotein cholesterol (LDLC) levels. Variants in four genes have been reported to cause the classical autosomal-dominant form of the disease. FH is largely under-diagnosed in European countries. As FH increases the risk for coronary artery disease (CAD) and myocardial infarction (MI), it might be specifically overlooked in the large number of such patients. Here, we systematically examined the frequency of potential FH-causing variants by exome sequencing in 255 German patients with premature MI and a positive family history for CAD. We further performed co-segregation analyses in an average of 5.5 family members per MI patient. In total, we identified 11 potential disease-causing variants that co-segregate within the families, that is, 5% of patients with premature MI and positive CAD family history had FH. Eight variants were previously reported as disease-causing and three are novel (LDLR.c.811G>A p.(V271I)), PCSK9.c.610G>A (p.(D204N)) and STAP1.c.139A>G (p.(T47A))). Co-segregation analyses identified multiple additional family members carrying one of these FH variants and the clinical phenotype of either FH (n=2) or FH and premature CAD (n=15). However, exome sequencing also revealed that some variants in FH genes, which have been reported to cause FH, do not co-segregate with FH. The data reveal that a large proportion of FH patients escape the diagnosis, even when they have premature MI. Hence, systematic molecular-genetic screening for FH in such patients may reveal a substantial number of cases and thereby allow a timely LDLC-lowering in both FH/MI patients as well as their variant-carrying family members.
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Affiliation(s)
- Ingrid Brænne
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Mariana Kleinecke
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Benedikt Reiz
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marcus Fischer
- Klinik und Poliklinik für Innere Medizin II, Universitätsklinikum Regensburg, Regensburg, Germany
| | - Thorsten Kessler
- Deutsches Herzzentrum München, Technische Universität München, München, Germany
| | - Christian Hengstenberg
- Deutsches Herzzentrum München, Technische Universität München, München, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Jeanette Erdmann
- Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, München, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
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3
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Jeenduang N, Porntadavity S, von Nickisch-Rosenegk M, Bier FF, Promptmas C. Two-dye based arrayed primer extension for simultaneous multigene detection in lipid metabolism. Clin Chim Acta 2015; 442:36-43. [PMID: 25591965 DOI: 10.1016/j.cca.2015.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 01/24/2023]
Abstract
BACKGROUND Cardiovascular disease (CVD) is one of the major causes of death worldwide. Numerous genetic risk factors in lipid metabolism, including mutations of LDLR, APOB, and PCSK9, as well as polymorphisms of CETP and APOE, have been found to associate with CVD. METHODS In this study, a two-dye based arrayed primer extension (APEX) microarray assay for simultaneous multigene (LDLR, APOB, PCSK9, CETP, and APOE) detection was developed. The DNA templates, originating from 1 DNA sample of known genotype and 7 blind DNA samples, were amplified by uniplex PCR. RESULTS Optimized conditions for the APEX reaction were determined to include a hybridization temperature of 55°C and a DNA template size of 50-150bp. The total assay including PCR, purification, fragmentation, APEX reaction, and image analysis could be performed in 6h. In total, 48 genotypes were identified among 8 individual DNA samples by APEX analysis. CONCLUSIONS The data suggest that this APEX microarray offers a robust, fast, and versatile option for screening these genotypes in hypercholesterolemia patients.
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Affiliation(s)
- Nutjaree Jeenduang
- School of Allied Health Science and Public Health, Walailak University, Nakhon Si Thammarat 80161, Thailand; Department of Nanobiotechnology and Nanomedicine, Fraunhofer Institute for Biomedical Engineering (IBMT), Potsdam-Golm 14476, Germany
| | - Sureerut Porntadavity
- Department of Clinical Chemistry, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Markus von Nickisch-Rosenegk
- Department of Nanobiotechnology and Nanomedicine, Fraunhofer Institute for Biomedical Engineering (IBMT), Potsdam-Golm 14476, Germany
| | - Frank F Bier
- Department of Nanobiotechnology and Nanomedicine, Fraunhofer Institute for Biomedical Engineering (IBMT), Potsdam-Golm 14476, Germany
| | - Chamras Promptmas
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom 73170, Thailand.
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Alharbi KK, Hou G, Chen XH, Gaunt TR, Syddall HE, Sayer AA, Dennison EM, Phillips DIW, Cooper C, Day INM. Population mutation scanning of human GHR by meltMADGE and identification of a paucimorphic variant. Genet Test Mol Biomarkers 2011; 15:855-60. [PMID: 21689014 DOI: 10.1089/gtmb.2011.0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Current studies of human genetic diversity are focused in two areas: first, detection of rare mutations in highly selected clinical cases; and second, in common single-nucleotide polymorphism (SNP) and haplotype effects in the general population. Less frequent SNPs and "paucimorphisms" remain underexplored, although lower frequency coding SNPs are more likely to have functional impact. We have developed a cost-efficient mutation scanning technology, meltMADGE, for population mutation scanning. Previous research in GHR has explored its role in extreme (-3 SD) growth retardation and, subsequently, "moderate" (-2 SD) growth retardation cases. Here, we describe meltMADGE assays for the entire coding region of GHR. As a first step we have established long polymerase chain reaction subbanks for GHR from 2423 unselected subjects and have applied meltMADGE scanning assays of exons 4 and 5 to these subbanks. A novel paucimorphism present at 439+30A>C (allele frequency: 0.0021) in intron 5 (location chr5:42,695,221 in GRCh37/hg19) was identified in 10 individuals, confirmed by sequencing and analysis made for major phenotypic effects. This approach is relevant to the deep sampling of populations for less frequent sequence diversity, some of which is expected to exert significant phenotypic effects.
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Affiliation(s)
- Khalid K Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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Izar MC, Machado VA, Fonseca FA. Genetic screening for homozygous and heterozygous familial hypercholesterolemia. Appl Clin Genet 2010; 3:147-57. [PMID: 23776359 PMCID: PMC3681171 DOI: 10.2147/tacg.s13490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Familial hypercholesterolemia (FH) is a common inherited disorder that results in premature atherosclerosis. Diagnosis of FH is suspected on the basis of clinical criteria, but confirmation requires genetic testing. In the era of statins, early diagnosis and initiation of treatment can modify disease progression and outcomes. Therefore, cascade screening with a combination of lipid concentration measurements and DNA testing should be used to identify relatives of index cases with a clinical diagnosis of FH. Autosomal dominant FH is related to mutations in the low-density lipoprotein receptor (LDLR), apolipoprotein B-100 (APOB), or proprotein convertase subtilisin/kexin type 9 (PCSK9) genes. Genetic screening of the LDLR gene is challenging to achieve at a feasible cost, especially in people who do not have a founder effect. Nucleotide sequencing of all exons and flanking splicing regions in combination with multiplex ligation probe amplification to detect large insertions or deletions is considered the gold-standard approach to screen for LDLR mutations. Alternatively, the cDNA can be sequenced; however, this procedure is not suitable for use in large populations, because of the need of RNA extraction. Multiplex analysis can be appropriate for population with founder effects or a low number of different mutations. Finally, there are many techniques for a mutation scanning approach, which have some benefits over sequencing, and also with the potential for detecting known and novel mutations. Familial defective Apo B is amenable to genetic diagnosis by screening for a few mutations. Recently, gain-of-function mutations in PCSK9 gene have been demonstrated to cause FH phenotype. Strategies for population screening, cost-effectiveness of genetic screening, ethical aspects, and insurance policies are discussed and need implementation worldwide.
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Affiliation(s)
- Maria C Izar
- Cardiology Division, Department of Medicine, Federal University of São Paulo, UNIFESP, São Paulo, SP, Brazil
| | - Valéria A Machado
- Cardiology Division, Department of Medicine, Federal University of São Paulo, UNIFESP, São Paulo, SP, Brazil
| | - Francisco A Fonseca
- Cardiology Division, Department of Medicine, Federal University of São Paulo, UNIFESP, São Paulo, SP, Brazil
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6
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Alharbi KK, Aldahmesh MA, Gaunt TR, Rassoulian H, Guthrie PAI, Rodriguez S, Boustred CR, Spanakis E, Day INM. MeltMADGE for mutation scanning of specific genes in population studies. Nat Protoc 2010; 5:1800-12. [PMID: 21030955 PMCID: PMC3575632 DOI: 10.1038/nprot.2010.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MeltMADGE reconfigures the mutation scanning process of denaturing gradient gel electrophoresis so that the independent variable is time rather than space and the dependent (denaturing) variable is temperature rather than concentration of chemical denaturant. Use of a thermal ramp enables the use of a homogeneous gel and therefore of high-density arrays of wells such as those of microplate array diagonal gel electrophoresis (MADGE). In this configuration, electrophoresis of products on 10-12 96-well meltMADGE gels can be conducted in a 1- to 2-liter tank in a 1- to 2-h run, enabling the scanning of a target amplicon in over 1,000 subjects simultaneously. Gels are read by imaging the fluorescence of UV-excited ethidium bromide, giving a simple, economical system for identifying rarer sequence variants in target genes; it is suitable for large-scale case-control or population studies and other comparable applications. Different amplicons with similar melting characteristics can also be combined in the same run.
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Affiliation(s)
- Khalid K Alharbi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, P.O.Box 10219, Riyadh 11433, Saudi Arabia
| | - Mohammed A Aldahmesh
- Developmental Genetics Unit, Research Centre, King Faisal Specialist Hospital P.O.Box 3354, MBC 03, Riyadh 11211 Saudi Arabia
| | - Tom R Gaunt
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Hamid Rassoulian
- Medical Physics & Clinical Engineering, Nottingham University Hospitals NHS Trust, Queens Medical Centre, West Block, Floor-A, Derby Road, Nottingham, NG7 2UH, United Kingdom
| | - Philip AI Guthrie
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Santiago Rodriguez
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Christopher R Boustred
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Emmanuel Spanakis
- Sanofi-Aventis R&D, Biologics Dept - Stem Cells, 13 quai Jules Guesde, F-94403 VITRY-SUR-SEINE, France
| | - Ian NM Day
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
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7
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Haplotype analyses, mechanism and evolution of common double mutants in the human LDL receptor gene. Mol Genet Genomics 2010; 283:565-74. [PMID: 20428891 DOI: 10.1007/s00438-010-0541-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 04/07/2010] [Indexed: 12/15/2022]
Abstract
Familial hypercholesterolemia (FH), an autosomal dominant inherited disorder resulting in increased levels of circulating plasma low-density lipoprotein (LDL), tendon xanthomas and premature coronary artery disease (CAD), is caused by defects in the LDL receptor gene (LDLR). Three widespread LDLR alterations not causing FH (c.1061-8T>C, c.2177C>T and c.829G>A) and one mutation (c.12G>A) with narrow geographical distribution and thought to cause disease were investigated. In an attempt to improve knowledge on their origin, spread and possible selective effects, estimations of the ages of these variants (t generations) and haplotype analysis were performed by genotyping 86 healthy individuals and 98 FH patients in Spain for five LDLR SNPs: c.81T>C, c.1413G>A, c.1725C>T, c.1959T>C, and c.2232G>A; most patients carried two of these LDLR variants simultaneously. It was found that both the c.1061-8T>C (t = 54) and c.2177C>T alterations (t = 62) arose at about the same time (54 and 62 generations ago, respectively) in the CGCTG haplotype, while the c.12G>A mutation (t = 70) appeared in a CGCCG haplotype carrying an earlier c.829G>A alteration (t = 83). The estimated ages of selectively neutral alterations could explain their distribution by migrations. The origin of the c.12G>A mutation could be in the Iberian Peninsula; despite its estimated age, a low selective pressure could explain its conservation in Spain from where it could have spread to China and Mexico, since the sixteenth century through the Spanish/Portuguese colonial expeditions.
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Abstract
dbSNP is a general catalog of genetic polymorphism maintained by NCBI, mainly collating information for single nucleotide variations, many of which will be single nucleotide polymorphisms (SNPs), but also including small indels. It takes submissions from many sources, now also including large numbers of sequence variants identified by next-generation sequencing. A number of differently designed studies have attempted to estimate the error rates in data archived in dbSNP. Most recently, a study added to earlier studies identifying specific issues for duplicons and copy number variations (CNVs); earlier analyses have focused on stop codons, splice sites, and the general content of dbSNP. This article overviews dbSNP itself, these studies, and their implications.
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Affiliation(s)
- Ian N M Day
- MRC Centre (CAiTE) and Bristol Genetic Epidemiology Laboratories, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
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9
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A novel splice site mutation of the LDL receptor gene in a Tunisian hypercholesterolemic family. Clin Chim Acta 2008; 392:25-9. [DOI: 10.1016/j.cca.2008.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 02/21/2008] [Accepted: 02/22/2008] [Indexed: 11/23/2022]
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10
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A novel mutation of the apolipoprotein A-I gene in a family with familial combined hyperlipidemia. Atherosclerosis 2008; 198:145-51. [DOI: 10.1016/j.atherosclerosis.2007.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 09/01/2007] [Accepted: 09/06/2007] [Indexed: 11/21/2022]
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Glynou K, Laios E, Drogari E, Tsaoussis V. Development of a universal chemiluminometric genotyping method for high-throughput detection of 7 LDLR gene mutations in Greek population. Clin Biochem 2008; 41:335-42. [PMID: 18206115 DOI: 10.1016/j.clinbiochem.2007.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 12/12/2007] [Accepted: 12/12/2007] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Familial hypercholesterolemia (FH) is caused by mutations in the LDL receptor (LDLR) gene. We report the application of a universal method with high allele discrimination properties to the simultaneous genotyping of 7 LDLR mutations in Greeks, in dry-reagent format. DESIGN AND METHODS We genotyped mutations C858A, C939A, G1285A, T1352C, G1646A, G1775A, C/T81G. Unpurified amplicons from a multiplex PCR that produced fragments encompassing all 7 mutations were subjected to probe extension reactions in the presence of fluorescein-modified dCTP, and a microtiter well-based assay of extension products with a peroxidase-antifluorescein conjugate and a chemiluminogenic substrate. We used lyophilized dry reagents and assigned genotypes by the signal ratio of normal-to-mutant-specific probe. RESULTS We standardized the method and optimised all steps for specificity. The method was validated by genotyping blindly 119 (833 genotypings). Results were fully concordant with other methods used as standards. CONCLUSIONS This method is accurate, simple, rapid and robust. The microtiter well format allows genotyping of a large number of samples in parallel for several mutations.
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12
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Gaunt TR, Rodríguez S, Day IN. Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'. BMC Bioinformatics 2007; 8:428. [PMID: 17980034 PMCID: PMC2180187 DOI: 10.1186/1471-2105-8-428] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 11/02/2007] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The frequency of a haplotype comprising one allele at each of two loci can be expressed as a cubic equation (the 'Hill equation'), the solution of which gives that frequency. Most haplotype and linkage disequilibrium analysis programs use iteration-based algorithms which substitute an estimate of haplotype frequency into the equation, producing a new estimate which is repeatedly fed back into the equation until the values converge to a maximum likelihood estimate (expectation-maximisation). RESULTS We present a program, "CubeX", which calculates the biologically possible exact solution(s) and provides estimated haplotype frequencies, D', r2 and chi2 values for each. CubeX provides a "complete" analysis of haplotype frequencies and linkage disequilibrium for a pair of biallelic markers under situations where sampling variation and genotyping errors distort sample Hardy-Weinberg equilibrium, potentially causing more than one biologically possible solution. We also present an analysis of simulations and real data using the algebraically exact solution, which indicates that under perfect sample Hardy-Weinberg equilibrium there is only one biologically possible solution, but that under other conditions there may be more. CONCLUSION Our analyses demonstrate that lower allele frequencies, lower sample numbers, population stratification and a possible |D'| value of 1 are particularly susceptible to distortion of sample Hardy-Weinberg equilibrium, which has significant implications for calculation of linkage disequilibrium in small sample sizes (eg HapMap) and rarer alleles (eg paucimorphisms, q < 0.05) that may have particular disease relevance and require improved approaches for meaningful evaluation.
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Affiliation(s)
- Tom R Gaunt
- Bristol Genetic Epidemology Laboratories (BGEL) and MRC Centre for Causal Analyses in Translational Epidemiology (CAiTE), Department of Social Medicine, University of Bristol, Canynge Hall, Whiteladies Road, Bristol, BS8 2PR, UK.
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Rodriguez S, Gaunt TR, Day INM. Molecular genetics of human growth hormone, insulin-like growth factors and their pathways in common disease. Hum Genet 2007; 122:1-21. [PMID: 17534663 DOI: 10.1007/s00439-007-0378-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2006] [Accepted: 05/08/2007] [Indexed: 12/29/2022]
Abstract
The human growth hormone gene (GH1) and the insulin-like growth factor 1 and 2 genes (IGF1 and IGF2) encode the central elements of a key pathway influencing growth in humans. This "growth pathway" also includes transcription factors, agonists, antagonists, receptors, binding proteins, and endocrine factors that constitute an intrincate network of feedback loops. GH1 is evolutionarily coupled with other genes in linkage disequilibrium in 17q24.2, and the same applies to IGF2 in 11p15.5. In contrast, IGF1 in 12q22-24.1 is not in strong linkage disequilibrium with neighbouring genes. Knowledge of the functional architecture of these regions is important for the understanding of the combined evolution and function of GH1, IGF2 and IGF1 in relation to complex diseases. A number of mutations accounting for rare Mendelian disorders have been described in GH-IGF elements. The constellation of genes in this key pathway contains potential candidates in a number of complex diseases, including growth disorders, metabolic syndrome, diabetes (notably IGF2BP2) cardiovascular disease, and central nervous system diseases, and in longevity, aging and cancer. We review these genes and their associations with disease phenotypes, with special attention to metabolic risk traits.
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Affiliation(s)
- Santiago Rodriguez
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology (CAiTE), Department of Social Medicine, University of Bristol, Canynge Hall, Whiteladies Road, Bristol, BS8 2PR, UK.
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14
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Alharbi KK, Spanakis E, Tan K, Smith MJ, Aldahmesh MA, O'Dell SD, Sayer AA, Lawlor DA, Ebrahim S, Davey Smith G, O'Rahilly S, Farooqi S, Cooper C, Phillips DIW, Day INM. Prevalence and functionality of paucimorphic and privateMC4Rmutations in a large, unselected European British population, scanned by meltMADGE. Hum Mutat 2007; 28:294-302. [PMID: 17072869 DOI: 10.1002/humu.20404] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identification of unknown mutations has remained laborious, expensive, and only viable for studies of selected cases. Population-based "reference ranges" of rarer sequence diversity are not available. However, the research and diagnostic interpretation of sequence variants depends on such information. Additionally, this is the only way to determine prevalence of severe, moderate, and silent mutations and is also relevant to the development of screening programs. We previously described a system, meltMADGE, suitable for mutation scanning at the population level. Here we describe its application to a population-based study of MC4R (melanocortin 4 receptor) mutations, which are associated with obesity. We developed nine assays representing MC4R and examined a population sample of 1,100 subjects. Two "paucimorphisms" were identified (c.307G>A/p.Val103Ile in 27 subjects and c.-178A>C in 22 subjects). Neither exhibited any anthropometric effects, whereas there would have been >90% power to detect a body mass index (BMI) effect of 0.5 kg/m(2) at P=0.01. Two "private" variants were also identified. c.335C>T/p.Thr112Met has been previously described and appears to be silent. A novel variant, c.260C>A/p.Ala87Asp, was observed in a subject with a BMI of 31.5 kg/m(2) (i.e., clinically obese) but not on direct assay of a further 3,525 subjects. This mutation was predicted to be deleterious and analysis using a cyclic AMP (cAMP) responsive luciferase reporter assay showed substantial loss of function of the mutant receptor. This population-based mutation scan of MC4R suggests that there is no severe MC4R mutation with high prevalence in the United Kingdom, but that obesity-causing MC4R mutation at 1 in 1,100 might represent one of the commonest autosomal dominant disorders in man.
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Affiliation(s)
- Khalid K Alharbi
- Human Genetics Division, School of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
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Laios E, Drogari E. Analysis of LDLR mutations in familial hypercholesterolemia patients in Greece by use of the NanoChip® Microelectronic Array Technology. Clin Chim Acta 2006; 374:93-9. [PMID: 16828076 DOI: 10.1016/j.cca.2006.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 05/26/2006] [Accepted: 05/26/2006] [Indexed: 01/24/2023]
Abstract
BACKGROUND Three mutations in the low density lipoprotein receptor (LDLR) gene account for 49% of familial hypercholesterolemia (FH) cases in Greece. METHODS We used the microelectronic array technology of the NanoChip Molecular Biology Workstation to develop a multiplex method to analyze these single-nucleotide polymorphisms (SNPs). Primer pairs amplified the region encompassing each SNP. The biotinylated PCR amplicon was electronically addressed to streptavidin-coated microarray sites. Allele-specific fluorescently labeled oligonucleotide reporters were designed and used for detection of wild-type and SNP sequences. Genotypes were compared to PCR-restriction fragment length polymorphism (PCR-RFLP). RESULTS We developed three monoplex assays (1 SNP/site) and an optimized multiplex assay (3SNPs/site). We performed 92 Greece II, 100 Genoa, and 98 Afrikaner-2 NanoChip monoplex assays (addressed to duplicate sites and analyzed separately). Of the 580 monoplex genotypings (290 samples), 579 agreed with RFLP. Duplicate sites of one sample were not in agreement with each other. Of the 580 multiplex genotypings, 576 agreed with the monoplex results. Duplicate sites of three samples were not in agreement with each other, indicating requirement for repetition upon which discrepancies were resolved. CONCLUSIONS The multiplex assay detects common LDLR mutations in Greek FH patients and can be extended to accommodate additional mutations.
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Affiliation(s)
- Eleftheria Laios
- Unit on Metabolic Diseases, Choremio Research Laboratory, University of Athens, 1st Department of Pediatrics, Aghia Sophia Children's Hospital, Athens 11527, Greece.
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Graham CA, Wright WT, McIlhatton BP, Young IS, Nicholls DP. The LDLR variant T705I does not cause the typical phenotype of familial hypercholesterolaemia. Atherosclerosis 2006; 188:218-9. [PMID: 16735037 DOI: 10.1016/j.atherosclerosis.2006.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 04/07/2006] [Indexed: 11/22/2022]
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Comai L, Henikoff S. TILLING: practical single-nucleotide mutation discovery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 45:684-94. [PMID: 16441355 DOI: 10.1111/j.1365-313x.2006.02670.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In the post-genomic sequencing era, an expanding portfolio of genomic technologies has been applied to the study of gene function. Reverse genetics approaches that provide targeted inactivation of genes identified by sequence analysis include TILLING (for Targeting Local Lesions IN Genomes). TILLING searches the genomes of mutagenized organisms for mutations in a chosen gene, typically single base-pair substitutions. This review covers practical aspects of the technology, ranging from building the mutagenized population to mutation discovery, and discusses possible improvements to current protocols and the impact of new genomic methods for mutation discovery in relation to the future of the TILLING approach.
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Affiliation(s)
- Luca Comai
- Department of Biology, Box 355325, University of Washington, Seattle, WA 98195, USA.
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