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Abstract
Parasites still impose a high death and disability burden on human populations, and are therefore likely to act as selective factors for genetic adaptations. Genetic epidemiological investigation of parasitic diseases is aimed at disentangling the mechanisms underlying immunity and pathogenesis by looking for associations or linkages between loci and susceptibility phenotypes. Until recently, most studies used a candidate gene approach and were relatively underpowered, with few attempts at replicating findings in different populations. However, in the last 5 years, genome-wide and/or multicentre studies have been conducted for severe malaria, visceral leishmaniasis, and cardiac Chagas disease, providing some novel important insights. Furthermore, studies of helminth infections have repeatedly shown the involvement of common loci in regulating susceptibility to distinct diseases such as schistosomiasis, ascariasis, trichuriasis, and onchocherciasis. As more studies are conducted, evidence is increasing that at least some of the identified susceptibility loci are shared not only among parasitic diseases but also with immunological disorders such as allergy or autoimmune disease, suggesting that parasites may have played a role in driving the evolution of the immune system.
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Affiliation(s)
- V D Mangano
- Department of Public Health and Infectious Diseases, University of Rome 'La Sapienza', Rome, Italy; Istituto Pasteur, Fondazione Cenci Bolognetti, University of Rome 'La Sapienza', Rome, Italy
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102
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Paradisi I, De Freitas L, Arias S. Most frequent mutation c.3402delC (p.Ala1135GlnfsX13) among Wilson disease patients in Venezuela has a wide distribution and two old origins. Eur J Med Genet 2014; 58:59-65. [PMID: 25497208 DOI: 10.1016/j.ejmg.2014.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 12/04/2014] [Indexed: 01/09/2023]
Abstract
Wilson disease is an infrequent autosomal recessive disorder caused by mutations in the ATP7B gene (13q14.3) producing pathologic phenotypes due to copper accumulation in critical tissues. The aim of the research was to probe Wilson disease genetic epidemiology in Venezuela, through the identification in diagnosed index cases, of ATP7B locus mutations, their geographic distribution, frequency, in-phase haplotypes and probable ethnic ancestry. During the last three decades 33 independent Wilson disease families from the country at large were ascertained and diagnosed through severely reduced ceruloplasmin activity, higher urinary copper excretion, and specific clinical signs. Molecular studies of the ATP7B gene were accomplished in 26 of the families. Disease prevalence was estimated as 1:94,000 families between 1985 and 2013, showing geographic aggregation in the state of Zulia with 1:27,000 families in it. DNA analysis in 26 families revealed 13 different mutations. The c.3402delC was the most frequent one (26.9%), presenting two independent in-phase haplotypes, both of likely European descent; which is followed by the not previously reported p.G691V (9.6%) and by the frequent European H1069Q (7.7%). Known mutations c.51 + 4A > T, c.1285 + 5G > T, M645R, T788I, V845SfsX28, T977M, L1088X, T1220M, R1319X and a novel P767L showed frequencies between 5.8 and 1.9%. Despite the ample mutation heterogeneity for Wilson disease in the country, the findings provide a diagnostic algorithm to ease mutation assessment in new patients; the predominant c.3402delC displayed wide geographic distribution and two genetic origins.
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Affiliation(s)
- Irene Paradisi
- Laboratorio de Genética Humana, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela.
| | - Laura De Freitas
- Laboratorio de Genética Humana, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela; Departamento de Ciencias Fisiológicas, Laboratorio de Genética Molecular, Universidad de Carabobo (UC), Valencia, Venezuela
| | - Sergio Arias
- Laboratorio de Genética Humana, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
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103
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Wu L, Schaid DJ, Sicotte H, Wieben ED, Li H, Petersen GM. Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations. J Med Genet 2014; 52:10-6. [PMID: 25371537 DOI: 10.1136/jmedgenet-2014-102697] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Whole exome sequencing (WES) provides an unprecedented opportunity to identify the potential aetiological role of rare functional variants in human complex diseases. Large-scale collaborations have generated germline WES data on patients with a number of diseases, especially cancer, but less often on healthy controls under the same sequencing procedures. These data can be a valuable resource for identifying new disease susceptibility loci if study designs are appropriately applied. This review describes suggested strategies and technical considerations when focusing on case-only study designs that use WES data in complex disease scenarios. These include variant filtering based on frequency and functionality, gene prioritisation, interrogation of different data types and targeted sequencing validation. We propose that if case-only WES designs were applied in an appropriate manner, new susceptibility genes containing rare variants for human complex diseases can be detected.
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Affiliation(s)
- Lang Wu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
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104
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Abstract
Early observations, candidate gene studies and, more recently, genome-wide association studies have shown that susceptibility to tuberculosis has a host genetic component. Because the value of candidate gene studies has been doubted due to major limitations such as lack of sufficient power and small study groups, lack of reproducibility in independent groups and, often, ambiguous or even contrasting results in attempts of replication, much hope and expectancy has been put on the progress the genome-wide association approach has created. However, much less than initially expected became clear by the results obtained in genome-wide studies, emphasizing the need of increasing sample sizes, e.g. through meta-analyses, and of increasing the density of genetic variants studied across the human genome. A further reason why a rather low number of associated genetic variants were identified to date in infectious diseases in general and tuberculosis in particular might be the fact that selection acts strongly in diseases that affect the reproductive success. As in most genome-wide association studies performed so far, significant signals, often most likely surrogate marker only, have been found in non-coding regions of genomes, the identification of truly causative genetic variation and of the functionality of associated factors needs urgent attention. In the following we briefly discuss genetic studies in tuberculosis and describe new technologies that are currently employed in the search for responsible genetic elements involved in tuberculosis susceptibility.
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Affiliation(s)
- Christian G Meyer
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Thorsten Thye
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
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105
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Abstract
'Isolated' populations did not exist unproblematically for life scientists to study. This article examines the practical and conceptual labour, and the historical contingencies that rendered populations legible as 'isolates' for population geneticists. Though a standard historiographical narrative tells us that population geneticists were moving from typological understandings of biological variation to processual ones, cultural variation was understood as vulnerable to homogenisation. I chart the importance that D. Carleton Gajdusek placed on isolates from his promotion of genetic epidemiology in WHO technical reports and at a Cold Spring Harbour symposium to his fieldwork routines and collection practices in a group of South Pacific islands. His fieldwork techniques combined social, cultural and historical knowledge of the research subjects in order to isolate biological descent using genealogies. Having isolated a population, Gajdusek incorporated biological materials derived from that population into broad categories of 'Melanesian' and 'race' to generate statements about the genetics of abnormal haemoglobins and malaria. Alongside an analysis of Gajdusek's practices, I present different narratives of descent, kinship and identities learned during my ethnographic work in Vanuatu. These alternatives show tacit decisions made pertaining to scale in the production of 'isolates'.
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Affiliation(s)
- Alexandra Widmer
- Department of Anthropology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.
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106
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Li A, Meyre D. Jumping on the Train of Personalized Medicine: A Primer for Non-Geneticist Clinicians: Part 2. Fundamental Concepts in Genetic Epidemiology. ACTA ACUST UNITED AC 2014; 10:101-117. [PMID: 25598767 PMCID: PMC4287874 DOI: 10.2174/1573400510666140319235334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 02/07/2014] [Accepted: 04/18/2014] [Indexed: 12/12/2022]
Abstract
With the decrease in sequencing costs, personalized genome sequencing will eventually become common in medical practice. We therefore write this series of three reviews to help non-geneticist clinicians to jump into the fast-moving field of personalized medicine. In the first article of this series, we reviewed the fundamental concepts in molecular genetics. In this second article, we cover the key concepts and methods in genetic epidemiology including the classification of genetic disorders, study designs and their implementation, genetic marker selection, genotyping and sequencing technologies, gene identification strategies, data analyses and data interpretation. This review will help the reader critically appraise a genetic association study. In the next article, we will discuss the clinical applications of genetic epidemiology in the personalized medicine area.
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Affiliation(s)
- Aihua Li
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON L8N 3Z5, Canada
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107
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Ramos YFM, Metrustry S, Arden N, Bay-Jensen AC, Beekman M, de Craen AJM, Cupples LA, Esko T, Evangelou E, Felson DT, Hart DJ, Ioannidis JPA, Karsdal M, Kloppenburg M, Lafeber F, Metspalu A, Panoutsopoulou K, Slagboom PE, Spector TD, van Spil EWE, Uitterlinden AG, Zhu Y, Valdes AM, van Meurs JBJ, Meulenbelt I. Meta-analysis identifies loci affecting levels of the potential osteoarthritis biomarkers sCOMP and uCTX-II with genome wide significance. J Med Genet 2014; 51:596-604. [PMID: 25057126 DOI: 10.1136/jmedgenet-2014-102478] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Research for the use of biomarkers in osteoarthritis (OA) is promising, however, adequate discrimination between patients and controls may be hampered due to innate differences. We set out to identify loci influencing levels of serum cartilage oligomeric protein (sCOMP) and urinary C-telopeptide of type II collagen (uCTX-II). METHODS Meta-analysis of genome-wide association studies was applied to standardised residuals of sCOMP (N=3316) and uCTX-II (N=4654) levels available in 6 and 7 studies, respectively, from TreatOA. Effects were estimated using a fixed-effects model. Six promising signals were followed up by de novo genotyping in the Cohort Hip and Cohort Knee study (N = 964). Subsequently, their role in OA susceptibility was investigated in large-scale genome-wide association studies meta-analyses for OA. Differential expression of annotated genes was assessed in cartilage. RESULTS Genome-wide significant association with sCOMP levels was found for a SNP within MRC1 (rs691461, p = 1.7 × 10(-12)) and a SNP within CSMD1 associated with variation in uCTX-II levels with borderline genome-wide significance (rs1983474, p = 8.5 × 10(-8)). Indication for association with sCOMP levels was also found for a locus close to the COMP gene itself (rs10038, p = 7.1 × 10(-6)). The latter SNP was subsequently found to be associated with hip OA whereas COMP expression appeared responsive to the OA pathophysiology in cartilage. CONCLUSIONS We have identified genetic loci affecting either uCTX-II or sCOMP levels. The genome wide significant association of MRC1 with sCOMP levels was found likely to act independent of OA subtypes. Increased sensitivity of biomarkers with OA may be accomplished by taking genetic variation into account.
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Affiliation(s)
- Yolande F M Ramos
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands
| | - Sarah Metrustry
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Nigel Arden
- NIHR Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UK Arthritis Research UK, Sport, Exercise and Osteoarthritis Centre of Excellence, London, UK
| | | | - Marian Beekman
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands
| | - Anton J M de Craen
- Department of Gerontology and Geriatrics, LUMC, Leiden, The Netherlands The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA The Framingham Heart Study, Framingham, Massachusetts, USA
| | - Tõnu Esko
- Institute of Molecular and Cell Biology and Estonian Genome Center, University of Tartu, Tartu, Estonia Department of Endocrinology, Children's Hospital Boston, Boston, Massachusetts, USA Broad Institute, Cambridge, Massachusetts, USA
| | - Evangelos Evangelou
- Department of Hygiene & Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - David T Felson
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Deborah J Hart
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - John P A Ioannidis
- Department of Hygiene & Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece Department of Medicine, Stanford Prevention Research Center, Stanford, USA Department of Health Research and Policy, Stanford University School of Medicine, Stanford, USA Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, USA
| | - Morten Karsdal
- Department of Rheumatology, Nordic Bioscience, Herlev, Denmark
| | - Margreet Kloppenburg
- Department of Rheumatology & Clinical Epidemiology, LUMC, Leiden, The Netherlands
| | - Floris Lafeber
- Department of Rheumatology & Clinical Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Andres Metspalu
- Institute of Molecular and Cell Biology and Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - P Eline Slagboom
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Erwin W E van Spil
- Department of Rheumatology & Clinical Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Andre G Uitterlinden
- The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Yanyan Zhu
- Global Analytical Science, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | | | | | - Ana M Valdes
- Academic Rheumatology, University of Nottingham, Nottingham, UK
| | - Joyce B J van Meurs
- The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ingrid Meulenbelt
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands The Netherlands Genomics Initiative-Sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, The Netherlands
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108
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Evans DG, Harkness E, Lalloo F, Howell A. Long-term prospective clinical follow-up after BRCA1/2 presymptomatic testing: BRCA2 risks higher than in adjusted retrospective studies. J Med Genet 2014; 51:573-80. [PMID: 25053764 DOI: 10.1136/jmedgenet-2014-102336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND The risks of breast cancer associated with BRCA1 and BRCA2 mutations vary considerably across studies but few have assessed prospective risks, which are likely to provide more reliable risk estimates for women undergoing presymptomatic testing. METHODS Prospective breast cancer risks were assessed in 254 unaffected women with BRCA1 mutations and 238 with BRCA2 mutations. Rates of breast cancer were calculated allowing for lead time bias and censored at time of risk reducing mastectomy. Degree of family history was assessed using the Manchester score and genotyping was undertaken using 18 single-nucleotide polymorphisms (SNPs) linked to breast cancer. RESULTS Nineteen breast cancers occurred in women undergoing presymptomatic testing for BRCA1 and 23 for BRCA2. Breast cancer incidence for BRCA2 was marginally higher than BRCA1 at 20.05 per 1000 in BRCA2 compared with 16.20 per 1000 in BRCA1. Penetrance estimates to 70 years of age adjusted for a 6-month lead time and oophorectomy using Kaplan-Meier analysis were 55.1% (95% CI 36.5% to 75.6%) for BRCA1 and 71.5% (95% CI 53.2% to 87.6%). Breast cancer cases were associated with stronger family histories and higher SNP aggregate scores in BRCA2. CONCLUSIONS Prospective breast cancer risks in women in the UK are high especially for BRCA2 families ascertained on the basis of high risk. Women undergoing presymptomatic testing for BRCA2 should be quoted a wide range of possible breast cancer risks and should be steered within that range based on degree of family history, non-genetic risk factors and possibly SNP testing.
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Affiliation(s)
- D Gareth Evans
- Genesis Breast Cancer Prevention Centre, University Hospital of South Manchester NHS Trust, Manchester, UK Manchester Centre for Genomic Medicine, Central Manchester Foundation Trust, St. Mary's Hospital, Manchester, UK Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Christie Hospital, Manchester, UK The University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, UK
| | - Elaine Harkness
- Genesis Breast Cancer Prevention Centre, University Hospital of South Manchester NHS Trust, Manchester, UK The University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, UK Centre for Imaging Sciences, University of Manchester, Manchester, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Central Manchester Foundation Trust, St. Mary's Hospital, Manchester, UK
| | - Anthony Howell
- Genesis Breast Cancer Prevention Centre, University Hospital of South Manchester NHS Trust, Manchester, UK Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Christie Hospital, Manchester, UK The University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, UK
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109
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Helgadottir H, Höiom V, Jönsson G, Tuominen R, Ingvar C, Borg A, Olsson H, Hansson J. High risk of tobacco-related cancers in CDKN2A mutation-positive melanoma families. J Med Genet 2014; 51:545-52. [PMID: 24935963 PMCID: PMC4112445 DOI: 10.1136/jmedgenet-2014-102320] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Germline mutations in the tumour suppressor gene CDKN2A occur in 5-20% of familial melanoma cases. A single founder mutation, p.Arg112dup, accounts for the majority of CDKN2A mutations in Swedish carriers. In a national program, carriers of p.Arg112dup mutation have been identified. The aim of this study was to assess cancer risks in p.Arg112dup carriers and their first degree relatives (FDRs) and second degree relatives (SDRs). METHODS In this prospective cohort study, cancer diagnoses in carriers (n=120), non-carriers (n=111), carriers' FDRs (n=275) and SDRs (n=321) and controls (n=3976) were obtained from the Swedish Cancer Registry. Relative risks (RRs) for cancers were calculated (number of cancers/person years). Two-sided 95% CIs were calculated for all RRs. RESULTS In carriers prospective RR for non-melanoma cancers was 5.0 (95% CI 3.7 to 7.3), for pancreatic cancer 43.8 (95% CI 13.8 to 139.0), for cancers in upper digestive tissues 17.1 (95% CI 6.3 to 46.5), and in respiratory tissues 15.6 (5.4 to 46.0). In FDRs and SDRs RRs were significantly elevated for cancers in pancreas, respiratory and upper digestive tissues. In ever-smoking carriers compared with never-smoking carriers, the odds ratio (OR) of cancers in pancreas, respiratory or upper digestive tissues was 9.3 (95% CI 1.9 to 44.7). CONCLUSIONS CDKN2A p.Arg112dup mutation carriers from melanoma-prone families and their FDRs and SDRs have elevated risk for pancreatic, lung, head and neck and gastro-oesophageal carcinomas. These cancers were mainly seen in ever-smoking carriers. Germline CDKN2A mutations may confer an increased sensitivity to carcinogens in tobacco smoke. CDKN2A mutation carriers should be counselled to abstain from smoking.
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Affiliation(s)
- Hildur Helgadottir
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Göran Jönsson
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Rainer Tuominen
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Ingvar
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Håkan Olsson
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Johan Hansson
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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110
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Shui IM, Lindström S, Kibel AS, Berndt SI, Campa D, Gerke T, Penney KL, Albanes D, Berg C, Bueno-de-Mesquita HB, Chanock S, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giles GG, Henderson B, Hoover R, Johansson M, Le Marchand L, Ma J, Navarro C, Overvad K, Schumacher FR, Severi G, Siddiq A, Stampfer M, Stevens VL, Travis RC, Trichopoulos D, Vineis P, Mucci LA, Yeager M, Giovannucci E, Kraft P. Prostate cancer (PCa) risk variants and risk of fatal PCa in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium. Eur Urol 2014; 65:1069-75. [PMID: 24411283 PMCID: PMC4006298 DOI: 10.1016/j.eururo.2013.12.058] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 12/23/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND Screening and diagnosis of prostate cancer (PCa) is hampered by an inability to predict who has the potential to develop fatal disease and who has indolent cancer. Studies have identified multiple genetic risk loci for PCa incidence, but it is unknown whether they could be used as biomarkers for PCa-specific mortality (PCSM). OBJECTIVE To examine the association of 47 established PCa risk single-nucleotide polymorphisms (SNPs) with PCSM. DESIGN, SETTING, AND PARTICIPANTS We included 10 487 men who had PCa and 11 024 controls, with a median follow-up of 8.3 yr, during which 1053 PCa deaths occurred. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The main outcome was PCSM. The risk allele was defined as the allele associated with an increased risk for PCa in the literature. We used Cox proportional hazards regression to calculate the hazard ratios of each SNP with time to progression to PCSM after diagnosis. We also used logistic regression to calculate odds ratios for each risk SNP, comparing fatal PCa cases to controls. RESULTS AND LIMITATIONS Among the cases, we found that 8 of the 47 SNPs were significantly associated (p<0.05) with time to PCSM. The risk allele of rs11672691 (intergenic) was associated with an increased risk for PCSM, while 7 SNPs had risk alleles inversely associated (rs13385191 [C2orf43], rs17021918 [PDLIM5], rs10486567 [JAZF1], rs6465657 [LMTK2], rs7127900 (intergenic), rs2735839 [KLK3], rs10993994 [MSMB], rs13385191 [C2orf43]). In the case-control analysis, 22 SNPs were associated (p<0.05) with the risk of fatal PCa, but most did not differentiate between fatal and nonfatal PCa. Rs11672691 and rs10993994 were associated with both fatal and nonfatal PCa, while rs6465657, rs7127900, rs2735839, and rs13385191 were associated with nonfatal PCa only. CONCLUSIONS Eight established risk loci were associated with progression to PCSM after diagnosis. Twenty-two SNPs were associated with fatal PCa incidence, but most did not differentiate between fatal and nonfatal PCa. The relatively small magnitudes of the associations do not translate well into risk prediction, but these findings merit further follow-up, because they may yield important clues about the complex biology of fatal PCa. PATIENT SUMMARY In this report, we assessed whether established PCa risk variants could predict PCSM. We found eight risk variants associated with PCSM: One predicted an increased risk of PCSM, while seven were associated with decreased risk. Larger studies that focus on fatal PCa are needed to identify more markers that could aid prediction.
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Affiliation(s)
- Irene M Shui
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA.
| | - Sara Lindström
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Adam S Kibel
- Department of Surgery, Division of Urology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Daniele Campa
- Genomic Epidemiology Group, German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany
| | - Travis Gerke
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Kathryn L Penney
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christine Berg
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, MD, USA
| | - H Bas Bueno-de-Mesquita
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands; School of Public Health, Imperial College London, London, United Kingdom
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | | | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - J Michael Gaziano
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Aging, Brigham and Women's Hospital, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Brian Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, Lyon, France; Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Jing Ma
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Carmen Navarro
- Department of Epidemiology, Murcia Regional Health Authority, Murcia, Spain; Department of Health and Social Sciences, Universidad de Murcia, Murcia, Spain
| | - Kim Overvad
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia; HuGeF Foundation, Torino, Italy
| | - Afshan Siddiq
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
| | - Meir Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece; Hellenic Health Foundation, Athens, Greece
| | - Paolo Vineis
- HuGeF Foundation, Torino, Italy; School of Public Health, Imperial College London, London, United Kingdom
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
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Dahgam S, Modig L, Torinsson Naluai Å, Olin AC, Nyberg F. Haplotypes of the inducible nitric oxide synthase gene are strongly associated with exhaled nitric oxide levels in adults: a population-based study. J Med Genet 2014; 51:449-54. [PMID: 24729625 DOI: 10.1136/jmedgenet-2013-101897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Previous genetic association studies have reported evidence for association of single-nucleotide polymorphisms (SNPs) in the NOS2 gene, encoding inducible nitric oxide synthase (iNOS), to variation in levels of fractional exhaled nitric oxide (FENO) in children and adults. In this study, we evaluated 10 SNPs in the region of chromosome 17 from 26.07 Mb to 26.13 Mb to further understand the contribution of NOS2 to variation in levels of FENO. METHODS In a cohort of 5912 adults 25-75 years of age, we investigated the relationship between NOS2 haplotypes and FENO, and effect modification by asthma. RESULTS Seven common (frequency ≥5%) haplotypes (H1-H7) were inferred from all possible haplotype combinations. One haplotype (H3) was significantly associated with lower levels of FENO: -5.8% (95% CI -9.8 to -1.7; p=0.006) compared with the most common baseline haplotype H1. Two haplotypes (H5 and H6) were significantly associated with higher levels of FENO: +10.7% (95% CI 5.0 to 16.7; p=0.0002) and +14.9% (95% CI 10.6 to 19.3; p=7.8×10(-13)), respectively. The effect of haplotype H3 was mainly seen in subjects with asthma (-21.6% (95% CI -33.5 to -5.9)) and was not significant in subjects without asthma (-4.2% (95% CI -8.4 to 0.2)). The p value for interaction between H3 and asthma status was 0.004. CONCLUSIONS Our findings suggest that several common haplotypes in the NOS2 gene contribute to variation in FENO in adults. We also saw some evidence of effect modification by asthma status on haplotype H3.
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Affiliation(s)
- Santosh Dahgam
- Occupational and Environmental Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Lars Modig
- Department of Public Health and Clinical Medicine, Occupational and Environmental Medicine, University of Umeå, Umeå, Sweden
| | - Åsa Torinsson Naluai
- Department of Medical and Clinical Genetics, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anna-Carin Olin
- Occupational and Environmental Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Nyberg
- Occupational and Environmental Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden AstraZeneca R&D, Mölndal, Sweden
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Wang JW, Tang X, Li N, Wu YQ, Li S, Li J, Qin XY, Zhang ZX, Hu YH, Chen DF. The impact of lipid-metabolizing genetic polymorphisms on body mass index and their interactions with soybean food intake: a study in a Chinese population. Biomed Environ Sci 2014; 27:176-85. [PMID: 24709098 DOI: 10.3967/bes2014.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 07/18/2013] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To evaluate the association of known polymorphisms in the lipid metabolic pathway with body mass index (BMI), and estimate their interactions with soybean food intake. METHODS A community-based cross-sectional survey was conducted in a Chinese Han population. BMI, soybean food intake, and single nucleotide polymorphisms of rs599839, rs3846662, rs3846663, rs12916, rs174547, rs174570, rs4938303, and rs1558861 were measured in 944 subjects. A multivariate logistic regression was used to analyze the association of the studied polymorphisms with BMIs. The expectation-maximization algorithm was employed to evaluate the extent of linkage disequilibrium between pairwise polymorphisms. The gene-environment interaction was assessed in the general multifactor dimensionality reduction model. RESULTS The polymorphisms of rs3846662 and rs3846663 were associated with 10% highest BMIs when comparing to the 10% lowest values both in individuals and haplotype-based association tests. Although no statistically significant gene-environment interactions were found, people with the haplotype composed of C allele in rs3846662 and T allele in rs3846663 and low frequency of soybean intake had significantly higher risk to overweight and obesity as compared with those with the haplotype consisting of T allele in rs3846662 and C allele in rs3846663 and highly frequent soybean food intake, with an odds ratio of 1.64 (95% confidence interval: 1.15-2.34, P<0.01) after adjusting for the common confounders. CONCLUSION Our study has suggested that rs3846662 and rs3846663 may be the potential candidate polymorphisms for obesity, and their effect on the pathogenesis could be mediated by the frequency of soybean food intake.
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Affiliation(s)
- Jin Wei Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Xun Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Na Li
- Fangshan District Bureau of Health, Beijing 102401, China
| | - Yi Qun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Shuai Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Jin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Xue Ying Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Zong Xin Zhang
- The First Hospital of Fangshan District, Beijing 102400, China
| | - Yong Hua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Da Fang Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
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Jervis S, Song H, Lee A, Dicks E, Tyrer J, Harrington P, Easton DF, Jacobs IJ, Pharoah PPD, Antoniou AC. Ovarian cancer familial relative risks by tumour subtypes and by known ovarian cancer genetic susceptibility variants. J Med Genet 2014; 51:108-13. [PMID: 24277755 DOI: 10.1136/jmedgenet-2013-102015] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Family history is one of the most important risk factors for epithelial ovarian cancer (EOC). Little is known, however, on how EOC familial relative risks (FRRs) vary by factors such as tumour subtype or the combined effects of common EOC susceptibility alleles. In addition, no data currently exist on the FRRs associated with EOC after exclusion of BRCA1 or BRCA2 mutation carriers. METHODS EOC FRRs were computed from observed EOCs in relatives of 1548 patients with EOC recruited between 1999 and 2010 from a population-based cohort study with known BRCA1 and BRCA2 mutation status and tumour subtype, compared with the number expected in the general population. RESULTS The EOC FRR to all first-degree relatives was estimated to be 2.96 (95% CI 2.35 to 3.72) but there was no evidence of difference in the FRRs for mothers, sisters and daughters. There was significant evidence that the FRR for relatives of patients with EOC diagnosed under age 50 years is higher than that for older patients (4.72 (95% CI 3.21 to 6.95) and 2.53 (95% CI 1.91 to 3.35), p-diff=0.0052) and a suggestion that the FRR in relatives of patients with serous disease is higher than that for non-serous tumours (3.64 (95% CI 2.72 to 4.87) and 2.25 (95% CI 1.56 to 3.26), p-diff=0.0023). The FRR to relatives of cases without a deleterious mutation in BRCA1 or BRCA2 was estimated to be over twice that of the general population (2.24 (95% CI 1.71 to 2.94)). BRCA1 and BRCA2 mutations were estimated to account for about 24% of the EOC FRR to first-degree relatives. FRRs were found to increase with increasing polygenic risk score of the index patient, although the trend was not significant. CONCLUSIONS These estimates could be useful in the counselling of relatives of patients with ovarian cancer.
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Affiliation(s)
- Sarah Jervis
- Department of Public and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
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Lemaitre RN, Johnson CO, Hesselson S, Sotoodehnia N, McKnight B, Sitlani CM, Rea TD, King IB, Kwok PY, Mak A, Li G, Brody J, Larson E, Mozaffarian D, Psaty BM, Huertas-Vazquez A, Tardif JC, Albert CM, Lyytikäinen LP, Arking DE, Kääb S, Huikuri HV, Krijthe BP, Eijgelsheim M, Wang YA, Reinier K, Lehtimäki T, Pulit SL, Brugada R, Müller-Nurasyid M, Newton-Cheh CH, Karhunen PJ, Stricker BH, Goyette P, Rotter JI, Chugh SS, Chakravarti A, Jouven X, Siscovick DS. Common variation in fatty acid metabolic genes and risk of incident sudden cardiac arrest. Heart Rhythm 2014; 11:471-7. [PMID: 24418166 DOI: 10.1016/j.hrthm.2014.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND There is limited information on genetic factors associated with sudden cardiac arrest (SCA). OBJECTIVE To assess the association of common variation in genes in fatty acid pathways with SCA risk. METHODS We selected 85 candidate genes and 1155 single nucleotide polymorphisms (SNPs) tagging common variation in each gene. We investigated the SNP associations with SCA in a population-based case-control study. Cases (n = 2160) were from a repository of SCA in the greater Seattle area. Controls (n = 2615), frequency-matched on age and sex, were from the same area. We used linear logistic regression to examine SNP associations with SCA. We performed permutation-based p-min tests to account for multiple comparisons within each gene. The SNP associations with a corrected P value of <.05 were then examined in a meta-analysis of these SNP associations in 9 replication studies totaling 2129 SCA cases and 23,833 noncases. RESULTS Eight SNPs in or near 8 genes were associated with SCA risk in the discovery study, one of which was nominally significant in the replication phase (rs7737692, minor allele frequency 36%, near the LPCAT1 gene). For each copy of the minor allele, rs7737692 was associated with 13% lower SCA risk (95% confidence interval -21% to -5%) in the discovery phase and 9% lower SCA risk (95% confidence interval -16% to -1%) in the replication phase. CONCLUSIONS While none of the associations reached significance with Bonferroni correction, a common genetic variant near LPCAT1, a gene involved in the remodeling of phospholipids, was nominally associated with incident SCA risk. Further study is needed to validate this observation.
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Souza KR, Ribeiro G, Silva dos Santos CG, de Lima EC, Melo PRS, Reis MG, Blanton RE, Silva LK. Vector control measures failed to affect genetic structure of Aedes aegypti in a sentinel metropolitan area of Brazil. Acta Trop 2013; 128:598-605. [PMID: 24028791 DOI: 10.1016/j.actatropica.2013.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/22/2013] [Accepted: 09/02/2013] [Indexed: 11/17/2022]
Abstract
In order to evaluate subpopulation differentiation, effective population size (Ne) and evidence for population bottlenecks at various geographic levels, Aedes aegypti larvae were collected longitudinally from 2007 to 2009 from four areas in the city of Salvador, Brazil. The DNA from each larva was isolated and genotyped with five independent microsatellite markers. FST and Jost's D revealed significant population structuring (P<0.05) at the municipal and regional levels, while only RST was able to detect genetic differentiation at the level of strata within these areas. Ne analysis from longitudinal data did not show any evidence of significant change in population structure. The census population measured by the house index, however, showed a significant trend toward decrease in these areas. Active vector control measures did contribute to vector reduction, but this was not enough to decrease A. aegypti population genetic diversity in Salvador. The understanding of A. aegypti population dynamics may be helpful for planning and evaluation of control measures to make them more effective.
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Affiliation(s)
- Kathleen R Souza
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, BA, Brazil.
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Meyer S, Tischkowitz M, Chandler K, Gillespie A, Birch JM, Evans DG. Fanconi anaemia, BRCA2 mutations and childhood cancer: a developmental perspective from clinical and epidemiological observations with implications for genetic counselling. J Med Genet 2013; 51:71-5. [PMID: 24259538 DOI: 10.1136/jmedgenet-2013-101642] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fanconi anaemia (FA) is an inherited condition characterised by congenital and developmental abnormalities and a strong cancer predisposition. In around 3-5% of cases FA is caused by biallelic mutations in the BRCA2 gene. Individuals heterozygous for BRCA2 mutations have an increased risk of inherited breast and ovarian cancer. We reviewed the mutation spectrum in BRCA2-associated FA, and the spectrum and frequency of BRCA2 mutations in distinct populations. The rarity of FA due to biallelic BRCA2 mutations supports a fundamental role of BRCA2 for prevention of malignant transformation during development. The spectrum of malignancies seen associated with FA support the concept of a tissue selectivity of BRCA2 mutations for development of FA-associated cancers. This specificity is illustrated by the distinct FA-associated BRCA2 mutations that appear to predispose to specific brain or haematological malignancies. For some populations, the number of FA-patients with biallelic BRCA2 disruption is smaller than that expected from the carrier frequency, and this implies that some pregnancies with biallelic BRCA2 mutations do not go to term. The apparent discrepancy between expected and observed incidence of BRCA2 mutation-associated FA in high-frequency carrier populations has important implications for the genetic counselling of couples with recurrent miscarriages from high-risk populations.
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Affiliation(s)
- Stefan Meyer
- Department of Paediatric and Adolescent Oncology, University of Manchester, Manchester, UK
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Weeke P, Parvez B, Blair M, Short L, Ingram C, Kucera G, Stubblefield T, Roden DM, Darbar D. Candidate gene approach to identifying rare genetic variants associated with lone atrial fibrillation. Heart Rhythm 2013; 11:46-52. [PMID: 24120998 DOI: 10.1016/j.hrthm.2013.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Rare variants in candidate atrial fibrillation (AF) genes have been associated with AF in small kindreds. The extent to which such polymorphisms contribute to AF is unknown. OBJECTIVE The purpose of this study was to determine the spectrum and prevalence of rare amino acid coding (AAC) variants in candidate AF genes in a large cohort of unrelated lone AF probands. METHODS We resequenced 45 candidate genes in 303 European American (EA) lone AF probands (186 lone AF probands screened for each gene on average [range 89-303], 63 screened for all) identified in the Vanderbilt AF Registry (2002-2012). Variants detected were screened against 4300 EAs from the Exome Sequencing Project (ESP) to identify very rare (minor allele frequency ≤0.04%) AAC variants and these were tested for AF co-segregation in affected family members where possible. RESULTS Median age at AF onset was 46.0 years [interquartile range 33.0-54.0], and 35.6% had a family history of AF. Overall, 63 very rare AAC variants were identified in 60 of 303 lone AF probands, and 10 of 19 (52.6%) had evidence of co-segregation with AF. Among the 63 lone AF probands who had 45 genes screened, the very rare variant burden was 22%. Compared with the 4300 EA ESP, the proportion of lone AF probands with a very rare AAC variant in CASQ2 and NKX2-5 was increased 3-5-fold (P <.05). CONCLUSION No very rare AAC variants were identified in ~80% of lone AF probands. Potential reasons for the lack of very rare AAC variants include a complex pattern of inheritance, variants in as yet unidentified AF genes or in noncoding regions, and environmental factors.
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Affiliation(s)
- Peter Weeke
- Department of Medicine, Vanderbilt University, Nashville, Tennessee; Department of Cardiology, Copenhagen University Hospital, Gentofte, Denmark
| | - Babar Parvez
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Marcia Blair
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Laura Short
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Christie Ingram
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Gayle Kucera
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | | | - Dan M Roden
- Departments of Medicine and Pharmacology, Vanderbilt University, Nashville, Tennessee
| | - Dawood Darbar
- Department of Medicine, Vanderbilt University, Nashville, Tennessee.
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Kjaergaard AD, Johansen JS, Nordestgaard BG, Bojesen SE. Genetic variants in CHI3L1 influencing YKL-40 levels: resequencing 900 individuals and genotyping 9000 individuals from the general population. J Med Genet 2013; 50:831-7. [PMID: 24062521 DOI: 10.1136/jmedgenet-2013-101908] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Despite its important role in many serious diseases, the genetic background for plasma YKL-40 has still not been systematically catalogued. Therefore, we aimed at identifying genetic variants in CHI3L1 influencing plasma YKL-40 levels in the general population. METHODS We resequenced the promoter, all 10 exons and exon-flanking intron segments of CHI3L1 in 904 individuals from the Danish general population (n=8899) with extreme plasma YKL-40 levels, adjusted for age. To potentially identify clinically important genetic variants with elevated plasma YKL-40 levels, we included twice as many individuals with the highest plasma YKL-40 levels (n=603) compared with the lowest plasma YKL-40 levels (n=301). Next, we mapped linkage disequilibrium for all variants with a minor allele frequency (MAF)>0.005. Finally, all participants were genotyped for eight variants that had divergent MAFs in the two extreme plasma YKL-40 groups. RESULTS We identified 59 genetic variants in CHI3L1. Fifteen of the genetic variants were associated with plasma YKL-40 levels. Three promoter SNPs, 1 non-synonymous SNP, and four intronic SNPs in CHI3L1 were associated with plasma YKL-40 levels at or below genome-wide association significance levels (unadjusted p for trend: from 4 × 10(-8) to 6 × 10(-243); age adjusted percentiles p for trend: from 3 × 10(-12) to 2 × 10(-304)). CONCLUSIONS In a systematic search to identify genetic variants influencing plasma YKL-40 levels, we identified eight SNPs associated with plasma YKL-40 levels in the general population.
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Affiliation(s)
- Alisa D Kjaergaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Herlev, Denmark
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119
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Li J, Foo JN, Schoof N, Varghese JS, Fernandez-Navarro P, Gierach GL, Quek ST, Hartman M, Nord S, Kristensen VN, Pollán M, Figueroa JD, Thompson DJ, Li Y, Khor CC, Humphreys K, Liu J, Czene K, Hall P. Large-scale genotyping identifies a new locus at 22q13.2 associated with female breast size. J Med Genet 2013; 50:666-73. [PMID: 23825393 DOI: 10.1136/jmedgenet-2013-101708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Individual differences in breast size are a conspicuous feature of variation in human females and have been associated with fecundity and advantage in selection of mates. To identify common variants that are associated with breast size, we conducted a large-scale genotyping association meta-analysis in 7169 women of European descent across three independent sample collections with digital or screen film mammograms. METHODS The samples consisted of the Swedish KARMA, LIBRO-1 and SASBAC studies genotyped on iCOGS, a custom illumina iSelect genotyping array comprising of 211 155 single nucleotide polymorphisms (SNPs) designed for replication and fine mapping of common and rare variants with relevance to breast, ovary and prostate cancer. Breast size of each subject was ascertained by measuring total breast area (mm(2)) on a mammogram. RESULTS We confirm genome-wide significant associations at 8p11.23 (rs10086016, p=1.3×10(-14)) and report a new locus at 22q13 (rs5995871, p=3.2×10(-8)). The latter region contains the MKL1 gene, which has been shown to impact endogenous oestrogen receptor α transcriptional activity and is recruited on oestradiol sensitive genes. We also replicated previous genome-wide association study findings for breast size at four other loci. CONCLUSIONS A new locus at 22q13 may be associated with female breast size.
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Affiliation(s)
- Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
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Galesloot TE, Geurts-Moespot AJ, den Heijer M, Sweep FCGJ, Fleming RE, Kiemeney LALM, Vermeulen SH, Swinkels DW. Associations of common variants in HFE and TMPRSS6 with iron parameters are independent of serum hepcidin in a general population: a replication study. J Med Genet 2013; 50:593-8. [PMID: 23794717 DOI: 10.1136/jmedgenet-2013-101673] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Genome-wide association studies have convincingly shown that single nucleotide polymorphisms (SNPs) in HFE and TMPRSS6 are associated with iron parameters. It was commonly thought that these associations could be explained by the intermediate effect on hepcidin concentration. A recent study in an isolated Italian population, however, concluded that these associations were not exclusively dependent on hepcidin values. We report here the second study to investigate the role of hepcidin in the associations between common variants in HFE and TMPRSS6 with iron parameters. METHODS We extracted 101 SNPs in HFE and TMPRSS6 from genome-wide imputed SNP data of 1832 individuals from the general population (Nijmegen Biomedical Study). Single locus and haplotype associations with serum iron parameters and hepcidin were studied using linear regression analyses. RESULTS We found that HFE rs1800562 and TMPRSS6 rs855791 are the main determinants of HFE and TMPRSS6 related variation in serum iron, ferritin, transferrin saturation, and total iron binding capacity. These SNPs are associated with the ratios hepcidin/ferritin (p<1×10(-5)) and hepcidin/transferrin saturation (p<1×10(-3)), but not with serum hepcidin (p>0.2). Adjustment for hepcidin or the ratio hepcidin/ferritin did not decrease the strength of the SNP-iron parameter associations. CONCLUSIONS Our results do not support an intermediate role for hepcidin in the SNP-iron parameter associations, which confirms previous findings, and indicate a pleiotropic SNP effect on the hepcidin ratios and the iron parameters. Taken together, this suggests that there might be other, yet unknown, serum hepcidin independent mechanisms which play a role in the association of HFE and TMPRSS6 variants with serum iron parameters.
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Affiliation(s)
- Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
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Croucher PJ, Mascheretti S, Garbelotto M. Combining field epidemiological information and genetic data to comprehensively reconstruct the invasion history and the microevolution of the sudden oak death agent Phytophthora ramorum (Stramenopila: Oomycetes) in California. Biol Invasions 2013; 15:2281-97. [PMID: 24078788 DOI: 10.1007/s10530-013-0453-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 03/18/2013] [Indexed: 11/27/2022]
Abstract
Understanding the migration patterns of invasive organisms is of paramount importance to predict and prevent their further spread. Previous attempts at reconstructing the entire history of the sudden oak death (SOD) epidemic in California were limited by: (1) incomplete sampling; (2) the inability to include infestations caused by a single genotype of the pathogen; (3) collapsing of non-spatially contiguous yet genetically similar samples into large meta-samples that confounded the coalescent analyses. Here, we employ an intensive sampling coverage of 832 isolates of Phytopthora ramorum (the causative agent of SOD) from 60 California forests, genotyped at nine microsatellite loci, to reconstruct its invasion. By using age of infestation as a constraint on coalescent analyses, by dividing genetically indistinguishable meta-populations into highly-resolved sets of spatially contiguous populations, and by using Bruvo genetic distances for most analyses, we reconstruct the entire history of the epidemic and convincingly show infected nursery plants are the original source for the entire California epidemic. Results indicate that multiple human-mediated introductions occurred in most counties and that further disease sources were represented by large wild infestations. The study also identifies minor introductions, some of them relatively recent, linked to infected ornamental plants. Finally, using archival isolates collected soon after the discovery of the pathogen in California, we corroborate that the epidemic is likely to have resulted form 3 to 4 core founder individuals evolved from a single genotype. This is probably the most complete reconstruction ever completed for an invasion by an exotic forest pathogen, and the approach here described may be useful for the reconstruction of invasions by any clonally reproducing organism with a relatively limited natural dispersal range.
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Zheng HF, Duncan EL, Yerges-Armstrong LM, Eriksson J, Bergström U, Leo PJ, Leslie WD, Goltzman D, Blangero J, Hanley DA, Carless MA, Streeten EA, Lorentzon M, Brown MA, Spector TD, Pettersson-Kymmer U, Ohlsson C, Mitchell BD, Richards JB. Meta-analysis of genome-wide studies identifies MEF2C SNPs associated with bone mineral density at forearm. J Med Genet 2013; 50:473-8. [PMID: 23572186 DOI: 10.1136/jmedgenet-2012-101287] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Forearm fractures affect 1.7 million individuals worldwide each year and most occur earlier in life than hip fractures. While the heritability of forearm bone mineral density (BMD) and fracture is high, their genetic determinants are largely unknown. AIM To identify genetic variants associated with forearm BMD and forearm fractures. METHODS BMD at distal radius, measured by dual-energy x-ray absorptiometry, was tested for association with common genetic variants. We conducted a meta-analysis of genome-wide association studies for BMD in 5866 subjects of European descent and then selected the variants for replication in 715 Mexican American samples. Gene-based association was carried out to supplement the single-nucleotide polymorphism (SNP) association test. We then tested the BMD-associated SNPs for association with forearm fracture in 2023 cases and 3740 controls. RESULTS We found that five SNPs in the introns of MEF2C were associated with forearm BMD at a genome-wide significance level (p<5×10(-8)) in meta-analysis (lead SNP, rs11951031[T] -0.20 SDs per allele, p=9.01×10(-9)). The gene-based association test suggested an association between MEF2C and forearm BMD (p=0.003). The association between MEF2C variants and risk of fracture did not achieve statistical significance (SNP rs12521522[A]: OR=1.14 (95% CI 0.92 to 1.35), p=0.14). Meta-analysis also revealed two genome-wide suggestive loci at CTNNA2 and 6q23.2. CONCLUSIONS These findings demonstrate that variants at MEF2C were associated with forearm BMD, implicating this gene in the determination of BMD at forearm.
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Affiliation(s)
- Hou-Feng Zheng
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, Lady Davis Institute, Jewish General Hospital, McGill University, 3755, Côte Ste-Catherine Road, Montreal, Québec H3T 1E2, Canada.
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Abstract
With the advent of modern genomic methods to adjust for population stratification, the use of external or publicly available controls has become an attractive option for reducing the cost of large-scale case-control genetic association studies. In this article, we study the estimation of joint effects of genetic and environmental exposures from a case-control study where data on genome-wide markers are available on the cases and a set of external controls while data on environmental exposures are available on the cases and a set of internal controls. We show that under such a design, one can exploit an assumption of gene-environment independence in the underlying population to estimate the gene-environment joint effects, after adjustment for population stratification. We develop a semiparametric profile likelihood method and related pseudolikelihood and working likelihood methods that are easy to implement in practice. We propose variance estimators for the methods based on asymptotic theory. Simulation is used to study the performance of the methods, and data from a multi-centre genome-wide association study of bladder cancer is further used to illustrate their application.
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Affiliation(s)
- YI-HAU CHEN
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - NILANJAN CHATTERJEE
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, U.S.A
| | - RAYMOND J. CARROLL
- Department of Statistics, Texas A&M University, College Station, Texas 77843-3143, U.S.A
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Davey Smith G. Use of genetic markers and gene-diet interactions for interrogating population-level causal influences of diet on health. Genes Nutr 2011; 6:27-43. [PMID: 21437028 PMCID: PMC3040803 DOI: 10.1007/s12263-010-0181-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/07/2010] [Indexed: 01/20/2023]
Abstract
Differences in diet appear to contribute substantially to the burden of disease in populations, and therefore changes in diet could lead to major improvements in public health. This is predicated on the reliable identification of causal effects of nutrition on health, and unfortunately nutritional epidemiology has deficiencies in terms of identifying these. This is reflected in the many cases where observational studies have suggested that a nutritional factor is protective against disease, and randomized controlled trials have failed to verify this. The use of genetic variants as proxy measures of nutritional exposure-an application of the Mendelian randomization principle-can contribute to strengthening causal inference in this field. Genetic variants are not subject to bias due to reverse causation (disease processes influencing exposure, rather than vice versa) or recall bias, and if obvious precautions are applied are not influenced by confounding or attenuation by errors. This is illustrated in the case of epidemiological studies of alcohol intake and various health outcomes, through the use of genetic variants related to alcohol metabolism (in ALDH2 and ADH1B). Examples from other areas of nutritional epidemiology and of the informative nature of gene-environment interactions interpreted within the Mendelian randomization framework are presented, and the potential limitations of the approach addressed.
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Affiliation(s)
- George Davey Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN UK
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Li N, Guo Y, Zhou L, Wang H, Yao X, Luo W, Chang J. Genetic variation and association analyses of NEDD4 gene in Kazak Chinese patients with hypertension. Int J Mol Epidemiol Genet 2010; 1:226-235. [PMID: 21537394 PMCID: PMC3076774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/15/2010] [Indexed: 05/30/2023]
Abstract
To analyze the association between the genetic variations of neural precursor cell expressed developmentally down-regulated 4 gene (NEDD4) and hypertension in Kazakh Chinese. The sequences of NEDD4 gene exons were sequenced in 96 Kazakh Chinese with hypertension to identify representative variations. A case-control study was conducted by genotyping the representative variations in 287 Kazakh hypertensives and 411 normotensives. Replication population was 343 Uygur hypertensives and 724 normotensives. All subjects were selected from population-based cross-sectional studies of metabolic disease. Thirteen novel and 15 known single nucleotide polymorphism (SNPs) or mutations, including 6 missense mutations, were identified. Of the four representative SNPs geno-typed, only rs2303580 was association with hypertension in Kazakh (additive P/Pc=0.020/0.160) without Bonferroni's correction. The result was replicated in Uygur (additive/dominant P=0.089/0.028, Pc=0.174/0.056). By adjusting for age and BMI, the observed association would no longer be statistically significant in Kazakh (additive OR (95%CI) 1.035(0.802-1.336), but remained statistically significant in Uygur ( additive/dominant ORs (95%CI) 1.323 (1.069-1.637), 1.521(1.146-2.020)). The rs2303580 genotypes were not association with blood pressure levels in Kazakh. Although by multiple linear regression analysis and by applying Bonferroni's correction, the genotypes were significant association with diastolic blood pressure levels (AA>AG>GG) in Uygur normotensive controls (P/Pc=0.003/0.018), the direction of difference was not in accordance with the association between the qualitative hypertension phenotype and the genotype shown (G risk allele). Our data indicates that the association between the NEDD4 genetic polymorphisms and hypertension phenotype should be replicated in further studies using larger and racially diverse populations.
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Affiliation(s)
- Nanfang Li
- The Department of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region; The Center of Diagnosis Treatment and Research of Hypertension in Xinjiang. No.91, Tianchi Road, Urumqi, Xinjiang 830001, China
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Alavantic D, Djuric T. Risk factors of atherosclerosis: A review of genetic epidemiology data from a Serbian population. Exp Clin Cardiol 2006; 11:78-82. [PMID: 18651039 PMCID: PMC2274853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Determining common risk factors for the onset and progression of atherosclerosis and cardiovascular diseases, which are known to be multi-factorial and polygenic diseases, represents a challenge for medicine in the future. In recent years, there have been breakthroughs in the determination of pathogenesis, risk estimating methodologies, modifications of genetic risk in prophylaxis and in establishing new therapeutic targets in pharmacology. The role of genetic epidemiology is to provide necessary data about genetic characteristics of different populations, as well as gene-gene and gene-environment interactions, that lead to the development of diseases. The aim is to define high-risk haplotypes and primary targets for a new generation of pharmaceutical products and tools designed for the diagnosis and therapy of these disorders. The present review provides examples from the authors' genetic epidemiology studies regarding the association of candidate genes with risk factors of atherosclerosis, such as dyslipidemias, hypertension and diabetes mellitus, in a Serbian population, along with basic assumptions that come with this type of research. The main results of these studies are discussed, as well as problems that should be taken into consideration in future evaluations of disease risk in a population.
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Affiliation(s)
- Dragan Alavantic
- VINCA Institute of Nuclear Sciences, Laboratory for Radiology and Molecular Genetics, Belgrade, Serbia and Montenegro
| | - Tamara Djuric
- VINCA Institute of Nuclear Sciences, Laboratory for Radiology and Molecular Genetics, Belgrade, Serbia and Montenegro
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