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Nln I, Shum J, Ghodke-Puranik Y, Tipon R, Triese D, Amin S, Makol A, Osborn T, Chowdhary V, Thanarajasingam U, Wampler Muskardin TL, Oke V, Gunnarsson I, Zickert A, Zervou MI, Boumpas DT, Svenungsson E, Goulielmos GN, Niewold TB. Regional european genetic ancestry predicts type I interferon level and risk of severe viral infection. QJM 2024:hcae052. [PMID: 38530799 DOI: 10.1093/qjmed/hcae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Viral infection outcomes vary widely between individuals, ranging from mild symptoms to severe organ failure and death, and it is clear that host genetic factors play a role in this variability. Type I interferon (IFN) is a critical anti-viral cytokine, and we have previously noted differences in type I IFN levels between world populations. METHODS In this study, we investigate the interrelationship between regional European genetic ancestry, type I IFN levels, and severe viral infection outcomes. RESULTS In cohorts of European ancestry lupus patients living in Europe, we noted higher IFN in the Northwestern populations as compared to Southeastern populations. In an independent cohort of European ancestry lupus patients from the United States with varying proportional regional European genetic admixture, we observed the same Northwest vs. Southeast European ancestry IFN gradient. We developed a model to predict type I IFN level based on regional European ancestry (AUC = 0.73, p = 6.1e-6). Examining large databases containing serious viral outcomes data, we found that lower predicted IFN in the corresponding European country was significantly correlated with increased viral infection fatality rate, including COVID-19, viral hepatitis, and HIV [Correlation coefficients: -0.79 (p = 4e-2), -0.94 (p = 6e-3), and -0.96 (p = 8e-2) respectively]. CONCLUSIONS This association between predicted type I IFN level and viral outcome severity suggests a potential causal relationship, as greater intrinsic type I IFN is beneficial in host defense against viruses. Genetic testing could provide insight into individual and population level risk of fatality due to viruses prior to infection, across a wide range of viral pathogens.
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Affiliation(s)
- Ilona Nln
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY
| | | | - Yogita Ghodke-Puranik
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY
| | | | | | | | - Ashima Makol
- Division of Rheumatology, Mayo Clinic, Rochester, MN
| | - Thomas Osborn
- Division of Rheumatology, Mayo Clinic, Rochester, MN
| | | | | | | | - Vilija Oke
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Agneta Zickert
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Maria I Zervou
- Laboratory of Molecular Medicine and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | | | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - George N Goulielmos
- Laboratory of Molecular Medicine and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Timothy B Niewold
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY
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2
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Mihić L, Janičić B, Marchetti I, Novović Z, Sica C, Bottesi G, Belopavlović R, Jakšić N. Comorbidity among depression, anxiety and stress symptoms in naturalistic clinical samples: A cross-cultural network analysis. Clin Psychol Psychother 2023. [PMID: 37940606 DOI: 10.1002/cpp.2927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Comorbidity between depression and anxiety is well-established across various settings and cultures. We approached comorbidity from the network psychopathology perspective and examined the depression, anxiety/autonomic arousal and stress/tension symptoms in naturalistic clinical samples from Serbia, Italy and Croatia. This was a multisite study in which regularized partial correlation networks of the symptoms, obtained via self-reports on the Depression Anxiety and Stress Scales-21 (DASS-21) in three cross-cultural, clinical samples (total N = 874), were compared with respect to centrality, edge weights, community structure and bridge centrality. A moderate degree of similarity in a number of network indices across the three networks was observed. While negative mood emerged to be the most central node, stress/tension nodes were the most likely bridge symptoms between depressive and anxiety/autonomic arousal symptoms. We demonstrated that the network structure and features in mixed clinical samples were similar across three different languages and cultures. The symptoms such as agitation, restlessness and inability to relax functioned as bridges across the three symptom communities explored in this study. Important theoretical and clinical implications were derived.
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Affiliation(s)
- Ljiljana Mihić
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Bojan Janičić
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Igor Marchetti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Zdenka Novović
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Claudio Sica
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Gioia Bottesi
- Department of General Psychology, University of Padova, Padova, Italy
| | - Radomir Belopavlović
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Nenad Jakšić
- Department of Psychiatry and Psychological Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
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Mirza-Davies A, Foley S, Caseras X, Baker E, Holmans P, Escott-Price V, Jones DK, Harrison JR, Messaritaki E. The impact of genetic risk for Alzheimer's disease on the structural brain networks of young adults. Front Neurosci 2022; 16:987677. [PMID: 36532292 PMCID: PMC9748570 DOI: 10.3389/fnins.2022.987677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction We investigated the structural brain networks of 562 young adults in relation to polygenic risk for Alzheimer's disease, using magnetic resonance imaging (MRI) and genotype data from the Avon Longitudinal Study of Parents and Children. Methods Diffusion MRI data were used to perform whole-brain tractography and generate structural brain networks for the whole-brain connectome, and for the default mode, limbic and visual subnetworks. The mean clustering coefficient, mean betweenness centrality, characteristic path length, global efficiency and mean nodal strength were calculated for these networks, for each participant. The connectivity of the rich-club, feeder and local connections was also calculated. Polygenic risk scores (PRS), estimating each participant's genetic risk, were calculated at genome-wide level and for nine specific disease pathways. Correlations were calculated between the PRS and (a) the graph theoretical metrics of the structural networks and (b) the rich-club, feeder and local connectivity of the whole-brain networks. Results In the visual subnetwork, the mean nodal strength was negatively correlated with the genome-wide PRS (r = -0.19, p = 1.4 × 10-3), the mean betweenness centrality was positively correlated with the plasma lipoprotein particle assembly PRS (r = 0.16, p = 5.5 × 10-3), and the mean clustering coefficient was negatively correlated with the tau-protein binding PRS (r = -0.16, p = 0.016). In the default mode network, the mean nodal strength was negatively correlated with the genome-wide PRS (r = -0.14, p = 0.044). The rich-club and feeder connectivities were negatively correlated with the genome-wide PRS (r = -0.16, p = 0.035; r = -0.15, p = 0.036). Discussion We identified small reductions in brain connectivity in young adults at risk of developing Alzheimer's disease in later life.
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Affiliation(s)
- Anastasia Mirza-Davies
- School of Medicine, University Hospital Wales, Cardiff University, Cardiff, United Kingdom
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Sonya Foley
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Xavier Caseras
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Emily Baker
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Judith R. Harrison
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- Institute for Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eirini Messaritaki
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- BRAIN Biomedical Research Unit, School of Medicine, Cardiff University, Cardiff, United Kingdom
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4
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Markiewicz E, Idowu OC. Evaluation of Personalized Skincare Through in-silico Gene Interactive Networks and Cellular Responses to UVR and Oxidative Stress. Clin Cosmet Investig Dermatol 2022; 15:2221-2243. [PMID: 36284733 PMCID: PMC9588296 DOI: 10.2147/ccid.s383790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Abstract
Purpose Personalized approaches in dermatology are designed to match the specific requirements based on the individual genetic makeup. One major factor accounting for the differences in skin phenotypes is single nucleotide polymorphism (SNP) within several genes with diverse roles that extend beyond skin tone and pigmentation. Therefore, the cellular sensitivities to the environmental stress and damage linked to extrinsic aging could also underlie the individual characteristics of the skin and dictate the unique skin care requirements. This study aimed to identify the likely biomarkers and molecular signatures expressed in skin cells of different ethnic backgrounds, which could aid further the design of personalized skin products based on specific demands. Methods Using data mining and in-silico modeling, the association of SNP-affected genes with three major skin types of European, Asian and African origin was analyzed and compared within the structure-function gene interaction networks. Cultured dermal fibroblasts were subsequently subjected to ultraviolet radiation and oxidative stress and analyzed for DNA damage and senescent markers. The protective applications of two cosmetic ingredients, Resveratrol and Quercetin, were validated in both cellular and in-silico models. Results Each skin type was characterized by the presence of SNPs in the genes controlling facultative and constitutive pigmentation, which could also underlie the major differences in responses to photodamage, such as oxidative stress, inflammation, and barrier homeostasis. Skin-type-specific dermal fibroblasts cultured in-vitro demonstrated distinctive sensitivities to ultraviolet radiation and oxidative stress, which could be modulated further by the bioactive compounds with the predicted capacities to interact with some of the genes in the in-silico models. Conclusion Evaluation of the SNP-affected gene networks and likely sensitivities of skin cells, defined as low threshold levels to extrinsic stress factors, can provide a valuable tool for the design and formulation of personalized skin products that match more accurately diverse ethnic backgrounds.
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Affiliation(s)
- Ewa Markiewicz
- Hexis Lab, The Catalyst, Newcastle Helix, Newcastle upon Tyne, UK
| | - Olusola C Idowu
- Hexis Lab, The Catalyst, Newcastle Helix, Newcastle upon Tyne, UK,Correspondence: Olusola C Idowu, HexisLab Limited, The Catalyst, Newcastle Helix, Newcastle upon Tyne, NE4 5TG, UK, Tel +44 1394 825487, Email
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Santos-Araújo C, Mendonça L, Carvalho DS, Bernardo F, Pardal M, Couceiro J, Martinho H, Gavina C, Taveira-Gomes T, Dinis-Oliveira RJ. Twenty years of real-world data to estimate chronic kidney disease prevalence and staging in an unselected population. Clin Kidney J 2022; 16:111-124. [PMID: 36726443 PMCID: PMC9871850 DOI: 10.1093/ckj/sfac206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic kidney disease (CKD) represents a global public health burden, but its true prevalence is not fully characterized in the majority of countries. We studied the CKD prevalence in adult users of the primary, secondary and tertiary healthcare units of an integrated health region in northern Portugal (n = 136 993; representing ∼90% of the region's adult population). Of these, 45 983 (33.6%) had at least two estimated glomerular filtration rate (eGFR) assessments and 30 534 (22.2%) had at least two urinary albumin:creatinine ratio (UACR) assessments separated by at least 3 months. CKD was defined according to the Kidney Disease: Improving Global Outcomes (KDIGO) guidelines as a persistent decrease in eGFR (<60 ml/min/1.73 m2) and/or an increase in UACR (≥30 mg/g). The estimated overall prevalence of CKD was 9.8% and was higher in females (5.5%) than males (4.2%). From these, it was possible to stratify 4.7% according to KDIGO guidelines. The prevalence of CKD was higher in older patients (especially in patients >70 years old) and in patients with comorbidities. This is the first real-world-based study to characterize CKD prevalence in a large, unselected Portuguese population. It probably provides the nearest estimate of the true CKD prevalence and may help healthcare providers to guide CKD-related policies and strategies focused on prevention and on the improvement of cardiovascular disease and other outcomes.
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Affiliation(s)
- Carla Santos-Araújo
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal,Nephrology Department, Pedro Hispano Hospital, Senhora da Hora, Matosinhos, Portugal
| | - Luís Mendonça
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal,Nephrology Department, Centro Hospitalar Universitário São João, EPE, Porto, Portugal
| | - Daniel Seabra Carvalho
- Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
| | | | - Marisa Pardal
- Medical Department, AstraZeneca, Barcarena, Portugal
| | - João Couceiro
- Medical Department, AstraZeneca, Barcarena, Portugal
| | - Hugo Martinho
- Medical Department, AstraZeneca, Barcarena, Portugal
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Lucock MD, Jones PR, Veysey M, Thota R, Garg M, Furst J, Martin C, Yates Z, Scarlett CJ, Jablonski NG, Chaplin G, Beckett EL. Biophysical evidence to support and extend the vitamin D-folate hypothesis as a paradigm for the evolution of human skin pigmentation. Am J Hum Biol 2021; 34:e23667. [PMID: 34418235 DOI: 10.1002/ajhb.23667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To test the "vitamin D-folate hypothesis for the evolution of human skin pigmentation." METHODS Total ozone mapping spectrometer (TOMS) satellite data were used to examine surface UV-irradiance in a large (n = 649) Australian cross-sectional study population. Genetic analysis was used to score vitamin D- and folate-related gene polymorphisms (n = 22), along with two pigmentation gene variants (IRF4-rs12203592/HERC2-rs12913832). Red cell folate and vitamin D3 were measured by immunoassay and HPLC, respectively. RESULTS Ultraviolet radiation (UVR) and pigmentation genes interact to modify blood vitamin levels; Light skin IRF4-TT genotype has greatest folate loss while light skin HERC2-GG genotype has greatest vitamin D3 synthesis (reflected in both TOMS and seasonal data). UV-wavelength exhibits a dose-response relationship in folate loss within light skin IRF4-TT genotype (305 > 310 > 324 > 380 nm). Significant vitamin D3 photosynthesis only occurs within light skin HERC2-GG genotype, and is maximal at 305 nm. Three dietary antioxidants (vitamins C, E, and β-carotene) interact with UVR and pigmentation genes preventing oxidative loss of labile reduced folate vitamers, with greatest benefit in light skin IRF4-TT subjects. The putative photosensitiser, riboflavin, did not sensitize red cell folate to UVR and actually afforded protection. Four genes (5xSNPs) influenced blood vitamin levels when stratified by pigmentation genotype; MTHFR-rs1801133/rs1801131, TS-rs34489327, CYP24A-rs17216707, and VDR-ApaI-rs7975232. Lightest IRF4-TT/darkest HERC2-AA genotype combination (greatest folate loss/lowest vitamin D3 synthesis) has 0% occurrence. The opposing, commonest (39%) compound genotype (darkest IRF4-CC/lightest HERC2-GG) permits least folate loss and greatest synthesis of vitamin D3 . CONCLUSION New biophysical evidence supports the vitamin D-folate hypothesis for evolution of skin pigmentation.
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Affiliation(s)
- Mark D Lucock
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Patrice R Jones
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | | | - Rohith Thota
- Nutraceuticals Research Group, University of Newcastle, Callaghan, New South Wales, Australia.,Metabolism and Nutrition, Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Manohar Garg
- Nutraceuticals Research Group, University of Newcastle, Callaghan, New South Wales, Australia
| | - John Furst
- Maths and Physical Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Charlotte Martin
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Zoe Yates
- Biomedical Sciences and Pharmacy, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Christopher J Scarlett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Nina G Jablonski
- Anthropology Department, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Chaplin
- Anthropology Department, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Emma L Beckett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
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Huebner M, Börnigen D, Deckert A, Holle R, Meisinger C, Müller-Nurasyid M, Peters A, Rathmann W, Becher H. Genetic Variation and Cardiovascular Risk Factors: A Cohort Study on Migrants from the Former Soviet Union and a Native German Population. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18126215. [PMID: 34201265 PMCID: PMC8227685 DOI: 10.3390/ijerph18126215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/17/2022]
Abstract
Resettlers are a large migrant group of more than 2 million people in Germany who migrated mainly from the former Soviet Union to Germany after 1989. We sought to compare the distribution of the major risk factors for cardiovascular disease (CVD) and to investigate the overall genetic differences in a study population which consisted of resettlers and native (autochthone) Germans. This was a joint analysis of two cohort studies which were performed in the region of Augsburg, Bavaria, Germany, with 3363 native Germans and 363 resettlers. Data from questionnaires and physical examinations were used to compare the risk factors for cardiovascular diseases between the resettlers and native Germans. A population-based genome-wide association analysis was performed in order to identify the genetic differences between the two groups. The distribution of the major risk factors for CVD differed between the two groups. The resettlers lead a less active lifestyle. While female resettlers smoked less than their German counterparts, the men showed similar smoking behavior. SNPs from three genes (BTNL2, DGKB, TGFBR3) indicated a difference in the two populations. In other studies, these genes have been shown to be associated with CVD, rheumatoid arthritis and osteoporosis, respectively.
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Affiliation(s)
- Marianne Huebner
- Institute for Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany;
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48864, USA
| | - Daniela Börnigen
- Bioinformatics Core Facility, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany;
| | - Andreas Deckert
- Institute of Global Health, Epidemiology and Biostatistics, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany;
| | - Rolf Holle
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, GmbH, 85764 Neuherberg, Germany;
| | - Christa Meisinger
- German Research Center for Environmental Health, Institute of Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (C.M.); (A.P.)
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Annette Peters
- German Research Center for Environmental Health, Institute of Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (C.M.); (A.P.)
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764 Neuherberg, Germany;
- German Diabetes Center, Institute for Biometrics and Epidemiology, 40225 Duesseldorf, Germany
| | - Heiko Becher
- Institute for Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany;
- Correspondence: ; Tel.: +49-(0)40-7410-59550
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Parfenchyk MS, Kotava SA. The Theoretical Framework for the Panels of DNA Markers Formation in the Forensic Determination of an Individual Ancestral Origin. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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9
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Harrison JR, Mistry S, Muskett N, Escott-Price V. From Polygenic Scores to Precision Medicine in Alzheimer's Disease: A Systematic Review. J Alzheimers Dis 2020; 74:1271-1283. [PMID: 32250305 PMCID: PMC7242840 DOI: 10.3233/jad-191233] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Late-onset Alzheimer's disease (AD) is highly heritable. The effect of many common genetic variants, single nucleotide polymorphisms (SNPs), confer risk. Variants are clustered in areas of biology, notably immunity and inflammation, cholesterol metabolism, endocytosis, and ubiquitination. Polygenic scores (PRS), which weight the sum of an individual's risk alleles, have been used to draw inferences about the pathological processes underpinning AD. OBJECTIVE This paper aims to systematically review how AD PRS are being used to study a range of outcomes and phenotypes related to neurodegeneration. METHODS We searched the literature from July 2008-July 2018 following PRISMA guidelines. RESULTS 57 studies met criteria. The AD PRS can distinguish AD cases from controls. The ability of AD PRS to predict conversion from mild cognitive impairment (MCI) to AD was less clear. There was strong evidence of association between AD PRS and cognitive impairment. AD PRS were correlated with a number of biological phenotypes associated with AD pathology, such as neuroimaging changes and amyloid and tau measures. Pathway-specific polygenic scores were also associated with AD-related biologically relevant phenotypes. CONCLUSION PRS can predict AD effectively and are associated with cognitive impairment. There is also evidence of association between AD PRS and other phenotypes relevant to neurodegeneration. The associations between pathway specific polygenic scores and phenotypic changes may allow us to define the biology of the disease in individuals and indicate who may benefit from specific treatments. Longitudinal cohort studies are required to test the ability of PGS to delineate pathway-specific disease activity.
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Affiliation(s)
- Judith R. Harrison
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, UK
| | - Sumit Mistry
- MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, UK
| | - Natalie Muskett
- Cardiff University Medical School, University Hospital of Wales, Cardiff, UK
| | - Valentina Escott-Price
- Dementia Research Institute & the MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, UK
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10
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Del Bino S, Duval C, Bernerd F. Clinical and Biological Characterization of Skin Pigmentation Diversity and Its Consequences on UV Impact. Int J Mol Sci 2018; 19:ijms19092668. [PMID: 30205563 PMCID: PMC6163216 DOI: 10.3390/ijms19092668] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Skin color diversity is the most variable and noticeable phenotypic trait in humans resulting from constitutive pigmentation variability. This paper will review the characterization of skin pigmentation diversity with a focus on the most recent data on the genetic basis of skin pigmentation, and the various methodologies for skin color assessment. Then, melanocyte activity and amount, type and distribution of melanins, which are the main drivers for skin pigmentation, are described. Paracrine regulators of melanocyte microenvironment are also discussed. Skin response to sun exposure is also highly dependent on color diversity. Thus, sensitivity to solar wavelengths is examined in terms of acute effects such as sunburn/erythema or induced-pigmentation but also long-term consequences such as skin cancers, photoageing and pigmentary disorders. More pronounced sun-sensitivity in lighter or darker skin types depending on the detrimental effects and involved wavelengths is reviewed.
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Affiliation(s)
- Sandra Del Bino
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
| | - Christine Duval
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
| | - Françoise Bernerd
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
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Gassner C, Degenhardt F, Meyer S, Vollmert C, Trost N, Neuenschwander K, Merki Y, Portmann C, Sigurdardottir S, Zorbas A, Engström C, Gottschalk J, Amar El Dusouqui S, Waldvogel-Abramovski S, Rigal E, Tissot JD, Tinguely C, Mauvais SM, Sarraj A, Bessero D, Stalder M, Infanti L, Buser A, Sigle J, Weingand T, Castelli D, Braisch MC, Thierbach J, Heer S, Schulzki T, Krawczak M, Franke A, Frey BM. Low-Frequency Blood Group Antigens in Switzerland. Transfus Med Hemother 2018; 45:239-250. [PMID: 30283273 DOI: 10.1159/000490714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022] Open
Abstract
Background High-frequency blood group antigens (HFA) are present in >90% of the human population, according to some reports even in >99% of individuals. Therefore, patients lacking HFA may become challenging for transfusion support because compatible blood is hardly found, and if the patient carries alloantibodies, the cross-match will be positive with virtual every red cell unit tested. Methods In this study, we applied high-throughput blood group SNP genotyping on >37,000 Swiss blood donors, intending to identify homozygous carriers of low-frequency blood group antigens (LFA). Results 326 such individuals were identified and made available to transfusion specialists for future support of patients in need of rare blood products. Conclusion Thorough comparison of minor allele frequencies using population genetics revealed heterogeneity of allele distributions among Swiss blood donors which may be explained by the topographical and cultural peculiarities of Switzerland. Moreover, geographically localized donor subpopulations are described which contain above-average numbers of individuals carrying rare blood group genotypes.
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Affiliation(s)
- Christoph Gassner
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stefan Meyer
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | | | - Nadine Trost
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | - Kathrin Neuenschwander
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | - Yvonne Merki
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | - Claudia Portmann
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | - Sonja Sigurdardottir
- Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Department of Molecular Diagnostics & Research (MOC), Schlieren, Switzerland
| | - Antigoni Zorbas
- Blood Transfusion Service Zürich, SRC, Schlieren, Switzerland
| | | | | | | | | | - Emmanuel Rigal
- Blood Transfusion Service Genève, SRC, Geneva, Switzerland
| | - Jean-Daniel Tissot
- Blood Transfusion Service Vaud, SRC (recently merged with Interregional Blood Transfusion, SRC, Ltd., Bern), Lausanne, Switzerland
| | | | - Simon M Mauvais
- Blood Transfusion Service Neuchâtel-Jura, SRC, Neuchâtel, Switzerland
| | - Amira Sarraj
- Blood Transfusion Service Neuchâtel-Jura, SRC, Neuchâtel, Switzerland
| | - Daniel Bessero
- Blood Transfusion Service Valais, SRC (recently merged with Interregional Blood Transfusion, SRC, Ltd., Bern), Sion, Switzerland
| | - Michele Stalder
- Blood Transfusion Service Valais, SRC (recently merged with Interregional Blood Transfusion, SRC, Ltd., Bern), Sion, Switzerland
| | - Laura Infanti
- Blood Transfusion Service beider Basel, SRC, Basel, Switzerland
| | - Andreas Buser
- Blood Transfusion Service beider Basel, SRC, Basel, Switzerland
| | - Jörg Sigle
- Blood Transfusion Service Aargau-Solothurn, SRC, Aarau, Switzerland
| | - Tina Weingand
- Blood Transfusion Service Zentralschweiz, SRC, Luzern, Switzerland
| | - Damiano Castelli
- Blood Transfusion Service Svizzera Italiana, SRC, Lugano, Switzerland
| | - Monica C Braisch
- Blood Transfusion Service Ostschweiz, SRC, St. Gallen, Switzerland
| | - Jutta Thierbach
- Blood Transfusion Service Ostschweiz, SRC, St. Gallen, Switzerland
| | - Sonja Heer
- Blood Transfusion Service Graubünden, SRC, Chur, Switzerland
| | - Thomas Schulzki
- Blood Transfusion Service Graubünden, SRC, Chur, Switzerland
| | - Michael Krawczak
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Beat M Frey
- Blood Transfusion Service Zürich, SRC, Schlieren, Switzerland
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12
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Brück K, Stel VS, Gambaro G, Hallan S, Völzke H, Ärnlöv J, Kastarinen M, Guessous I, Vinhas J, Stengel B, Brenner H, Chudek J, Romundstad S, Tomson C, Gonzalez AO, Bello AK, Ferrieres J, Palmieri L, Browne G, Capuano V, Van Biesen W, Zoccali C, Gansevoort R, Navis G, Rothenbacher D, Ferraro PM, Nitsch D, Wanner C, Jager KJ. CKD Prevalence Varies across the European General Population. J Am Soc Nephrol 2016; 27:2135-47. [PMID: 26701975 PMCID: PMC4926978 DOI: 10.1681/asn.2015050542] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022] Open
Abstract
CKD prevalence estimation is central to CKD management and prevention planning at the population level. This study estimated CKD prevalence in the European adult general population and investigated international variation in CKD prevalence by age, sex, and presence of diabetes, hypertension, and obesity. We collected data from 19 general-population studies from 13 European countries. CKD stages 1-5 was defined as eGFR<60 ml/min per 1.73 m(2), as calculated by the CKD-Epidemiology Collaboration equation, or albuminuria >30 mg/g, and CKD stages 3-5 was defined as eGFR<60 ml/min per 1.73 m(2) CKD prevalence was age- and sex-standardized to the population of the 27 Member States of the European Union (EU27). We found considerable differences in both CKD stages 1-5 and CKD stages 3-5 prevalence across European study populations. The adjusted CKD stages 1-5 prevalence varied between 3.31% (95% confidence interval [95% CI], 3.30% to 3.33%) in Norway and 17.3% (95% CI, 16.5% to 18.1%) in northeast Germany. The adjusted CKD stages 3-5 prevalence varied between 1.0% (95% CI, 0.7% to 1.3%) in central Italy and 5.9% (95% CI, 5.2% to 6.6%) in northeast Germany. The variation in CKD prevalence stratified by diabetes, hypertension, and obesity status followed the same pattern as the overall prevalence. In conclusion, this large-scale attempt to carefully characterize CKD prevalence in Europe identified substantial variation in CKD prevalence that appears to be due to factors other than the prevalence of diabetes, hypertension, and obesity.
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Affiliation(s)
- Katharina Brück
- European Renal Association-European Dialysis and Transplant Association Registry, Department of Medical Informatics, Amsterdam Medical Center, Amsterdam, The Netherlands;
| | - Vianda S Stel
- European Renal Association-European Dialysis and Transplant Association Registry, Department of Medical Informatics, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Giovanni Gambaro
- Division of Nephrology and Dialysis, Columbus-Gemelli University Hospital, Catholic University of the Sacred Heart, Rome, Italy
| | - Stein Hallan
- Department of Nephrology, St. Olav's Hospital/Faculty of Medicine, The Norwegian University of Science and Technology, Trondheim, Norway
| | - Henry Völzke
- Department of Clinical Epidemiology research, University Medicine Greifswald, Greifswald, Germany
| | - Johan Ärnlöv
- Department of Medical Sciences/Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Mika Kastarinen
- Finnish Medicines Agency, Department of Internal Medicine and Nephrology, Kuopio/National Institute for Health and Welfare, Helsinki, Finland
| | - Idris Guessous
- Department of Community Medicine, Primary Care and Emergency medicine, Geneva University Hospital, Geneva, Switzerland
| | - José Vinhas
- Department of Medicine, Setubal Hospital Centre, Setubal, Portugal
| | - Bénédicte Stengel
- Research Centre in Epidemiology and Population Health, INSERM Unit 1018, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center/Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Jerzy Chudek
- Department of Pathophysiology, Medical Faculty/Department of Nephrology Endocrinology and Metabolic Diseases, Medical University of Silesia, Katowice, Poland
| | - Solfrid Romundstad
- Department of Nephrology, Levanger Hospital, Health Trust Nord-Trøndelag/The Norwegian University of Science and Technology, Norway
| | - Charles Tomson
- Department of Nephrology, Freeman Hospital, Newcastle upon Tyne, UK
| | | | - Aminu K Bello
- Department of Medicine, University of Alberta, Edmonton, Canada
| | - Jean Ferrieres
- Department of Cardiology, Toulouse University School of Medicine, Rangueil Hospital, Toulouse, France
| | - Luigi Palmieri
- Department of Epidemiology of Cerebro and Cardiovascular Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Gemma Browne
- Department of Epidemiology & Public Health, University College Cork & Mercy University Hospital, Cork, Ireland
| | - Vincenzo Capuano
- Unità Operativa di Cardiologia ed UTIC, Mercato S. Severino Hospital, Salerno, Italy
| | - Wim Van Biesen
- Department of Nephrology, Ghent University Hospital, Ghent, Belgium
| | - Carmine Zoccali
- Consiglio Nazionale delle Ricerche-Istituto di Fisiologia Clinica, Clinical Epidemiology and Pathophysiology of Renal Diseases and Hypertension, Reggio Calabria, Italy
| | - Ron Gansevoort
- Department of Nephrology/Graduate School of Medical Sciences and
| | - Gerjan Navis
- Department of Epidemiology of Cerebro and Cardiovascular Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Pietro Manuel Ferraro
- Division of Nephrology and Dialysis, Columbus-Gemelli University Hospital, Catholic University of the Sacred Heart, Rome, Italy
| | - Dorothea Nitsch
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine and University College London, Centre for Nephrology, London, United Kingdom; and
| | - Christoph Wanner
- Department of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - Kitty J Jager
- European Renal Association-European Dialysis and Transplant Association Registry, Department of Medical Informatics, Amsterdam Medical Center, Amsterdam, The Netherlands
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Leslie R, O'Donnell CJ, Johnson AD. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics 2014; 30:i185-94. [PMID: 24931982 DOI: 10.1093/bioinformatics/btu273] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
SUMMARY We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). MOTIVATION To create a high-quality resource to facilitate further use and interpretation of human GWAS results in order to address important scientific questions. RESULTS GWAS have grown exponentially, with increases in sample sizes and markers tested, and continuing bias toward European ancestry samples. GRASP contains >100 000 phenotypes, roughly: eQTLs (71.5%), metabolite QTLs (21.2%), methylation QTLs (4.4%) and diseases, biomarkers and other traits (2.8%). cis-eQTLs, meQTLs, mQTLs and MHC region SNPs are highly enriched among significant results. After removing these categories, GRASP still contains a greater proportion of studies and results than comparable GWAS catalogs. Cardiovascular disease and related risk factors pre-dominate remaining GWAS results, followed by immunological, neurological and cancer traits. Significant results in GWAS display a highly gene-centric tendency. Sex chromosome X (OR = 0.18[0.16-0.20]) and Y (OR = 0.003[0.001-0.01]) genes are depleted for GWAS results. Gene length is correlated with GWAS results at nominal significance (P ≤ 0.05) levels. We show this gene-length correlation decays at increasingly more stringent P-value thresholds. Potential pleotropic genes and SNPs enriched for multi-phenotype association in GWAS are identified. However, we note possible population stratification at some of these loci. Finally, via re-annotation we identify compelling functional hypotheses at GWAS loci, in some cases unrealized in studies to date. CONCLUSION Pooling summary-level GWAS results and re-annotating with bioinformatics predictions and molecular features provides a good platform for new insights. AVAILABILITY The GRASP database is available at http://apps.nhlbi.nih.gov/grasp.
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Affiliation(s)
- Richard Leslie
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USACardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher J O'Donnell
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USACardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew D Johnson
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
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14
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Kowalczyk M, Owczarek A, Suchanek R, Paul-Samojedny M, Fila-Danilow A, Borkowska P, Kucia K, Kowalski J. Heat shock protein 70 gene polymorphisms are associated with paranoid schizophrenia in the Polish population. Cell Stress Chaperones 2014; 19:205-15. [PMID: 23893339 PMCID: PMC3933617 DOI: 10.1007/s12192-013-0446-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 07/01/2013] [Accepted: 07/10/2013] [Indexed: 01/01/2023] Open
Abstract
HSP70 genes have been considered as promising schizophrenia candidate genes based on their protective role in the central nervous system under stress conditions. In this study, we analyzed the potential implication of HSPA1A +190G/C, HSPA1B +1267A/G, and HSPA1L +2437T/C polymorphisms in the susceptibility to paranoid schizophrenia in a homogenous Caucasian Polish population. In addition, we investigated the association of the polymorphisms with the clinical variables of the disease. Two hundred and three patients with paranoid schizophrenia and 243 healthy controls were enrolled in the study. Polymorphisms of HSPA1A, -1B, and -1L genes were genotyped using the PCR-RFLP technique. Analyses were conducted in entire groups and in subgroups that were stratified according to gender. There were significant differences in the genotype and allele frequencies of HSPA1A polymorphism between the patients and controls. The +190CC genotype and +190C allele were over-represented in the patients and significantly increased the risk for developing schizophrenia (OR = 3.45 and OR = 1.61, respectively). Interestingly, such a risk was higher for females with the +190CC genotype than for males with the +190CC genotype (OR = 5.78 vs. OR = 2.76). We also identified the CGT haplotype as a risk haplotype for schizophrenia and demonstrated the effects of HSPA1A and HSPA1B genotypes on the psychopathology and age of onset. Our study provided the first evidence that the HSPA1A polymorphism may potentially increase the risk of developing paranoid schizophrenia. Further independent analyses in different populations to evaluate the role of gender are needed to replicate these results.
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Affiliation(s)
- Malgorzata Kowalczyk
- Department of Medical Genetics, Medical University of Silesia, Ostrogorska 30, 41-200, Sosnowiec, Poland,
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15
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Pato MT, Sobell JL, Medeiros H, Abbott C, Skar B, Buckley PF, Bromet EJ, Escamilla MA, Fanous AH, Lehrer DS, Macciardi F, Malaspina D, McCarroll SA, Marder SR, Moran J, Morley CP, Nicolini H, Perkins DO, Purcell SM, Rapaport MH, Sklar P, Smoller JW, Knowles JA, Pato CN. The genomic psychiatry cohort: partners in discovery. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:306-12. [PMID: 23650244 PMCID: PMC3729260 DOI: 10.1002/ajmg.b.32160] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/14/2013] [Indexed: 01/04/2023]
Abstract
The Genomic Psychiatry Cohort (GPC) is a longitudinal resource designed to provide the necessary population-based sample for large-scale genomic studies, studies focusing on Research Domain Criteria (RDoC) and/or other alternate phenotype constructs, clinical and interventional studies, nested case-control studies, long-term disease course studies, and genomic variant-to-phenotype studies. We provide and will continue to encourage access to the GPC as an international resource. DNA and other biological samples and diagnostic data are available through the National Institute of Mental Health (NIMH) Repository. After appropriate review and approval by an advisory board, investigators are able to collaborate in, propose, and co-lead studies involving cohort participants.
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Affiliation(s)
- Michele T. Pato
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Janet L. Sobell
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helena Medeiros
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Colony Abbott
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brooke Skar
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Peter F. Buckley
- Department of Psychiatry, Georgia Regents University, Augusta, GA, USA
| | - Evelyn J. Bromet
- Department of Psychiatry and Behavioral Science, State University of New York, Stony Brook, NY, USA
| | - Michael A. Escamilla
- Department of Psychiatry, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Ayman H. Fanous
- Department of Psychiatry, Veterans Administration Medical Center, Washington, DC, USA
| | | | - Fabio Macciardi
- Department of Psychiatry, University of California, Irvine, CA, USA
| | | | - Steve A. McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Stephen R. Marder
- Department of Psychiatry, University of California, Los Angeles, CA, USA
| | - Jennifer Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher P. Morley
- Departments of Family Medicine, Public Health and Preventive Medicine, and Psychiatry and Behavioral Science, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | | | - Diana O. Perkins
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Shaun M. Purcell
- Center for Human Genome Research, Massachusetts General Hospital, Boston, MA, USA
| | - Mark H. Rapaport
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Pamela Sklar
- Department of Psychiatry, Mt. Sinai School of Medicine, New York, NY, USA
| | | | - James A. Knowles
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Carlos N. Pato
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
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16
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Liu F, Wen B, Kayser M. Colorful DNA polymorphisms in humans. Semin Cell Dev Biol 2013; 24:562-75. [PMID: 23587773 DOI: 10.1016/j.semcdb.2013.03.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/26/2013] [Indexed: 10/26/2022]
Abstract
In this review article we summarize current knowledge on how variation on the DNA level influences human pigmentation including color variation of iris, hair, and skin. We review recent progress in the field of human pigmentation genetics by focusing on the genes and DNA polymorphisms discovered to be involved in determining human pigmentation traits, their association with diseases particularly skin cancers, and their power to predict human eye, hair, and skin colors with potential utilization in forensic investigations.
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Affiliation(s)
- Fan Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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17
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Population structure, migration, and diversifying selection in the Netherlands. Eur J Hum Genet 2013; 21:1277-85. [PMID: 23531865 DOI: 10.1038/ejhg.2013.48] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 01/04/2013] [Accepted: 02/20/2013] [Indexed: 12/21/2022] Open
Abstract
Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the Dutch North-South PC showed correlations with genome-wide homozygosity (r=0.245), which may reflect a serial-founder effect due to northwards migration, and also with height (♂: r=0.142, ♀: r=0.153). The divergence between subpopulations identified by PCs is partly driven by selection pressures. The first three PCs showed significant signals for diversifying selection (545 SNPs - the majority within 184 genes). The strongest signal was observed between North and South for the functional SNP in HERC2 that determines human blue/brown eye color. Thus, this study demonstrates how to increase ancestry signals in a relatively homogeneous population and how those signals can reveal evolutionary history.
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18
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Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations. PLoS One 2012; 7:e48294. [PMID: 23118974 PMCID: PMC3485197 DOI: 10.1371/journal.pone.0048294] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 09/25/2012] [Indexed: 12/21/2022] Open
Abstract
Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.
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19
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Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
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Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
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20
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Richards AL, Jones L, Moskvina V, Kirov G, Gejman PV, Levinson DF, Sanders AR, Purcell S, Visscher PM, Craddock N, Owen MJ, Holmans P, O’Donovan MC. Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain. Mol Psychiatry 2012; 17:193-201. [PMID: 21339752 PMCID: PMC4761872 DOI: 10.1038/mp.2011.11] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 01/12/2011] [Accepted: 01/19/2011] [Indexed: 12/11/2022]
Abstract
It is widely thought that alleles that influence susceptibility to common diseases, including schizophrenia, will frequently do so through effects on gene expression. As only a small proportion of the genetic variance for schizophrenia has been attributed to specific loci, this remains an unproven hypothesis. The International Schizophrenia Consortium (ISC) recently reported a substantial polygenic contribution to that disorder, and that schizophrenia risk alleles are enriched among single-nucleotide polymorphisms (SNPs) selected for marginal evidence for association (P<0.5) from genome-wide association studies (GWAS). It follows that if schizophrenia susceptibility alleles are enriched for those that affect gene expression, those marginally associated SNPs, which are also expression quantitative trait loci (eQTLs), should carry more true association signals compared with SNPs that are not marginally associated. To test this, we identified marginally associated (P<0.5) SNPs from two of the largest available schizophrenia GWAS data sets. We assigned eQTL status to those SNPs based upon an eQTL data set derived from adult human brain. Using the polygenic score method of analysis reported by the ISC, we observed and replicated the observation that higher probability cis-eQTLs predicted schizophrenia better than those with a lower probability for being a cis-eQTL. Our data support the hypothesis that alleles conferring risk of schizophrenia are enriched among those that affect gene expression. Moreover, our data show that notwithstanding the likely developmental origin of schizophrenia, studies of adult brain tissue can, in principle, allow relevant susceptibility eQTLs to be identified.
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Affiliation(s)
- Alexander L Richards
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Valentina Moskvina
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Pablo V Gejman
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Northshore University Health System Research Institute, 1001 University Place, Evanston, IL 60201, USA
| | | | - Alan R Sanders
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Northshore University Health System Research Institute, 1001 University Place, Evanston, IL 60201, USA
| | | | | | - Shaun Purcell
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Massachusetts 02114, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Massachusetts 02114, USA
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Peter M Visscher
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane 4006, Australia
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Michael C O’Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
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The last two millennias echo-catastrophes are the driving forces for the potential genetic advantage mechanisms in celiac disease. Med Hypotheses 2011; 77:773-6. [DOI: 10.1016/j.mehy.2011.07.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/17/2011] [Indexed: 11/23/2022]
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Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 2011; 12:245-74. [PMID: 21801023 DOI: 10.1146/annurev-genom-090810-183123] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift. Surveying this structure gives us a scientific perspective on human origins, sheds light on evolutionary processes that shape both human adaptation and disease, and is integral to effectively carrying out the mission of global medical genetics and personalized medicine. Surveys of population structure have been ongoing for decades, but in the past three years, single-nucleotide-polymorphism (SNP) array technology has provided unprecedented detail on human population structure at global and regional scales. These studies have confirmed well-known relationships between distantly related populations and uncovered previously unresolvable relationships among closely related human groups. SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences. Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era.
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Affiliation(s)
- John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90403, USA.
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23
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Humphreys K, Grankvist A, Leu M, Hall P, Liu J, Ripatti S, Rehnström K, Groop L, Klareskog L, Ding B, Grönberg H, Xu J, Pedersen NL, Lichtenstein P, Mattingsdal M, Andreassen OA, O'Dushlaine C, Purcell SM, Sklar P, Sullivan PF, Hultman CM, Palmgren J, Magnusson PKE. The genetic structure of the Swedish population. PLoS One 2011; 6:e22547. [PMID: 21829632 PMCID: PMC3150368 DOI: 10.1371/journal.pone.0022547] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 06/29/2011] [Indexed: 11/26/2022] Open
Abstract
Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise Fst) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions.
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Affiliation(s)
- Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Grankvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Monica Leu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jianjun Liu
- Human Genetics Laboratory, Genome Institute of Singapore, Singapore, Singapore
| | - Samuli Ripatti
- Institute for Molecular Medicine, Finland, FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Karola Rehnström
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Lars Klareskog
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bo Ding
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jianfeng Xu
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Morten Mattingsdal
- Institute of Clinical Medicine, Section Psychiatry, University of Oslo, Oslo, Norway
- Sørlandet Hospital HF, Kristiansand, Norway
| | - Ole A. Andreassen
- Institute of Clinical Medicine, Section Psychiatry, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Colm O'Dushlaine
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Shaun M. Purcell
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Pamela Sklar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Juni Palmgren
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Mathematical Statistics, Stockholm University, Stockholm, Sweden
- Swedish eScience Research Center, Stockholm, Sweden
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Abstract
In view of the population-specific heterogeneity in reported genetic risk factors for Parkinson's disease (PD), we conducted a genome-wide association study (GWAS) in a large sample of PD cases and controls from the Netherlands. After quality control (QC), a total of 514,799 SNPs genotyped in 772 PD cases and 2024 controls were included in our analyses. Direct replication of SNPs within SNCA and BST1 confirmed these two genes to be associated with PD in the Netherlands (SNCA, rs2736990: P = 1.63 × 10(-5), OR = 1.325 and BST1, rs12502586: P = 1.63 × 10(-3), OR = 1.337). Within SNCA, two independent signals in two different linkage disequilibrium (LD) blocks in the 3' and 5' ends of the gene were detected. Besides, post-hoc analysis confirmed GAK/DGKQ, HLA and MAPT as PD risk loci among the Dutch (GAK/DGKQ, rs2242235: P = 1.22 × 10(-4), OR = 1.51; HLA, rs4248166: P = 4.39 × 10(-5), OR = 1.36; and MAPT, rs3785880: P = 1.9 × 10(-3), OR = 1.19).
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Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK. Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples. INVESTIGATIVE GENETICS 2011; 2:1. [PMID: 21208434 PMCID: PMC3025953 DOI: 10.1186/2041-2223-2-1] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 01/05/2011] [Indexed: 12/02/2022]
Abstract
Background Using DNA to determine an individual's ancestry from among human populations is generally interesting and useful for many purposes, including admixture mapping, controlling for population structure in disease or trait association studies and forensic ancestry inference. However, to estimate ancestry, including possible admixture within an individual, as well as heterogeneity within a group of individuals, allele frequencies are necessary for what are believed to be the contributing populations. For this purpose, panels of ancestry informative markers (AIMs) have been developed. Results We are presenting our work on one such panel, composed of 128 ancestry informative single-nucleotide polymorphisms (AISNPs) already proposed in the literature. Compared to previous studies of these AISNPs, we have studied three times the number of individuals (4,871) in three times as many population samples (119). We have validated this panel for many ancestry assignment and admixture studies, especially those that were the rationale for the original selection of the 128 SNPs: African Americans and Mexican Americans. At the same time, the limitations of the panel for distinguishing ancestry and quantifying admixture among Eurasian populations are noted. Conclusion We demonstrate the simultaneous importance of the specific set of population samples and their relative sample sizes in the use of the structure program to determine which groups cluster together and consequently influence the ability of a marker panel to infer ancestry. We demonstrate the strengths and weaknesses of this particular panel of AISNPs in a global context.
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Affiliation(s)
- Judith R Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
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