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Schraiber JG, Edge MD. Heritability within groups is uninformative about differences among groups: Cases from behavioral, evolutionary, and statistical genetics. Proc Natl Acad Sci U S A 2024; 121:e2319496121. [PMID: 38470926 PMCID: PMC10962975 DOI: 10.1073/pnas.2319496121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give-directly or indirectly-some support to claims that aggregate heritable variation within groups can be related to heritable variation among groups. We consider three families of approaches: the "between-group heritability" sometimes invoked in behavior genetics, the statistic [Formula: see text] used in empirical work in evolutionary quantitative genetics, and methods based on variation in ancestry in an admixed population, used in anthropological and statistical genetics. We take up these examples to show mathematically that information on within-group genetic and phenotypic information in the aggregate cannot separate among-group differences into genetic and environmental components, and we provide simulation results that support our claims. We discuss these results in terms of the long-running debate on this topic.
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Affiliation(s)
- Joshua G. Schraiber
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA90089-2911
| | - Michael D. Edge
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA90089-2911
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Schraiber JG, Edge MD. Heritability within groups is uninformative about differences among groups: cases from behavioral, evolutionary, and statistical genetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.06.565864. [PMID: 37986815 PMCID: PMC10659290 DOI: 10.1101/2023.11.06.565864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give-directly or indirectly-some support to claims that aggregate heritable variation within groups can be related to heritable variation among groups. We consider three families of approaches: the "between-group heritability" sometimes invoked in behavior genetics, the statistic P S T used in empirical work in evolutionary quantitative genetics, and methods based on variation in ancestry in an admixed population, used in anthropological and statistical genetics. We take up these examples to show mathematically that information on within-group genetic and phenotypic information in the aggregate cannot separate among-group differences into genetic and environmental components, and we provide simulation results that support our claims. We discuss these results in terms of the long-running debate on this topic.
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Affiliation(s)
- Joshua G. Schraiber
- Department of Quantitative and Computational Biology, University of Southern California
| | - Michael D. Edge
- Department of Quantitative and Computational Biology, University of Southern California
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Abstract
Historically, rheumatic diseases have not received much attention in Africa, particularly in sub-Saharan Africa, possibly owing to a focus on the overwhelming incidence of infectious diseases and the decreased life span of the general population in this region. Global attention and support, together with better health policies and planning, have improved outcomes for many infectious diseases; thus, increasing attention is being turned to chronic non-communicable diseases. Rheumatic diseases were previously considered to be rare among Africans but there is now a growing interest in these conditions, particularly as the number of rheumatologists on the continent increases. This interest has resulted in a growing number of publications from Africa on the more commonly encountered rheumatic diseases, as well as case reports of rare diseases. Despite the limited amount of available data, some aspects of the epidemiology, genetics and clinical and laboratory features of rheumatic diseases in African populations are known, as is some detail on the use of therapeutics. Similarities and differences in these conditions can be seen across the multi-ethnic and genetically diverse African continent, and it is hoped that increased awareness of rheumatic diseases in Africa will lead to earlier diagnosis and better outcomes for patients. The prevalence of rheumatic diseases is increasing in African countries, leading to an increased need for specialist rheumatologists and disease-modifying drugs. In this Review, the authors outline what is currently known about the state of rheumatic diseases in Africa. In the past, there has been an emphasis on communicable diseases in Africa, but attention has now shifted towards non-communicable diseases such as rheumatic diseases. Common rheumatic diseases are seen in Africa and are both comparable and different from presentations seen outside of Africa. Diverse genetic and environmental factors affect the presentation of common rheumatic diseases among different African nations. A shortage of appropriately trained staff, laboratory testing capacity and effective medications exists across the whole continent. Advocacy and research are needed to increase awareness of the risk factors, presentations and management of rheumatic diseases in Africa. Specialized treatment guidelines are needed for resource-poor countries in Africa.
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Mario-Vásquez JE, Naranjo-González CA, Montiel J, Zuluaga LM, Vásquez AM, Tobón-Castaño A, Bedoya G, Segura C. Association of variants in IL1B, TLR9, TREM1, IL10RA, and CD3G and Native American ancestry on malaria susceptibility in Colombian populations. INFECTION GENETICS AND EVOLUTION 2020; 87:104675. [PMID: 33316430 DOI: 10.1016/j.meegid.2020.104675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/19/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
Host genetics is an influencing factor in the manifestation of infectious diseases. In this study, the association of mild malaria with 28 variants in 16 genes previously reported in other populations and/or close to ancestry-informative markers (AIMs) selected was evaluated in an admixed 736 Colombian population sample. Additionally, the effect of genetic ancestry on phenotype expression was explored. For this purpose, the ancestral genetic composition of Turbo and El Bagre was determined. A higher Native American ancestry trend was found in the population with lower malaria susceptibility [odds ratio (OR) = 0.416, 95% confidence interval (95% CI) = 0.234-0.740, P = 0.003]. Three AIMs presented significant associations with the disease phenotype (MID1752, MID921, and MID1586). The first two were associated with greater malaria susceptibility (D/D, OR = 2.23, 95% CI = 1.06-4.69, P = 0.032 and I/D-I/I, OR = 2.14, 95% CI = 1.18-3.87, P = 0.011, respectively), and the latter has a protective effect on the appearance of malaria (I/I, OR = 0.18, 95% CI = 0.08-0.40, P < 0.0001). After adjustment by age, sex, municipality, and genetic ancestry, genotype association analysis showed evidence of association with malaria susceptibility for variants in or near IL1B, TLR9, TREM1, IL10RA, and CD3G genes: rs1143629-IL1B (G/A-A/A, OR = 0.41, 95% CI = 0.21-0.78, P = 0.0051), rs352139-TLR9 (T/T, OR = 0.28, 95% CI = 0.11-0.72, P = 0.0053), rs352140-TLR9 (C/C, OR = 0.41, 95% CI = 0.20-0.87, P = 0.019), rs2234237-TREM1 (T/A-A/A, OR = 0.43, 95% CI = 0.23-0.79, P = 0.0056), rs4252246-IL10RA (C/A-A/A, OR = 2.11, 95% CI = 1.18-3.75, P = 0.01), and rs1561966-CD3G (A/A, OR = 0.20, 95% CI = 0.06-0.69, P = 0.0058). The results showed the participation of genes involved in immunological processes and suggested an effect of ancestral genetic composition over the traits analyzed. Compared to the paisa population (Antioquia), Turbo and El Bagre showed a strong decrease in European ancestry and an increase in African and Native American ancestries. Also, a novel association of two single nucleotide polymorphisms with malaria susceptibility was identified in this study.
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Affiliation(s)
- Jorge Eliécer Mario-Vásquez
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | | | - Jehidys Montiel
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Lina M Zuluaga
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Ana M Vásquez
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Alberto Tobón-Castaño
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Gabriel Bedoya
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | - Cesar Segura
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia.
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Samuels DC, Below JE, Ness S, Yu H, Leng S, Guo Y. Alternative Applications of Genotyping Array Data Using Multivariant Methods. Trends Genet 2020; 36:857-867. [PMID: 32773169 PMCID: PMC7572808 DOI: 10.1016/j.tig.2020.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
One of the forerunners that pioneered the revolution of high-throughput genomic technologies is the genotyping microarray technology, which can genotype millions of single-nucleotide variants simultaneously. Owing to apparent benefits, such as high speed, low cost, and high throughput, the genotyping array has gained lasting applications in genome-wide association studies (GWAS) and thus accumulated an enormous amount of data. Empowered by continuous manufactural upgrades and analytical innovation, unconventional applications of genotyping array data have emerged to address more diverse genetic problems, holding promise of boosting genetic research into human diseases through the re-mining of the rich accumulated data. Here, we review several unconventional genotyping array analysis techniques that have been built on the idea of large-scale multivariant analysis and provide empirical application examples. These unconventional outcomes of genotyping arrays include polygenic score, runs of homozygosity (ROH)/heterozygosity ratio, distant pedigree computation, and mitochondrial DNA (mtDNA) copy number inference.
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Affiliation(s)
- David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Jennifer E Below
- Devision of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Scott Ness
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA
| | - Hui Yu
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA
| | - Shuguang Leng
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA
| | - Yan Guo
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA.
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Association of Native American ancestry and common variants in ACE, ADIPOR2, MTNR1B, GCK, TCF7L2 and FTO genes with glycemic traits in Colombian population. Gene 2018; 677:198-210. [DOI: 10.1016/j.gene.2018.07.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
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Bhattacharya J, Pappas K, Toz B, Aranow C, Mackay M, Gregersen PK, Doumbo O, Traore AK, Lesser ML, McMahon M, Utset T, Silverman E, Levy D, McCune WJ, Jolly M, Wallace D, Weisman M, Romero-Diaz J, Diamond B. Serologic features of cohorts with variable genetic risk for systemic lupus erythematosus. Mol Med 2018; 24:24. [PMID: 30134810 PMCID: PMC6016868 DOI: 10.1186/s10020-018-0019-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is an autoimmune disease with genetic, hormonal, and environmental influences. In Western Europe and North America, individuals of West African descent have a 3-4 fold greater incidence of SLE than Caucasians. Paradoxically, West Africans in sub-Saharan Africa appear to have a low incidence of SLE, and some studies suggest a milder disease with less nephritis. In this study, we analyzed sera from African American female SLE patients and four other cohorts, one with SLE and others with varying degrees of risk for SLE in order to identify serologic factors that might correlate with risk of or protection against SLE. METHODS Our cohorts included West African women with previous malaria infection assumed to be protected from development of SLE, clinically unaffected sisters of SLE patients with high risk of developing SLE, healthy African American women with intermediate risk, healthy Caucasian women with low risk of developing SLE, and women with a diagnosis of SLE. We developed a lupus risk index (LRI) based on titers of IgM and IgG anti-double stranded DNA antibodies and levels of C1q. RESULTS The risk index was highest in SLE patients; second highest in unaffected sisters of SLE patients; third highest in healthy African-American women and lowest in healthy Caucasian women and malaria-exposed West African women. CONCLUSION This risk index may be useful in early interventions to prevent SLE. In addition, it suggests new therapeutic approaches for the treatment of SLE.
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Affiliation(s)
- Jyotsna Bhattacharya
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr, Manhasset, NY, 11030, USA
| | - Karalyn Pappas
- Department of Statistical Science, Cornell University, Ithaca, NY, USA
| | - Bahtiyar Toz
- Department of Internal Medicine, Istanbul University, Istanbul, Turkey
| | - Cynthia Aranow
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr, Manhasset, NY, 11030, USA
| | - Meggan Mackay
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr, Manhasset, NY, 11030, USA
| | - Peter K Gregersen
- The Feinstein Institute for Medical Research, Center for Genomics and Human Genetics, Manhasset, NY, USA
| | | | - Abdel Kader Traore
- Deputy of the Department of Internal Medicine, University Hospital, Bamako, Mali
| | - Martin L Lesser
- The Feinstein Institute for Medical Research, Center of Biostatistics Unit Manhasset, Manhasset, NY, USA
| | - Maureen McMahon
- UCLA David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Tammy Utset
- University of Chicago Medical Center, Chicago, IL, USA
| | - Earl Silverman
- Hospital for Sick Children, University of Toronto, Toronto, ON M5G, 1X8, Canada
| | - Deborah Levy
- Hospital for Sick Children, University of Toronto, Toronto, ON M5G, 1X8, Canada
| | | | | | - Daniel Wallace
- Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Juanita Romero-Diaz
- Instituto Nacional de Ciencias Medicas y Nutrician Salvador Zubiran, Mexico City, Mexico
| | - Betty Diamond
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr, Manhasset, NY, 11030, USA.
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Gergianaki I, Bertsias G. Systemic Lupus Erythematosus in Primary Care: An Update and Practical Messages for the General Practitioner. Front Med (Lausanne) 2018; 5:161. [PMID: 29896474 PMCID: PMC5986957 DOI: 10.3389/fmed.2018.00161] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/08/2018] [Indexed: 12/29/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is a complex chronic autoimmune disease that manifests a wide range of organ involvement. Traditionally, the diagnosis and management of SLE is provided at secondary and tertiary centers to ensure prompt initiation of treatment, adequate control of flares and prevention of irreversible organ damage. Notwithstanding, the role of primary care in SLE is also emerging as there are still significant unmet needs such as the diagnostic delay at the community level and the high burden of therapy- and disease-related comorbidities. In the present review, we summarize practical messages for primary care physicians and general practitioners (GPs) concerning early diagnosis and proper referral of patients with SLE. In addition, we discuss the main comorbidities complicating the disease course and the recommended preventative measures, and we also provide an update on the role and current educational needs of GPs regarding the disease.
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Affiliation(s)
- Irini Gergianaki
- Rheumatology, Clinical Immunology and Allergy, University of Crete Faculty of Medicine, Iraklio, Greece
| | - George Bertsias
- Rheumatology, Clinical Immunology and Allergy, University of Crete Faculty of Medicine, Iraklio, Greece
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Genetic Ancestry and Susceptibility to Late-Onset Alzheimer Disease (LOAD) in the Admixed Colombian Population. Alzheimer Dis Assoc Disord 2018; 31:225-231. [PMID: 28369008 DOI: 10.1097/wad.0000000000000195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Differences in the prevalence of dementia among populations and in the effect of apolipoprotein E (APOE) on the emergence of Alzheimer disease (AD), which is the main type of dementia, have been reported. METHODS This study estimated the ancestry of a group of individuals with late-onset Alzheimer disease (LOAD) (N=280) and established whether there were any differences when compared with a control group (N=357) in a sample of the Colombian population. RESULTS When the analyses were adjusted for known risk factors such as age, sex, presence of APOE[Latin Small Letter Open E]4, socioeconomic status, educational attainment, and place of birth, African ancestry was associated with an increased LOAD risk (odds ratio: 1.55; 95% confidence interval, 1.09-2.03; P=0.029), whereas Native American ancestry was associated with lower risk (odds ratio: 0.75; 95% confidence interval, 0.61-0.98; P=0.046), for every 10% increase in ancestry. In addition, there were significant differences in the proportion of Native American ancestry between carriers and noncarriers of the APOE[Latin Small Letter Open E]4 allele (Mann-Whitney U test, P=0.047), with noncarriers having higher mean Native American ancestry when compared with carriers. CONCLUSIONS Our results are consistent with the presence of variants of African origin in the genome of the Colombian population and different from APOE[Latin Small Letter Open E]4 that represents a risk factor for the development of LOAD, whereas variants of Native American origin may be conferring protection. However, unknown environmental factors or epigenetic differences among continental groups could also explain the observed associations.
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Variants in the TNFA, IL6 and IFNG genes are associated with the dengue severity in a sample from Colombian population. BIOMEDICA 2017; 37:486-497. [DOI: 10.7705/biomedica.v37i4.3305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 12/09/2016] [Indexed: 01/26/2023]
Abstract
Introducción. La composición genética del huésped determina, entre otros aspectos, el perfil clínico del dengue, lo cual se debería al efecto de variantes en los genes que codifican citocinas proinflamatorias.Objetivo. Evaluar la asociación entre las variantes de tres polimorfismos en los genes candidatos TNFA, IL6 e IFNG con la gravedad del dengue en una población colombiana.Materiales y métodos. Se evaluaron los polimorfismos rs1800750, rs2069843 y rs2069705 de los genes TNFA, IL6 e IFNG, respectivamente, en 226 pacientes con dengue. Los genotipos se tipificaron usando la reacción en cadena de la polimerasa (PCR) y los polimorfismos de la longitud de los fragmentos de restricción (Restriction Fragment Length Polymorphism, RFLP). Para determinar el riesgo de diferentes fenotipos del dengue, se compararon las frecuencias alélicas con la prueba de ji al cuadrado, y los genotipos y los haplotipos, con regresión logística. Por último, los análisis se ajustaron utilizando datos de autoidentificación o del componente genético ancestral.Resultados. El alelo A del rs2069843, ajustado por autoidentificación, se asoció con casos de dengue hemorrágico en afrocolombianos. En la muestra completa, dicho polimorfismo, ajustado por componente genético ancestral, fue reproducible. Además, hubo asociaciones significativas entre las combinaciones alélicas GGT y GAC de los rs1800750, rs2069843 y rs2069705 en pacientes con dengue hemorrágico, con ajuste por componente genético ancestral y sin él. Además, la combinación alélica AGC produjo 58,03 pg/ml más de interleucina 6 que la GGC, independientemente de los componentes genéticos europeo, amerindio y africano.Conclusión. Las variantes de los polimorfismos GGT y GAC de los rs1800750, rs2069843 y rs2069705 en los genes TNFA, IL6 e IFNG, respectivamente, se correlacionaron con la gravedad del dengue en esta muestra de población colombiana.
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Moreno DJ, Ruiz S, Ríos Á, Lopera F, Ostos H, Via M, Bedoya G. Association of GWAS Top Genes With Late-Onset Alzheimer's Disease in Colombian Population. Am J Alzheimers Dis Other Demen 2017; 32:27-35. [PMID: 28084078 PMCID: PMC10857032 DOI: 10.1177/1533317516679303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The association of variants in CLU, CR1, PICALM, BIN1, ABCA7, and CD33 genes with late-onset Alzheimer's disease (LOAD) was evaluated and confirmed through genome-wide association study. However, it is unknown whether these associations can be replicated in admixed populations. METHODS The association of 14 single-nucleotide polymorphisms in those genes was evaluated in 280 LOAD cases and 357 controls from the Colombian population. RESULTS In a multivariate analysis using age, gender, APOE∊4 status, and admixture covariates, significant associations were obtained ( P < .05) for variants in BIN1 (rs744373, odds ratio [OR]: 1.42), CLU (rs11136000, OR: 0.66), PICALM (rs541458, OR: 0.69), ABCA7 (rs3764650, OR: 1.7), and CD33 (rs3865444, OR: 1.12). Likewise, a significant interaction effect was observed between CLU and CR1 variants with APOE. CONCLUSION This study replicated the associations previously reported in populations of European ancestry and shows that APOE variants have a regulatory role on the effect that variants in other loci have on LOAD, reflecting the importance of gene-gene interactions in the etiology of neurodegenerative diseases.
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Affiliation(s)
| | - Susana Ruiz
- Grupo de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Ángela Ríos
- Grupo de Neuropsicología, Universidad Surcolombiana, Neiva, Colombia
| | - Francisco Lopera
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - Henry Ostos
- Grupo de Medicina Genómica, Universidad Surcolombiana, Neiva, Colombia
| | - Marc Via
- Psicologia Clínica i Psicobiologia and Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Gabriel Bedoya
- Grupo de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
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Thrombotic Thrombocytopenic Purpura in Black People: Impact of Ethnicity on Survival and Genetic Risk Factors. PLoS One 2016; 11:e0156679. [PMID: 27383202 PMCID: PMC4934773 DOI: 10.1371/journal.pone.0156679] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/18/2016] [Indexed: 02/06/2023] Open
Abstract
Black people are at increased risk of thrombotic thrombocytopenic purpura (TTP). Whether clinical presentation of TTP in Black patients has specific features is unknown. We assessed here differences in TTP presentation and outcome between Black and White patients. Clinical presentation was comparable between both ethnic groups. However, prognosis differed with a lower death rate in Black patients than in White patients (2.7% versus 11.6%, respectively, P = .04). Ethnicity, increasing age and neurologic involvement were retained as risk factors for death in a multivariable model (P < .05 all). Sixty-day overall survival estimated by the Kaplan-Meier curves and compared with the Log-Rank test confirmed that Black patients had a better survival than White patients (P = .03). Salvage therapies were similarly performed between both groups, suggesting that disease severity was comparable. The comparison of HLA-DRB1*11, -DRB1*04 and -DQB1*03 allele frequencies between Black patients and healthy Black individuals revealed no significant difference. However, the protective allele against TTP, HLA-DRB1*04, was dramatically decreased in Black individuals in comparison with White individuals. Black people with TTP may have a better survival than White patients despite a comparable disease severity. A low natural frequency of HLA-DRB1*04 in Black ethnicity may account for the greater risk of TTP in this population.
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Alarcón GS, Bastian HM, Beasley TM, Roseman JM, Tan FK, Fessler BJ, Vilá LM, McGwin G. Systemic lupus erythematosus in a multi-ethnic cohort (LUMINA): contributions of admixture and socioeconomic status to renal involvement. Lupus 2016; 15:26-31. [PMID: 16482742 DOI: 10.1191/0961203306lu2260oa] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Renal involvement in systemic lupus erythematosus (SLE) is more frequent in minorities. We examined whether genetic or socioeconomic status (SES) explain these disparities in a large multiethnic (Hispanics from Texas and Puerto Rico, African Americans and Caucasians) SLE cohort. Renal involvement was defined as WHO Class II-V and/or proteinuria (>0.5 g/24 h or 3+) attributable to SLE and/or abnormal urinary sediment, proteinuria 2+, elevated serum creatinine/decreased creatinine clearance twice, 6 months apart present any time over the course of the disease. Ancestry informative markers (AIMS) were used to define the admixture proportions in each patient and group. Logistic regression models were examined to determine the percentage variance ( R2) in renal involvement related to ethnicity that is explained by socio-economic status (SES) and admixture (adjusting for age, gender and disease duration, basic model). Four-hundred and fifty-nine (out of 575) patients were included; renal involvement occurred in 44.6% Texas Hispanics, 11.3% Puerto Rico Hispanics, 45.8% African Americans, 18.3% Caucasians. SES accounted for 14.5% of the variance due to ethnicity (after adjusting for basic model variables), admixture 36.8% and both, 12.2%; 45.9% of the variance remained unexplained. Alternative models for decreased glomerula filtration rate and end-stage renal disease were comparable in the distribution of the explanatory variables. Our data indicate that genetic factors appear to be more important than SES in explaining the ethnic disparities in the occurrence of renal involvement.
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Affiliation(s)
- G S Alarcón
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, 35294, USA.
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Vučković F, Krištić J, Gudelj I, Teruel M, Keser T, Pezer M, Pučić-Baković M, Štambuk J, Trbojević-Akmačić I, Barrios C, Pavić T, Menni C, Wang Y, Zhou Y, Cui L, Song H, Zeng Q, Guo X, Pons-Estel BA, McKeigue P, Leslie Patrick A, Gornik O, Spector TD, Harjaček M, Alarcon-Riquelme M, Molokhia M, Wang W, Lauc G. Association of systemic lupus erythematosus with decreased immunosuppressive potential of the IgG glycome. Arthritis Rheumatol 2016. [PMID: 26200652 PMCID: PMC4626261 DOI: 10.1002/art.39273] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Objective Glycans attached to the Fc portion of IgG are important modulators of IgG effector functions. Interindividual differences in IgG glycome composition are large and they associate strongly with different inflammatory and autoimmune diseases. IKZF1, HLA–DQ2A/B, and BACH2 genetic loci that affect IgG glycome composition show pleiotropy with systemic lupus erythematosus (SLE), indicating a potentially causative role of aberrant IgG glycosylation in SLE. We undertook this large multicenter case–control study to determine whether SLE is associated with altered IgG glycosylation. Methods Using ultra‐performance liquid chromatography analysis of released glycans, we analyzed the composition of the IgG glycome in 261 SLE patients and 247 matched controls of Latin American Mestizo origin (the discovery cohort) and in 2 independent replication cohorts of different ethnicity (108 SLE patients and 193 controls from Trinidad, and 106 SLE patients and 105 controls from China). Results Multiple statistically significant differences in IgG glycome composition were observed between patients and controls. The most significant changes included decreased galactosylation and sialylation of IgG (which regulate proinflammatory and antiinflammatory actions of IgG) as well as decreased core fucose and increased bisecting N‐acetylglucosamine (which affect antibody‐dependent cell‐mediated cytotoxicity). Conclusion The IgG glycome in SLE patients is significantly altered in a way that decreases immunosuppressive action of circulating immunoglobulins. The magnitude of observed changes is associated with the intensity of the disease, indicating that aberrant IgG glycome composition or changes in IgG glycosylation may be an important molecular mechanism in SLE.
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Affiliation(s)
- Frano Vučković
- Genos Ltd., Glycoscience Research Laboratory, Zagreb, Croatia
| | | | - Ivan Gudelj
- Genos Ltd., Glycoscience Research Laboratory, Zagreb, Croatia
| | - Maria Teruel
- Pfizer-University of Granada-Junta de Andalucia Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | | | - Marija Pezer
- Genos Ltd., Glycoscience Research Laboratory, Zagreb, Croatia
| | | | - Jerko Štambuk
- Genos Ltd., Glycoscience Research Laboratory, Zagreb, Croatia
| | | | - Clara Barrios
- King's College London, London, UK, and Hospital del Mar and Institut Mar d'Investigacions Mediques, Barcelona, Spain
| | | | | | | | - Yong Zhou
- Beijing Tiantan Hospital and Capital Medical University, Beijing, China
| | - Liufu Cui
- Affiliated Kailuan General Hospital of Hebei United University, Tangshan, China
| | - Haicheng Song
- Affiliated Kailuan General Hospital of Hebei United University, Tangshan, China
| | - Qiang Zeng
- International Medical Center and Chinese People's Liberation Army General Hospital, Beijing, China
| | - Xiuhua Guo
- Capital Medical University, Beijing, China
| | | | | | | | | | | | | | - Marta Alarcon-Riquelme
- Pfizer-University of Granada-Junta de Andalucia Centre for Genomics and Oncological Research (GENYO), Granada, Spain, and Oklahoma Medical Research Foundation, Oklahoma City
| | | | - Wei Wang
- Capital Medical University, Beijing, China, and Edith Cowan University, Perth, Western Australia, Australia
| | - Gordan Lauc
- Genos Ltd., Glycoscience Research Laboratory, and University of Zagreb, Zagreb, Croatia
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Seldin MF. The genetics of human autoimmune disease: A perspective on progress in the field and future directions. J Autoimmun 2015; 64:1-12. [PMID: 26343334 PMCID: PMC4628839 DOI: 10.1016/j.jaut.2015.08.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/23/2015] [Indexed: 12/18/2022]
Abstract
Progress in defining the genetics of autoimmune disease has been dramatically enhanced by large scale genetic studies. Genome-wide approaches, examining hundreds or for some diseases thousands of cases and controls, have been implemented using high throughput genotyping and appropriate algorithms to provide a wealth of data over the last decade. These studies have identified hundreds of non-HLA loci as well as further defining HLA variations that predispose to different autoimmune diseases. These studies to identify genetic risk loci are also complemented by progress in gene expression studies including definition of expression quantitative trait loci (eQTL), various alterations in chromatin structure including histone marks, DNase I sensitivity, repressed chromatin regions as well as transcript factor binding sites. Integration of this information can partially explain why particular variations can alter proclivity to autoimmune phenotypes. Despite our incomplete knowledge base with only partial definition of hereditary factors and possible functional connections, this progress has and will continue to facilitate a better understanding of critical pathways and critical changes in immunoregulation. Advances in defining and understanding functional variants potentially can lead to both novel therapeutics and personalized medicine in which therapeutic approaches are chosen based on particular molecular phenotypes and genomic alterations.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA; Division of Rheumatology and Allergy, Department of Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA.
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Girkin CA, Nievergelt CM, Kuo JZ, Maihofer AX, Huisingh C, Liebmann JM, Ayyagari R, Weinreb RN, Ritch R, Zangwill LM. Biogeographic Ancestry in the African Descent and Glaucoma Evaluation Study (ADAGES): Association With Corneal and Optic Nerve Structure. Invest Ophthalmol Vis Sci 2015; 56:2043-9. [PMID: 25744975 DOI: 10.1167/iovs.14-15719] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PURPOSE We determined if quantitative measurements of biogeographic ancestry (BGA) correlate with variations in optic disc area, corneal thickness (CCT), and retinal nerve fiber layer (RNFL) thickness. METHODS Data were obtained from 656 participants in the African Descent and Glaucoma Evaluation Study (ADAGES) cohort who consented to BGA testing. Data for CCT, optic disc area, and RNFL thickness were obtained from subjects in the ADAGES study who also had participated in the current substudy. A total of 31 ancestry informative markers (AIMs) with large allele frequencies differences between populations was used to calculate admixture proportion (implemented in STRUCTURE). Correlations with BGA adjusted for diagnosis, age, and sex for CCT and optic disc area using the whole group and RNFL thickness adjusted for age and sex for the normal study participants were determined. RESULTS The mean percentage of African admixture was 79.6% in the self-described African Descent (AD) group and 3.5% in the European Descent (ED) group. Percent African ancestry was significantly correlated with CCT (ρ = -0.27, P < 0.0001) and disc area (ρ = 0.15, P < 0.0001), but only marginally associated with RNFL thickness (ρ = 0.20, P = 0.092) in adjusted models. CONCLUSIONS The BGA correlates with variation in ocular features that significantly differ across racial groups and that have been associated with the development of glaucoma. While BGA can provide an objective measurement of the biologic component of self-described race for ocular research, for most nongenetic epidemiologic studies, self-described race may adequately describe the associations with these ocular characteristics. (ClinicalTrials.gov number, NCT00221923.).
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Affiliation(s)
- Christopher A Girkin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California, San Diego, San Diego, California, United States
| | - Jane Z Kuo
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States Pathway Genomics Corporation, San Diego, California, United States
| | - Adam X Maihofer
- Department of Psychiatry, University of California, San Diego, San Diego, California, United States
| | - Carrie Huisingh
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Radha Ayyagari
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
| | - Robert N Weinreb
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
| | - Robert Ritch
- Department of Ophthalmology, New York Eye and Ear Infirmary, New York, New York, United States
| | - Linda M Zangwill
- Department of Ophthalmology, University of California, San Diego, San Diego, California, United States
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17
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Epidemiology and classification of systemic lupus erythematosus. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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18
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Reynolds RJ, Ahmed AF, Danila MI, Hughes LB, Gregersen PK, Raychaudhuri S, Plenge RM, Bridges SL. HLA-DRB1-associated rheumatoid arthritis risk at multiple levels in African Americans: hierarchical classification systems, amino acid positions, and residues. Arthritis Rheumatol 2014; 66:3274-82. [PMID: 25524867 PMCID: PMC4273668 DOI: 10.1002/art.38855] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/19/2014] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To evaluate HLA-DRB1 genetic risk of rheumatoid arthritis (RA) in African Americans by 3 validated allele classification systems and by amino acid position and residue, and to compare genetic risk between African American and European ancestries. METHODS Four-digit HLA-DRB1 genotyping was performed on 561 autoantibody-positive African American cases and 776 African American controls. Association analysis was performed on Tezenas du Montcel (TdM), de Vries (DV), and Mattey classification system alleles and separately by amino acid position and individual residues. RESULTS TdM S2 and S3P alleles were associated with RA (odds ratio [95% confidence interval] 2.8 [2.0-3.9] and 2.1 [1.7-2.7], respectively). The DV (P = 3.2 × 10(-12)) and Mattey (P = 6.5 × 10(-13)) system alleles were both protective in African Americans. Amino acid position 11 (permutation P < 0.00001) accounted for nearly all variability explained by HLA-DRB1, although conditional analysis demonstrated that position 57 was also significant (0.01 ≤ permutation P ≤ 0.05). The valine and aspartic acid residues at position 11 conferred the highest risk of RA in African Americans. CONCLUSION With some exceptions, the genetic risk conferred by HLA-DRB1 in African Americans is similar to that in individuals of European ancestry at multiple levels: classification system (e.g., TdM), amino acid position (e.g., 11), and residue (Val11). Unlike that reported for individuals of European ancestry, amino acid position 57 was associated with RA in African Americans, but positions 71 and 74 were not. Asp11 (odds ratio 1 in European ancestry) corresponds to the 4-digit classical allele *09:01, which is also a risk allele for RA in Koreans.
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Affiliation(s)
| | | | | | | | - CLEAR Investigators
- Richard D. Brasington, Jr. MD (Washington University at St. Louis), Leigh F. Callahan, PhD (University of North Carolina at Chapel Hill), Doyt L. Conn, MD (Emory University), Beth L. Jonas, MD (University of North Carolina at Chapel Hill), Larry W. Moreland, MD (University of Pittsburgh), Edwin A. Smith, MD (Medical University of South Carolina)
| | | | - Soumya Raychaudhuri
- Brigham & Women's Hospital, Harvard Medical School, Division of Genetics & Rheumatology, Boston, MA
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Almal SH, Padh H. Frequency distribution of autoimmunity associated FCGR3B gene copy number in Indian population. Int J Immunogenet 2014; 42:26-30. [PMID: 25428402 DOI: 10.1111/iji.12165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/12/2014] [Accepted: 10/23/2014] [Indexed: 11/27/2022]
Abstract
Amongst several human genome variations, copy number variations (CNVs) are considered as an important source of variability contributing to susceptibility to wide range of diseases. Although CNV is scattered for genes throughout the human genome, several of autoimmunity related genes have CN variation and therefore play an important role in susceptibility to autoimmune diseases. The association of the Fc gamma receptor 3B (FCGR3B) gene copy number in autoimmunity is well characterized in various populations studied. The Fc gamma receptor is a low affinity, glycosylphosphatidylinositol-linked receptor for IgG molecule predominantly expressed on human neutrophils. The variable gene copy number of FCGR3B is found to be involved in the impaired clearance of immune complexes, which significantly contribute to the pathogenesis of several autoimmune diseases such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), type-1 diabetes and others. The FCGR3B copy number ranged from 0 to ≥ 2 copies per diploid genome in other populations, but yet not explored in Indian population. Hence, this study aims to evaluate the variation in the frequency distribution of FCGR3B CNV in Indian population. FCGR3B gene copy number varied significantly when compared to other population of the world. This observation will help us in exploring the potential role of CNV in FCGR3B gene and its association to autoimmune disorders in Indian population.
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Affiliation(s)
- S H Almal
- Department of Cell and Molecular Biology, B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
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20
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Familial clustering of systemic lupus erythematosus in the cayman islands. W INDIAN MED J 2014; 63:325-8. [PMID: 25429475 DOI: 10.7727/wimj.2013.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/30/2013] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To describe the unusual clustering of systemic lupus erythematosus (SLE) in a family from the Cayman Islands. METHOD An observational retrospective study of SLE was done following an index case of mixed connective tissue disease in a 51-year old West Indian woman of African descent. Her two daughters of the same father, who is of Cayman Islands origin, were also diagnosed with SLE. A family tree was subsequently drawn up to 1890 to identify other cases in the same family. RESULTS There were 13 cases identified and all occurred between the 6th and the 8th generation. A family tree linked all cases to a man from the Cayman Islands who died in 1890. The nine cases with full medical records showed eight females and one male (8:1). The mean age at diagnosis was 29 years; polyarthritis occured in all nine patients (100%), kidney involvement in 6/9 (66.6%), skin rash in 6/9 (66.6%), pleuritis and pericarditis in 6/9 (66.6%) and anaemia in 6/9 (66.6%). The autoantibodies were mainly ANA in all patients (100%) and anti-dsDNA in 8/9 (88.8%). CONCLUSION The unusual extensive familial clustering in this study represents the first to be described in a West Indian population where SLE is most prevalent and may suggest a genetic predisposition.
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21
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Lim SS, Bayakly AR, Helmick CG, Gordon C, Easley K, Drenkard C. The incidence and prevalence of systemic lupus erythematosus, 2002-2004: The Georgia Lupus Registry. Arthritis Rheumatol 2014; 66:357-68. [PMID: 24504808 PMCID: PMC4617771 DOI: 10.1002/art.38239] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/15/2013] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The Georgia Lupus Registry is a population-based registry designed to improve our ability to estimate the incidence and prevalence of systemic lupus erythematosus (SLE) in a large population. METHODS Potential cases of SLE were identified from multiple sources during the years 2002 through 2004. Cases were defined according to the American College of Rheumatology (ACR) criteria for SLE or a combined definition. Age-standardized rates were determined and stratified by race and sex. With capture-recapture analyses, we estimated the under-ascertainment of cases. RESULTS Using the ACR case definition, the overall crude and age-adjusted incidence rate was 5.6 per 100,000, with capture-recapture and combined definition rates being slightly higher. The age-adjusted incidence rate in women was >5 times higher than that for men (9.2 versus 1.8). Black women had an incidence rate nearly 3 times higher than that in white women, with a significantly higher rate in the group ages 30-59 years. The overall crude and age-adjusted prevalence rates were 74.4 and 73 per 100,000, respectively. The age-adjusted prevalence rate in women was nearly 9 times higher than that for men (127.6 versus 14.7). Black women had very high rates (196.2). A striking difference was seen in the proportion of prevalent cases with end-stage renal disease, with 7-fold greater involvement among black patients. CONCLUSION With the more complete case-finding methods we used, the incidence and prevalence rates of SLE are among the highest reported in the US. The results continue to underscore striking sex, age, and racial disparities between black patients and white patients with SLE.
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Affiliation(s)
- S. Sam Lim
- Emory University, Department of Medicine, Division of Rheumatology, Atlanta, GA
| | | | | | | | - Kirk Easley
- Emory University, Rollins School of Public Health, Department of Biostatistics and Bioinformatics, Atlanta, GA
| | - Cristina Drenkard
- Emory University, Department of Medicine, Division of Rheumatology, Atlanta, GA
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22
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Li M, Zhang W, Leng X, Li Z, Ye Z, Li C, Li X, Zhu P, Wang Z, Zheng Y, Li X, Zhang M, Zhang F, Zhao Y, Zeng X. Chinese SLE Treatment and Research group (CSTAR) registry: I. Major clinical characteristics of Chinese patients with systemic lupus erythematosus. Lupus 2013; 22:1192-9. [PMID: 23963101 DOI: 10.1177/0961203313499086] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Chinese systemic lupus erythematosus (SLE) treatment and research group (CSTAR) provides major clinical characteristics of SLE in China and establishes a platform to provide resources for future basic and clinical studies. CSTAR originated as a multicentre, consecutive, and prospective design. The data were collected online from 104 rheumatology centers, which covered 30 provinces in China. The registered patients were required to meet four or more of the American College of Rheumatology (ACR) criteria for the classification of SLE. All CSTAR centers use the same protocol-directed methods to provide uniform evaluations, which included demographic data, clinical features, laboratory examinations, and disease activity evaluations. The patient samples, including DNA samples and sera, were also collected for further quality controls and additional studies. Preliminary analysis from 2104 baseline evaluations was available for this analysis. Of 1914 female and 190 male patients (F:M=10.1), the mean age at onset was 29.2 y with confirmed diagnosis one year later at the age of 30.3 y. Eighty four (4.2%) of 2002 patients had a family history of rheumatic diseases, including 34 (1.7%) cases with SLE. In addition, one hundred and seven (5.2%) abnormal pregnancies were recorded among 2026 experiences. The characteristics of the CSTAR cohort were compared to similarly sized cohorts from other studies. We found that 56.1% of patients presented with concurrent hematological disorders compared to only 18.2% of European patients. Moreover, 47.4% of patients presented with nephropathy compared to 27.9% of European patients. Conversely, neurological manifestations were only seen in 4.8% of Chinese SLE patients compared to 19.4% of European patients, 12.1% of U.S. patients, 22.8% of Malaysian patients and 26.4% of Latin Americans. Pulmonary arterial hypertension and interstitial lung diseases were complications identified in 3.8% and 4.2% of Chinese lupus patients, respectively. The CSTAR registry has provided epidemiological data and phenotypes of Chinese patients with SLE, and has demonstrated several differences between ethnicities. Clinical data and biologic samples would be valuable resources for future translational studies with national and international collaboration.
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Affiliation(s)
- M Li
- 1Department of Rheumatology, Peking Union Medical College Hospital, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
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Torres JB, Stone AC, Kittles R. An anthropological genetic perspective on Creolization in the Anglophone Caribbean. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:135-43. [PMID: 23553646 DOI: 10.1002/ajpa.22261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 02/14/2013] [Indexed: 01/23/2023]
Abstract
Variable socio-cultural influences developed in the colonial Caribbean as a result of competing European hegemonic rule. In this study, we examine how colonial regulations regarding social hierarchies and mate choice worked to influence the genetic landscape of contemporary African Caribbean populations. To this end, 420 individuals from Dominica, Grenada, St. Kitts, St. Lucia, St. Thomas, St. Vincent, Jamaica, and Trinidad were genotyped for 105 autosomal ancestry informative markers. Based on these data, population substructure and admixture were assessed using an exact test, a model-based clustering method, and principal components analysis. On average, individual admixture estimates of the pooled African Caribbean sample were 77% (SD ± 18%) West African, 15% (SD ± 15%) European, and 7.7% (SD ± 8%) Native American. In general, ancestry estimates were significantly different between Dominica and all other islands. Genetic structure analyses indicated subdivision into two subpopulations on most islands. Finally, unlike all of the other Caribbean populations that clustered adjacent to African populations, the Dominican population was more intermediate between the three parental groups in the principal components plot. As a result of the significant French influence throughout Dominican history, Dominica did not have the same cultural influences that typified other Anglophone colonies. Consequently, there were different social hierarchies and resulting mate choices on Dominica compared with the other considered islands. This study highlights the complex socio-cultural history of a broad region of the Caribbean and attests to the interplay between social and biological factors in shaping the genetic diversity present in present-day communities.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, IN 46556, USA.
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Rumpel JA, Ahmedani BK, Peterson EL, Wells KE, Yang M, Levin AM, Yang JJ, Kumar R, Burchard EG, Williams LK. Genetic ancestry and its association with asthma exacerbations among African American subjects with asthma. J Allergy Clin Immunol 2012; 130:1302-6. [PMID: 23069492 DOI: 10.1016/j.jaci.2012.09.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/17/2012] [Accepted: 09/01/2012] [Indexed: 02/04/2023]
Abstract
BACKGROUND There are large and persisting disparities in severe asthma exacerbations by race-ethnicity, and African American subjects are among those at greatest risk. It is unclear whether this increased risk solely represents differences in environmental exposures and health care or whether there is a predisposing genetic component. OBJECTIVE We sought to assess the relationship between genetic ancestry and severe exacerbations among African American subjects with asthma. METHODS Participants were part of the Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-ethnicity (SAPPHIRE). These subjects were 12 to 56 years of age, received care from a single large health system, and had a physician's diagnosis of asthma. Genetic ancestry was estimated by using a set of validated ancestry informative markers. Severe exacerbations (ie, asthma-related emergency department visits, hospitalizations, and burst oral steroid use) were prospectively identified from health care claims. RESULTS We assessed genetic ancestry in 392 African American subjects with asthma. The average proportion of African ancestry was 76.1%. A significant interaction was identified between ancestry and sex on severe exacerbations, such that the risk was significantly higher with increasing African ancestry among male but not female subjects. The association among male subjects persisted after adjusting for potential confounders (relative rate, 4.30 for every 20% increase in African ancestry; P = .029). CONCLUSIONS African ancestry was significantly and positively associated with severe exacerbations among male African American subjects. These findings suggest that a portion of the risk of asthma exacerbations in this high-risk group is attributable to a genetic risk factor that partitions with ancestry.
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Affiliation(s)
- Jennifer A Rumpel
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
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Flower C, Hennis AJM, Hambleton IR, Nicholson GD, Liang MH. Systemic lupus erythematosus in an African Caribbean population: incidence, clinical manifestations, and survival in the Barbados National Lupus Registry. Arthritis Care Res (Hoboken) 2012; 64:1151-8. [PMID: 22392730 DOI: 10.1002/acr.21656] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To assess the epidemiology, clinical features, and outcomes of systemic lupus erythematosus (SLE) in the predominantly African Caribbean population of Barbados. METHODS A national registry of all patients diagnosed with SLE was established in 2007. Complete case ascertainment was facilitated by collaboration with the island's sole rheumatology service, medical practitioners, and the lupus advocacy group. Informed consent was required for inclusion. RESULTS Between January 1, 2000 and December 31, 2009, there were 183 new cases of SLE (98% African Caribbean) affecting 172 women and 11 men for unadjusted annual incidence rates of 12.21 (95% confidence interval [95% CI] 10.46-14.18) and 0.84 (95% CI 0.42-1.51) per 100,000 person-years, respectively. Excluding pediatric cases (ages <18 years), the unadjusted incidence rate among women was 15.14 per 100,000 person-years. The principal presenting manifestations were arthritis (84%), nephritis (47%), pleuritis (41.5%), malar rash (36.4%), and discoid lesions (33.1%). Antinuclear antibody positivity was 95%. The overall 5-year survival rate was 79.9% (95% CI 69.6-87.1), decreasing to 68% in patients with nephritis. A total of 226 persons with SLE were alive at the end of the study for point prevalences of 152.6 (95% CI 132.8-174.5) and 10.1 (95% CI 5.4-17.2) per 100,000 among women and men, respectively. CONCLUSION Rates of SLE in Barbadian women are among the highest reported to date, with clinical manifestations similar to African American women and high mortality. Further study of this population and similar populations of West African descent might assist our understanding of environmental, genetic, and health care issues underpinning disparities in SLE.
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Affiliation(s)
- Cindy Flower
- The University of the West Indies, Bridgetown, Barbados.
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Gilkeson G, James J, Kamen D, Knackstedt T, Maggi D, Meyer A, Ruth N. The United States to Africa lupus prevalence gradient revisited. Lupus 2012; 20:1095-103. [PMID: 21917913 DOI: 10.1177/0961203311404915] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has a significantly higher prevalence, morbidity and mortality in African Americans compared with Americans of European descent. The pathogenesis of lupus is unclear but appears to be a result of environmental factors interacting with a genetically susceptible host. Despite the high disease load of SLE in African Americans, there is the perception that lupus is relatively rare in Africa. This prevalence gradient suggests that comparative studies of related cohorts from the two continents may provide insight into the genetic/environmental interactions that result in the development of lupus. To define if a lupus gradient exists, we began a study of autoimmunity prevalence utilizing two unique cohorts. The first is the Gullah population of the Sea Islands of South Carolina, who are unique in their low genetic admixture and their known ancestral heritage. The second is the population of young women served by the West Africa Fistula Foundation in Bo, Sierra Leone. Anthropologic studies indicate a direct ancestral link between the Gullah population and Sierra Leoneans. Since it is impossible to perform an epidemiologic study of lupus in Sierra Leone at this time, we assessed the prevalence of lupus serum autoantibodies, serologic evidence of specific infections and levels of serum 25-OH vitamin D in young women in the two cohorts who have no known relatives with lupus. Our results indicate similar prevalence of serum antinuclear antibodies in the two cohorts, though there was a significantly increased prevalence of antiphospholipid and anti-Sm antibodies in the Sierra Leone cohort. Seropositivity to common viral infections was significantly higher in women from Sierra Leone, while serum 25-OH vitamin D levels were markedly lower in the Gullah population. These data suggest that the prevalence of autoimmunity is similar in the two populations, but that there are significant environmental differences that may impact progression to autoimmune disease. Further studies comparing these two cohorts is likely to provide important insight into the impact of environmental factors on development of lupus.
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Affiliation(s)
- Gs Gilkeson
- Department of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC 29412, USA.
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Aghdassi E, Ma DWL, Morrison S, Hillyer LM, Clarke S, Gladman DD, Urowitz MB, Fortin PR. Alterations in circulating fatty acid composition in patients with systemic lupus erythematosus: a pilot study. JPEN J Parenter Enteral Nutr 2011; 35:198-208. [PMID: 21378249 DOI: 10.1177/0148607110386378] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Circulating fatty acids (FAs) may play a role in the disease pathogenesis of patients with systemic lupus erythematosus (SLE). OBJECTIVES To compare red blood cell (RBC) and plasma FA composition: (1) between female SLE patients and age-matched healthy female (HF) controls and in SLE with history of cardiovascular disease (CVD) and those with no history (SLE+CVD vs SLE-CVD); and (2) between SLE patients who were or were not receiving prednisone treatment at the time of blood sampling. METHODS This cross-sectional study consisted of 33 female patients with SLE (11 SLE+CVD, 22 SLE-CVD) and 20 HF controls. Demographics, CVD risk, medication profile, blood biochemistry, and FA composition of RBC and plasma total lipids were determined. RESULTS Waist circumference and body mass index were higher in SLE patients than in HF controls. These variables along with serum triglycerides, blood glucose, and systolic blood pressure were higher in SLE+CVD than SLE-CVD patients. RBC FA composition showed lower eicosapentaenoic acid (EPA, ω-3 active metabolite) and ω-3 index (EPA+ docosahexaenoic acid) in SLE patients compared with HF controls. The ratio of the RBC inflammatory metabolite, arachidonic acid, to the anti-inflammatory metabolite EPA was also significantly higher in SLE patients than in HF controls. No differences were seen in plasma FA between SLE and HF groups. However, SLE-CVD patients had a more favorable lipid profile than SLE+CVD patients. In SLE patients, the use of prednisone resulted in alteration of both RBC and plasma FA composition. CONCLUSION SLE patients, regardless of their history of CVD, have altered plasma and RBC FA composition favoring inflammation. The use of prednisone was associated with differences in FA profile.
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Affiliation(s)
- Elaheh Aghdassi
- Division of Health Care and Outcome Research, Toronto Western Research Institute, Ontario, Canada
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Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, Kao WHL, Ruczinski I, Fornage M, Siscovick DS, Zhu X, Larkin E, Lange LA, Cupples LA, Yang Q, Akylbekova EL, Musani SK, Divers J, Mychaleckyj J, Li M, Papanicolaou GJ, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante SJ, Bandera EV, Ingles SA, Press MF, Chanock SJ, Deming SL, Rodriguez-Gil JL, Palmer CD, Buxbaum S, Ekunwe L, Hirschhorn JN, Henderson BE, Myers S, Haiman CA, Reich D, Patterson N, Wilson JG, Price AL. Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium. PLoS Genet 2011; 7:e1001371. [PMID: 21541012 PMCID: PMC3080860 DOI: 10.1371/journal.pgen.1001371] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 03/10/2011] [Indexed: 12/24/2022] Open
Abstract
While genome-wide association studies (GWAS) have primarily examined populations of European ancestry, more recent studies often involve additional populations, including admixed populations such as African Americans and Latinos. In admixed populations, linkage disequilibrium (LD) exists both at a fine scale in ancestral populations and at a coarse scale (admixture-LD) due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered SNP association (LD mapping) or admixture association (mapping by admixture-LD), but not both. Here, we introduce a new statistical framework for combining SNP and admixture association in case-control studies, as well as methods for local ancestry-aware imputation. We illustrate the gain in statistical power achieved by these methods by analyzing data of 6,209 unrelated African Americans from the CARe project genotyped on the Affymetrix 6.0 chip, in conjunction with both simulated and real phenotypes, as well as by analyzing the FGFR2 locus using breast cancer GWAS data from 5,761 African-American women. We show that, at typed SNPs, our method yields an 8% increase in statistical power for finding disease risk loci compared to the power achieved by standard methods in case-control studies. At imputed SNPs, we observe an 11% increase in statistical power for mapping disease loci when our local ancestry-aware imputation framework and the new scoring statistic are jointly employed. Finally, we show that our method increases statistical power in regions harboring the causal SNP in the case when the causal SNP is untyped and cannot be imputed. Our methods and our publicly available software are broadly applicable to GWAS in admixed populations.
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Affiliation(s)
- Bogdan Pasaniuc
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Noah Zaitlen
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Canada
- Département de Médecine, Université de Montréal, Montréal, Canada
| | - Gary K. Chen
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Arti Tandon
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - W. H. Linda Kao
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine and Division of Epidemiology, School of Public Health, University of Texas Health Sciences Center at Houston, Houston, Texas, United States of America
| | - David S. Siscovick
- Departments of Medicine and Epidemiology, University of Washington, Seattle, Washington, United States of America
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Emma Larkin
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Qiong Yang
- Department of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Ermeg L. Akylbekova
- Jackson Heart Study, Jackson State University, Jackson, Mississippi, United States of America
| | - Solomon K. Musani
- University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Jasmin Divers
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Joe Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George J. Papanicolaou
- National Heart, Lung, and Blood Institute (NHLBI), Division of Cardiovascular Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Esther M. John
- Northern California Cancer Center, Fremont, California, United States of America
- Stanford University School of Medicine and Stanford Cancer Center, Stanford, California, United States of America
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, California, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Regina G. Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sarah J. Nyante
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Sue A. Ingles
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Michael F. Press
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sandra L. Deming
- Institute for Medicine and Public Health, Vanderbilt Epidemiology Center, Nashville, Tennessee, United States of America
| | - Jorge L. Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Cameron D. Palmer
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Divisions of Genetics and Endocrinology and Program in Genomics, Children’s Hospital Boston, Boston, Massachusetts, United States of America
| | - Sarah Buxbaum
- Jackson Heart Study, Jackson State University, Jackson, Mississippi, United States of America
| | - Lynette Ekunwe
- Jackson Heart Study, Jackson State University, Jackson, Mississippi, United States of America
| | - Joel N. Hirschhorn
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Divisions of Genetics and Endocrinology and Program in Genomics, Children’s Hospital Boston, Boston, Massachusetts, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Simon Myers
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Christopher A. Haiman
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - David Reich
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nick Patterson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - James G. Wilson
- University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- V. A. Medical Center, Jackson, Mississippi, United States of America
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
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Molokhia M, Fanciulli M, Petretto E, Patrick AL, McKeigue P, Roberts AL, Vyse TJ, Aitman TJ. FCGR3B copy number variation is associated with systemic lupus erythematosus risk in Afro-Caribbeans. Rheumatology (Oxford) 2011; 50:1206-10. [PMID: 21296850 DOI: 10.1093/rheumatology/keq456] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To evaluate FCGR3B copy number variation (CNV) in African and European populations and to determine if FCGR3B copy number is associated with SLE and SLE nephritis risk in Afro-Caribbeans, adjusting for African genetic ancestry. METHODS We estimated FCGR3B to determine if there were ethnic variations in CNV (unrelated unadmixed Europeans and Africans). We then examined CNV at FCGR3B in relation to SLE and SLE nephritis within a case-control collection of 134 cases of SLE (37 with SLE nephritis) and 589 population controls of mainly Afro-Caribbean descent resident in Trinidad. RESULTS We found a significant difference in copy number FCGR3B distribution between unadmixed African and European UK cohorts, with 27 (29%) vs 3 (5%) for those with low (0 or 1) copy FCGR3B, respectively, P = 0.002. In a Trinidadian SLE case-control study, low FCGR3B CNV was associated with SLE risk 1.7 (95% CI 1.1, 2.8), P = 0.02, which remained after adjustment for African genetic ancestry; odds ratios (ORs) 1.7 (95% CI 1.0, 2.8), P = 0.04. CONCLUSION Our studies suggest that FCGR3B low copy number is associated with SLE risk in Afro-Caribbean populations independently of CNV due to African ancestry.
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Affiliation(s)
- Mariam Molokhia
- Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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Pedroza LSRA, Sauma MFLC, Vasconcelos JM, Takeshita LYC, Ribeiro-Rodrigues EM, Sastre D, Barbosa CM, Chies JAB, Veit TD, Lima CPS, Oliveira LF, Henderson BL, Castro APG, Maia MHT, Barbosa FB, Santos SEB, Guerreiro JF, Sena L, Santos EJM. Systemic lupus erythematosus: association with KIR and SLC11A1 polymorphisms, ethnic predisposition and influence in clinical manifestations at onset revealed by ancestry genetic markers in an urban Brazilian population. Lupus 2011; 20:265-73. [PMID: 21233146 DOI: 10.1177/0961203310385266] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder of the connective tissue with a wide and heterogeneous spectrum of manifestations, with renal and neurological involvement usually related to worse prognosis. SLE more frequently affects females of reproductive age, and a high prevalence and renal manifestation seem to be associated with non-European ethnicity. The present study aims to investigate candidate loci to SLE predisposition and evaluate the influence of ethnic ancestry in the disease risk and clinical phenotypic heterogeneity of lupus at onset. Samples represented by 111 patients and 345 controls, originated from the city of Belém, located in the Northern Region of Brazil, were investigated for polymorphisms in HLA-G, HLA-C, SLC11A1, MTHFR, CASP8 and 15 KIR genes, in addition to 89 Amerindian samples genotyped for SLC11A1. We also investigated 48 insertion/deletion ancestry markers to characterize individual African, European and Amerindian ancestry proportions in the samples. Predisposition to SLE was associated with GTGT deletion at the SLC11A1 3'UTR, presence of KIR2DS2 +/KIR2DS5 +/KIR3DS1 + profile, increased number of stimulatory KIR genes, and European and Amerindian ancestries. The ancestry analysis ruled out ethnic differences between controls and patients as the source of the observed associations. Moreover, the African ancestry was associated with renal manifestations.
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Affiliation(s)
- L S R A Pedroza
- 1Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
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Genetic susceptibility to systemic lupus erythematosus protects against cerebral malaria in mice. Proc Natl Acad Sci U S A 2010; 108:1122-7. [PMID: 21187399 DOI: 10.1073/pnas.1017996108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plasmodium falciparum has exerted tremendous selective pressure on genes that improve survival in severe malarial infections. Systemic lupus erythematosus (SLE) is an autoimmune disease that is six to eight times more prevalent in women of African descent than in women of European descent. Here we provide evidence that a genetic susceptibility to SLE protects against cerebral malaria. Mice that are prone to SLE because of a deficiency in FcγRIIB or overexpression of Toll-like receptor 7 are protected from death caused by cerebral malaria. Protection appears to be by immune mechanisms that allow SLE-prone mice better to control their overall inflammatory responses to parasite infections. These findings suggest that the high prevalence of SLE in women of African descent living outside of Africa may result from the inheritance of genes that are beneficial in the immune control of cerebral malaria but that, in the absence of malaria, contribute to autoimmune disease.
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Aghdassi E, Zhang W, St-Pierre Y, Clarke AE, Morrison S, Peeva V, Landolt-Marticorena C, Su J, Reich H, Scholey J, Herzenberg A, Pope JE, Peschken C, Wither JE, Fortin PR. Healthcare cost and loss of productivity in a Canadian population of patients with and without lupus nephritis. J Rheumatol 2010; 38:658-66. [PMID: 21159829 DOI: 10.3899/jrheum.100482] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To compare the healthcare cost and loss of productivity in patients with systemic lupus erythematosus (SLE) with (LN) and without lupus nephritis (lupus nephritis-negative, LNN). METHOD Patients were classified into those with active (ALN and ALNN) and inactive disease (ILN and ILNN). Patients reported on visits to healthcare professionals and use of diagnostic tests, medications, assistive devices, alternative treatments, hospital emergency visits, surgical procedures, and hospitalizations as well as loss of productivity in the 4 weeks preceding enrollment. RESULTS Enrollment was 141 patients, 79 with LN and 62 LNN. Patients with LN were more likely to visit rheumatologists and nephrologists, undergo diagnostic tests, and had higher costs for medications than patients who were LNN. The annual healthcare cost averaged $CAN 12,597 ± 9946 for patients with LN and $10,585 ± 13,149 for patients who were LNN, a difference of $2012 (95% CI -$2075, $6100). Patients with ALN had more diagnostic tests and surgical procedures, contributing to a significantly higher annual direct cost ($14,224 ± 10,265) compared to patients with ILN ($9142 ± 8419) and a difference of $5082 (95% CI $591, $9573). The healthcare cost was not different between patients with ALNN and patients with ILNN. In patients with LN and patients who were LNN, < 50% were employed and on average missed 6.5-9 days of work per month. The loss of productivity was significantly higher for caregivers of patients with LN than caregivers of patients who were LNN. CONCLUSION Healthcare cost and loss of productivity were similar between patients with LN and patients who were LNN; the loss of productivity for caregivers is higher for patients with LN; and the healthcare cost is greater in ALN than in ILN.
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Affiliation(s)
- Elaheh Aghdassi
- Department of Medicine, Division of Rheumatology, University Health Network, University of Toronto, Canada
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Chen G, Shriner D, Zhou J, Doumatey A, Huang H, Gerry NP, Herbert A, Christman MF, Chen Y, Dunston GM, Faruque MU, Rotimi CN, Adeyemo A. Development of admixture mapping panels for African Americans from commercial high-density SNP arrays. BMC Genomics 2010; 11:417. [PMID: 20602785 PMCID: PMC2996945 DOI: 10.1186/1471-2164-11-417] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 07/05/2010] [Indexed: 01/07/2023] Open
Abstract
Background Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs) for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. Results We developed two panels of AIMs (~2,000 markers each) based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. Conclusions Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1) no de novo genotyping needs to be done, thereby saving costs, and (2) markers can be filtered for various quality measures and replacement markers (to minimize gaps) can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1) the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2) clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from SNP chip genotype data provides a fresh opportunity to conduct admixture mapping for disease genes in admixed populations when genome-wide association data exist or are planned.
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Affiliation(s)
- Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Calvo-Alén J, Alarcón GS. Systemic lupus erythematosus and ethnicity: nature versus nurture or nature and nurture? Expert Rev Clin Immunol 2010; 3:589-601. [PMID: 20477163 DOI: 10.1586/1744666x.3.4.589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ethnic variation in the frequency and outcome of systemic lupus erythematosus (SLE) has been recognized for decades. The reasons underlying these discrepancies are not completely understood but it is most likely that both genetic and nongenetic factors are responsible for them. Sorting out the extent to which these factors, particularly those of a nongenetic nature, exert their influence in SLE is not easy given inherent methodological difficulties in studying them. To establish this review properly, we would like to make it clear from the outset that ethnicity is a broad construct that implies not only biological but also nonbiological features including cultural and sociodemographic, among others. We will then describe the epidemiological differences of SLE among Caucasian and non-Caucasian populations followed by a succinct review of the genetic predisposition to SLE with special emphasis in ethnic heterogeneity. Differences in disease activity, lupus nephritis, damage and mortality as a function of ethnic group will then be described. Finally, we will present a comprehensive model of the influence of ethnicity on SLE.
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Affiliation(s)
- Jaime Calvo-Alén
- Hospital Sierrallana, Av. Manuel Teira s/n, Sección de Reumatología, 39300 Torrelavega, Cantabria, Spain.
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Borchers AT, Naguwa SM, Shoenfeld Y, Gershwin ME. The geoepidemiology of systemic lupus erythematosus. Autoimmun Rev 2009; 9:A277-87. [PMID: 20036343 DOI: 10.1016/j.autrev.2009.12.008] [Citation(s) in RCA: 223] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with manifold clinical manifestations and immunological abnormalities, affecting primarily women. Although accurate current data on its incidence and prevalence are largely lacking, there are numerous indications that SLE is far less common in Europeans and their descendants compared to all other ethnicities. The clinical manifestations of the disease show geographic or ethnic variation, generally being less severe in patients of European ancestry than in African, Asian, certain "Hispanic" or mestizo, and various indigenous populations. In particular, renal involvement is far more common in non-European patients. Genetic as well as environmental, sociodemographic and sociocultural factors are likely to contribute to the differences in the incidence and clinical expression of SLE.
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Affiliation(s)
- Andrea T Borchers
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Davis, CA 95616, USA
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Abstract
Genetic, environmental, and hormonal factors contribute to disease susceptibility in systemic lupus erythematosus. Among environmental factors, infectious agents play a major role. When considering the complex relationship between genetic predisposition and infections in the pathogenesis of systemic lupus erythematosus, we have to consider that infectious agents can interact with the immune system in several ways. For example, molecular mimicry, altered apoptosis of the host cells, exposure of as yet masked antigens to the immune system by a given microorganism, and direct viral invasion of immunocompetent cells are all mechanisms that may give rise to dysfunction of the immune system; in addition, some genetically determined deficit of the immune system, such as complement deficiency or deficit of mannose binding lectine, may cause insufficient clearance of infectious agents, whose persistence in the host may determine autoimmunity. Finally, evidence has been emerging suggesting that the production of autoantibodies, by infected B-lymphocytes, may be drawn by altered expression of particular microRNA in these cells. In this paper, we review some of the distinct scenarios that can account for the role of infectious agents, acting on a genetically prone host, in determining systemic lupus erythematosus.
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Halder I, Yang BZ, Kranzler HR, Stein MB, Shriver MD, Gelernter J. Measurement of admixture proportions and description of admixture structure in different U.S. populations. Hum Mutat 2009; 30:1299-309. [PMID: 19572378 PMCID: PMC2867064 DOI: 10.1002/humu.21045] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Variation in individual admixture proportions leads to heterogeneity within populations. Though novel methods and marker panels have been developed to quantify individual admixture, empirical data describing individual admixture distributions are limited. We investigated variation in individual admixture in four U.S. populations (European American [EA], African American [AA], Hispanics from Connecticut [East Coast, or EC], and Hispanics from California [West Coast, or WC]) assuming three-way intermixture among Europeans, Africans, and Indigenous Americans. Admixture estimates were inferred using a panel of 36 microsatellites and one SNP, which have significant allele frequency differences between ancestral populations, and by using both a maximum likelihood (ML)-based method and a Bayesian method implemented in the program STRUCTURE. Simulation studies showed that estimates obtained with this marker panel are within 96% of expected values. EAs had the lowest non-European admixture with both methods, but showed greater homogeneity with STRUCTURE than with ML. All other samples showed a high degree of variation in admixture estimates with both methods, were highly concordant, and showed evidence of admixture stratification. With both methods, AA subjects had on average, 16% European and <10% Indigenous American admixture. EC Hispanics had higher mean African admixture and the WC Hispanics had higher mean Indigenous American admixture, possibly reflecting their different continental origins.
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Affiliation(s)
- Indrani Halder
- Department of Anthropology, Pennsylvania State University, University Park, PA 16801
| | - Bao-Zhu Yang
- Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, CT, USA
- VA CT Healthcare Center 116A2; 950 Campbell Avenue; West Haven, CT 06516
| | - Henry R. Kranzler
- Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Murray B. Stein
- Departments of Psychiatry and Family and Preventive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, University Park, PA 16801
| | - Joel Gelernter
- Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
- VA CT Healthcare Center 116A2; 950 Campbell Avenue; West Haven, CT 06516
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Zuo L, Luo X, Listman JB, Kranzler HR, Wang S, Anton RF, Blumberg HP, Stein MB, Pearlson GD, Covault J, Charney DS, van Kammen DP, Price LH, Lappalainen J, Cramer J, Krystal JH, Gelernter J. Population admixture modulates risk for alcohol dependence. Hum Genet 2009; 125:605-13. [PMID: 19306106 PMCID: PMC2777998 DOI: 10.1007/s00439-009-0647-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/25/2009] [Indexed: 11/29/2022]
Abstract
The admixture of different ancestral populations in America may have important implications for the risk for psychiatric disorders, as it appears to have for other medical disorders. The present study investigated the role of population admixture in risk for several psychiatric disorders in European-Americans (EAs) and African-Americans (AAs). This is a multisite study with 3,792 subjects recruited from across the United States, including 3,119 EAs and 673 AAs. These subjects included healthy controls and those with substance dependence (SD) [including alcohol dependence (AD), cocaine dependence, and opioid dependence], social phobia, affective disorders, and schizophrenia. In addition, DNA was included from 78 West Africans. The degree of admixture for each subject was estimated by analysis of a set of ancestry-informative genetic markers using the program STRUCTURE, and was compared between cases and controls. As noted previously, the degree of admixture in AAs was higher than EAs. In EAs, the degree of admixture (with African ancestry) was significantly lower in patients with SD (mainly AD) than controls (P = 0.009 for SD; P = 0.008 for AD). This finding suggests that population admixture may modulate risk for alcohol dependence. Population admixture might protect against alcohol dependence by increasing average heterozygosity and reducing the risk of deleterious recessive alleles. We cannot exclude the possibility that the results might have been influenced by selection bias due to the multisite nature of the study.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | | | - Henry R. Kranzler
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Raymond F. Anton
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Hilary P. Blumberg
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | - Murray B. Stein
- Departments of Psychiatry and Family and Preventive Medicine, University of California, La Jolla, San Diego, CA, USA
| | - Godfrey D. Pearlson
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
| | - Jonathan Covault
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Dennis S. Charney
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | | | - Lawrence H. Price
- Department of Psychiatry and Human Behavior, Butler Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Jaakko Lappalainen
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | - Joyce Cramer
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
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Amerindian ancestry in Argentina is associated with increased risk for systemic lupus erythematosus. Genes Immun 2008; 9:389-93. [PMID: 18401351 DOI: 10.1038/gene.2008.25] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previous studies have demonstrated that in admixed populations, West African ancestry is associated with an increased prevalence of systemic lupus erythematosus (SLE). In the current study, the effect of Amerindian ancestry in SLE was examined in an admixed population in Argentina. The Argentine population is predominantly European with approximately 20% Amerindian admixture, and a very small (<2%) contribution from West Africa. The results indicate that Amerindian admixture in this population is associated with a substantial increase in SLE susceptibility risk (Odds Ratio=7.94, P=0.00006). This difference was not due to known demographic factors, including site of collection, age and gender. In addition, there were trends towards significance for Amerindian ancestry influencing renal disease, age of onset and anti-SSA antibodies. These studies suggest that populations with Amerindian admixture, like those with West African admixture, should be considered in future studies to identify additional allelic variants that predispose to SLE.
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Molokhia M, Maconochie N, Patrick AL, Doyle P. Cross-sectional analysis of adverse outcomes in 1,029 pregnancies of Afro-Caribbean women in Trinidad with and without systemic lupus erythematosus. Arthritis Res Ther 2008; 9:R124. [PMID: 18042277 PMCID: PMC2246243 DOI: 10.1186/ar2332] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 10/23/2007] [Accepted: 11/27/2007] [Indexed: 11/16/2022] Open
Abstract
The objective of the study was to examine pregnancy outcomes in women with systemic lupus erythematosus (SLE) and population controls in Trinidad. We performed a cross-sectional analysis of adverse outcomes in pregnancies of Afro-Caribbean women with SLE and without SLE. One hundred and twenty-two female adult cases of SLE and 203 neighbourhood age-matched women without SLE were interviewed concerning details of their reproductive history, and the anticardiolipin antibody (ACL) status was established for women with SLE. A total of 1,029 pregnancies were reported (356 by women with SLE, 673 by women without SLE). In women with ≥ 1 pregnancy the total number of pregnancies was similar in women with a diagnosis of SLE and women without; however, a lower proportion of women with SLE had ever been pregnant compared with women without SLE (80% versus 91%, P = 0.002). In multivariate logistic regression analyses adjusted for maternal age, district of residence, pregnancy order and smoking, SLE pregnancies were more than twice as likely to end in foetal death than non-SLE pregnancies (odds ratio (OR), 2.4; 95% confidence interval (CI), 1.2–4.7). This effect was driven by a large increase in the odds of stillbirth (OR, 8.5; 95% CI, 2.5–28.8). The odds of early miscarriage (OR, 1.4; 95% CI, 0.6–3.1) and of mid-trimester miscarriage (OR, 1.9; 95% CI, 0.4–9.5) were higher, but were not statistically significantly different, in SLE pregnancies than in non-SLE pregnancies. The odds of ectopic pregnancy (OR, 7.5; 95% CI, 0.9–62.5) and of preterm birth (OR, 3.4; 95% CI, 1.2–10.0) were higher in SLE pregnancies conceived after diagnosis than in non-SLE pregnancies. There was no evidence of raised levels of IgG or IgM ACL among the majority (93/97 women, 96%) of SLE cases who reported sporadic mid-trimester miscarriage or stillbirth, although there was evidence of high levels of IgM and IgG ACL among women reporting three or more miscarriages and three consecutive miscarriages, and of raised IgG ACL among those experiencing ectopic pregnancy. In conclusion, we found evidence for a large increase in risk of stillbirth in the pregnancies of Afro-Caribbean Trinidadian women with SLE (not accounted for by high ACL status). There was some evidence of an increased risk of preterm delivery and ectopic pregnancy in pregnancies conceived after a diagnosis of maternal SLE.
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Affiliation(s)
- Mariam Molokhia
- Non-Communicable Disease Epidemiology Unit, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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Halder I, Shriver M, Thomas M, Fernandez JR, Frudakis T. A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. Hum Mutat 2008; 29:648-58. [DOI: 10.1002/humu.20695] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Frudakis TN, Thomas MJ, Ginjupalli SN, Handelin B, Gabriel R, Gomez HJ. CYP2D6*4 polymorphism is associated with statin-induced muscle effects. Pharmacogenet Genomics 2007; 17:695-707. [PMID: 17700359 DOI: 10.1097/fpc.0b013e328012d0a9] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Statin use is associated with a variety of overtly related muscle symptoms including muscle pain, myalgia, creatine kinase elevations without pain with myolysis and myositis (rhabdomyolysis), a potentially fatal side effect that led to the withdrawal of cerivastatin in 2001. Unintended drug response phenotypes have an impact on patient compliance and sometimes patient health and the assessment of risk on an individual basis could enhance therapeutic benefit. We therefore investigated whether common single nucleotide polymorphisms were associated with the expression of broadly grouped atorvastatin-induced muscle events in a case-control study (n=263 samples, n=388 SNPs). Of a number of associations identified in a discovery sample (51 atorvastatin-induced muscle and 55 normal) only those corresponding to the CYP2D6*4 allele were significantly associated in the sample (24 atorvastatin-induced muscle and 133 normal) (Discovery P=0.004, odds ratio=3.6; Validation P=0.036, odds ratio=2.7; total P=0.001, odds ratio=2.5). The frequency of the CYP2D6*4 allele was about 50% in atorvastatin-induced muscle patients but only 28% in controls, similar to that of other patient types (28.5%). The association was independent of various demographic variables and not explained by gross demographic, clinical or population-structure differences among cases and controls. Surprisingly, the CYP2D6*4 allele appeared similarly distributed among controls and patients expressing simvastatin-induced muscle events (n=169, frequency in case participants=49.2%, P=0.067, odds ratio=1.7). Our results suggest that the CYP2D6*4 allele is associated with broadly related muscle events caused by at least two structurally dissimilar HMG-CoA reductase inhibitors, and as such, may have implications for a better understanding of this statin-wide phenomena.
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Frudakis T, Terravainen T, Thomas M. Multilocus OCA2 genotypes specify human iris colors. Hum Genet 2007; 122:311-26. [PMID: 17619204 DOI: 10.1007/s00439-007-0401-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 06/25/2007] [Indexed: 01/18/2023]
Abstract
Human iris color is a quantitative, multifactorial phenotype that exhibits quasi-Mendelian inheritance. Recent studies have shown that OCA2 polymorphism underlies most of the natural variability in human iris pigmentation but to date, only a few associated polymorphisms in this gene have been described. Herein, we describe an iris color score (C) for quantifying iris melanin content in-silico and undertake a more detailed survey of the OCA2 locus (n = 271 SNPs). In 1,317 subjects, we confirmed six previously described associations and identified another 27 strongly associated with C that were not explained by continental population stratification (OR 1.5-17.9, P = 0.03 to <0.001). Haplotype analysis with respect to these 33 SNPs revealed six haplotype blocks and 11 hap-tags within these blocks. To identify genetic features for best-predicting iris color, we selected sets of SNPs by parsing P values among possible combinations and identified four discontinuous and non-overlapping sets across the LD blocks (p-Selected SNP sets). In a second, partially overlapping sample of 1,072, samples with matching diplotypes comprised of these p-Selected OCA2 SNPs exhibited a rate of C concordance of 96.3% (n = 82), which was significantly greater than that obtained from randomly selected samples (62.6%, n = 246, P<0.0001). In contrast, the rate of C concordance using diplotypes comprised of the 11 identified hap-tags was only 83.7%, and that obtained using diplotypes comprised of all 33 SNPs organized as contiguous sets along the locus (defined by the LD block structure) was only 93.3%. These results confirm that OCA2 is the major human iris color gene and suggest that using an empirical database-driven system, genotypes from a modest number of SNPs within this gene can be used to accurately predict iris melanin content from DNA.
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Affiliation(s)
- Tony Frudakis
- DNAPrint Genomics, Inc, 1621 W. University Pkwy, Sarasota, FL 34243, USA.
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Molokhia M, McKeigue P. Systemic lupus erythematosus: genes versus environment in high risk populations. Lupus 2007; 15:827-32. [PMID: 17153858 DOI: 10.1177/0961203306070007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The risks of systemic lupus erythematosus (SLE) are known to vary considerably with ethnic origin. Prevalence of lupus is increased in African-American, Afro-Caribbean, Native American, Asian Indian, Polynesian and Chinese populations compared with people of European descent. The consistency with which high prevalence of lupus occurs in these populations descent living in different environments suggests that genetic factors are likely to underlie the high risk in this group. However the increased risk of lupus in high risk groups such as West Africans compared with Europeans does not appear to be accounted for by differences in allele frequencies at any of the loci where associations with SLE have been found, including those in the HLA region. To date the contribution of environmental factors to a complex disease such as lupus is still not fully understood. This article explores possible environmental risk factors for SLE in high risk ethnic groups. Smoking, occupational exposures to silica and exposure to infection in childhood may explain some non-genetic risk factors for SLE in these groups.
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Affiliation(s)
- M Molokhia
- Department of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
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Seldin MF. Admixture mapping as a tool in gene discovery. Curr Opin Genet Dev 2007; 17:177-81. [PMID: 17466511 PMCID: PMC3146309 DOI: 10.1016/j.gde.2007.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 03/11/2007] [Indexed: 12/20/2022]
Abstract
Admixture mapping is a rapidly developing method to map susceptibility alleles in complex genetic disease associated with continental ancestry. Theoretically, when admixture between continental populations has occurred relatively recently, the chromosomal segments derived from the parental populations can be deduced from the differences in genotype allele frequencies. Progress in computational algorithms, in identification of ancestry informative single nucleotide polymorphisms, and in recent studies applying these tools suggests that this approach will complement other strategies for identifying the variation that underlies many complex diseases.
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Affiliation(s)
- Michael F Seldin
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, Room 4453, Tupper Hall Department of Biological Chemistry, One Shields Avenue, University of California, Davis, CA 95616, USA.
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Abstract
Systemic lupus erythematosus is an autoimmune connective-tissue disorder with a wide range of clinical features, which predominantly affects women, especially from certain ethnic groups. Diagnosis is based on clinical assessment supported by investigations, including the finding of autoantibodies. Treatments range from antimalarial agents to corticosteroids and immunosuppressive agents. This Seminar draws attention to advances in the epidemiology, genetics, cardiovascular risks, lupus nephritis, CNS disease, the antiphospholipid syndrome, assessment of disease activity and damage, and pregnancy related and quality of life issues. New therapeutic approaches, such as biological agents and mycophenolate mofetil, will also be discussed.
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Affiliation(s)
- David P D'Cruz
- Lupus Research Unit, Rayne Institute, St Thomas' Hospital, London SE1 7EH, UK. david.d'
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Peralta CA, Ziv E, Katz R, Reiner A, Burchard EG, Fried L, Kwok PY, Psaty B, Shlipak M. African ancestry, socioeconomic status, and kidney function in elderly African Americans: a genetic admixture analysis. J Am Soc Nephrol 2006; 17:3491-6. [PMID: 17082243 DOI: 10.1681/asn.2006050493] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Kidney disease is a major public health problem in the United States that affects African Americans disproportionately. The relative contribution of environmental and genetic factors to the increased burden of kidney disease among African Americans is unknown. The associations of genetic African ancestry and socioeconomic status with kidney function were studied cross-sectionally and longitudinally among 736 community-dwelling African Americans who were aged >65 yr and participating in the Cardiovascular Health Study. Genetic African ancestry was determined by genotyping 24 biallelic ancestry-informative markers and combining this information statistically to generate an estimate of ancestry for each individual. Kidney function was evaluated by cystatin C and estimated GFR (eGFR) using the Modification of Diet in Renal Disease equation. Longitudinal changes in serum creatinine and eGFR were estimated using baseline and follow-up values. In cross-sectional analyses, there was no association between genetic African ancestry and either measure of kidney function (P = 0.36 for cystatin C and 0.68 for eGFR). African ancestry was not associated with change in serum creatinine > or =0.05 mg/dl per yr (odds ratio [OR] 0.94; 95% confidence interval [CI] 0.83 to 1.06) or with change in eGFR > or =3 ml/min per 1.73 m(2) per yr (OR 1.02; 95% CI 0.92 to 1.13). In contrast, self reported African-American race was strongly associated with increased risk for kidney disease progression compared with white individuals for change in creatinine (OR 1.77; 95% CI 1.33 to 2.36) and for change in eGFR (OR 3.21; 95% CI 2.54 to 4.06). Among self-identified African Americans, low income (< US dollars 8000/yr) was strongly associated with prevalent kidney dysfunction by cystatin C >1.29 g/dl (adjusted OR 2.7; 95% CI 1.0 to 7.5) or by eGFR <60 ml/min per 1.73 m(2) (adjusted OR 3.2; 95% CI 1.1 to 9.4) compared with those with incomes >US dollars 35,000/yr. Alleles that are known to be present more frequently in the African ancestral group were not associated with kidney dysfunction or kidney disease progression. Rather, kidney dysfunction in elderly African Americans seems more attributable to differences in environmental and social factors.
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Affiliation(s)
- Carmen A Peralta
- Department of Medicine, University of California at San Francisco, San Francisco, California 94124, USA
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George A, Ogunbiyi A. Systemic lupus erythematosus: a rarity in West Africa, or a yet to be investigated entity. Lupus 2006; 14:924-5. [PMID: 16335588 DOI: 10.1191/0961203305lu2190xx] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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