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Brugger SW, Davis MF. Influence of Admixture on Phenotypes. Curr Protoc 2023; 3:e953. [PMID: 38146906 DOI: 10.1002/cpz1.953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Individuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been developed and optimized with such genomes in mind. African-descent and Latino individuals generally possess genomes of greater architectural complexity due to mosaic genomic ancestry, which can extensively and intricately impact phenotypic expression. As such, genetic analyses of admixed individuals require that genetic admixture be quantified to accurately model the impact of genetic variation on phenotypic expression. In this overview, we explore how fundamental genetic concepts such as linkage disequilibrium and differential allele frequency interact with genetic admixture to uniquely influence phenotypes in admixed individuals. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Steven W Brugger
- Department of Molecular Biology and Microbiology, Brigham Young University, Provo, Utah
| | - Mary F Davis
- Department of Molecular Biology and Microbiology, Brigham Young University, Provo, Utah
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2
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Levin AM, She R, Chen Y, Adrianto I, Datta I, Loveless IM, Garman L, Montgomery CG, Li J, Iannuzzi MC, Rybicki BA. Identification of Environmental Exposures Associated with Risk of Sarcoidosis in African Americans. Ann Am Thorac Soc 2023; 20:1274-1282. [PMID: 37209419 PMCID: PMC10502890 DOI: 10.1513/annalsats.202208-722oc] [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: 08/22/2022] [Accepted: 05/19/2023] [Indexed: 05/22/2023] Open
Abstract
Rationale: Sarcoidosis is a racially disparate granulomatous disease likely caused by environmental exposures, genes, and their interactions. Despite increased risk in African Americans, few environmental risk factor studies in this susceptible population exist. Objectives: To identify environmental exposures associated with the risk of sarcoidosis in African Americans and those that differ in effect by self-identified race and genetic ancestry. Methods: The study sample comprised 2,096 African Americans (1,205 with and 891 without sarcoidosis) compiled from three component studies. Unsupervised clustering and multiple correspondence analyses were used to identify underlying clusters of environmental exposures. Mixed-effects logistic regression was used to evaluate the association of these exposure clusters and the 51 single-component exposures with risk of sarcoidosis. A comparison case-control sample of 762 European Americans (388 with and 374 without sarcoidosis) was used to assess heterogeneity in exposure risk by race. Results: Seven exposure clusters were identified, five of which were associated with risk. The exposure cluster with the strongest risk association was composed of metals (P < 0.001), and within this cluster, exposure to aluminum had the highest risk (odds ratio, 3.30; 95% confidence interval [95% CI], 2.23-4.09; P < 0.001). This effect also differed by race (P < 0.001), with European Americans having no significant association with exposure (odds ratio, 0.86; 95% CI, 0.56-1.33). Within African Americans, the increased risk was dependent on genetic African ancestry (P = 0.047). Conclusions: Our findings support African Americans having sarcoidosis environmental exposure risk profiles that differ from those of European Americans. These differences may underlie racially disparate incidence rates that are partially explained by genetic variation differing by African ancestry.
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Affiliation(s)
- Albert M. Levin
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Ruicong She
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Yalei Chen
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indra Adrianto
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indrani Datta
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Ian M. Loveless
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Lori Garman
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; and
| | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; and
| | - Jia Li
- Department of Public Health Science and
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Michael C. Iannuzzi
- Department of Medical Education, School of Medicine, City University of New York, New York, New York
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Xiong Y, Kullberg S, Garman L, Pezant N, Ellinghaus D, Vasila V, Eklund A, Rybicki BA, Iannuzzi MC, Schreiber S, Müller-Quernheim J, Montgomery CG, Grunewald J, Padyukov L, Rivera NV. Sex differences in the genetics of sarcoidosis across European and African ancestry populations. Front Med (Lausanne) 2023; 10:1132799. [PMID: 37250650 PMCID: PMC10213734 DOI: 10.3389/fmed.2023.1132799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/10/2023] [Indexed: 05/31/2023] Open
Abstract
Background Sex differences in the susceptibility of sarcoidosis are unknown. The study aims to identify sex-dependent genetic variations in two clinical sarcoidosis phenotypes: Löfgren's syndrome (LS) and non-Löfgren's syndrome (non-LS). Methods A meta-analysis of genome-wide association studies was conducted on Europeans and African Americans, totaling 10,103 individuals from three population-based cohorts, Sweden (n = 3,843), Germany (n = 3,342), and the United States (n = 2,918), followed by an SNP lookup in the UK Biobank (UKB, n = 387,945). A genome-wide association study based on Immunochip data consisting of 141,000 single nucleotide polymorphisms (SNPs) was conducted in the sex groups. The association test was based on logistic regression using the additive model in LS and non-LS sex groups independently. Additionally, gene-based analysis, gene expression, expression quantitative trait loci (eQTL) mapping, and pathway analysis were performed to discover functionally relevant mechanisms related to sarcoidosis and biological sex. Results We identified sex-dependent genetic variations in LS and non-LS sex groups. Genetic findings in LS sex groups were explicitly located in the extended Major Histocompatibility Complex (xMHC). In non-LS, genetic differences in the sex groups were primarily located in the MHC class II subregion and ANXA11. Gene-based analysis and eQTL enrichment revealed distinct sex-specific gene expression patterns in various tissues and immune cell types. In LS sex groups, a pathway map related to antigen presentation machinery by IFN-gamma. In non-LS, pathway maps related to immune response lectin-induced complement pathway in males and related to maturation and migration of dendritic cells in skin sensitization in females were identified. Conclusion Our findings provide new evidence for a sex bias underlying sarcoidosis genetic architecture, particularly in clinical phenotypes LS and non-LS. Biological sex likely plays a role in disease mechanisms in sarcoidosis.
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Affiliation(s)
- Ying Xiong
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Kullberg
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Lori Garman
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Nathan Pezant
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Vasiliki Vasila
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Anders Eklund
- Department of Respiratory Medicine and Allergy, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, United States
| | - Michael C. Iannuzzi
- Zucker School of Medicine, Staten Island University Hospital, Northwell/Hofstra University, Staten Island, NY, United States
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Clinic for Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Joachim Müller-Quernheim
- Department of Pneumology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Courtney G. Montgomery
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Johan Grunewald
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Natalia V. Rivera
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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4
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Elkins KM, Garloff AT, Zeller CB. Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen kits. J Forensic Sci 2023; 68:608-613. [PMID: 36762775 DOI: 10.1111/1556-4029.15215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/15/2023] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
Multiplex DNA typing methods using massively parallel sequencing can be used to predict externally visible characteristics (EVCs) in forensic DNA phenotyping through the analysis of single-nucleotide polymorphisms. The focus of EVC determination has focused on hair color, eye color, and skin tone as well as visible biogeographical ancestry features. In this study, we researched off-label applications beyond what is currently marketed by the manufacturer of the Verogen ForenSeq kit primer set B and Imagen primer set E SNP loci. We investigated additional EVC predictions by examining published genome wide sequencing studies and reported allele-specific gene expression and predictive values. We have identified 15 SNPs included in the ForenSeq kit panel and Imagen kits that have additional EVC prediction capabilities beyond what is published in the Verogen manuals. The additional EVCs that can be predicted include hair graying, ephelides hyperpigmented spots, dermatoheliosis, facial pigmented spots, standing height, pattern balding, helix-rolling ear morphology, hair shape, hair thickness, facial morphology, eyebrow thickness, sarcoidosis, obesity, vitiligo, and tanning propensity. The loci can be used to augment and refine phenotype predictions with software such as MetaHuman for missing persons, cold case, and historic case investigations.
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Affiliation(s)
- Kelly M Elkins
- TU Human Remains Identification Laboratory (THRIL), Chemistry Department, Forensic Science Program, Towson University, Towson, Maryland, USA
| | - Alexis T Garloff
- TU Human Remains Identification Laboratory (THRIL), Chemistry Department, Forensic Science Program, Towson University, Towson, Maryland, USA
| | - Cynthia B Zeller
- TU Human Remains Identification Laboratory (THRIL), Chemistry Department, Forensic Science Program, Towson University, Towson, Maryland, USA
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Garman L, Montgomery CG, Rivera NV. Recent advances in sarcoidosis genomics: epigenetics, gene expression, and gene by environment (G × E) interaction studies. Curr Opin Pulm Med 2020; 26:544-553. [PMID: 32701681 PMCID: PMC7735660 DOI: 10.1097/mcp.0000000000000719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW We aim to review the most recent findings in genomics of sarcoidosis and highlight the gaps in the field. RECENT FINDINGS Original explorations of sarcoidosis subphenotypes, including cases associated with the World Trade Center and ocular sarcoidosis, have identified novel risk loci. Innovative gene--environment interaction studies utilizing modern analytical techniques have discovered risk loci associated with smoking and insecticide exposure. The application of whole-exome sequencing has identified genetic variants associated with persistent sarcoidosis and rare functional variations. A single epigenomics study has provided background knowledge of DNA methylation mechanisms in comparison with gene expression data. The application of machine-learning techniques has suggested new drug repositioning for the treatment of sarcoidosis. Several gene expression studies have identified prominent inflammatory pathways enriched in the affected tissue. SUMMARY Certainly, sarcoidosis research has recently advanced in the exploration of disease subphenotypes, utilizing novel analytical techniques, and including measures of clinical variation. Nevertheless, large-scale and diverse cohorts investigated with advanced sequencing methods, such as whole-genome and single-cell RNA sequencing, epigenomics, and meta-analysis coupled with cutting-edge analytic approaches, when employed, will broaden and translate genomics findings into clinical applications, and ultimately open venues for personalized medicine.
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Affiliation(s)
- Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Courtney G. Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Natalia V. Rivera
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center of Molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
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Chen Y, Adrianto I, Ianuzzi MC, Garman L, Montgomery CG, Rybicki BA, Levin AM, Li J. Extended methods for gene-environment-wide interaction scans in studies of admixed individuals with varying degrees of relationships. Genet Epidemiol 2019; 43:414-426. [PMID: 30793815 DOI: 10.1002/gepi.22196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/26/2018] [Accepted: 01/24/2019] [Indexed: 11/08/2022]
Abstract
The etiology of many complex diseases involves both environmental exposures and inherited genetic predisposition as well as interactions between them. Gene-environment-wide interaction studies (GEWIS) provide a means to identify the interactions between genetic variation and environmental exposures that underlie disease risk. However, current GEWIS methods lack the capability to adjust for the potentially complex correlations in studies with varying degrees of relationships (both known and unknown) among individuals in admixed populations. We developed novel generalized estimating equation (GEE) based methods-GEE-adaptive and GEE-joint-to account for phenotypic correlations due to kinship while accounting for covariates, including, measures of genome-wide ancestry. In simulation studies of admixed individuals, both methods controlled family-wise error rates, an advantage over the case-only approach. They demonstrated higher power than traditional case-control methods across a wide range of underlying alternative hypotheses, especially where both marginal and interaction effects were present. We applied the proposed method to conduct a GEWIS of a known sarcoidosis risk factor (insecticide exposure) and risk of sarcoidosis in African Americans and identified two novel loci with suggestive evidence of G × E interaction.
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Affiliation(s)
- Yalei Chen
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan.,Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indra Adrianto
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan.,Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Michael C Ianuzzi
- Department of Internal Medicine, Northwell Staten Island University Hospital, Staten Island, New York, New York
| | - Lori Garman
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Courtney G Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan.,Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Jia Li
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan.,Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
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Common variants of T-cells contribute differently to phenotypic variation in sarcoidosis. Sci Rep 2017; 7:5623. [PMID: 28717140 PMCID: PMC5514043 DOI: 10.1038/s41598-017-05754-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/02/2017] [Indexed: 12/30/2022] Open
Abstract
The involvement of the immune system, particularly the role of T-cells, in sarcoidosis is unclear. The existence of higher CD4+ T-cells and increased CD4/CD8 ratio may indicate a pathogenic role of T-cells in the disease. In this study, we quantified the contribution of T-cells associated variants and of CD4/CD8 ratio in sarcoidosis phenotypes, Löfgren’s syndrome (LS) and non- Löfgren’s syndrome (non-LS). We employed a polygenic-based approach using genome-wide association studies results on relative levels of T-cells in healthy individuals to measure the genetic contribution of T-cells in sarcoidosis entities. Results revealed that the genetic architecture of LS is highly influenced by genetic variants associated with CD8+ T-cells and CD4/CD8 ratio, explaining up to 7.94% and 6.49% of LS variation, respectively; whereas, the genetic architecture of non-LS is minimally influenced by T-cells, explaining a phenotypic variation of <1%. Moreover, pleiotropy assessment between T-cells and LS/non-LS associated-variants led to the discovery of highly scored pathway maps that shared common factors related to antigen presentation and T-cell regulatory mechanisms. Differences in significant polygenic scores, presence of pleiotropy, and distinct genetic factors provide further insights on how genetic variants and genes associated with relative levels of T-cell subtypes contribute differently to sarcoidosis phenotypes.
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9
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Abstract
PURPOSE OF REVIEW Nonnecrotizing granulomas in the affected organ are the hallmark of sarcoidosis. This review summarizes most recent genetic findings in sarcoidosis with a focus on genes that might influence granuloma formation or resolution. Specific results in multiple ethnic groups and certain clinical subphenotypes, such as extra-pulmonary organ involvement, are discussed. RECENT FINDINGS Associations of genetic variants in antigen-presenting molecules (HLA-DRB1) were shown to confer risk to sarcoidosis and certain disease phenotypes in populations of different ethnic origins. Specific DRB1 alleles, such as *0301 and *0302, appear to confer protection against chronic disease, but in an ethnic-specific manner illustrating the extensive genetic heterogeneity and complexity at this locus. Mechanistic studies of putative sarcoid antigens lend further credence to a role of HLA-DRB1 in disease pathogenesis. With relevance to granuloma formation, genes involved in apoptotic processes and immune cell activation were further confirmed (ANXA11 and BTNL2) in multiple ethnicities; others were newly identified (XAF1). Linking mechanism to clinical application, a TNF variant was shown to correlate with anti-TNF response in sarcoidosis patients. SUMMARY The investigation of known and novel risk variants for sarcoidosis and specific clinical phenotypes in various ethnicities highlights the genetic complexity of the disease. Detailed subanalysis of disease phenotypes revealed the potential for prediction of extra-pulmonary organ involvement and therapy response based on the patient's genotype.
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Levin AM, Adrianto I, Datta I, Iannuzzi MC, Trudeau S, Li J, Drake WP, Montgomery CG, Rybicki BA. Association of HLA-DRB1 with Sarcoidosis Susceptibility and Progression in African Americans. Am J Respir Cell Mol Biol 2015; 53:206-16. [PMID: 25506722 DOI: 10.1165/rcmb.2014-0227oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
HLA-DRB1 is a sarcoidosis risk gene, and the *03:01 allele is strongly associated with disease resolution in European sarcoidosis cases. Whereas the HLA-DRB1 variation is associated with sarcoidosis susceptibility in African Americans, DRB1 risk alleles are not as well defined, and associations with disease resolution have not been studied. Associations between genotyped and imputed HLA-DRB1 alleles and disease susceptibility/resolution were evaluated in a sample of 1,277 African-American patients with sarcoidosis and 1,467 control subjects. In silico binding assays were performed to assess the functional significance of the associated alleles. Increased disease susceptibility was associated with the HLA-DRB1 alleles *12:01 (odds ratio [OR], 2.11; 95% confidence interval [CI], 1.65-2.69; P = 3.2 × 10(-9)) and *11:01 (OR, 1.69; 95% CI, 1.42-2.01; P = 3.0 × 10(-9)). The strongest protective association was found with *03:01 (OR, 0.56; 95% CI, 0.44-0.73; P = 1.0 × 10(-5)). The African-derived allele *03:02 was associated with decreased risk of persistent radiographic disease (OR, 0.52; 95% CI, 0.37-0.72; P = 1.3 × 10(-4)), a finding consistent across the three component studies comprising the analytic sample. The DRB1*03:01 association with disease persistence was dependent upon local ancestry, with carriers of at least one European allele at DRB1 at a decreased risk of persistent disease (OR, 0.36; 95% CI, 0.14-0.94; P = 0.037). Results of in silico binding analyses showed that DRB1*03:01 consistently demonstrated the highest binding affinities for six bacterial peptides previously found in sarcoidosis granulomas, whereas *12:01 displayed the lowest binding affinities. This study has identified DRB1*03:01 and *03:02 as novel alleles associated with disease susceptibility and course in African Americans. Further investigation of DRB1*03 alleles may uncover immunologic factors that favor sarcoidosis protection and resolution among African Americans.
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Affiliation(s)
- Albert M Levin
- 1 Department of Public Health Sciences and.,2 Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Indra Adrianto
- 3 Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Indrani Datta
- 1 Department of Public Health Sciences and.,2 Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Michael C Iannuzzi
- 4 Department of Medicine, Upstate Medical University, Syracuse, New York; and
| | | | - Jia Li
- 1 Department of Public Health Sciences and.,2 Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan
| | - Wonder P Drake
- 5 Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Courtney G Montgomery
- 3 Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
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11
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Abstract
Sarcoidosis is a disease with highly variable presentation and progression; although it is hypothesized that disease phenotype is related to genetic variation, how much of this variability is driven by genetic factors is not known. The HLA region is the most strongly and consistently associated genetic risk factor for sarcoidosis, supporting the notion that sarcoidosis is an exposure-mediated immunologic disease. Most of the genetic etiology of sarcoidosis remains unknown in terms of the specific variants that increase risk in various populations, their biologic functions, and how they interact with environmental exposures.
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Affiliation(s)
| | - Nabeel Hamzeh
- Division of Environmental Occupational Health and Sciences, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Lisa A Maier
- Division of Environmental Occupational Health and Sciences, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
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12
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Abstract
Sarcoidosis is a multisystem inflammatory disease, the aetiology of which has still to be resolved. The proposed mechanism is that a susceptible genotype is exposed to one or more potential antigens. A sustained inflammatory response follows, which ultimately results in pathognomonic granuloma formation. Various clinical phenotypes exist with specific genetic associations influencing disease susceptibility, protection, and clinical progression. Occupational and environmental factors, including microbial elements, may then effect the development of this disease. Sarcoidosis is a heterogeneous disease, showing geographic and racial variation in clinical presentation. It demonstrates a familial tendency and clear genotype associations. Additionally, it appears to cluster within closely associated populations (eg, work colleagues) and appears to be related to selected occupations and environmental exposures. Frequently occult, but occasionally fatal, this disease has a very variable prognosis. It is also unusual in having no specific biomarker. The epidemiology and multiple factors that appear to influence the aetiology of sarcoidosis illustrate why this disease state is frequently described as a clinical enigma.
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Affiliation(s)
- Simon Dubrey
- Department of Cardiology, Hillingdon Hospital, Uxbridge, Middlesex, UK
| | - Shreena Shah
- The Medical Admissions Unit, Queens Hospital, Romford, Essex, UK
| | - Timothy Hardman
- Niche Science & Technology Ltd., Unit 26, Richmond-Upon-Thames, London, UK
| | - Rakesh Sharma
- Department of Cardiology, The Royal Brompton Hospital, London, UK
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Tchernev G, Cardoso JC, Chokoeva AA, Verma SB, Tana C, Ananiev J, Gulubova M, Philipov S, Kanazawa N, Nenoff P, Lotti T, Wollina U. The "mystery" of cutaneous sarcoidosis: facts and controversies. Int J Immunopathol Pharmacol 2014; 27:321-30. [PMID: 25280023 DOI: 10.1177/039463201402700302] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The reason why the cutaneous form of sarcoidosis is well known in the literature is because of its spectrum of manifestations granting it the fame of a Great Imitator. The mystery shrouding the pathogenesis of this rare cutaneous disease is still there (in spite of the fundamental progress of the various diagnostic methods in current day medicine). The production of the morphological substrate - the epithelioid cell granuloma - which is considered to be characteristic of skin sarcoidosis, could, however, also be the end result of a reaction to i) various specific infectious agents such as Leishmaniasis cutis, coccidioidomycosis, etc., ii) certain residual bacterial or other mycobacterial antigens which, at the moment of setting the diagnosis are - by definition - non-infectious but still immunogenic, as well as iii) different tumor antigens in lesional tissue or other location. Often, differentiating between sarcodiosis and a sarcoid-like reaction, based on the updated criteria for cutaneous sarcoidosis, is problematic to downright impossible. A future characterization of the genetic signature of the two conditions, as well as the implementation of additional mandatory panels for i) the identification of certain infectious or ii) non-infectious but immunogenic and iii) tumor antigens in the epithelioid cell granuloma (or in another location in the organism), could be a considerable contribution to the process of differentiating between the two above-mentioned conditions. This will create conditions for greater accuracy when setting the subsequent therapeutic approaches.
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Affiliation(s)
- G Tchernev
- Policlinic for Dermatology and Venerology, Saint Kliment Ohridski University, Medical Faculty, University Hospital Lozenetz, Sofia, Bulgaria
| | - J C Cardoso
- Dermatology Department University Hospital of Coimbra, Pinto, Coimbra, Portugal
| | - A A Chokoeva
- Department of Dermatology and Venereology, Medical University of Plovdiv, Plovdiv, Bulgaria
| | | | - C Tana
- Department of Medicine and Science of Aging "G. d'Annunzio" University, Chieti, Italy
| | - J Ananiev
- Department of General and Clinical Pathology, Medical Faculty, Trakia University, Stara Zagora, Bulgaria
| | - M Gulubova
- Department of General and Clinical Pathology, Medical Faculty, Trakia University, Stara Zagora, Bulgaria
| | - S Philipov
- Department of General and Clinical Pathology, Medical Faculty, "Saint Kliment Ohridski University", Sofia, Bulgaria
| | - N Kanazawa
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - P Nenoff
- Laboratory for Medical Microbiology, Mölbis, Germany
| | - T Lotti
- Dermatology Department, University of Rome "G. Marconi" Rome, Italy
| | - U Wollina
- Department of Dermatology and Allergology, Hospital Dresden-Friedrichstadt, Academic Teaching Hospital of the Technical University of Dresden, Dresden, Germany
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Parker MM, Foreman MG, Abel HJ, Mathias RA, Hetmanski JB, Crapo JD, Silverman EK, Beaty TH. Admixture mapping identifies a quantitative trait locus associated with FEV1/FVC in the COPDGene Study. Genet Epidemiol 2014; 38:652-9. [PMID: 25112515 DOI: 10.1002/gepi.21847] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/31/2022]
Abstract
African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3,300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1 /FVC (P = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1 /FVC (P = 2.1 × 10(-6) ) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1 /FVC (P = 1.76 × 10(-6) ). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1 /FVC ratio among African Americans in the COPDGene Study.
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Affiliation(s)
- Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland, United States of America
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Li J, Yang J, Levin AM, Montgomery CG, Datta I, Trudeau S, Adrianto I, McKeigue P, Iannuzzi MC, Rybicki BA. Efficient generalized least squares method for mixed population and family-based samples in genome-wide association studies. Genet Epidemiol 2014; 38:430-8. [PMID: 24845555 DOI: 10.1002/gepi.21811] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 03/26/2014] [Accepted: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Genome-wide association studies (GWAS) that draw samples from multiple studies with a mixture of relationship structures are becoming more common. Analytical methods exist for using mixed-sample data, but few methods have been proposed for the analysis of genotype-by-environment (G×E) interactions. Using GWAS data from a study of sarcoidosis susceptibility genes in related and unrelated African Americans, we explored the current analytic options for genotype association testing in studies using both unrelated and family-based designs. We propose a novel method-generalized least squares (GLX)-to estimate both SNP and G×E interaction effects for categorical environmental covariates and compared this method to generalized estimating equations (GEE), logistic regression, the Cochran-Armitage trend test, and the WQLS and MQLS methods. We used simulation to demonstrate that the GLX method reduces type I error under a variety of pedigree structures. We also demonstrate its superior power to detect SNP effects while offering computational advantages and comparable power to detect G×E interactions versus GEE. Using this method, we found two novel SNPs that demonstrate a significant genome-wide interaction with insecticide exposure-rs10499003 and rs7745248, located in the intronic and 3' UTR regions of the FUT9 gene on chromosome 6q16.1.
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Affiliation(s)
- Jia Li
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, United States of America
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Admixture fine-mapping in African Americans implicates XAF1 as a possible sarcoidosis risk gene. PLoS One 2014; 9:e92646. [PMID: 24663488 PMCID: PMC3963923 DOI: 10.1371/journal.pone.0092646] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 02/25/2014] [Indexed: 12/23/2022] Open
Abstract
Sarcoidosis is a complex, multi-organ granulomatous disease with a likely genetic component. West African ancestry confers a higher risk for sarcoidosis than European ancestry. Admixture mapping provides the most direct method to locate genes that underlie such ethnic variation in disease risk. We sought to identify genetic risk variants within four previously-identified ancestry-associated regions—6p24.3–p12.1, 17p13.3–13.1, 2p13.3–q12.1, and 6q23.3–q25.2—in a sample of 2,727 African Americans. We used logistic regression fit by generalized estimating equations and the MIX score statistic to determine which variants within ancestry-associated regions were associated with risk and responsible for the admixture signal. Fine mapping was performed by imputation, based on a previous genome-wide association study; significant variants were validated by direct genotyping. Within the 6p24.3–p12.1 locus, the most significant ancestry-adjusted SNP was rs74318745 (p = 9.4*10−11), an intronic SNP within the HLA-DRA gene that did not solely explain the admixture signal, indicating the presence of more than a single risk variant within this well-established sarcoidosis risk region. The locus on chromosome 17p13.3–13.1 revealed a novel sarcoidosis risk SNP, rs6502976 (p = 9.5*10−6), within intron 5 of the gene X-linked Inhibitor of Apoptosis Associated Factor 1 (XAF1) that accounted for the majority of the admixture linkage signal. Immunohistochemical expression studies demonstrated lack of expression of XAF1 and a corresponding high level of expression of its downstream target, X-linked Inhibitor of Apoptosis (XIAP) in sarcoidosis granulomas. In conclusion, ancestry and association fine mapping revealed a novel sarcoidosis susceptibility gene, XAF1, which has not been identified by previous genome-wide association studies. Based on the known biology of the XIAP/XAF1 apoptosis pathway and the differential expression patterns of XAF1 and XIAP in sarcoidosis granulomas, we suggest that this pathway may play a role in the maintenance of sarcoidosis granulomas.
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Bensen JT, Xu Z, McKeigue PM, Smith GJ, Fontham ET, Mohler JL, Taylor JA. Admixture mapping of prostate cancer in African Americans participating in the North Carolina-Louisiana Prostate Cancer Project (PCaP). Prostate 2014; 74:1-9. [PMID: 24037755 PMCID: PMC3934014 DOI: 10.1002/pros.22722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/22/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Few genetic risk factors have been uncovered that contribute specifically to the racial disparity in prostate cancer (CaP) observed in African Americans (AA). With the advent of ancestry informative marker (AIM) single nucleotide polymorphism (SNP) panels and powerful genetic strategies such as mapping by admixture linkage disequilibrium (MALD) it is possible to discover genes that underlie ethnic variation in disease risk. METHODS One thousand one hundred thirty AA CaP cases enrolled in the North Carolina-Louisiana Prostate Cancer Project (PCaP) were genotyped using a 1,509 AIM SNP panel. MALD was performed using ADMIXMAP to test for linkage between CaP risk and ancestry estimates at each AIM SNP. RESULTS The largest increase of African ancestry was observed at marker rs12543473 (P = 0.0011), located on chromosome 8q24.21, and the greatest excess of European ancestry was observed at marker rs10768140 (P = 0.0004) at chromosome 11p13. CONCLUSIONS The study confirmed the 8q24 risk loci and identified a novel genomic region on 11p13 that is associated with CaP risk. These findings should be replicated in larger AA populations and combined with fine mapping data to further refine the novel 11p13 CaP risk loci.
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Affiliation(s)
- Jeannette T. Bensen
- Department of Epidemiology University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7435
- Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7435
| | - Zongli Xu
- Epidemiology Branch National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
| | - Paul M. McKeigue
- Center for Population Health Sciences, University of Edinburgh Medical School, Tevoit Place, Edinburgh , United Kingdom
| | - Gary J. Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Elizabeth T.H. Fontham
- School of Public Health, Louisiana State University Health Science Center, New Orleans, Louisiana 70112
| | - James L. Mohler
- Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7435
- Department of Surgery, Division of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7435
- Department of Urology, Roswell Park Cancer Institute, Buffalo, New York 14263
- Department of Urology, University of Buffalo School of Medicine and Biotechnology, Buffalo, New York, 14214
| | - Jack A. Taylor
- Epidemiology Branch National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
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Nolan D, Kraus WE, Hauser E, Li YJ, Thompson DK, Johnson J, Chen HC, Nelson S, Haynes C, Gregory SG, Kraus VB, Shah SH. Genome-wide linkage analysis of cardiovascular disease biomarkers in a large, multigenerational family. PLoS One 2013; 8:e71779. [PMID: 23936524 PMCID: PMC3732259 DOI: 10.1371/journal.pone.0071779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 07/03/2013] [Indexed: 12/13/2022] Open
Abstract
Given the importance of cardiovascular disease (CVD) to public health and the demonstrated heritability of both disease status and its related risk factors, identifying the genetic variation underlying these susceptibilities is a critical step in understanding the pathogenesis of CVD and informing prevention and treatment strategies. Although one can look for genetic variation underlying susceptibility to CVD per se, it can be difficult to define the disease phenotype for such a qualitative analysis and CVD itself represents a convergence of diverse etiologic pathways. Alternatively, one can study the genetics of intermediate traits that are known risk factors for CVD, which can be measured quantitatively. Using the latter strategy, we have measured 21 cardiovascular-related biomarkers in an extended multigenerational pedigree, the CARRIAGE family (Carolinas Region Interaction of Aging, Genes, and Environment). These biomarkers belong to inflammatory and immune, connective tissue, lipid, and hemostasis pathways. Of these, 18 met our quality control standards. Using the pedigree and biomarker data, we have estimated the broad sense heritability (H2) of each biomarker (ranging from 0.09–0.56). A genome-wide panel of 6,015 SNPs was used subsequently to map these biomarkers as quantitative traits. Four showed noteworthy evidence for linkage in multipoint analysis (LOD score ≥ 2.6): paraoxonase (chromosome 8p11, 21), the chemokine RANTES (22q13.33), matrix metalloproteinase 3 (MMP3, 17p13.3), and granulocyte colony stimulating factor (GCSF, 8q22.1). Identifying the causal variation underlying each linkage score will help to unravel the genetic architecture of these quantitative traits and, by extension, the genetic architecture of cardiovascular risk.
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Affiliation(s)
- Daniel Nolan
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
| | - William E. Kraus
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Elizabeth Hauser
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
| | - Yi-Ju Li
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
| | - Dana K. Thompson
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Jessica Johnson
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
| | - Hsiang-Cheng Chen
- Division of Rheumatology, Immunology and Allergy, Tri-Service General Hospital, Taipei, Taiwan
| | - Sarah Nelson
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Carol Haynes
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
| | - Simon G. Gregory
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
| | - Virginia B. Kraus
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Svati H. Shah
- Center for Human Genetics, Duke University, Durham, North Carolina, United States of America
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Davis MB, Liu X, Wang S, Reeves J, Khramtsov A, Huo D, Olopade OI. Expression and sub-cellular localization of an epigenetic regulator, co-activator arginine methyltransferase 1 (CARM1), is associated with specific breast cancer subtypes and ethnicity. Mol Cancer 2013; 12:40. [PMID: 23663560 PMCID: PMC3663705 DOI: 10.1186/1476-4598-12-40] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 04/03/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Co-Activator Arginine Methyltransferase 1(CARM1) is an Estrogen Receptor (ER) cofactor that remodels chromatin for gene regulation via methylation of Histone3. We investigated CARM1 levels and localization across breast cancer tumors in a cohort of patients of either European or African ancestry. METHODS We analyzed CARM1 levels using tissue microarrays with over 800 histological samples from 549 female cancer patients from the US and Nigeria, Africa. We assessed associations between CARM1 expression localized to the nucleus and cytoplasm for 11 distinct variables, including; ER status, Progesterone Receptor status, molecular subtypes, ethnicity, HER2+ status, other clinical variables and survival. RESULTS We found that levels of cytoplasmic CARM1 are distinct among tumor sub-types and increased levels are associated with ER-negative (ER-) status. Higher nuclear CARM1 levels are associated with HER2 receptor status. EGFR expression also correlates with localization of CARM1 into the cytoplasm. This suggests there are distinct functions of CARM1 among molecular tumor types. Our data reveals a basal-like subtype association with CARM1, possibly due to expression of Epidermal Growth Factor Receptor (EGFR). Lastly, increased cytoplasmic CARM1, relative to nuclear levels, appear to be associated with self-identified African ethnicity and this result is being further investigated using quantified genetic ancestry measures. CONCLUSIONS Although it is known to be an ER cofactor in breast cancer, CARM1 expression levels are independent of ER. CARM1 has distinct functions among molecular subtypes, as is indicative of its sub-cellular localization and it may function in subtype etiology. These sub-cellular localization patterns, indicate a novel role beyond its ER cofactor function in breast cancer. Differential localization among ethnic groups may be due to ancestry-specific polymorphisms which alter the gene product.
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Affiliation(s)
- Melissa B Davis
- The Institute for Genomics and Systems Biology, University of Chicago Biological Sciences Division, Chicago, IL, USA
- Department of Human Genetics, University of Chicago Biological Sciences Division, Chicago, IL, USA
- Georgia Health Sciences University, Athens, GA 30602, USA
- University of Georgia Medical Partnership, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Xinyu Liu
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Shiyao Wang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Jaxk Reeves
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Andrey Khramtsov
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago Medicine, Chicago, IL 60637, USA
| | - Dezheng Huo
- Department of Health Studies, Center for Clinical Cancer Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Olufunmilayo I Olopade
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago Medicine, Chicago, IL 60637, USA
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Cozier Y, Ruiz-Narvaez E, McKinnon C, Berman J, Rosenberg L, Palmer J. Replication of genetic loci for sarcoidosis in US black women: data from the Black Women's Health Study. Hum Genet 2013; 132:803-10. [PMID: 23543185 DOI: 10.1007/s00439-013-1292-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/18/2013] [Indexed: 01/08/2023]
Abstract
In the United States, incidence and mortality from sarcoidosis, a chronic, granulomatous disease, are increased in black women. In data from the Black Women's Health Study, a follow-up of US black women, we assessed two SNPs (rs2076530 and rs9268480) previously identified in the BTNL2 gene (chromosome 6p21), of which rs4424066 and rs3817963 are perfect proxies, to determine if they represent independent signals of disease risk. We also assessed whether local ancestry in four genomic regions previously identified through admixture mapping was associated with sarcoidosis. Finally, we assessed the relation of global percent African ancestry to risk. We conducted a nested case-control study of 486 sarcoidosis cases and 943 age- and geography-matched controls. Both BTNL2 SNPs were associated with risk of sarcoidosis in separate models, but in a combined analysis the increased risk was due to the A-allele of the rs3817963 SNP; each copy of the A-allele was associated with a 40 % increase in risk of sarcoidosis (p = 0.02) and was confirmed by our haplotypic analysis. Local African ancestry around the rs30533 ancestry informative marker at chromosome 5q31 was associated with a 29 % risk reduction (p = 0.01). Therefore, we adjusted our analysis of global African ancestry for number of copies of African alleles in rs30533. Subjects in the highest quintile of percent African ancestry had a 54 % increased risk of sarcoidosis. The present results from a population of African-American women support the role of the BTNL2 gene and the 5q31 locus in the etiology of sarcoidosis, and also demonstrate that percent African ancestry is associated with disease risk.
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Affiliation(s)
- Yvette Cozier
- Slone Epidemiology Center, Boston University, Boston, USA.
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McKeigue PM, Colombo M, Agakov F, Datta I, Levin A, Favro D, Gray-Montgomery C, Iannuzzi MC, Rybicki BA. Extending admixture mapping to nuclear pedigrees: application to sarcoidosis. Genet Epidemiol 2013; 37:256-66. [PMID: 23371909 DOI: 10.1002/gepi.21710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 11/08/2012] [Accepted: 12/17/2012] [Indexed: 11/08/2022]
Abstract
We describe statistical methods that extend the application of admixture mapping from unrelated individuals to nuclear pedigrees, allowing existing pedigree-based collections to be fully exploited. Computational challenges have been overcome by developing a fast algorithm that exploits the factorial structure of the underlying model of ancestry transitions. This has been implemented as an extension of the program ADMIXMAP. We demonstrate the application of the method to a study of sarcoidosis in African Americans that has previously been analyzed only as an admixture mapping study restricted to unrelated individuals. Although the ancestry signals detected in this pedigree analysis are generally similar to those detected in the earlier analysis of unrelated cases, we are able to extract more information and this yields a much sharper exclusion map; using the classical criterion of an LOD score of minus 2, the pedigree analysis is able to exclude a risk ratio of 2 or more associated with African ancestry over 96% of the genome, compared with only 83% in the earlier analysis of unrelated individuals only. Although the pedigree extension of ADMIXMAP can use ancestry-informative markers only at relatively low density, it can use imputed ancestry states from programs such as WINPOP or HAPMIX that use dense SNP marker genotypes for admixture mapping. This extends both the efficiency and the range of application of this powerful gene mapping method.
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Affiliation(s)
- Paul M McKeigue
- Centre for Population Health Sciences, Medical School, University of Edinburgh, Teviot Place, Edinburgh EH9 9AG, United Kingdom.
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Levin AM, Iannuzzi MC, Montgomery CG, Trudeau S, Datta I, McKeigue P, Fischer A, Nebel A, Rybicki BA. Association of ANXA11 genetic variation with sarcoidosis in African Americans and European Americans. Genes Immun 2012; 14:13-8. [PMID: 23151485 DOI: 10.1038/gene.2012.48] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A recent genome-wide association study in a German population and two subsequent studies in European populations found that a non-synonymous single-nucleotide polymorphism (SNP), rs1049550, within the annexin A11 (ANXA11) gene was associated with susceptibility to sarcoidosis. We sought to identify additional ANXA11 variants independently associated with sarcoidosis, determine whether any sarcoidosis-associated ANXA11 variants were associated with chest radiographic phenotypes, and explore human leukocyte antigen (HLA) SNP-SNP interactions with ANXA11. A total of 209 SNPs spanning 100 kb including the 5' promoter, coding, and 3' untranslated regions of ANXA11 were genotyped for 1689 sarcoidosis cases and 1252 controls. After adjustment for rs1049550, two additional novel ANXA11 sarcoidosis associations were identified only in African Americans--rs61860052 (odds ratio (OR)=0.62; 95% confidence interval (CI)=0.40-0.97) and rs4377299 (OR=1.31; 95% CI=1.06-1.63). These associations were more pronounced in radiologically-classified Scadding stage IV sarcoidosis cases. We also identified a significant SNP-SNP interaction between rs1049550 and a sarcoidosis risk SNP (rs9268839) near the HLA-DRA locus. This further genetic dissection of ANXA11 may provide additional insight into the immune dysregulation characteristic of sarcoidosis pathophysiology.
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Affiliation(s)
- A M Levin
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI 48202, USA
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25
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Adrianto I, Lin CP, Hale JJ, Levin AM, Datta I, Parker R, Adler A, Kelly JA, Kaufman KM, Lessard CJ, Moser KL, Kimberly RP, Harley JB, Iannuzzi MC, Rybicki BA, Montgomery CG. Genome-wide association study of African and European Americans implicates multiple shared and ethnic specific loci in sarcoidosis susceptibility. PLoS One 2012; 7:e43907. [PMID: 22952805 PMCID: PMC3428296 DOI: 10.1371/journal.pone.0043907] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/27/2012] [Indexed: 12/21/2022] Open
Abstract
Sarcoidosis is a systemic inflammatory disease characterized by the formation of granulomas in affected organs. Genome-wide association studies (GWASs) of this disease have been conducted only in European population. We present the first sarcoidosis GWAS in African Americans (AAs, 818 cases and 1,088 related controls) followed by replication in independent sets of AAs (455 cases and 557 controls) and European Americans (EAs, 442 cases and 2,284 controls). We evaluated >6 million SNPs either genotyped using the Illumina Omni1-Quad array or imputed from the 1000 Genomes Project data. We identified a novel sarcoidosis-associated locus, NOTCH4, that reached genome-wide significance in the combined AA samples (rs715299, P(AA-meta) = 6.51 × 10(-10)) and demonstrated the independence of this locus from others in the MHC region in the same sample. We replicated previous European GWAS associations within HLA-DRA, HLA-DRB5, HLA-DRB1, BTNL2, and ANXA11 in both our AA and EA datasets. We also confirmed significant associations to the previously reported HLA-C and HLA-B regions in the EA but not AA samples. We further identified suggestive associations with several other genes previously reported in lung or inflammatory diseases.
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Affiliation(s)
- Indra Adrianto
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Chee Paul Lin
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Jessica J. Hale
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Indrani Datta
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Ryan Parker
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Kenneth M. Kaufman
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- The United States Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Christopher J. Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Kathy L. Moser
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John B. Harley
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- The United States Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Michael C. Iannuzzi
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
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Abstract
Patients with sarcoidosis can be subgrouped according to organ engagement and clinical manifestations. One such subgroup is Löfgren's syndrome (LS), constituting a distinct group of sarcoidosis patients with typical clinical manifestations, separate genetic associations and an immune response that seems to differ from that of non-LS patients. In particular, LS patients have strong associations with HLA-DRB1 alleles, and the well-known association with HLA-DRB1*03 is particularly striking. This particular HLA-DRB1 allele is also a very strong marker within that particular group of patients for a prognostically favorable disease course. This article will mainly discuss genetic associations with LS, and the possible implications of such associations.
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Affiliation(s)
- Johan Grunewald
- Department of Medicine, Division of Respiratory Medicine, Karolinska Institutet, Lung Research Laboratory L4:01, Karolinska University Hospital Solna, S-171 76 Stockholm, Sweden.
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Abstract
STUDY DESIGN Case report of occult presentation of asymptomatic vertebral sarcoidosis. OBJECTIVE To illustrate a case of vertebral sarcoidosis with occult presentation and subsequent spontaneous resolution. SUMMARY OF BACKGROUND DATA Vertebral sarcoidosis is an uncommon disorder characterized by noncaseating granulomatous infiltration of the spine. It most commonly affects the thoracic spine. The disc spaces are usually preserved; clinical presentation and imaging characteristics are variable. METHODS Case presentation and report. RESULTS A 41-year-old man with classic pulmonary sarcoidosis presented after a work-related back injury. Magnetic resonance injury of his spine demonstrated multiple enhancing lesions throughout the thoracic and lumbar vertebrae. Classic granulomas were identified on subsequently obtained core biopsy specimens, and the diagnosis of vertebral sarcoidosis was made. CONCLUSION To our knowledge, this is the first case of concomitant pulmonary and asymptomatic vertebral sarcoidosis with spontaneous resolution of the vertebral manifestations without definitive treatment. A broad differential diagnosis should be entertained for new enhancing spine lesions including noninfectious inflammatory diseases such as sarcoidosis.
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