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El-Halwagi A, Agarwal SK. Insights into the genetic landscape of systemic sclerosis. Best Pract Res Clin Rheumatol 2024:101981. [PMID: 39068103 DOI: 10.1016/j.berh.2024.101981] [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: 04/30/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
Systemic sclerosis (SSc) is a complex autoimmune disease that clinically manifests as progressive fibrosis of the skin and internal organs. Autoimmunity and endothelial dysfunction play important roles in the development of SSc but the causes of SSc remain unknown. Accumulating evidence, first from familial aggregation studies and subsequently from candidate gene association studies and genome wide association studies underscore the crucial contributions of genetics to the development of SSc. The identification of polymorphisms in the HLA region as well as non-HLA loci is important for understanding the risks of developing SSc but can also provide important pathogenic insight in SSc. While not translating into clinic practice yet, understanding the genetic landscape of SSc will hopefully assist in the diagnosis and management of patients with and/or at risk of developing SSc in the future. Herein we review the studies that investigate genetic risks of SSc susceptibility.
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Affiliation(s)
- Ali El-Halwagi
- Section of Immunology, Allergy and Rheumatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sandeep K Agarwal
- Section of Immunology, Allergy and Rheumatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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Zhong T, Hou D, Zhao Q, Zhan S, Wang L, Li L, Zhang H, Zhao W, Yang S, Niu L. Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds. BMC Genomics 2024; 25:480. [PMID: 38750582 PMCID: PMC11094944 DOI: 10.1186/s12864-024-10396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its "year-round estrus and multiple births" and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep's high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.
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Affiliation(s)
- Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Dunying Hou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhao
- College of Animal Science, Xichang University, Xichang, 615013, China
| | - Shizhong Yang
- Academy of Agricultural Sciences Liangshan, Xichang, 615000, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
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Abstract
PURPOSE OF REVIEW To review susceptibility genes and how they could integrate in systemic sclerosis (SSc) pathophysiology providing insight and perspectives for innovative therapies. RECENT FINDINGS SSc is a rare disease characterized by vasculopathy, dysregulated immunity and fibrosis. Genome-Wide association studies and ImmunoChip studies performed in recent years revealed associated genetic variants mainly localized in noncoding regions and mostly affecting the immune system of SSc patients. Gene variants were described in innate immunity (IRF5, IRF7 and TLR2), T and B cells activation (CD247, TNFAIP3, STAT4 and BLK) and NF-κB pathway (TNFAIP3 and TNIP1) confirming previous biological data. In addition to impacting immune response, CSK, DDX6, DNASE1L3 and GSDMA/B could also act in the vascular and fibrotic components of SSc. SUMMARY Although genetic studies highlighted the dysregulated immune response in SSc, future research must focus on a deeper characterization of these variants with determination of their functional effects. Moreover, the role of these genes or others on specific vasculopathy and fibrosis would provide insight. Establishment of polygenic score or integrated genome approaches could identify new targets specific of SSc clinical features. This will allow physicians to propose new therapies to SSc patients.
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Mehta BK, Espinoza ME, Hinchcliff M, Whitfield ML. Molecular "omic" signatures in systemic sclerosis. Eur J Rheumatol 2020; 7:S173-S180. [PMID: 33164732 DOI: 10.5152/eurjrheum.2020.19192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/05/2020] [Indexed: 01/15/2023] Open
Abstract
Systemic sclerosis (SSc) is a connective tissue disorder characterized by immunologic, vascular, and extracellular matrix abnormalities. Variation in the proportion and/or timing of activation in the deregulated molecular pathways that underlie SSc may explain the observed clinical heterogeneity in terms of disease phenotype and treatment response. In recent years, SSc research has generated massive amounts of "omics" level data. In this review, we discuss the body of "omics" level work in SSc and how each layer provides unique insight to our understanding of SSc. We posit that effective integration of genomic, transcriptomic, metagenomic, and epigenomic data is an important step toward precision medicine and is vital to the identification of effective therapeutic options for patients with SSc.
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Affiliation(s)
- Bhaven K Mehta
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Monica E Espinoza
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Monique Hinchcliff
- Department of Rheumatology, Allergy & Immunology, Yale School of Medicine, New Haven, CT, USA
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA
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Benfaremo D, Svegliati Baroni S, Manfredi L, Moroncini G, Gabrielli A. Putative functional pathogenic autoantibodies in systemic sclerosis. Eur J Rheumatol 2020; 7:S181-S186. [PMID: 33164733 PMCID: PMC7647689 DOI: 10.5152/eurjrheum.2020.19131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/06/2020] [Indexed: 01/19/2023] Open
Abstract
Systemic sclerosis (scleroderma, SSc) is a systemic disease characterized by vascular lesions, fibrosis, and circulating autoantibodies. A complex interplay between innate and adaptive immunity, and with regard to the latter, between humoral and cellular immunity, is believed to be involved in SSc pathogenesis. Lately, close attention has been paid to the role of B cells which, once activated, release profibrotic cytokines, promote profibrotic Th2 differentiation, and produce autoantibodies. Several novel interesting autoantibodies, targeting antigens within the extracellular matrix or on the cell surface, rather than the nuclear antigens of canonical SSc-autoantibodies, have been recently described in patients with SSc. As they show stimulatory or inhibitory activity or react with structures involved in the pathogenesis of SSc lesions, they can be considered as potentially pathogenic. In this paper, we will review those which have been better characterized.
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Affiliation(s)
- Devis Benfaremo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | | | - Lucia Manfredi
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | - Gianluca Moroncini
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | - Armando Gabrielli
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
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Radic M, Frech TM. Big data in systemic sclerosis: Great potential for the future. JOURNAL OF SCLERODERMA AND RELATED DISORDERS 2020; 5:172-177. [DOI: 10.1177/2397198320929805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
Since it was first used in 1997, the term “big data” has been popularized; however, the concept of big data is relatively new to medicine. Big data refers to a method and technique to systematically retrieve, collect, manage, and analyze very large and complex sets of structured and unstructured data that cannot be sufficiently processed using traditional methods of processing data. Integrating big data in rare diseases with low prevalence and incidence, like systemic sclerosis is of particular importance. We conducted a literature review of use of big data in systemic sclerosis. The volume of data on systemic sclerosis has grown steadily in the recent years; however, big data methods have not been readily used. This inexhaustible source of data needs to be used more to unleash its full potential.
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Affiliation(s)
- Mislav Radic
- Department of Rheumatology, University of Utah, Salt Lake City, UT, USA
- Center of Excellence for Systemic Sclerosis Ministry of Health Republic of Croatia, Division of Rheumatology and Clinical Immunology, University Hospital Centre Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Tracy M Frech
- Department of Rheumatology, University of Utah, Salt Lake City, UT, USA
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Abstract
Systemic sclerosis (SSc) is a severe autoimmune disease that is characterized by vascular abnormalities, immunological alterations and fibrosis of the skin and internal organs. The results of genetic studies in patients with SSc have revealed statistically significant genetic associations with disease manifestations and progression. Nevertheless, genetic susceptibility to SSc is moderate, and the functional consequences of genetic associations remain only partially characterized. A current hypothesis is that, in genetically susceptible individuals, epigenetic modifications constitute the driving force for disease initiation. As epigenetic alterations can occur years before fibrosis appears, these changes could represent a potential link between inflammation and tissue fibrosis. Epigenetics is a fast-growing discipline, and a considerable number of important epigenetic studies in SSc have been published in the past few years that span histone post-translational modifications, DNA methylation, microRNAs and long non-coding RNAs. This Review describes the latest insights into genetic and epigenetic contributions to the pathogenesis of SSc and aims to provide an improved understanding of the molecular pathways that link inflammation and fibrosis. This knowledge will be of paramount importance for the development of medicines that are effective in treating or even reversing tissue fibrosis.
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Gourh P, Remmers EF, Boyden SE, Alexander T, Morgan ND, Shah AA, Mayes MD, Doumatey A, Bentley AR, Shriner D, Domsic RT, Medsger TA, Steen VD, Ramos PS, Silver RM, Korman B, Varga J, Schiopu E, Khanna D, Hsu V, Gordon JK, Saketkoo LA, Gladue H, Kron B, Criswell LA, Derk CT, Bridges SL, Shanmugam VK, Kolstad KD, Chung L, Jan R, Bernstein EJ, Goldberg A, Trojanowski M, Kafaja S, Maksimowicz-McKinnon KM, Mullikin JC, Adeyemo A, Rotimi C, Boin F, Kastner DL, Wigley FM. Brief Report: Whole-Exome Sequencing to Identify Rare Variants and Gene Networks That Increase Susceptibility to Scleroderma in African Americans. Arthritis Rheumatol 2018; 70:1654-1660. [PMID: 29732714 PMCID: PMC6160338 DOI: 10.1002/art.40541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/26/2018] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Whole-exome sequencing (WES) studies in systemic sclerosis (SSc) patients of European American (EA) ancestry have identified variants in the ATP8B4 gene and enrichment of variants in genes in the extracellular matrix (ECM)-related pathway that increase SSc susceptibility. This study was undertaken to evaluate the association of the ATP8B4 gene and the ECM-related pathway with SSc in a cohort of African American (AA) patients. METHODS SSc patients of AA ancestry were enrolled from 23 academic centers across the US under the Genome Research in African American Scleroderma Patients consortium. Unrelated AA individuals without serologic evidence of autoimmunity who were enrolled in the Howard University Family Study were used as unaffected controls. Functional variants in genes reported in the 2 WES studies in EA patients with SSc were selected for gene association testing using the optimized sequence kernel association test (SKAT-O) and pathway analysis by Ingenuity Pathway Analysis in 379 patients and 411 controls. RESULTS Principal components analysis demonstrated that the patients and controls had similar ancestral backgrounds, with roughly equal proportions of mean European admixture. Using SKAT-O, we examined the association of individual genes that were previously reported in EA patients and none remained significant, including ATP8B4 (P = 0.98). However, we confirmed the previously reported association of the ECM-related pathway with enrichment of variants within the COL13A1, COL18A1, COL22A1, COL4A3, COL4A4, COL5A2, PROK1, and SERPINE1 genes (corrected P = 1.95 × 10-4 ). CONCLUSION In the largest genetic study in AA patients with SSc to date, our findings corroborate the role of functional variants that aggregate in a fibrotic pathway and increase SSc susceptibility.
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Affiliation(s)
- Pravitt Gourh
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elaine F. Remmers
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven E. Boyden
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Theresa Alexander
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nadia D. Morgan
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ami A. Shah
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Maureen D. Mayes
- Division of Rheumatology and Clinical Immunogenetics, University of Texas McGovern Medical School, Houston, TX
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robyn T. Domsic
- Division of Rheumatology, University of Pittsburgh, Pittsburgh, PA
| | | | - Virginia D. Steen
- Division of Rheumatology, Georgetown University School of Medicine, Washington, DC
| | - Paula S. Ramos
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC
| | - Richard M. Silver
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC
| | - Benjamin Korman
- Division of Rheumatology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - John Varga
- Division of Rheumatology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Elena Schiopu
- University of Michigan Scleroderma Program, Ann Arbor, MI 48105
| | - Dinesh Khanna
- University of Michigan Scleroderma Program, Ann Arbor, MI 48105
| | - Vivien Hsu
- Division of Rheumatology, Robert Wood Johnson University, New Brunswick, NJ
| | - Jessica K. Gordon
- Department of Rheumatology, Hospital for Special Surgery, New York, NY
| | - Lesley Ann Saketkoo
- Division of Rheumatology, Tulane University School of Medicine, New Orleans, LA
| | - Heather Gladue
- Department of Rheumatology, Arthritis and Osteoporosis Consultants of the Carolinas, Charlotte, NC
| | - Brynn Kron
- Division of Rheumatology, University of California San Francisco, San Francisco, CA
| | - Lindsey A. Criswell
- Division of Rheumatology, University of California San Francisco, San Francisco, CA
| | - Chris T. Derk
- Division of Rheumatology, University of Pennsylvania, Philadelphia, PA
| | - S. Louis Bridges
- Director, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL
| | - Victoria K. Shanmugam
- Division of Rheumatology, The George Washington University, School of Medicine and Health Sciences, Washington, D.C
| | | | - Lorinda Chung
- Stanford University School of Medicine, Stanford, CA
- Palo Alto VA Health Care System Palo Alto VA Health Care System
| | - Reem Jan
- Division of Rheumatology, University of Chicago Pritzker School of Medicine, Chicago, IL
| | | | - Avram Goldberg
- Division of Rheumatology, New York University Langone Medical Center, New York, NY
| | - Marcin Trojanowski
- Division of Rheumatology, Boston University School of Medicine, Boston, MA
| | - Suzanne Kafaja
- Division of Rheumatology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | | | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Rockville, MD
| | | | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francesco Boin
- Division of Rheumatology, University of California San Francisco, San Francisco, CA
| | - Daniel L. Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fredrick M. Wigley
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Tsou PS, Sawalha AH. Unfolding the pathogenesis of scleroderma through genomics and epigenomics. J Autoimmun 2017; 83:73-94. [PMID: 28526340 DOI: 10.1016/j.jaut.2017.05.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 12/12/2022]
Abstract
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated. The non-HLA genes associated with SSc are involved in various functions, with the most robust associations including genes for B and T cell activation and innate immunity. Other pathways include genes involved in extracellular matrix deposition, cytokines, and autophagy. Among these genes, IRF5, STAT4, and CD247 were replicated most frequently while SNPs rs35677470 in DNASE1L3, rs5029939 in TNFAIP3, and rs7574685 in STAT4 have the strongest associations with SSc. In addition to genetic predisposition, it became clear that environmental factors and epigenetic influences also contribute to the development of SSc. Epigenetics, which refers to studies that focus on heritable phenotypes resulting from changes in chromatin structure without affecting the DNA sequence, is one of the most rapidly expanding fields in biomedical research. Indeed extensive epigenetic changes have been described in SSc. Alteration in enzymes and mediators involved in DNA methylation and histone modification, as well as dysregulated non-coding RNA levels all contribute to fibrosis, immune dysregulation, and impaired angiogenesis in this disease. Genes that are affected by epigenetic dysregulation include ones involved in autoimmunity, T cell function and regulation, TGFβ pathway, Wnt pathway, extracellular matrix, and transcription factors governing fibrosis and angiogenesis. In this review, we provide a comprehensive overview of the current findings of SSc genetic susceptibility, followed by an extensive description and a systematic review of epigenetic research that has been carried out to date in SSc. We also summarize the therapeutic potential of drugs that affect epigenetic mechanisms, and outline the future prospective of genomics and epigenomics research in SSc.
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Affiliation(s)
- Pei-Suen Tsou
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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