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Identification of novel associations and localization of signals in idiopathic inflammatory myopathies using genome‐wide imputation

Simon Rothwell, Christopher I. Amos, Frederick W. Miller, Lisa G. Rider, Ingrid E. Lundberg, Peter K. Gregersen, Jiri Vencovsky, Neil McHugh, Vidya Limaye, Albert Selva‐O'Callaghan, et al.
(2023) ARTHRITIS & RHEUMATOLOGY. 75(6). p.1021-1027
Author
Organization
Abstract
ObjectiveThe idiopathic inflammatory myopathies (IIMs) are heterogeneous diseases thought to be initiated by immune activation in genetically predisposed individuals. We imputed variants from the ImmunoChip array using a large reference panel to fine-map associations and identify novel associations in IIM. MethodsWe analyzed 2,565 Caucasian IIM patient samples collected through the Myositis Genetics Consortium (MYOGEN) and 10,260 ethnically matched control samples. We imputed 1,648,116 variants from the ImmunoChip array using the Haplotype Reference Consortium panel and conducted association analysis on IIM and clinical and serologic subgroups. ResultsThe HLA locus was consistently the most significantly associated region. Four non-HLA regions reached genome-wide significance, SDK2 and LINC00924 (both novel) and STAT4 in the whole IIM cohort, with evidence of independent variants in STAT4, and NAB1 in the polymyositis (PM) subgroup. We also found suggestive evidence of association with loci previously associated with other autoimmune rheumatic diseases (TEC and LTBR). We identified more significant associations than those previously reported in IIM for STAT4 and DGKQ in the total cohort, for NAB1 and FAM167A-BLK loci in PM, and for CCR5 in inclusion body myositis. We found enrichment of variants among DNase I hypersensitivity sites and histone marks associated with active transcription within blood cells. ConclusionWe found novel and strong associations in IIM and PM and localized signals to single genes and immune cell types.
Keywords
Immunology, Rheumatology, Immunology and Allergy

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MLA
Rothwell, Simon, et al. “Identification of Novel Associations and Localization of Signals in Idiopathic Inflammatory Myopathies Using Genome‐wide Imputation.” ARTHRITIS & RHEUMATOLOGY, vol. 75, no. 6, Wiley, 2023, pp. 1021–27, doi:10.1002/art.42434.
APA
Rothwell, S., Amos, C. I., Miller, F. W., Rider, L. G., Lundberg, I. E., Gregersen, P. K., … the Myositis Genetics Consortium, [missing]. (2023). Identification of novel associations and localization of signals in idiopathic inflammatory myopathies using genome‐wide imputation. ARTHRITIS & RHEUMATOLOGY, 75(6), 1021–1027. https://doi.org/10.1002/art.42434
Chicago author-date
Rothwell, Simon, Christopher I. Amos, Frederick W. Miller, Lisa G. Rider, Ingrid E. Lundberg, Peter K. Gregersen, Jiri Vencovsky, et al. 2023. “Identification of Novel Associations and Localization of Signals in Idiopathic Inflammatory Myopathies Using Genome‐wide Imputation.” ARTHRITIS & RHEUMATOLOGY 75 (6): 1021–27. https://doi.org/10.1002/art.42434.
Chicago author-date (all authors)
Rothwell, Simon, Christopher I. Amos, Frederick W. Miller, Lisa G. Rider, Ingrid E. Lundberg, Peter K. Gregersen, Jiri Vencovsky, Neil McHugh, Vidya Limaye, Albert Selva‐O’Callaghan, Michael G. Hanna, Pedro M. Machado, Lauren M. Pachman, Ann M. Reed, Øyvind Molberg, Olivier Benveniste, Pernille Mathiesen, Timothy Radstake, Andrea Doria, Jan De Bleecker, Boel De Paepe, Britta Maurer, William E. Ollier, Leonid Padyukov, Terrance P. O’Hanlon, Annette Lee, Lucy R. Wedderburn, Hector Chinoy, Janine A. Lamb, and [missing] the Myositis Genetics Consortium. 2023. “Identification of Novel Associations and Localization of Signals in Idiopathic Inflammatory Myopathies Using Genome‐wide Imputation.” ARTHRITIS & RHEUMATOLOGY 75 (6): 1021–1027. doi:10.1002/art.42434.
Vancouver
1.
Rothwell S, Amos CI, Miller FW, Rider LG, Lundberg IE, Gregersen PK, et al. Identification of novel associations and localization of signals in idiopathic inflammatory myopathies using genome‐wide imputation. ARTHRITIS & RHEUMATOLOGY. 2023;75(6):1021–7.
IEEE
[1]
S. Rothwell et al., “Identification of novel associations and localization of signals in idiopathic inflammatory myopathies using genome‐wide imputation,” ARTHRITIS & RHEUMATOLOGY, vol. 75, no. 6, pp. 1021–1027, 2023.
@article{01HNFG1DHC491JFBMH0MT9HREY,
  abstract     = {{ObjectiveThe idiopathic inflammatory myopathies (IIMs) are heterogeneous diseases thought to be initiated by immune activation in genetically predisposed individuals. We imputed variants from the ImmunoChip array using a large reference panel to fine-map associations and identify novel associations in IIM. MethodsWe analyzed 2,565 Caucasian IIM patient samples collected through the Myositis Genetics Consortium (MYOGEN) and 10,260 ethnically matched control samples. We imputed 1,648,116 variants from the ImmunoChip array using the Haplotype Reference Consortium panel and conducted association analysis on IIM and clinical and serologic subgroups. ResultsThe HLA locus was consistently the most significantly associated region. Four non-HLA regions reached genome-wide significance, SDK2 and LINC00924 (both novel) and STAT4 in the whole IIM cohort, with evidence of independent variants in STAT4, and NAB1 in the polymyositis (PM) subgroup. We also found suggestive evidence of association with loci previously associated with other autoimmune rheumatic diseases (TEC and LTBR). We identified more significant associations than those previously reported in IIM for STAT4 and DGKQ in the total cohort, for NAB1 and FAM167A-BLK loci in PM, and for CCR5 in inclusion body myositis. We found enrichment of variants among DNase I hypersensitivity sites and histone marks associated with active transcription within blood cells. ConclusionWe found novel and strong associations in IIM and PM and localized signals to single genes and immune cell types.}},
  author       = {{Rothwell, Simon and Amos, Christopher I. and Miller, Frederick W. and Rider, Lisa G. and Lundberg, Ingrid E. and Gregersen, Peter K. and Vencovsky, Jiri and McHugh, Neil and Limaye, Vidya and Selva‐O'Callaghan, Albert and Hanna, Michael G. and Machado, Pedro M. and Pachman, Lauren M. and Reed, Ann M. and Molberg, Øyvind and Benveniste, Olivier and Mathiesen, Pernille and Radstake, Timothy and Doria, Andrea and De Bleecker, Jan and De Paepe, Boel and Maurer, Britta and Ollier, William E. and Padyukov, Leonid and O'Hanlon, Terrance P. and Lee, Annette and Wedderburn, Lucy R. and Chinoy, Hector and Lamb, Janine A. and the Myositis Genetics Consortium, [missing]}},
  issn         = {{2326-5191}},
  journal      = {{ARTHRITIS & RHEUMATOLOGY}},
  keywords     = {{Immunology,Rheumatology,Immunology and Allergy}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{1021--1027}},
  publisher    = {{Wiley}},
  title        = {{Identification of novel associations and localization of signals in idiopathic inflammatory myopathies using genome‐wide imputation}},
  url          = {{http://doi.org/10.1002/art.42434}},
  volume       = {{75}},
  year         = {{2023}},
}
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