Fine mapping seronegative and seropositive rheumatoid arthritis to shared and distinct HLA alleles by adjusting for the effects of heterogeneity.

PubWeight™: 1.34‹?› | Rank: Top 10%

🔗 View Article (PMC 3980428)

Published in Am J Hum Genet on March 20, 2014

Authors

Buhm Han1, Dorothée Diogo2, Steve Eyre3, Henrik Kallberg4, Alexandra Zhernakova5, John Bowes3, Leonid Padyukov4, Yukinori Okada2, Miguel A González-Gay6, Solbritt Rantapää-Dahlqvist7, Javier Martin8, Tom W J Huizinga9, Robert M Plenge10, Jane Worthington3, Peter K Gregersen11, Lars Klareskog4, Paul I W de Bakker12, Soumya Raychaudhuri13

Author Affiliations

1: Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA.
2: Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA; Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
3: Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester M13 9PT, UK; NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PT, UK.
4: Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, 171 76 Stockholm, Sweden.
5: Department of Rheumatology, Leiden University Medical Centre, 2300 RC Leiden, the Netherlands; Department of Genetics, University Medical Center Groningen and University of Groningen, 9700 RB Groningen, the Netherlands.
6: Rheumatology Division, Hospital Universitario Marqués de Valdecilla, Instituto de Formación e Investigación Marqués de Valdecilla, 39008 Santander, Spain.
7: Department of Public Health and Clinical Medicine and Department of Rheumatology, Umeå University, 901 85 Umeå, Sweden.
8: Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Cientificas, 18100 Armilla, Granada, Spain.
9: Department of Rheumatology, Leiden University Medical Centre, 2300 RC Leiden, the Netherlands.
10: Merck Research Laboratories, Merck & Co. Inc., Boston, MA 02115, USA.
11: The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, NY 11030, USA.
12: Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Epidemiology and Medical Genetics, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands.
13: Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA; Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA; Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester M13 9PT, UK. Electronic address: soumya@broadinstitute.org.

Articles citing this

Dense genotyping of immune-related susceptibility loci reveals new insights into the genetics of psoriatic arthritis. Nat Commun (2015) 1.70

Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes. Am J Hum Genet (2014) 1.26

Construction of a population-specific HLA imputation reference panel and its application to Graves' disease risk in Japanese. Nat Genet (2015) 1.02

Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk. Nat Genet (2015) 1.00

Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis. Proc Natl Acad Sci U S A (2016) 0.98

The genetics of rheumatoid arthritis: risk and protection in different stages of the evolution of RA. Rheumatology (Oxford) (2014) 0.96

Interactions between amino acid-defined major histocompatibility complex class II variants and smoking in seropositive rheumatoid arthritis. Arthritis Rheumatol (2015) 0.95

Genetics, environment, and gene-environment interactions in the development of systemic rheumatic diseases. Rheum Dis Clin North Am (2014) 0.93

New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. Int J Epidemiol (2015) 0.93

Genetics of autoimmune diseases: perspectives from genome-wide association studies. Int Immunol (2016) 0.93

Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases. Nat Genet (2015) 0.91

PTPN22 is associated with susceptibility to psoriatic arthritis but not psoriasis: evidence for a further PsA-specific risk locus. Ann Rheum Dis (2015) 0.90

Human leukocyte antigen polymorphisms and personalized medicine for rheumatoid arthritis. J Hum Genet (2015) 0.90

Molecular mechanisms for contribution of MHC molecules to autoimmune diseases. Curr Opin Immunol (2014) 0.88

Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet (2016) 0.88

Genetics of immune-mediated disorders: from genome-wide association to molecular mechanism. Curr Opin Immunol (2014) 0.86

A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases. Nat Genet (2016) 0.85

Familial aggregation of arthritis-related diseases in seropositive and seronegative rheumatoid arthritis: a register-based case-control study in Sweden. Ann Rheum Dis (2014) 0.83

Coeliac disease and rheumatoid arthritis: similar mechanisms, different antigens. Nat Rev Rheumatol (2015) 0.83

Genetic sharing and heritability of paediatric age of onset autoimmune diseases. Nat Commun (2015) 0.81

Association of valine and leucine at HLA-DRB1 position 11 with radiographic progression in rheumatoid arthritis, independent of the shared epitope alleles but not independent of anti-citrullinated protein antibodies. Arthritis Rheumatol (2015) 0.80

The immunopathogenesis of seropositive rheumatoid arthritis: from triggering to targeting. Nat Rev Immunol (2016) 0.80

Genetic markers as therapeutic target in rheumatoid arthritis: A game changer in clinical therapy? Rheumatol Int (2016) 0.80

Genetic architectures of seropositive and seronegative rheumatic diseases. Nat Rev Rheumatol (2015) 0.79

Replication of Associations of Genetic Loci Outside the HLA Region With Susceptibility to Anti-Cyclic Citrullinated Peptide-Negative Rheumatoid Arthritis. Arthritis Rheumatol (2016) 0.78

Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis. Am J Hum Genet (2016) 0.77

Genetic studies of rheumatoid arthritis. Proc Jpn Acad Ser B Phys Biol Sci (2015) 0.77

Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Sci Transl Med (2017) 0.77

Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses. Am J Hum Genet (2015) 0.76

The Roles of Cigarette Smoking and the Lung in the Transitions Between Phases of Preclinical Rheumatoid Arthritis. Curr Rheumatol Rep (2016) 0.76

Fine-mapping the MHC locus in juvenile idiopathic arthritis (JIA) reveals genetic heterogeneity corresponding to distinct adult inflammatory arthritic diseases. Ann Rheum Dis (2016) 0.76

Update on the genetic architecture of rheumatoid arthritis. Nat Rev Rheumatol (2016) 0.76

VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis. Genes Immun (2017) 0.75

Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci. Sci Rep (2017) 0.75

Effects of C2ta genetic polymorphisms on MHC class II expression and autoimmune diseases. Immunology (2016) 0.75

Anti-citrullinated peptide/protein antibody (ACPA)-negative RA shares a large proportion of susceptibility loci with ACPA-positive RA: a meta-analysis of genome-wide association study in a Japanese population. Arthritis Res Ther (2015) 0.75

Family history of rheumatoid arthritis: an old concept with new developments. Nat Rev Rheumatol (2016) 0.75

Strategies for evaluating idiopathic inflammatory myopathy disease susceptibility genes. Curr Rheumatol Rep (2014) 0.75

rs2841277 (PLD4) is associated with susceptibility and rs4672495 is associated with disease activity in rheumatoid arthritis. Oncotarget (2017) 0.75

The association between the lymphocyte-monocyte ratio and disease activity in rheumatoid arthritis. Clin Rheumatol (2017) 0.75

MergeReference: A Tool for Merging Reference Panels for HLA Imputation. Genomics Inform (2017) 0.75

Articles cited by this

Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet (2006) 115.71

UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47

A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet (2009) 17.80

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet (2010) 9.90

Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med (2008) 9.68

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61

A new model for an etiology of rheumatoid arthritis: smoking may trigger HLA-DR (shared epitope)-restricted immune reactions to autoantigens modified by citrullination. Arthritis Rheum (2006) 9.52

Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet (2008) 7.07

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet (2012) 5.11

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet (2012) 4.46

Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene. Am J Hum Genet (2006) 4.22

Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci. Nat Genet (2010) 3.58

Prediction of coronary heart disease risk using a genetic risk score: the Atherosclerosis Risk in Communities Study. Am J Epidemiol (2007) 3.48

The genetic basis for the association of the 8.1 ancestral haplotype (A1, B8, DR3) with multiple immunopathological diseases. Immunol Rev (1999) 3.21

Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One (2013) 3.07

Regulation of anti-cyclic citrullinated peptide antibodies in rheumatoid arthritis: contrasting effects of HLA-DR3 and the shared epitope alleles. Arthritis Rheum (2005) 2.88

Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nat Genet (2013) 2.87

Value of anti-modified citrullinated vimentin and third-generation anti-cyclic citrullinated peptide compared with second-generation anti-cyclic citrullinated peptide and rheumatoid factor in predicting disease outcome in undifferentiated arthritis and rheumatoid arthritis. Arthritis Rheum (2009) 2.62

Overview of the MHC fine mapping data. Diabetes Obes Metab (2009) 2.24

Genetics and epigenetics of rheumatoid arthritis. Nat Rev Rheumatol (2013) 2.20

Autoantibodies recognizing carbamylated proteins are present in sera of patients with rheumatoid arthritis and predict joint damage. Proc Natl Acad Sci U S A (2011) 2.07

Different patterns of associations with anti-citrullinated protein antibody-positive and anti-citrullinated protein antibody-negative rheumatoid arthritis in the extended major histocompatibility complex region. Arthritis Rheum (2009) 1.87

Psoriasis and HLA-Cw6. Br J Dermatol (1980) 1.83

Interaction between smoking, the shared epitope, and anti-cyclic citrullinated peptide: a mixed picture in three large North American rheumatoid arthritis cohorts. Arthritis Rheum (2007) 1.83

HLA class I associations of ankylosing spondylitis in the white population in the United Kingdom. Ann Rheum Dis (1996) 1.79

Advances in the genetics of rheumatoid arthritis point to subclassification into distinct disease subsets. Arthritis Res Ther (2008) 1.61

Association of HLA-DR3 with anti-cyclic citrullinated peptide antibody-negative rheumatoid arthritis. Arthritis Rheum (2005) 1.55

Cumulative association of 22 genetic variants with seropositive rheumatoid arthritis risk. Ann Rheum Dis (2010) 1.53

Genetic and environmental determinants for disease risk in subsets of rheumatoid arthritis defined by the anticitrullinated protein/peptide antibody fine specificity profile. Ann Rheum Dis (2012) 1.53

Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08. Ann Neurol (2012) 1.19

HLA-Cw6 and HLA-DRB1*07 together are associated with less severe joint disease in psoriatic arthritis. Ann Rheum Dis (2007) 1.08

Rheumatoid arthritis: Are ACPA-positive and ACPA-negative RA the same disease? Nat Rev Rheumatol (2011) 1.03

All you wanted to know about anti-CCP but were afraid to ask. Autoimmun Rev (2010) 1.00

Rheumatoid arthritis: anti-Ro antibodies define a non-HLA-DR4 associated clinicoserological cluster. J Rheumatol (1993) 0.88