Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
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The genetic architectures of common, complex diseases are largely uncharacterized. We modeled the genetic architecture underlying genome-wide association study (GWAS) data for rheumatoid arthritis and developed a new method using polygenic risk-score analyses to infer the total liability-scale variance explained by associated GWAS SNPs. Using this method, we estimated that, together, thousands of SNPs from rheumatoid arthritis GWAS explain an additional 20% of disease risk (excluding known associated loci). We further tested this method on datasets for three additional diseases and obtained comparable estimates for celiac disease (43% excluding the major histocompatibility complex), myocardial infarction and coronary artery disease (48%) and type 2 diabetes (49%). Our results are consistent with simulated genetic models in which hundreds of associated loci harbor common causal variants and a smaller number of loci harbor multiple rare causal variants. These analyses suggest that GWAS will continue to be highly productive for the discovery of additional susceptibility loci for common diseases.
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ASD mutations with very high penetrance are exceptional (i.e., Rett syndrome mutations in MECP2 and CDKL5), and Mendelian diseases enriched for ASD have far less than complete penetrance (e.g., Fragile X syndrome and tuberous sclerosis).
“Indeed, ASD mutations with very high penetrance are exceptional (i.e., Rett syndrome mutations in MECP2 and CDKL5), and Mendelian diseases enriched for ASD have far less than complete penetrance (e.g., Fragile X syndrome and tuberous sclerosis). 78”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [78]
Karyotyping studies suggested that on the order of 5% of ASD cases have one of a large number of rare but relatively gross chromosomal abnormalities.
“Karyotyping studies suggested that on the order of 5% of ASD cases have one of a large number of rare but relatively gross chromosomal abnormalities. 14,78”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [78]
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- Authors
- Diabetes Genetics Replication and Meta-analysis Consortium, Stahl, E. A., Myocardial Infarction Genetics Consortium, Wegmann, D., Trynka, G., Gutierrez-Achury, J., Do, R., Voight, B. F., Kraft, P., Chen, R., Kallberg, H. J., Kurreeman, F. A. S., Kathiresan, S., Wijmenga, C., Gregersen, P. K., Alfredsson, L., Siminovitch, K. A., Worthington, J., de Bakker, P. I. W., Raychaudhuri, S., & Plenge, R. M.
- Affiliations
- Broad Institute (US)
- University of California, Los Angeles (US)
- University Medical Center Groningen (NL)
- University of Pennsylvania (US)
- Harvard University (US)
- Northwell Health (US)
- Karolinska Institutet (SE)
- Mount Sinai Hospital (CA)
- Manchester Academic Health Science Centre (GB)
- Corresponding author
- Stahl, Eli A
- Plenge, Robert M
- ORCID
- Venue
- Nature Genetics
- Published
- 2012-03-25
- Volume
- 44
- Issue
- 5
- Pages
- 483-489
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6560362
- OpenAlex
- W2153968413
- Cited by
- 388
- References
- 60
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 6 · 2023: 8 · 2022: 12 · 2021: 20 · 2020: 20 · 2019: 27 · 2018: 27 · 2017: 38 · 2016: 41 · 2015: 43 · 2014: 56 · 2013: 56 · 2012: 26
- FWCI
- 34.88
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- PubMed Central (acceptedVersion)
- Archivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele (submittedVersion)
- Site cant be reached (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion)
- Open Research (University of Surrey) (submittedVersion)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- Funders
- Burroughs Wellcome Fund
- Biogen
- Wellcome Trust (090532)
- Canada Research Chairs
- National Institutes of Health
- Canadian Institutes of Health Research (MOP79321, IIN84042)
- National Institute of General Medical Sciences (U01GM092691)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR044422, N01-AR-22263, R01 AR44422, K08AR055688, R01AR059648, R01AR056768, R01AR057108)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Rheumatology › Rheumatoid Arthritis Research and Therapies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- rheumatoid arthritis, polygenic risk score, polygenic architecture, Bayesian inference, genetic susceptibility, common genetic variants, celiac disease, myocardial infarction, coronary artery disease, type 2 diabetes, genetic susceptibility loci, genome-wide association study
- MeSH terms
- Arthritis, Rheumatoid, Bayes Theorem, Cardiovascular Diseases, Celiac Disease, Diabetes Mellitus, Type 2, Humans, Case-Control Studies, Genetic Predisposition to Disease, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic Loci
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