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Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry.
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In: Molecular psychiatry, vol 25, iss 10 (2020)
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Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry.
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In: Molecular psychiatry, vol 25, iss 10 (2020)
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Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis.
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In: Human molecular genetics, vol 27, iss 24 (2018)
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Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.
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In: Nature genetics, vol 50, iss 7 (2018)
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Global genetic differentiation of complex traits shaped by natural selection in humans.
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In: Nature communications, vol. 9, no. 1, pp. 1865 (2018)
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GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium.
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In: Molecular psychiatry, vol 22, iss 3 (2017)
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Functional annotation signatures of disease susceptibility loci improve SNP association analysis.
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Abstract:
BACKGROUND: Genetic association studies are conducted to discover genetic loci that contribute to an inherited trait, identify the variants behind these associations and ascertain their functional role in determining the phenotype. To date, functional annotations of the genetic variants have rarely played more than an indirect role in assessing evidence for association. Here, we demonstrate how these data can be systematically integrated into an association study's analysis plan. RESULTS: We developed a Bayesian statistical model for the prior probability of phenotype-genotype association that incorporates data from past association studies and publicly available functional annotation data regarding the susceptibility variants under study. The model takes the form of a binary regression of association status on a set of annotation variables whose coefficients were estimated through an analysis of associated SNPs in the GWAS Catalog (GC). The functional predictors examined included measures that have been demonstrated to correlate with the association status of SNPs in the GC and some whose utility in this regard is speculative: summaries of the UCSC Human Genome Browser ENCODE super-track data, dbSNP function class, sequence conservation summaries, proximity to genomic variants in the Database of Genomic Variants and known regulatory elements in the Open Regulatory Annotation database, PolyPhen-2 probabilities and RegulomeDB categories. Because we expected that only a fraction of the annotations would contribute to predicting association, we employed a penalized likelihood method to reduce the impact of non-informative predictors and evaluated the model's ability to predict GC SNPs not used to construct the model. We show that the functional data alone are predictive of a SNP's presence in the GC. Further, using data from a genome-wide study of ovarian cancer, we demonstrate that their use as prior data when testing for association is practical at the genome-wide scale and improves power to detect associations. CONCLUSIONS: We show how diverse functional annotations can be efficiently combined to create 'functional signatures' that predict the a priori odds of a variant's association to a trait and how these signatures can be integrated into a standard genome-wide-scale association analysis, resulting in improved power to detect truly associated variants.
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Keyword:
Disease Susceptibility; Female; Genetic Association Studies; Genetic Loci; Genome-Wide Association Study; Humans; Molecular Sequence Annotation; Ovarian Neoplasms; Polymorphism; Single Nucleotide
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URL: http://www.ncbi.nlm.nih.gov/pubmed/24886216
https://hdl.handle.net/10161/8882
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Genome-wide association analyses of child genotype effects and parent-of-origin effects in specific language impairment.
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In: Symplectic Elements at Oxford ; Europe PubMed Central ; PubMed (http://www.ncbi.nlm.nih.gov/pubmed/) ; Web of Science (Lite) (http://apps.webofknowledge.com/summary.do) ; Scopus (http://www.scopus.com/home.url) ; CrossRef (2014)
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A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci
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Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
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In: PLoS genetics, vol 7, iss 7 (2011)
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Identification of relations between risk factors and their pathologies or health conditions by mining scientific literature.
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In: ISSN: 0926-9630 ; EISSN: 1879-8365 ; Studies in Health Technology and Informatics ; https://hal-riip.archives-ouvertes.fr/pasteur-00606238 ; Studies in Health Technology and Informatics, IOS Press, 2010, 160 (Pt 2), pp.964-8. ⟨10.1111/j.1567-1364.2008.00361.x⟩ (2010)
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Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
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In: Symplectic Elements at Oxford ; Europe PubMed Central ; PubMed (http://www.ncbi.nlm.nih.gov/pubmed/) ; Web of Science (Lite) (http://apps.webofknowledge.com/summary.do) ; Scopus (http://www.scopus.com/home.url) ; CrossRef (2009)
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