ArticleAmerican journal of human genetics2012
Prioritizing genetic variants for causality on the basis of preferential linkage disequilibrium.
Article in American journal of human genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- TET2 germline variants promote kidney disease by impairing DNA repair and activating cytosolic nucleotide sensors.Nature communications · 2024Article
- Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression of RUVBL1 and prostate cancer progression.American journal of human genetics · 2023Article
- A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis.Nature communications · 2021Article
- Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation.Journal of neural transmission (Vienna, Austria : 1996) · 2020Review
- Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression.G3 (Bethesda, Md.) · 2017Article
- Gene-nutrient interactions and susceptibility to human obesity.Genes & nutrition · 2017Review
- Trans-ethnic follow-up of breast cancer GWAS hits using the preferential linkage disequilibrium approach.Oncotarget · 2016Article
- The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants.Human mutation · 2016Article
- New Genetic Approaches to AD: Lessons from APOE-TOMM40 Phylogenetics.Current neurology and neuroscience reports · 2016Review
- Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease.BMC genomics · 2015Article
- Accurate prediction of a minimal region around a genetic association signal that contains the causal variant.European journal of human genetics : EJHG · 2014Article
- Article
- Comparing the efficacy of SNP filtering methods for identifying a single causal SNP in a known association region.Annals of human genetics · 2014Article
- The genetics of childhood obesity and interaction with dietary macronutrients.Genes & nutrition · 2013Article
- Windfalls and pitfalls: Applications of population genetics to the search for disease genes.Evolution, medicine, and public health · 2013Article
- Leveraging prior information to detect causal variants via multi-variant regression.PLoS computational biology · 2013Article
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11 authors.
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Abstract
To date, the widely used genome-wide association studies (GWASs) of the human genome have reported thousands of variants that are significantly associated with various human traits. However, in the vast majority of these cases, the causal variants responsible for the observed associations remain unknown. In order to facilitate the identification of causal variants, we designed a simple computational method called the "preferential linkage disequilibrium (LD)" approach, which follows the variants discovered by GWASs to pinpoint the causal variants, even if they are rare compared with the discovery variants. The approach is based on the hypothesis that the GWAS-discovered variant is better at tagging the causal variants than are most other variants evaluated in the original GWAS. Applying the preferential LD approach to the GWAS signals of five human traits for which the causal variants are already known, we successfully placed the known causal variants among the top ten candidates in the majority of these cases. Application of this method to additional GWASs, including those of hepatitis C virus treatment response, plasma levels of clotting factors, and late-onset Alzheimer disease, has led to the identification of a number of promising candidate causal variants. This method represents a useful tool for delineating causal variants by bringing together GWAS signals and the rapidly accumulating variant data from next-generation sequencing.
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