ArticleEuropean journal of human genetics : EJHG2012
1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data.
Article in European journal of human genetics : EJHG, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 5 of them syntheses that pooled it.
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Who cites it
85 citing papers in PubMed, 5 syntheses or guidelines pooled it, 137 citations in OpenAlex.
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- Association of common polymorphisms in the IL2RA gene with type 1 diabetes: evidence of 32,646 individuals from 10 independent studies.Journal of cellular and molecular medicine · 2015Pooled it
- Integrating genetic, transcriptional, and functional analyses to identify 5 novel genes for atrial fibrillation.Circulation · 2014Pooled it
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- Genetic interactions and pleiotropy in metabolic diseases: Insights from a comprehensive GWAS analysis.Journal of cellular and molecular medicine · 2024Article
- Biomolecular Actions by Intestinal Endotoxemia in Metabolic Syndrome.International journal of molecular sciences · 2024Review
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- A genome-wide cross-trait analysis identifies shared loci and causal relationships of type 2 diabetes and glycaemic traits with polycystic ovary syndrome.Diabetologia · 2022Article
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- A Comparison of Methods for Gene-Based Testing That Account for Linkage Disequilibrium.Frontiers in genetics · 2022Article
- Genetic overlap between type 1 diabetes and other autoimmune diseases.Seminars in immunopathology · 2022Review
- Causal effects of inflammatory protein biomarkers on inflammatory diseases.Science advances · 2021Article
- Prediction of functional microexons by transfer learning.BMC genomics · 2021Article
- Gene-level analysis of rare variants in 379,066 whole exome sequences identifies an association of GIGYF1 loss of function with type 2 diabetes.Scientific reports · 2021Article
- Genome-wide Association Study of Estradiol Levels and the Causal Effect of Estradiol on Bone Mineral Density.The Journal of clinical endocrinology and metabolism · 2021Article
- Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes.Nature genetics · 2021Article
- Association of type 2 diabetes mellitus and periodontal disease susceptibility with genome-wide association-identified risk variants in a Southeastern Brazilian population.Clinical oral investigations · 2021Article
- How imputation can mitigate SNP ascertainment Bias.BMC genomics · 2021Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
Abstract
We hypothesize that imputation based on data from the 1000 Genomes Project can identify novel association signals on a genome-wide scale due to the dense marker map and the large number of haplotypes. To test the hypothesis, the Wellcome Trust Case Control Consortium (WTCCC) Phase I genotype data were imputed using 1000 genomes as reference (20100804 EUR), and seven case/control association studies were performed using imputed dosages. We observed two 'missed' disease-associated variants that were undetectable by the original WTCCC analysis, but were reported by later studies after the 2007 WTCCC publication. One is within the IL2RA gene for association with type 1 diabetes and the other in proximity with the CDKN2B gene for association with type 2 diabetes. We also identified two refined associations. One is SNP rs11209026 in exon 9 of IL23R for association with Crohn's disease, which is predicted to be probably damaging by PolyPhen2. The other refined variant is in the CUX2 gene region for association with type 1 diabetes, where the newly identified top SNP rs1265564 has an association P-value of 1.68 × 10(-16). The new lead SNP for the two refined loci provides a more plausible explanation for the disease association. We demonstrated that 1000 Genomes-based imputation could indeed identify both novel (in our case, 'missed' because they were detected and replicated by studies after 2007) and refined signals. We anticipate the findings derived from this study to provide timely information when individual groups and consortia are beginning to engage in 1000 genomes-based imputation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.