GREGOR: Evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

Bioinformatics

Volumn 31, Issue 16, 2015, Pages 2601-2606

  Schmidt, Ellen M ^a   Zhang, Ji ^b   Zhou, Wei ^a   Chen, Jin ^b   Mohlke, Karen L ^c   Chen, Y Eugene ^b   Willer, Cristen J ^a,b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANTIBODY SPECIFICITY; COMPUTER LANGUAGE; EPIGENETICS; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMAN; PHENOTYPE; PROCEDURES; QUANTITATIVE TRAIT LOCUS; REGULATORY SEQUENCE; SOFTWARE;

ALGORITHMS; EPIGENOMICS; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; ORGAN SPECIFICITY; PHENOTYPE; PROGRAMMING LANGUAGES; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID; SOFTWARE;

EID: 84939517308     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv201     Document Type: Article

References (24)

1. Abecasis, G. R. et al. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. Boyle, A. P. et al. (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. , 22, 1790-1797.
3. Claussnitzer, M. et al. (2014) Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms. Cell, 156, 343-358.
4. Coronary Artery Disease (C4D) Genetics Consortium(2011) A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease. Nat. Genet. , 43, 339-344.
5. Ehret, G. B. et al. (2011) Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature, 478, 103-109.
6. Ernst, J. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
7. Kichaev, G. et al. (2014) Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet. , 10, e1004722.
8. Lo, K. S. et al. (2014) Strategies to fine-map genetic associations with lipid levels by combining epigenomic annotations and liver-specific transcription profiles. Genomics, 104, 105-112.
9. Locke, A. E. et al. (2015) Genetic studies of body mass index yield new insights for obesity biology. Nature, 518, 197-206.
10. Maurano, M. T. et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science, 337, 1190-1195.
11. Morris, A. P. et al. (2012) Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat. Genet. , 44, 981-990.
12. Musunuru, K. et al. (2010) From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature, 466, 714-719.
13. Parker, S. C. et al. (2013) Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc. Natl Acad. Sci. U S A, 110, 17921-17926.
14. Pickrell, J. K. (2014) Joint analysis of functional genomic data and genomewide association studies of 18 human traits. Am. J. Hum. Genet. , 94, 559-573.
15. Schadt, E. E. et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol. , 6, e107.
16. Schaub, M. A. et al. (2012) Linking disease associations with regulatory information in the human genome. Genome Res. , 22, 1748-1759.
17. Schunkert, H. et al. (2011) Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat. Genet. , 43, 333-338.
18. Teslovich, T. M. et al. (2010) Biological, clinical and population relevance of 95 loci for blood lipids. Nature, 466, 707-713.
19. The ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
20. Thurman, R. E. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
21. Trynka, G. et al. (2013) Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet. , 45, 124-130.
22. Ward, L. D. and Kellis, M. (2012) HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. , 40, D930-D934.
23. Welter, D. et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. , 42, D1001-D1006.
24. Global Lipids Genetics Consortium et al. (2013) Discovery and refinement of loci associated with lipid levels. Nat. Genet. , 45, 1274-1283.