GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation

Bioinformatics

Volumn 32, Issue 4, 2016, Pages 542-548

  Lu, Qiongshi ^a   Yao, Xinwei ^a   Hu, Yiming ^a   Zhao, Hongyu ^a,b  

^a YALE UNIVERSITY   (United States)

^b VA Cooperative Studies Program Coordinating Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

CROHN DISEASE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HAPLOTYPE; HUMAN; PROCEDURES; QUANTITATIVE TRAIT LOCUS; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE;

BIOMARKERS; CROHN DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SCHIZOPHRENIA; SOFTWARE;

EID: 84959129294     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv610     Document Type: Article

References (29)

1. Ardlie, K. G. et al. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348, 648-660.
2. Bernstein, B. E. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
3. Chung, D. et al. (2014) GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation. PLoS Genet., 10, e1004787.
4. Cooper, G. M. and Shendure, J. (2011) Needles in stacks of needles: finding diseasecausal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 628-640.
5. Efron, B. (2010) Large-Scale Inference: Empirical Bayes Methods for Estimation, Testing, and Prediction. Cambridge University Press, New York.
6. Eicher, J. D. et al. (2015) GRASP v2. 0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. Nucleic Acids Res., 43, D799-D804.
7. Eichler, E. E. et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet., 11, 446-450.
8. Franke, A. et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet., 42, 1118-1125.
9. Fu, Y. et al. (2014) FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. Genome Biol., 15, 480.
10. Gibbs, J. R. et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet., 6, e1000952.
11. Hindorff, L. A. et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA, 106, 9362-9367.
12. Hou, L. and Zhao, H. (2013) A review of post-GWAS prioritization approaches. Front. Genet., 4, 280.
13. Kircher, M. et al. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet., 46, 310-315.
14. Kundaje, A. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
15. Lu, Q. et al. (2015) A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. Sci. Rep., 5, 10576.
16. Manolio, T. A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
17. Pruim, R. J. et al. (2010) LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics, 26, 2336-2337.
18. Rioux, J. D. et al. (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet., 39, 596-604.
19. Ripke, S. et al. (2011) Genome-wide association study identifies five new schizophrenia loci. Nat. Genet., 43, 969-976.
20. Ripke, S. et al. (2014) Biological insights from 108 schizophrenia-associated genetic loci. Nature, 511, 421-427.
21. Ritchie, G. R. et al. (2014) Functional annotation of noncoding sequence variants. Nat. Methods, 11, 294-296.
22. Sboner, A. et al. (2011) The real cost of sequencing: higher than you think!. Genome Biol., 12, 125.
23. Shihab, H. A. et al. (2015) An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics, 31, 1536-1543.
24. Visscher, P. M. et al. (2012) Five years of GWAS discovery. Am. J. Hum. Genet., 90, 7-24.
25. Wall, J. D. and Pritchard, J. K. (2003) Haplotype blocks and linkage disequilibrium in the human genome. Nature Rev. Genet., 4, 587-597.
26. Wang, Q. et al. (2015) A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Front. Genet., 6, 149.
27. Ward, L. D. and Kellis, M. (2012) Interpreting noncoding genetic variation in complex traits and human disease. Nat. Biotechnol., 30, 1095-1106.
28. Westra, H. J. et al. (2013) Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet., 45, 1238-1243.
29. Witte, J. S. et al. (2014)The contribution of genetic variants to disease depends on the ruler. Nat. Rev. Genet., 15, 765-776.