The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Linking disease associations with regulatory information in the human genome
Open accessAbstract
Genome-wide association studies have been successful in identifying single nucleotide polymorphisms (SNPs) associated with a large number of phenotypes. However, an associated SNP is likely part of a larger region of linkage disequilibrium. This makes it difficult to precisely identify the SNPs that have a biological link with the phenotype. We have systematically investigated the association of multiple types of ENCODE data with disease-associated SNPs and show that there is significant enrichment for functional SNPs among the currently identified associations. This enrichment is strongest when integrating multiple sources of functional information and when highest confidence disease-associated SNPs are used. We propose an approach that integrates multiple types of functional data generated by the ENCODE Consortium to help identify “functional SNPs” that may be associated with the disease phenotype. Our approach generates putative functional annotations for up to 80% of all previously reported associations. We show that for most associations, the functional SNP most strongly supported by experimental evidence is a SNP in linkage disequilibrium with the reported association rather than the reported SNP itself. Our results show that the experimental data sets generated by the ENCODE Consortium can be successfully used to suggest functional hypotheses for variants associated with diseases and other phenotypes.
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Cites
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Genomewide Association Analysis of Coronary Artery Disease
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Cited by
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
Annotation of functional variation in personal genomes using RegulomeDB
Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722
Self-citationAnalysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
International Multiple Sclerosis Genetics Consortium (IMSGC) (2013) · Nature Genetics · doi:10.1038/ng.2770 · Cited by 1,386
Integrative omics for health and disease
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Metadata
- Authors
- Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S., & Snyder, M.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2012-09
- Volume
- 22
- Issue
- 9
- Pages
- 1748-1759
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W4213327946
- Cited by
- 713
- References
- 15
- Type
- posted content
- Language
- en
- Open access
- hybrid
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- Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S., & Snyder, M. (2012). Linking disease associations with regulatory information in the human genome. Genome Research. https://doi.org/10.1101/gr.136127.111
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