Software:Gene Relationships Across Implicated Loci
Gene Relationships Across Implicated Loci (GRAIL) is a free web application developed by Soumya Raychaudhuri at the Broad Institute with the goal of determining the relationships among genes in different disease associated loci through statistical analysis.[1]
Mode of operation
When single-nucleotide polymorphisms (SNPs) are identified through a genome-wide association study (GWAS) as being possibly linked to a human disease, GRAIL works by comparing those with SNPs already identified in the scientific literature as being tied to the disease (using a text-mining algorithm going through PubMed abstracts),[1] and determines the degree of functional connectivity among the associated genes. SNPs identified with this method have been shown to be replicated in independent sets at a much higher probability than randomly selected ones.[2] GRAIL has also demonstrated better performance than other published algorithms.[3]
However, the software is still in its Beta phase, and has shown varied levels of success depending on the phenotype in question.[3]
References
- ↑ 1.0 1.1 "BROAD Institute website: GRAIL: Gene Relationships Across Implicated Loci". https://software.broadinstitute.org/mpg/grail/.
- ↑ Raychaudhuri, Soumya; Thomson, Brian P; Remmers, Elaine F; Eyre, Stephen; Hinks, Anne; Guiducci, Candace; Catanese, Joseph J; Xie, Gang et al. (2009-11-08). "Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk" (in En). Nature Genetics 41 (12): 1313–1318. doi:10.1038/ng.479. ISSN 1061-4036. PMID 19898481.
- ↑ 3.0 3.1 Raychaudhuri, Soumya; Plenge, Robert M.; Rossin, Elizabeth J.; Ng, Aylwin C. Y.; Consortium, International Schizophrenia; Purcell, Shaun M.; Sklar, Pamela; Scolnick, Edward M. et al. (2009-06-26). "Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions" (in en). PLOS Genetics 5 (6): e1000534. doi:10.1371/journal.pgen.1000534. ISSN 1553-7404. PMID 19557189.
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