By a News Reporter-Staff News Editor at Genomics & Genetics Weekly -- A new study on Applied Bioinformatics is now available. According to news reporting originating from Nashville, Tennessee, by NewsRx correspondents, research stated, "With the recent decreasing cost of genome sequence data, there has been increasing interest in rare variants and methods to detect their association to disease. We developed BioBin, a flexible collapsing method inspired by biological knowledge that can be used to automate the binning of low frequency variants for association testing."
Our news editors obtained a quote from the research from Vanderbilt University, "We also built the Library of Knowledge Integration (LOKI), a repository of data assembled from public databases, which contains resources such as: dbSNP and gene Entrez database information from the National Center for Biotechnology (NCBI), pathway information from Gene Ontology (GO), Protein families database (Pfam), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, NetPath -signal transduction pathways, Open Regulatory Annotation Database (ORegAnno), Biological General Repository for Interaction Datasets (BioGrid), Pharmacogenomics Knowledge Base (PharmGKB), Molecular INTeraction database (MINT), and evolutionary conserved regions (ECRs) from UCSC Genome Browser. The novelty of BioBin is access to comprehensive knowledge-guided multi-level binning. For example, bin boundaries can be formed using genomic locations from: functional regions, evolutionary conserved regions, genes, and/or pathways. We tested BioBin using simulated data and 1000 Genomes Project low coverage data to test our method with simulated causative variants and a pairwise comparison of rare variant (MAF Genomes Project data, CEU and YRI populations. Lastly, we were able to apply BioBin to natural biological data from dbGaP and identify an interesting candidate gene for further study."
According to the news editors, the research concluded: "We have established that BioBin will be a very practical and flexible tool to analyze sequence data and potentially uncover novel associations between low frequency variants and complex disease."
For more information on this research see: BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. Bmc Medical Genomics, 2013;6 Suppl 2():S6. (BioMed Central - www.biomedcentral.com/; Bmc Medical Genomics - www.biomedcentral.com/bmcmedgenomics/)
The news editors report that additional information may be obtained by contacting C.B. Moore, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, United States. Additional authors for this research include J.R. Wallace, A.T. Frase, S.A. Pendergrass and M.D Ritchie (see also Applied Bioinformatics).
Keywords for this news article include: Nashville, Tennessee, United States, Applied Bioinformatics, North and Central America.
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