PHENCODE: PAVING THE PATH BETWEEN PHENOTYPE AND GENOME
Belinda Giardine1, Riemer C.1, Hefferon T.2, Cutting G.3, Hsu F.4, Trumbower H.4, Kent W.J.4, Kern A.4, Kuhn R.4, Patrinos G.P.5, Hughes J.R.6, Higgs D.R.6, Chui D.H.K.7, Blumenfeld O.O.8, Scriver C.R9, Phommarinh M.9, Miller W.1, Hardison R.C.1 1Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA; 2National Human Genome Research Institute, Bethesda, MD; 3Johns Hopkins University School of Medicine, Baltimore, MD; 4Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA; 5Erasmus University, Rotterdam, Netherlands; 6Weatherall Institute of Molecular Medicine, Oxford, UK; 7Boston University, Boston, MA; 8Albert Einstein College of Medicine, Bronx, NY; 9Montreal Children’s Hospital Research Institute, Canada www.bx.psu.edu & genome-test.cse.ucsc.edu (coming soon at genome.ucsc.edu) PhenCode connects locus Example 1: Interesting ABO variation specific databases, How can 2 parents with O blood type have a child with A? phenotype databases and
According to the literature, a large genotype data in the number of alleles arose by UCSC Genome Browser. recombination or gene conversion. (Seltsam et al, Blood 2003) Example 1 goes from Phenotype to Genotype and features the BGMUT locus specific database hosted at NCBI’s dbRBC.
Example 2 goes from Genotype to Phenotype figure adapted from Yazer M.H., Transfusion Medicine Reviews 2005 and features the PAHdb locus specific database. PhenotypePhenotype The UCSC Genome browser shows the mutations on the ABO gene as well as a region with a high recombination rate. Phenotype data widely scattered
Dead From the source, PAHdb, we find out that the phenotype produced by End this mutation is non-PKU HPA (hyperphenylalaninemia). Querying on the phenotype shows that 129 other entries have the same phenotype. Dead Inconsistent End nomenclature
Dead Inconsistent End numbering systems
Dead Different data End formats Genotype
Dead Different reference End sequences
Example 2: The UCSC Genome Browser shows a well conserved landmark upstream from the PAH gene. A deletion in the Human Mutation track removes this region. Summary: The details page on the browser shows more information including a link to the data source. Two-way connections
Connecting existing resources not creating new ones
Enhancing usefulness of connected resources