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 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 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 arose by UCSC Genome Browser. recombination or 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 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 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