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PhenCode

PhenCode. Connecting Genotype and Phenotype. HbVar: Hemoglobin variants and thalassemia mutations. Began as Prof. Titus Huisman’s Syllabus of Hemoglobin Variants and Syllabus of Thalassemia Mutations Converted to on-line resource about 1997 Major curators now: Henri Wajcman, Ph.D.

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PhenCode

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  1. PhenCode Connecting Genotype and Phenotype

  2. HbVar: Hemoglobin variants and thalassemia mutations • Began as Prof. Titus Huisman’s Syllabus of Hemoglobin Variants and Syllabus of Thalassemia Mutations • Converted to on-line resource about 1997 • Major curators now: • Henri Wajcman, Ph.D. • George Patrinos, M.D., Ph.D. • David Chui, M.D.

  3. Current status of HbVar • Type Count • Total entries in database 1237 • Total hemoglobin variant entries 930 • Total thalassemia entries 355 • Entries both variant and thalassemia 48 • Entries involving the alpha1 gene 252 • Entries involving the alpha2 gene 287 • Entries involving the beta gene 688 http://www.bx.psu.edu/

  4. GenPhen • Records genotype and published phenotype data • Hemoglobin variants • Thalassemias • HPFH

  5. The Problem • Genotype is well covered by browsers such as those at UCSC and Ensembl • Phenotype data is scattered among literature articles and Locus Specific Databases (LSDBs) • No easy way of getting from one to another

  6. Difficulties in making the connection • Inconsistencies in fields, coordinate systems, and nomenclature • Standards are still being developed by the research community • Human Genome Variation Society (HGVS) • Mammalian Phenotype (MP) Ontology • Requires a large number of research groups, representing hundreds of databases, to work together

  7. Similar projects • OMIM • Lack of controlled vocabulary, inconsistent base numbering • HmutDb • Lacks plans for curation • Requires a reference sequence, but not chromosome coordinates • HGVbase • Not yet available; in progress for years • The WayStation and its associated central repository • Lacks funding • No chromosome coordinates

  8. PhenCode plan • Start by incorporating data from a few selected LSDBs as a proof of concept, and expand as more LSDB curators become interested • Currently we have HbVar, PAHdb, and are working on BGMUT, ARdb, and CFTR. • In addition, genome-wide variants have been imported from SwissProt • Work closely with the central repository and The WayStation for new mutations. • Use tools to map HGVS name to chromosome coordinates

  9. PhenCode plan continued • Keep a summary of the data in the central repository as a Human Mutation track at UCSC • Provide links to the LSDBs and other phenotype databases from the track to allow more in-depth queries • Build a companion Landmarks track containing reference points provided by the LSDB curators for each locus

  10. Recent additions • We have added data for the human phenylalanine hydroxylase gene (PAH). This data came from PAHdb at McGill University. • Deficiencies in PAH cause phenylketonuria (PKU)

  11. PAH gene in UCSC Browser

  12. Details page at browser

  13. Follow links back to PAHdb Liver-specific enhancer of human PAH.

  14. Examples • Examples are available at http://www.bx.psu.edu

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