PhenCode: Connecting genome to phenotype Belinda Giardine Cathy Riemer Ross Hardison Webb Miller Jim Kent PSU and UCSC

Aims of PhenCode   Connect genome data (evolutionary history, function) with phenotype and clinical data   Facilitate better understanding of the associations between genotype and phenotype   Generate novel explanations for mechanisms of disease

Connectivity in PhenCode

PhenCode tracks See rest of example on poster 1201C

Current data in PhenCode databases#entries links to source ARdb329no BGMUT1605yes BTKbase512yes CFMDB1,400yes HbVar1,530yes PAHdb513yes SRD5A242no Swiss-Prot22,454yes TOTAL28,382

Any LSDB with clearly defined mutations can join PhenCode   The essential information is the same as for HGVS style nomenclature or entry in Central Repository   Reference sequence   Position(s) in reference sequence   The change in amino acid or nucleotide sequence   This information, in combination with alignments between the reference sequence and the chromosome sequence, gives all the required information to add the mutations to the track.   Additional attributes such as the phenotype associated with the variant make the track even more useful.

URLs and Acknowledgements URLS genome.ucsc.edu UCSC and UCSC and PSU Work was supported by NIH grants HG (WM) and DK65806 (RH), NHGRI grant 1P41HG02371 (WJK)

Work accomplished Tools for converting from reference sequence coordinates to genome coordinates Tools for converting from reference sequence coordinates to genome coordinates Table schema fast enough for Genome Browser, and general enough to handle varied fields for details page Table schema fast enough for Genome Browser, and general enough to handle varied fields for details page Customized detail page, track coloring and filtering Customized detail page, track coloring and filtering Position box searches on HGVS names and common names for variants. Position box searches on HGVS names and common names for variants.

Composition of Locus Variants track

Work in progress Add more Locus Specific Databases Add more Locus Specific Databases Expand capabilities of tools used in mapping variants to genome Expand capabilities of tools used in mapping variants to genome Documentation Documentation Automation of track updates Automation of track updates