PhenCode: Paving the Path between Phenotype and Genome

PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans. It connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. PhenCode is a collaboration among researchers at Penn State, UC Santa Cruz, and locus experts at other institutions.

Information for users:

• Introduction
• How to view PhenCode tracks at the Genome Browser
• Examples
• Downloads
• Links to LSDB sources and related sites
• Frequently asked questions
• Mailing list for announcements
• Contact us

Statistics:

LSDB variants Swiss-Prot variants HGMD*

variants 34,213 56,396 76,011

genes 1,386 11,343 2,876

average variants per gene 25 5 26
*Note the HGMD variants are not included in PhenCode but are listed here for comparison.

Additional information for database curators:

• Participating in PhenCode
• Invitation handout from HGVS meeting (Oct 2006)
• Guidelines for data conversion
• Example of adding a new data source

Publications and Presentations:

References for citation:

• Citing these sources

Additional reports:

• Poster from HGVS meeting (Nov 2008)
• Miller, W. et al. (2007) 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. [more]
• Poster from ASHG meeting (Oct 2007)
• Poster from CSHL meeting (May 2007)
• Poster from ASHG meeting (Oct 2006)

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