October, 2006

Dear LSDB curators,

We would like to invite you to join in the PhenCode project, an effort to connect phenotype and clinical data in locus specific databases such as yours with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. It is a collaboration among Penn State, UC Santa Cruz, and locus experts at other institutions, providing connections between the LSDBs and the Browser. This project enhances the usefulness of the information in both the locus specific databases and in the Genome Browser. We are working with the Human Genome Variation Society, and this project is being developed in collaboration with the WayStation and is set to connect to the Central Repository when that becomes available.

To see the current PhenCode-related tracks, go to genome-test.cse.ucsc.edu (soon on genome.ucsc.edu) and open the Genome Browser with the Human March 2006 build. The Locus Variants track is located in the Phenotype and Disease Associations section, while the ORegAnno (Open Regulatory Annotation) track is located under Expression and Regulation. Additional documentation on this project is available via the PhenCode link at www.bx.psu.edu.

Joining the project can be as simple as giving us permission to download your data and convert it to genome coordinates. Of course we will state that your database is the source of the information, and will also provide links back to it. We find that two-way connections between the UCSC Browser and locus specific databases are particularly helpful, and we would be happy to advise you on how to connect to the UCSC Browser. The PhenCode documentation includes examples demonstrating the advantages of this two-way information flow, using our databases of hemoglobin variants and genotype-phenotype relationships (HbVar and GenPhen) by way of illustration. Genome Browser users may find mutations of interest, and follow links back to the source LSDB for more complete information; conversely, users starting at an LSDB can use its query interface to find mutations that fit various criteria, and then view them on the Browser in register with additional annotation tracks of their choice.

We think your database would be a valuable addition to this effort; please let us know if you'd like to work with us on this.


Belinda Giardine image of email address, Ross Hardison, Webb Miller, Jim Kent

The Pennsylvania State University
The University of California, Santa Cruz