PhenCode: Examples

Locus-specific databases of variants and other mutations form a key link between the abundance of genomic information and clinically important issues. Here we show how the PhenCode connections complete a path from genome sequence, to functional analysis, to human mutations, and on to phenotypes of groups of patients (and back again). Among the resources used are the following:

HbVar is a relational database of hemoglobin variants and thalassemia mutations derived initially from several books by Prof. Titus H.J. Huisman. Subsequent additions and updates have increased the number of entries to over 1230. Entries include a description of the variant and associated pathology, hematology, electrophoretic mobility, ethnic occurrence, structure studies, functional studies, and references.
GenPhen records anonymized data on the clinical presentation and other phenotypes of these mutations, in heterozygous and homozygous conditions. (It is currently a prototype with limited data.)
The ENCODE consortium (ENCyclopedia Of DNA Elements), supported by the National Human Genome Research Institute, aims to identify all of the functional elements in the human genome; its results are available at various sites, including the UCSC Genome Browser.

The connectivity among these resources, as well as other LSDBs and Genome Browser tracks, is illustrated in the following examples.

Example 1:	Using GenPhen to find candidate mutations for a thalassemia patient, then viewing them in register with ENCODE functional data at the Genome Browser.
Example 2:	Using PhenCode with the Genome Browser's resident tracks to examine multi-species conservation at the sites of observed mutations in the human PAH gene.
Example 3:	Using HbVar to search for hemoglobin mutations associated with particular laboratory findings and ethnicity.

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