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.
Using GenPhen to find candidate mutations for a thalassemia
patient, then viewing them in register with ENCODE functional
data at the Genome Browser.
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.
Using HbVar to search for hemoglobin mutations associated with
particular laboratory findings and ethnicity.
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