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PhenCode: Connecting genome to phenotype Belinda Giardine Cathy Riemer Ross Hardison Webb Miller Jim...
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Transcript of PhenCode: Connecting genome to phenotype Belinda Giardine Cathy Riemer Ross Hardison Webb Miller Jim...
PhenCode: PhenCode: Connecting Connecting genome to genome to phenotypephenotype
Belinda GiardineBelinda Giardine
Cathy RiemerCathy Riemer
Ross HardisonRoss Hardison
Webb MillerWebb Miller
Jim KentJim Kent
PSU and UCSCPSU and UCSC
Aims of PhenCodeAims 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 PhenCodeConnectivity in PhenCode
PhenCode tracksPhenCode tracksSee rest of example on poster 1201CSee rest of example on poster 1201C
Current data in PhenCodeCurrent data in PhenCode
databasesdatabases #entries#entries links to links to sourcesource
ARdbARdb 329329 nono
BGMUTBGMUT 16051605 yesyes
BTKbaseBTKbase 512512 yesyes
CFMDBCFMDB 1,4001,400 yesyes
HbVarHbVar 1,5301,530 yesyes
PAHdbPAHdb 513513 yesyes
SRD5A2SRD5A2 4242 nono
Swiss-ProtSwiss-Prot 22,45422,454 yesyes
TOTALTOTAL 28,38228,382
Any LSDB with clearly Any LSDB with clearly defined mutations can join defined mutations can join
PhenCodePhenCode 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 URLs and AcknowledgementsAcknowledgements
URLS genome.ucsc.edu www.bx.psu.edu
UCSC and UCSC and PSU Work was supported by NIH grants
HG002238 (WM) and DK65806 (RH), NHGRI grant 1P41HG02371 (WJK)
Work accomplishedWork accomplished
Tools for converting from reference Tools for converting from reference sequence coordinates to genome sequence coordinates to genome coordinatescoordinates
Table schema fast enough for Genome Table schema fast enough for Genome Browser, and general enough to handle Browser, and general enough to handle varied fields for details pagevaried fields for details page
Customized detail page, track coloring Customized detail page, track coloring and filteringand filtering
Position box searches on HGVS names Position box searches on HGVS names and common names for variants.and common names for variants.
Composition of Locus Variants Composition of Locus Variants tracktrack
Work in progressWork in progress
Add more Locus Specific DatabasesAdd more Locus Specific Databases Expand capabilities of tools used in Expand capabilities of tools used in
mapping variants to genomemapping variants to genome Documentation Documentation Automation of track updatesAutomation of track updates