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