1. PhenCode: Linking Human Mutation and Genome
Belinda Giardine
Cathy Riemer
Ross Hardison
Webb Miller
Jim Kent
PSU and UCSC

2. Aims 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

3. Connectivity in PhenCode

4. Current data in PhenCode
databases
#entries
associated with
ARdb
329
AIS, Prostatic cancer
BGMUT
1,941
Blood groups
CFMDB
1,433
Cystic fibrosis
HbVar
1,477
Hemoglobinopathies
IDbases
2,185
Immune deficiencies
LMDp
105
Muscular dystrophy
PAHdb
518
Phenylketonuria
SRD5A2 42
Prostate and breast cancer
Swiss-Prot
23,936
(broad polymorphism data)
TOTAL
31,966

5. LSDBs in the works RettBASE (Rett syndrome) dbPEX
(Zellweger syndrome, Refsum Disease Infinitile Form, Adrenoleukodystrophy Autosomal Neonatal Form)
LMDp (muscular dystrophy)
BIC (breast cancer)

6. Recent accomplishments
Added new LSDBs and updated old ones
Documentation is now available from the bx web site
The tools used in mapping the mutations to the genome are available also
Paper in Human Mutation
PhenCode: connecting ENCODE data with mutations and phenotype.

7. PhenCode example

8. Detail page at UCSC

9. Work in progress Add more Locus Specific Databases
Automation of track updates
Phenotype nomenclature

10. URLs and Acknowledgements
genome.ucsc.edu
UCSC and PSU
Work was supported by NIH grants HG (WM) and DK65806 (RH), NHGRI grant 1P41HG02371 (WJK)
Santa Cruz url has the tracks
Penn State has documentation on PhenCode