SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project.
The multidisciplinary UCSF Pharmacogenetics of Membrane Transporters project seeks to systematically identify sequence variants in transporters and to determine the functional significance of these variants through evaluation of relevant cellular and clinical phenotypes. The project is structured around four interacting cores: genomics, cellular phenotyping, clinical phenotyping, and bioinformatics. The bioinformatics core is responsible for collecting, storing, and analyzing the information obtained by the other cores and for presenting the results, in particular, for the genomic data. Most of this process is automated using locally developed software written in Python, an open source language well suited for rapid, modular development that meets requirements that are themselves constantly evolving. Here we present the details of transforming ABI trace file data into useful information for project investigators and a description of the types of data analysis and display that we have developed.
Stryke
Doug
D
Department of Pharmaceutical Chemistry, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
Huang
Conrad C
CC
Kawamoto
Michiko
M
Johns
Susan J
SJ
Carlson
Elaine J
EJ
Deyoung
Joseph A
JA
Leabman
Maya K
MK
Herskowitz
Ira
I
Giacomini
Kathleen M
KM
Ferrin
Thomas E
TE
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D005091:Exons; D014644:Genetic Variation; D006801:Humans; D020407:Internet; D026901:Membrane Transport Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D027701:Organic Cation Transport Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000075102:Organic Cation Transporter 2; D010597:Pharmacogenetics / Q000706:statistics & numerical data*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software
D026901:Membrane Transport Proteins; D027701:Organic Cation Transport Proteins; D000075102:Organic Cation Transporter 2; C491013:SLC22A2 protein, human