PACdb: a database for cell-based pharmacogenomics

Abstract

We have developed Pharmacogenomics And Cell database (PACdb), a results database that makes available relationships between single nucleotide polymorphisms, gene expression, and cellular sensitivity to various drugs in cell-based models to help determine genetic variants associated with drug response. The current version also supports summary analysis on differentially expressed genes between the HapMap samples of European and African ancestry, as well as queries for summary information of correlations between gene expression and pharmacological phenotypes. At present, data generated on the following anticancer agents are included: carboplatin, cisplatin, etoposide, daunorubicin, and cytarabine (Ara-C). The database is also available to assist in the investigation of the effects of potential confounding variables (e.g. cell proliferation rate) in lymphoblastoid cell lines. PACdb will be regularly updated to include more drugs and new datasets (e.g. baseline microRNA levels). PACdb will be linked into PharmGKB to benefit the next wave of pharmacogenetic and pharmacogenomic discovery.

Fig. 1

Pharmacogenomics And Cell database (PACdb) serves results from cell-based pharmacogenomic studies. CEU, Caucasian residents from Utah, USA; YRI, Yoruba people from Ibadan, Nigeria. Dashed arrows indicate future developments (e.g. more drugs and datasets).

Fig. 2

Genotype–Cytotoxicity Association Query Tool. With drug as input, single nucleotide polymorphisms (SNPs) that show association at a user-specified threshold are output, along with the relevant phenotype (e.g. area under the cellular survival curve and IC₅₀). Each SNP is annotated with host gene, function, and genomic RefSeq position. The results, as true of all Pharmacogenomics And Cell database (PACdb) queries, may be exported to a spreadsheet for further analysis.