PACdb: a Database for Cell-based Pharmacogenomics

Overview

Journal Pharmacogenet Genomics

Specialties Genetics
Pharmacology

Date 2010 Mar 11

PMID 20216476

Citations 33

Authors

Eric R Gamazon

Shiwei Duan

Wei Zhang

Rong Stephanie Huang

Emily O Kistner

Mary Eileen Dolan

Nancy J Cox

Affiliations

Soon will be listed here.

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.

Citing Articles

Pharmacogenomics Tools for Precision Public Health and Lessons for Low- and Middle-Income Countries: A Scoping Review.

Borbon A, Briceno J, Valderrama-Aguirre A Pharmgenomics Pers Med. 2025; 18:19-34.

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Response and Toxicity to Cytarabine Therapy in Leukemia and Lymphoma: From Dose Puzzle to Pharmacogenomic Biomarkers.

di Francia R, Crisci S, De Monaco A, Cafiero C, Re A, Iaccarino G Cancers (Basel). 2021; 13(5).

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Pharmacogenomics and COVID-19: clinical implications of human genome interactions with repurposed drugs.

Badary O Pharmacogenomics J. 2021; 21(3):275-284.

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Robust imaging and gene delivery to study human lymphoblastoid cell lines.

Jolly L, Sun Y, Carroll R, Homan C, Gecz J J Hum Genet. 2018; 63(9):945-955.

PMID: 29925960 DOI: 10.1038/s10038-018-0483-2.

Hypertension Susceptibility Loci are Associated with Anthracycline-related Cardiotoxicity in Long-term Childhood Cancer Survivors.

Hildebrandt M, Reyes M, Wu X, Pu X, Thompson K, Ma J Sci Rep. 2017; 7(1):9698.

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References

Abecasis G, Cardon L, Cookson W . A general test of association for quantitative traits in nuclear families. Am J Hum Genet. 2000; 66(1):279-92. PMC: 1288332. DOI: 10.1086/302698. View

Gamazon E, Zhang W, Konkashbaev A, Duan S, Kistner E, Nicolae D . SCAN: SNP and copy number annotation. Bioinformatics. 2009; 26(2):259-62. PMC: 2852202. DOI: 10.1093/bioinformatics/btp644. View

Huang R, Kistner E, Bleibel W, Shukla S, Dolan M . Effect of population and gender on chemotherapeutic agent-induced cytotoxicity. Mol Cancer Ther. 2007; 6(1):31-6. PMC: 2669540. DOI: 10.1158/1535-7163.MCT-06-0591. View

Huang R, Duan S, Bleibel W, Kistner E, Zhang W, Clark T . A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci U S A. 2007; 104(23):9758-63. PMC: 1887589. DOI: 10.1073/pnas.0703736104. View

Huang R, Duan S, Shukla S, Kistner E, Clark T, Chen T . Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach. Am J Hum Genet. 2007; 81(3):427-37. PMC: 1950832. DOI: 10.1086/519850. View

Frazer K, Ballinger D, Cox D, Hinds D, Stuve L, Boudreau A . A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449(7164):851-61. PMC: 2689609. DOI: 10.1038/nature06258. View

Sakai W, Swisher E, Karlan B, Agarwal M, Higgins J, Friedman C . Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers. Nature. 2008; 451(7182):1116-20. PMC: 2577037. DOI: 10.1038/nature06633. View

Zhang W, Duan S, Kistner E, Bleibel W, Huang R, Clark T . Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet. 2008; 82(3):631-40. PMC: 2427223. DOI: 10.1016/j.ajhg.2007.12.015. View

Huang R, Duan S, Kistner E, Bleibel W, Delaney S, Fackenthal D . Genetic variants contributing to daunorubicin-induced cytotoxicity. Cancer Res. 2008; 68(9):3161-8. PMC: 2714371. DOI: 10.1158/0008-5472.CAN-07-6381. View

10.

Huang R, Duan S, Kistner E, Hartford C, Dolan M . Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans. Mol Cancer Ther. 2008; 7(9):3038-46. PMC: 2743011. DOI: 10.1158/1535-7163.MCT-08-0248. View

11.

Zhang W, Duan S, Bleibel W, Wisel S, Huang R, Wu X . Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet. 2008; 125(1):81-93. PMC: 2665168. DOI: 10.1007/s00439-008-0601-x. View

12.

Bleibel W, Duan S, Huang R, Kistner E, Shukla S, Wu X . Identification of genomic regions contributing to etoposide-induced cytotoxicity. Hum Genet. 2008; 125(2):173-80. PMC: 2714550. DOI: 10.1007/s00439-008-0607-4. View

13.

Hartford C, Duan S, Delaney S, Mi S, Kistner E, Lamba J . Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity. Blood. 2008; 113(10):2145-53. PMC: 2652364. DOI: 10.1182/blood-2008-05-154302. View

14.

Cheung V, Spielman R . Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat Rev Genet. 2009; 10(9):595-604. PMC: 2989458. DOI: 10.1038/nrg2630. View

15.

Storey J, Tibshirani R . Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003; 100(16):9440-5. PMC: 170937. DOI: 10.1073/pnas.1530509100. View