Abstract

DEEPRESEQUENCING (DR) PLATFORM (BUDGET ONP. 21) The DR Platform will be devoted to more systematic analyses of sequence variation in genes that emerge as likely determinants of interindividual variability in drug response based on some combination of evidence for a role in a drug pathway, phenotype/genotype association, linkage analysis, and differential expression. These genes will arise from the studies performed in Steps 1 and 2, and the analyses carried out in this platform will be preliminary to the large-scale clinical studies planned in Step 3. The goal of this Platform is to obtain a more thorough characterization of the patterns of variation, with a special focus on identifying and understanding the patterns of functional variation in coding and noncoding regions, which in turn will inform the design of subsequent association and functional studies. Examples of how DR data on UGT1A and CYP3A genes will be used to design association and/or functional studies are provided in the CRC (p. 256) and CYP3A (p. 262) Projects, respectively.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01GM061393-09
Application #
7690737
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
Budget Start
2008-07-01
Budget End
2009-06-30
Support Year
9
Fiscal Year
2008
Total Cost
$209,944
Indirect Cost

  Institution

Name
University of Chicago
Department
Type
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637

  Publications

Zhou, Shuqin; Skaar, Debra J; Jacobson, Pamala A et al. (2018) Pharmacogenomics of Medications Commonly Used in the Intensive Care Unit. Front Pharmacol 9:1436
House, Larry; Seminerio, Michael J; Mirkov, Snezana et al. (2018) Metabolism of megestrol acetate in vitro and the role of oxidative metabolites. Xenobiotica 48:973-983
Gamazon, Eric R; Trendowski, Matthew R; Wen, Yujia et al. (2018) Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. Sci Rep 8:733
Li, M; Seiser, E L; Baldwin, R M et al. (2018) ABC transporter polymorphisms are associated with irinotecan pharmacokinetics and neutropenia. Pharmacogenomics J 18:35-42
Geeleher, Paul; Nath, Aritro; Wang, Fan et al. (2018) Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. Genome Biol 19:130
Wing, Claudia; Komatsu, Masaaki; Delaney, Shannon M et al. (2017) Application of stem cell derived neuronal cells to evaluate neurotoxic chemotherapy. Stem Cell Res 22:79-88
Rudin, Shoshana; Marable, Marcus; Huang, R Stephanie (2017) The Promise of Pharmacogenomics in Reducing Toxicity During Acute Lymphoblastic Leukemia Maintenance Treatment. Genomics Proteomics Bioinformatics 15:82-93
Geeleher, Paul; Huang, R Stephanie (2017) Exploring the Link between the Germline and Somatic Genome in Cancer. Cancer Discov 7:354-355
Geeleher, Paul; Zhang, Zhenyu; Wang, Fan et al. (2017) Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Genome Res 27:1743-1751
Eadon, Michael T; Hause, Ronald J; Stark, Amy L et al. (2017) Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach. Int J Mol Sci 18:

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