title: Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions.
abstract: The emergence and prevalence of drug resistance demands streamlined strategies to identify drug resistant variants in a fast, systematic and cost-effective way. Methods commonly used to understand and predict drug resistance rely on limited clinical studies from patients who are refractory to drugs or on laborious evolution experiments with poor coverage of the gene variants. Here, we report an integrative functional variomics methodology combining deep sequencing and a Bayesian statistical model to provide a comprehensive list of drug resistance alleles from complex variant populations. Dihydrofolate reductase, the target of methotrexate chemotherapy drug, was used as a model to identify functional mutant alleles correlated with methotrexate resistance. This systematic approach identified previously reported resistance mutations, as well as novel point mutations that were validated in vivo. Use of this systematic strategy as a routine diagnostics tool widens the scope of successful drug research and development.
authors: Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
authors: Lai H
authors: 0000-0001-8653-2734
authors: LH
authors: Wong
authors: Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
authors: Sunita
authors: S
authors: Sinha
authors: Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.
authors: Julien R
authors: JR
authors: Bergeron
authors: seqWell, Inc., Beverly, Massachusetts, United States of America.
authors: Joseph C
authors: JC
authors: Mellor
authors: Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
authors: Guri
authors: G
authors: Giaever
authors: Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors: Patrick
authors: 0000-0001-6097-6572
authors: P
authors: Flaherty
authors: Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
authors: Corey
authors: C
authors: Nislow
mesh_terms: D000483:Alleles; D001499:Bayes Theorem; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005493:Folic Acid Antagonists / Q000627:therapeutic use; D006801:Humans; D008727:Methotrexate / Q000627:therapeutic use; D009154:Mutation; D009369:Neoplasms / Q000188:drug therapy* / Q000235:genetics; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics / Q000378:metabolism*
chemical_list: D005493:Folic Acid Antagonists; D013762:Tetrahydrofolate Dehydrogenase; D008727:Methotrexate