Complex diseases, caused by several potentially epistatic genes in concert with the environment, contribute to the bulk of human disease. Examples of complex diseases include coronary artery disease and Type II diabetes, but the inter-individual variation in drug toxicity is also a complex disease. Unfortunately, progress at identifying the genetic loci (Quantitative Trait Loci or QTL) contributing to complex disease has been slow. This is particularly true in the field of pharmacogenomics, where it is difficult to recruit large homogenous sets of affected patients and the underlying etiology of toxicity is likely to be heterogeneous. In this proposal we explore the utility of identifying genes harboring standing genetic variation that mediate drug toxicity in Drosophila, with the goal of exporting newly discovered genes to humans. Genes that contribute to standing variation in drug toxicity in Drosophila may be better candidates for genes contributing to inter-individual variation in humans than genes identified through traditional mutagenic screens (e.g., X-ray or EMS). The initial drug we will examine is Methotrexate because of wide clinical use to treat cancer and arthritis, known toxicities, and conservation of target pathways from humans to Drosophila. The experiments are simple enough that we will extend our work to three additional drugs that exhibit toxicity in humans. We will elucidate the genetic architecture of Methotrexate and other drug toxicity in a collection of two sets of ~750 Drosophila RI lines, each initially derived from eight highly inbred founder lines. These RI lines give us a great deal of power to both identify and localize QTL, and also gives us the extremely important ability to estimate the population frequency of any mapped QTL. We will draw female flies from each RI line and expose them to concentrations of Methotrexate and other drugs chosen so that adult female flies exposed to the drug for three days display a marked reduction in fertility. We will determine if toxicity by genotype interactions are due to intermediate frequency or rare in frequency causative factors. As each of the founder inbred lines used to derive the ~1500 RI lines will have been completely sequenced, knowledge of the """"""""phase"""""""" of mapped QTL will allow the identification of the actual nucleotide sites that define mapped QTLs.

Public Health Relevance

Methotrexate is widely used as both a chemotherapy agent and to treat joint swelling in arthritis, yet in many cases it use is suspended as a result of toxic side effects. As Drosophila and humans share the genetic pathway Methotrexate targets, research will identify DNA polymorphisms in Drosophila that modulate toxicity. Future work can then ask if these same genes modulate toxicity in humans, possibly leading to genetic tests to identify patients who could most likely benefit from Methotrexate treatment. Similar outcomes are expected for additional chemotherapy agents.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Okita, Richard T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Irvine
Schools of Arts and Sciences
United States
Zip Code
Baldwin-Brown, James G; Long, Anthony D; Thornton, Kevin R (2014) The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol 31:1040-55
Burke, Molly K; Liti, Gianni; Long, Anthony D (2014) Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. Mol Biol Evol 31:3228-39
King, Elizabeth G; Kislukhin, Galina; Walters, Kelli N et al. (2014) Using Drosophila melanogaster to identify chemotherapy toxicity genes. Genetics 198:31-43
Burke, Molly K; King, Elizabeth G; Shahrestani, Parvin et al. (2014) Genome-wide association study of extreme longevity in Drosophila melanogaster. Genome Biol Evol 6:1-11
Long, Anthony D; Macdonald, Stuart J; King, Elizabeth G (2014) Dissecting complex traits using the Drosophila Synthetic Population Resource. Trends Genet 30:488-95
Thornton, Kevin R; Foran, Andrew J; Long, Anthony D (2013) Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genet 9:e1003258
Kislukhin, Galina; King, Elizabeth G; Walters, Kelli N et al. (2013) The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans. G3 (Bethesda) 3:1301-10
King, Elizabeth G; Macdonald, Stuart J; Long, Anthony D (2012) Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 191:935-49
King, Elizabeth G; Merkes, Chris M; McNeil, Casey L et al. (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res 22:1558-66
Kislukhin, Galina; Murphy, Maura L; Jafari, Mahtab et al. (2012) Chemotherapy-induced toxicity is highly heritable in Drosophila melanogaster. Pharmacogenet Genomics 22:285-9