Understanding general mechanisms of chemotherapy resistance can assist with the design of new drugs and guide cancer treatment decisions. Here we applied in vitro evolution and whole genome analysis (IVIEWGA) to the human, near-haploid cell line (HAP-1) to directly identify resistance alleles. Clones (28) resistant to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel), were evolved and compared to their isogenic parents via whole genome and whole exome sequencing (WES). High frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound were identified in only 21 genes: The set included clinically-relevant resistance genes or drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1), as well as new genes (SLC13A4). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments (via shRNA and CRISPR-Cas9 respectively) of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, identified and studied in an isogenic background in the laboratory.
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