Dissecting Complex Multi-Drug Resistance Traits with High-Order Genetic Analysis

Complex traits, including most common human genetic diseases, have remained opaque because of daunting experimental and statistical challenges in exhaustively testing variant combinations in multiple genes. We describe an ‘X-gene’ genetic analysis (XGA) approach that engineers and profiles combinatorial perturbations in multiple genes. This study demonstrates XGA on yeast ABC transporters by engineering 5,353 strains, each deleted for a random subset of 16 transporters, and profiling each strain’s resistance to 16 compounds.The submitted data contains reads from two sequencing runs used for XGA:1)Index-based PCR genotyping (RCP-PCR). This associates the genotype of each strain at 16 ABC transporters to a DNA barcode en masse.2)BarSeq fitness assay. Following genotyping, strains are pooled together by mating type, and grown under each of 16 drugs, as well as a solvent control (DMSO). High throughput sequencing of strain-specific DNA barcodes at multiple time points reconstructs the resistance of each strain to each drug. The deposited data consists of two runs - one corresponding to t = 0, 10, 20 generations, and another corresponding to t=0, 5, 15 generations.