PT - JOURNAL ARTICLE AU - Atray Dixit AU - Olena Kuksenko AU - David Feldman AU - Aviv Regev TI - Shuffle-Seq: <em>En masse</em> combinatorial encoding for <em>n</em>-way genetic interaction screens AID - 10.1101/861443 DP - 2019 Jan 01 TA - bioRxiv PG - 861443 4099 - http://biorxiv.org/content/early/2019/12/02/861443.short 4100 - http://biorxiv.org/content/early/2019/12/02/861443.full AB - Genetic interactions, defined as the non-additive phenotypic impact of combinations of genes, are a hallmark of the mapping from genotype to phenotype. However, genetic interactions remain challenging to systematically test given the massive number of possible combinations. In particular, while large-scale screening efforts in yeast have quantified pairwise interactions that affect cell viability, or synthetic lethality, between all pairs of genes as well as for a limited number of three-way interactions, it has previously been intractable to perform the large screens needed to comprehensively assess interactions in a mammalian genome. Here, we develop Shuffle-Seq, a scalable method to assay genetic interactions. Shuffle-Seq leverages the co-inheritance of genetically encoded barcodes in dividing cells and can scale in proportion to sequencing throughput. We demonstrate the technical validity of Shuffle-Seq and apply it to screening for mechanisms underlying drug resistance in a melanoma model. Shuffle-Seq should allow screens of hundreds of millions of combinatorial perturbations and facilitate the understanding of genetic dependencies and drug sensitivities.