@article {Dixit861443, author = {Atray Dixit and Olena Kuksenko and David Feldman and Aviv Regev}, title = {Shuffle-Seq: En masse combinatorial encoding for n-way genetic interaction screens}, elocation-id = {861443}, year = {2019}, doi = {10.1101/861443}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2019/12/02/861443}, eprint = {https://www.biorxiv.org/content/early/2019/12/02/861443.full.pdf}, journal = {bioRxiv} }