Fig. 1

Analysis Pipeline. This figure describes the analytical pipeline, from the raw data to the synergy scores. a All pairwise combinations between the selected drugs (108) where platted in a pseudo-random order on four 1536 plates, and viabilities were computed by dividing the number of cells in the well by the mean number of cells in the untreated wells. b Combination viabilities were modeled with the Bliss independence assumption, after passing to the logarithm, yielding a linear model of 5778 equations modeling the combination viabilities, and 108 unknown, representing the singlet viabilities. c Residuals of the linear system were used as a score for synergy. Variance in the DMSO wells was used to model sample error on the measurement of combination viability, yielding p values and q values for each combination. d For each cell line, if one of the two dose showed synergy, well considered the combination synergic in that cell line. e We counted the number of cell lines were the combination synergy was significant (absolute synergy score). f We computed the synergy specificity score from the absolute synergy scores (see methods). Synergy scores could be modeled using genomic features, as they are available for most cell lines used here on the GDSC project website (www.cancerrxgene.org)