Additional file 1: Fig. S1. (A) CRISPR-Cas9 library sequencing data analysis workflow. (B) The distribution of sgRNA frequencies of the corresponding replicates of N87 and OE19 cells. (C) Comparison of different treatment conditions and biological replicates in the N87 and OE19 lapatinib screening. Each square in the lower left half of the matrix compares the normalized sgRNA read count between two biological samples. Sample labels for each axis are indicated on the diagonal. For the sample labels, N87 and OE19 are the cell line names; D14 means vehicle day 14 and L14 means lapatinib treated day 14. The last number 1 or 2 means the replicates. The Pearson correlation coefficient can be found in each square in the upper right half of the matrix. For example, the number 0.947 on the second row of top row indicates that the correlation coefficient between N87 vehicle day replicate 1 and replicate 2 is 0.947. Wilcoxon rank-sum test indicated the following, **significant difference from the control, p < 2.2e-16. Fig. S2. Validation of the screen that disruption of a few other candidate genes individually in GC cell lines causes resistance to lapatinib. (A) Cell viability curve of KEAP1, BAX, MED24 or TADA1 knockout OE19 cells treated with indicated doses of lapatinib, respectively. OE19 cells were transduced with lentivirus carrying sgRNAs targeting the indicated gene individually. The drug resistance of gene knockout and the control cells were measured by the relative percentage of cell viability. (B) Cell viability curve of KCTD5 or NF1 knockout OE19 cells treated with indicated doses of lapatinib, respectively. OE19 cells were transduced with lentivirus carrying sgRNAs targeting the indicated gene individually. The drug resistance of gene knockout and the control cells were examined by the relative percentage of cell viability. Unpaired Student’s t test indicated the following: *significant difference from the control, p < 0.05; **significant difference from the control, p < 0.01. Fig. S3. Protein interaction networks and the predicted partners were analyzed by STRING on the validated genes. CSK, PTEN, KEAP1, BAX, MED24, TADA1, KCTD5, NF1 (validated genes) and HER2 (ERBB2) were mapped by searching the STRING for Protein interaction networks (A) and the predicted partners analysis (B). In the resulting protein association network, proteins are presented as nodes which are connected by lines whose thickness represents the confidence level. (C) Heat...