Supplementary Figures 1 - 5 from Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery

Supplementary Figure 1. Original comparison of 18 cell lines sequenced by COSMIC and CCLE to display that the conformity of missense mutation detection ranges from 56.75% in HCC2218 cell line to 12.90% in HCC1954. Supplementary Figure 2. Bamfile images of the CRUK MI sequencing shows good read coverage with the PAK4 p.E119Q mutation in 51% of reads compared to CCLE hybrid capture bamfiles of the same area with only 2 reads and neither read showing a mutation. Supplementary Figure 3. Western Blot showing empty vector, PAK4 wildtype, and p.E119Q mutant overexpression in 293T cells with the mutant showing enhanced ERK phosphorylation but no effect on JNK phosphorylation. Supplementary Figure 4. Chart demonstrating an increase in conformity of reported mutations when the CCLE data that has not been filtered for germ line SNPs is used. Supplementary Figure 5. Comparison of mutation detection in four cell lines between COSMIC, CCLE and our own institute (CRUK MI) reveals 29.41% of mutations are missed by CRUK MI but the discrepancy decreases to 17.65% when the comparison is repeated with CRUK MI data that has not been filtered for germ line SNPs.