1. Figure 1

2. Figure 2 Somatic Mutation Summary 1030478A281050716A 3051000A98-07-F009a tumor mutant reads > 10 normal mutant read = 0 tumor mutant fraction > 0.1 normal reference reads > 10

3. Figure 3 tumor normal P952R ESYT1 tumor normal K217Q RYBP validation by sanger sequencing of gDNA

4. Allelic gene expression analysis of mutated allele Figure 3B Look for better example?

5. Distribution of Ratio of cDNA ras over gDNA ras Ratio of cDNA-ras / gDNA-ras ras = mutant/(wt +mutant) Mean = 1.54, p-value = 0.0262

6. Samples used in this study Table 1 sample tumor content ERPRHER2stagegradeinvasionnodetype 1030478A28 100--+T3N33yespositiveinvasive ductal carcinoma 1050716A 100---T2N3c3yespositiveinvasive ductal carcinoma 3051000A 100--+T33yesinvasive ductal carcinoma 98-07-F009a 95---T2N03yesnegativeInvasive ductal carcinoma

7. Number of mutation validated by sanger sequencing of gDNA samplevalidated 1030478A282 1050716A7 3051000A4 98-07-F009a6 Table 2

8. genetumorAA changeSIFTdescriptioncomment ESYT198-07-F009aP952R0.0656extended synaptotagmin-like protein 1 GPRC5A1050716AS59C0.071G protein-coupled receptor, family C, group 5, member Atumor suppressor USP6NL3051000AV536I0.434USP6 N-terminal likeGAP activity SHQ198-07-F009aK193M0.0068protein SHQ1 homologsnoRNA regulation STAG198-07-F009aV935F0.1688stromal antigen 1, a component of cohesin mediates p53-dependent apoptosis RYBP1050716AK217Q0.0275RING1 and YY1 binding protein tumor suppressor stabilizes TP53 OSTF13051000AL20P0.0015osteoclast stimulating factor 1interact with SRC RAPH11050716AD1199NNARas association and pleckstrin homology domains 1RAS association INO80B1030478A28P306L0.0114INO80 complex subunit Btumor suppressor G3BP21050716AS48T0.3688GTPase activating protein (SH3 domain) binding protein 2oncogene sequests TP53 VIM1050716AE153A0.0014vimentincell migration ARID1B1050716AY1345NNAAT rich interactive domain 1B (SWI1-like) isoform 3 related to ARID1A, mutated in Ovarian clear cell carcinoma PSMD298-07-F009aE177K0.1939proteasome 26S non-ATPase subunit 2 SFRS898-07-F009aR811M0.0119splicing factor, arginine/serine-rich 8 isoform 2 PIK3CA3051000AG1049R0.386phosphoinositide-3-kinase, catalytic, alpha polypeptideoncogene KDM2A1030478A28S1095F0.007lysine (K)-specific demethylase 2A KDM2A binds to nonmethylated CpG islands PIM23051000AD198H0.0174pim-2 oncogeneoncogene KLC498-07-F009aE521Q0.152kinesin light chain 4 APOL21050716AA230T0.262apolipoprotein L2 Table 3

9. RNA-seq of CGI samples? Identify mutations and gene expression in large number of genes Using alellic gene expression can we classify mutations into driver and passenger? mRNA-seq of breast cancer samples selectively identified driver mutations?