Supplemental Figures S1-S42 from The Pan-Tumor Landscape of Gene Amplifications and Copy Number Amplification Ratio for Established and Emerging Clinical Targets

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Supplemental Figure 1: Modeled CN vs. AmpRatio Supplemental Figure 2: Amplification ratio purity invariance Supplemental Figure 3: Modeled gene CN vs. AmpRatio Supplemental Figure 4: CONSORT diagram Supplemental Figure 5: Pan-tumor MDM2 amplification landscape Supplemental Figure 6: MDM2 co-alteration landscape Supplemental Figure 7: Tissue ploidy distribution by tumor type Supplemental Figure 8: CN segment length vs. AmpRatio Supplemental Figure 9: Amplicon focality Supplemental Figure 10: Pan-tumor AmpRatio distribution of emerging targets Supplemental Figure 11: Breast ERBB2 co-alteration landscape Supplemental Figure 12: GE ERBB2 co-alteration landscape Supplemental Figure 13: CRC ERBB2 co-alteration landscape Supplemental Figure 14: Breast CGDB CONSORT diagram Supplemental Figure 15: GE CGDB CONSORT diagram Supplemental Figure 16: CRC CGDB CONSORT diagram Supplemental Figure 17: rwPFS for ERBB2-amplified mBC, aGE, and mCRC patients treated with trastuzumab-based regimens Supplemental Figure 18: Exploratory AmpRatio cutoffs for ERBB2-amplified mBC, aGE, and mCRC patients treated with trastuzumab-based regimens Supplemental Figure 19: Outcomes for ERBB2-amplified mBC patients treated with T-DXd Supplemental Figure 20: Exploratory AmpRatio cutoffs for ERBB2-amplified mBC patients treated with T-DXd Supplemental Figure 21: Performance of ERBB2 AmpRatio for predicting HER2-positivity Supplemental Figure 22: Association between ERBB2 AmpRatio and HER2 IHC/FISH Supplemental Figure 23: rwPFS on anti-HER2 regimens within HER2 IHC-defined subgroups Supplemental Figure 24: Exploratory AmpRatio cutoffs for anti-HER2 regimens within HER2 IHC-defined subgroups Supplemental Figure 25: Outcomes for HER2+ mBC patients treated with T-DXd Supplemental Figure 26: Exploratory AmpRatio cutoffs for HER2+ mBC patients treated with T-DXd Supplemental Figure 27: Outcomes for HER2+ mBC patients treated with T-DM1 Supplemental Figure 28: Exploratory AmpRatio cutoffs for HER2+ mBC patients treated with T-DM1 Supplemental Figure 29: Sensitivity analysis for outcomes of HER2+ mBC treated with 1L trastuzumab-based regimens Supplemental Figure 30: Sensitivity analysis for outcomes of HER2+ mBC treated with T-DXd Supplemental Figure 31: Sensitivity analysis for outcomes of HER2+ mBC treated with T-DM1 Supplemental Figure 32: Outcomes for HER2+ aGE patients treated with 1L trastuzumab-based regimens Supplemental Figure 33: Sensitivity analysis for outcomes of HER2+ aGE treated with 1L trastuzumab-based regimens Supplemental Figure 34: NSCLC MET co-alteration landscape Supplemental Figure 35: NSCLC EGFR co-alteration landscape Supplemental Figure 36: Ovarian CCNE1 amplification landscape Supplemental Figure 37: Serous Ovarian CCNE1 co-alteration landscape Supplemental Figure 38: ctDNA TF distribution by alteration type Supplemental Figure 39: ctDNA TF distribution by tumor type Supplemental Figure 40: All-gene liquid amplification concordance Supplemental Figure 41: Tissue and Liquid AmpRatio Correlation Supplemental Figure 42: Distribution of ctDNA TF and AmpRatio for discordant vs. concordant liquid samples.