Candice Francheska B. Tambaoan

Purpose: COPE evaluated serial circulating tumor DNA (ctDNA) profiling with molecular tumor board (MTB) review during first-line therapy for advanced non–small cell lung cancer (NSCLC). Experimental Design: COPE was a multicenter, randomized (2:1), noncomparative phase II trial. Arm A underwent serial plasma profiling with every report reviewed at a weekly virtual MTB; Arm B received standard management. The primary endpoint was 18-month overall survival (OS) in Arm A versus a prespecified 40% historical benchmark; no between-arm comparison was planned. Results: Among 176 patients, 117 were assigned to Arm A and 59 to Arm B. Eighteen-month OS was 53.8% (95% CI, 44.3–62.5) and 65.7% (95% CI, 52.0–76.3), respectively. Baseline plasma profiling provided contributory information in 32 of 35 patients with noncontributory or unavailable tissue, increasing genotyping success from 69% to 97%. Paired baseline and early on-treatment samples were available in 90 patients (median, 21 days; range, 19–64). ctDNA clearance was associated with higher objective response rate (83% vs. 52%), longer progression-free survival (22.9 vs. 5.4 months; P<0.001), and longer OS (not reached vs. 17.1 months; P=0.004) than persistent detection. Conclusions: Serial ctDNA profiling with weekly MTB review was operationally feasible and complemented tissue genotyping. Clinical benefit was not demonstrated; early ctDNA kinetics require validation in interventional trials.

Supplemental Table 1: Demographics and clinical characteristics of the ERBB2-amplified mBC cohort treated with first-line trastuzumab-based regimens Supplemental Table 2: Demographics and clinical characteristics of the ERBB2-amplified mBC cohort treated with T-DXd Supplemental Table 3: Demographics and clinical characteristics of the ERBB2-amplified aGE cohort treated with first-line trastuzumab-based regimens Supplemental Table 4: Demographics and clinical characteristics of the ERBB2-amplified CRC cohort treated with trastuzumab Supplemental Table 5: ERBB2 NGS and HER2 IHC/FISH concordance for 3,650 mBC patients Supplemental Table 6: Demographics and clinical characteristics of the HER2+ mBC cohort treated with 1L trastuzumab-based regimens Supplemental Table 7: Demographics and clinical characteristics of the HER2+ mBC cohort treated with T-DXd Supplemental Table 8: Demographics and clinical characteristics of the HER2+ mBC cohort treated with T-DM1 Supplemental Table 9: Demographics and clinical characteristics of the HER2-low/ultra-low mBC cohort treated with 2L + T-DXd Supplemental Table 10: ERBB2 NGS and HER2 IHC/FISH concordance for 1,168 aGE patients Supplemental Table 11: Demographics and clinical characteristics of the HER2+ aGE cohort treated with 1L trastuzumab-based regimens.

Purpose:Gene copy number (CN) amplifications and protein overexpression are common drug targets, and detection relies on various methodologies, including next-generation sequencing–based CN, immunohistochemistry (IHC), and in situ hybridization (ISH). We investigated the pan-tumor landscape of amplifications and developed AmpRatio, a novel method of CN quantitation.Experimental Design:Pan-tumor tissue (N = 486,340) and liquid (N = 85,635) samples underwent hybrid capture–based comprehensive genomic profiling. A genome-wide CN model for each sample was generated to estimate the purity, ploidy, and segment-level CN. AmpRatio was calculated by dividing gene CN/sample ploidy. A US-based deidentified clinicogenomic database was utilized to assess the relationship between ERBB2 AmpRatio and HER2 IHC/FISH and outcomes on anti-HER2 therapies.Results:Amplifications with varying degrees of gain were reported in 38.6% of pan-tumor tissue samples, most frequently MYC (5.6%), 11q13 (5.2%), ERBB2 (5.2%), and CCNE1 (3.2%). ERBB2 AmpRatio was associated with HER2 positivity by IHC/FISH in gastroesophageal [overall percent agreement (OPA) 90%] and breast (OPA 95%) cancers. Among patients treated with anti-HER2 therapies, ERBB2 AmpRatio significantly stratified outcomes within the ERBB2-amplified and IHC-defined HER2+ and HER2-low/ultralow populations. High concordance (sensitivity 88%) of amplification detection in liquid biopsy versus tissue was associated with higher AmpRatio and ctDNA tumor fraction ≥20%.Conclusions:CN amplifications are prevalent and diverse biomarkers, and AmpRatio is variable across genes and tumor types. ERBB2 AmpRatio is associated with outcomes to HER2-directed therapies and may have utility alongside IHC for clinical decision-making. With the increasing number of therapies targeting amplifications/overexpression, it will be important to define harmonized methods for CN quantification for optimal patient selection.

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.

PURPOSE: To evaluate neoadjuvant sacituzumab govitecan (SG), followed by radical cystectomy (RC), in patients with muscle-invasive bladder cancer (MIBC) who are ineligible for/refuse neoadjuvant chemotherapy (NAC). We report the results of the primary analysis and biomarker analyses of the phase II SURE-01 trial (ClinicalTrials.gov identifier: NCT05226117 ). PATIENTS AND METHODS: Patients were age 18 years and older, had Eastern Cooperative Oncology Group performance status 0-1, had histologically confirmed cT2-T4aN0M0 MIBC, were ineligible/refusing NAC, and were scheduled for RC received four cycles of SG 10 mg/kg on day 1 and day 8, once every 3 weeks, followed by RC. The primary outcome measure was the pathologic complete response (pT0N0) rate. Transcriptome-wide analyses and comprehensive genomic profiling assays were performed on baseline tumor samples. RESULTS: From March 2022 to July 2025, 44 patients were treated and efficacy evaluable. After the initial eight patients enrolled, the protocol was amended with a SG dose of 7.5 mg/kg, with primary prophylaxis for neutropenia, due to the occurrence of two deaths (one treatment-related). Subsequent grade 3-4 treatment-related adverse-events occurred in 5 patients (13.9%). Twenty-six patients (59.1%) had a cT3-4 stage and 20 (45.5%) had a variant histology. Fourteen patients (31.8%) refused to undergo RC, accounting for 12 repeating a transurethral resection of the bladder tumor and two undergoing active surveillance. The median follow-up was 22 months (IQR, 15-26). In the intention-to-treat population, although the protocol-defined ypT0N0 rate was 9.1% (95% CI, 2.5 to 21.7), the overall ypT0N0-x rate was 29.5% (95% CI, 16.7 to 45.2), with an enrichment of ypT0 responses in nonluminal subtypes (46% v 14% of luminal). The 24-month event-free survival (EFS) rate was 71.4% (95% CI, 58 to 87.8), with longer EFS for participants with lower TOP1-expressing tumors. CONCLUSION: Neoadjuvant SG, at the reduced dose of 7.5 mg/kg, was active with a manageable safety profile, corroborating TROP2 as a suitable target for MIBC.

Purpose: Gene copy number (CN) amplifications and protein overexpression are common drug targets, and detection relies on various methodologies, including next-generation sequencing–based CN, immunohistochemistry (IHC), and in situ hybridization (ISH). We investigated the pan-tumor landscape of amplifications and developed AmpRatio, a novel method of CN quantitation. Experimental Design: Pan-tumor tissue (N = 486,340) and liquid (N = 85,635) samples underwent hybrid capture–based comprehensive genomic profiling. A genome-wide CN model for each sample was generated to estimate the purity, ploidy, and segment-level CN. AmpRatio was calculated by dividing gene CN/sample ploidy. A US-based deidentified clinicogenomic database was utilized to assess the relationship between ERBB2 AmpRatio and HER2 IHC/FISH and outcomes on anti-HER2 therapies. Results: Amplifications with varying degrees of gain were reported in 38.6% of pan-tumor tissue samples, most frequently MYC (5.6%), 11q13 (5.2%), ERBB2 (5.2%), and CCNE1 (3.2%). ERBB2 AmpRatio was associated with HER2 positivity by IHC/FISH in gastroesophageal [overall percent agreement (OPA) 90%] and breast (OPA 95%) cancers. Among patients treated with anti-HER2 therapies, ERBB2 AmpRatio significantly stratified outcomes within the ERBB2-amplified and IHC-defined HER2+ and HER2-low/ultralow populations. High concordance (sensitivity 88%) of amplification detection in liquid biopsy versus tissue was associated with higher AmpRatio and ctDNA tumor fraction ≥20%. Conclusions: CN amplifications are prevalent and diverse biomarkers, and AmpRatio is variable across genes and tumor types. ERBB2 AmpRatio is associated with outcomes to HER2-directed therapies and may have utility alongside IHC for clinical decision-making. With the increasing number of therapies targeting amplifications/overexpression, it will be important to define harmonized methods for CN quantification for optimal patient selection.