<p>Supplementary Table 10. Whole-genome cfDNA sequencing quality metrics.</p>
ARTICLE ABSTRACT
HER2 targeting is increasingly relevant in metastatic urothelial cancer (mUC) because of emerging antibody–drug conjugates, in which assessment of tumor HER2/ERBB2 status could aid interpretation of ongoing trials. We evaluated whether precise ERBB2 genotype can be determined from mUC ctDNA and the relationship with tissue status.
ERBB2 genotype was determined through targeted sequencing of longitudinal samples from 226 patients with mUC. Heterogeneity was evaluated across ctDNA and metachronous tumor tissue ERBB2 genotype and compared with HER2 IHC.
Activating ERBB2 mutation and/or amplification was identified in 16% and 29% of patients by ctDNA and tissue sequencing, respectively. Alternatively, 55% of tissue samples were HER2 IHC positive. Agreement between HER2 IHC and ERBB2 genotype (by either ctDNA or tissue) was 64%, in contrast to 87% between patient-matched ctDNA and tissue genotypes. Across serial samples, genotype and IHC revealed marked heterogeneity in ERBB2 status. Factors linked with heterogeneity included ERBB2 amplifications on extrachromosomal DNA, detected through whole-genome sequencing of ctDNA and FISH, and subclonal ERBB2 mutations, which were evident in half of ctDNA and one-third of tissue samples.
We report a combined analysis of HER2 IHC and ERBB2 genotype in mUC ctDNA and archival tissue, revealing high spatiotemporal heterogeneity. Our data suggest that sole reliance on DNA- or protein-based HER2 assessment is insufficient to capture nuanced genomic indicators of HER2 pathway reliance and support a role for ctDNA alongside existing methods for characterizing HER2/ERBB2 status during biomarker development in mUC.
