Value-added clinical tumor/normal whole exome and whole transcriptome sequencing versus a DNA and RNA tumor only gene panel for managing breast cancer

Abstract As sequencing technologies advance, there is increasing interest in the value of more comprehensive molecular profiling techniques. Our laboratory has clinically validated two next generation sequencing (NGS) assays for detecting somatic variants in solid tumors. The Sema4 Signal Solid Tumor Panel, utilizes the Thermo Fisher 161 gene Oncomine Comprehensive v3 assay and the Sema4 Signal Whole Exome/Transcriptome Sequencing (WES/WTS) assay consists of whole transcriptome RNAseq for the tumor and whole exome sequencing for the tumor and normal DNA on the Illumina NovaSeq. We compiled a cohort of 224 breast tumors from 211 patients encompassing 10 histological subtypes (BRCA (102), IDC (74), ILC (21), BRCANOS (11), BRCNOS (4), IBC (1), ACBC (1), IMMC (1), MBC (2), MDLC (2), Other (5)). A total of 209 specimens were analyzed by our Solid Tumor panel, and 15 were analyzed by WES/WTS. ER/PR/HER2 status was available for 212 tumors with 36 triple-negative, 123 ER(+)/PR(+)/HER2(-), and 23 ER(+)/PR(+)/HER2(+). Treatment history was available for 151 patients. Of the 118 patients who self-reported racial identity, 8 identified as Asian, 33 identified as Black or African American, 77 identified as white. Sequencing with either the 161 gene panel or WES/WTS detected clinically significant variants in 95% (213/224) of the tumors sequenced. Targetable PIK3CA variants were reported in 36% (80/224) of tumors, as well as CCND1 amplification (16%, 26/224) and ESR1 resistance variants (10%, 24/224). Tier 1 drugs were reported in 35% (79/224) of tumors, as well as tier 2 drugs (4%, 10/224). At least 2 patients had tumor specimens obtained at time points spanning 18 or more months and acquired ESR1 p.Y537S and p.Y537C resistance mutations in the later specimens. A patient with triple-negative specimens, obtained in 2018 and 2020, had no change in clinically significant variants but had loss of variants of unknown significance in the later sample. Panel sequencing and WES/WTS are comparable in terms of known variant detection, but panel-based testing has considerable limitations for assessing disease progression and genomic complexity. For the 15 WES/WTS specimens, we were able to determine additional molecular features, including complex copy number state, which has relevance to prognostic information, tumor mutation burden, homologous recombination deficiency, and differential gene expression. Moreover, WES of the tumor and normal specimens resolved multiple germline variants that had been reported as somatic variants in a tumor-only report from a patient with triple-negative breast cancer. Our findings support the adoption of tumor/normal WES/WTS as a standard diagnostic tool for breast cancer patients. Citation Format: Kimberly S. Cole, Zhiqiang Li, Amy Tiersten, Wanying Zhang, Hussam Al-Kateb, Feras M. Hantash, Michael R. Rossi, Scott Newman, Xiang Zhou, Eric E. Schadt, Rong Chen, William K. Oh, Marc Y. Fink. Value-added clinical tumor/normal whole exome and whole transcriptome sequencing versus a DNA and RNA tumor only gene panel for managing breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-15.