Abstract P2-23-08: Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue
Authors: Huang Chi-Cheng , Tseng Ling-Ming 
Published: March 2023

Abstract
Purpose: In this study, we evaluated the concordance of targeted sequencing results between paired ctDNA and tumor samples from early breast cancers scheduled for curative surgery with or without adjuvant therapy. If high concordance was observed, pre-operative ctDNA testing could serve as a non-invasive surrogate for variants meant to be revealed after definite surgery. On the other hand, poor concordance may hamper wide clinical absorption of liquid biopsy early breast cancer.
Materials and Methods: The study VGH-TAYLOR: Comprehensive precision medicine research on the heterogeneity of Taiwanese breast cancer patients, consisted of three years enrollment and approximately four years follow-up after enrollment. Individual subject was assigned into Group 1 [planned to received surgery as first-line treatment and followed by adjuvant therapy, Group 2 [planned to receive neoadjuvant therapy as the first-line treatment and followed by surgery], and Group 3 [diagnosed with de novo and treatment naïve stage IV breast cancer, or stage IV breast cancer with recurrence beyond three years after surgery]. Molecular profiling and potential biomarkers were determined using Oncomine Comprehensive Assay v3 from FFPE tissues and Oncomine Breast cfDNA Assay v2 from plasma. Oncomine Comprehensive Assay is a targeted sequencing of NGS experiments were performed with TMO comprehensive using FFPE tissues, included 161 cancer-releant genes and types of mutation detected such as frameshift, missense, synonymous, SNV, Indel, and CNV. Oncomine Breast cfDNA Assay detects breast-derived cfDNA including hotspot genes: AKT1, EGFR, ERBB2, ERBB3, ESR1, FBXW7, KRAS, PIK3CA, SF3B1, TP53 (~152 hotspots), CNVs: CCND1, ERBB2, FGFR1, and full length TP53 (~80% coverage). Common genes interrogated by both ctDNA and TMO assay were identified, and concordance between paired targeted sequencing results from the same individuals were reported.
Results: We reported the mutational landscape of initial 612 patients interrogated with the Oncomine Breast cfDNA assay; 239 out of 612 patients reported at least one mutation (39%). Among 246 patients assayed for both ctDNA and tumor tissue, cfDNA assay detected 73 (29.6%) and TMO comprehensive assay detected 201 (81.7%) breast cancers with at least one variant (c2 test, p=0.001). Sixty-seven (25.6%) were tested positive for both liquid and tissue assays, while cfDNA and TMO comprehensive assay detected additional 10 (4%) and 138 (56%) cases, which were not identified by the other platform. Table 1 details the distributions of called variants among common targeted genes.
Conclusion: In current study, we evaluated the concordance of called variants between targeted sequencing from ctDNA and tumor tissue among an early breast cancer cohort in Taiwan. Only one-quarter of patients were positive for both cfDNA and TMO comprehensive assays from the same subject, indicating assay-specific sensitivity inevitably resulting in diagnostic discrepancy. Another plausible explanation came from the early stage nature of interrogated patients, which may inherit fewer ctDNA spillage from tumor and compromise detectability from liquid biopsy. The most prevalent mutant genes from both platforms were TP53 (68.3%) and KRAS (53.5%), both were well-known drivers in cancers. From breast cancer actionability, PIK3CA (39.4%) mutation is a biomarker for the FDA-approved PI3Ka inhibitor such as alpelisib, AKT1 (45.9%) mutation for agents such as capivasertib (AZD5363) and ipatasertib, and ERBB2 mutation for tyrosine kinase inhibitor such as neratinib. Our study showed that tumor should be the preferred source for targeted sequencing, and additional 4% of variants wound be revealed from liquid biopsy.
Table 1. Distributions of variants from common targeted genes (n=6) from cfDNA and TMO comprehensive assay.
Citation Format: Chi-Cheng Huang, Ling-Ming Tseng. Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-08.