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Huang CC, Tsai YF, Liu CY, Lien PJ, Lin YS, Chao TC, Feng CJ, Chen YJ, Lai JI, Cheng HF, Chen BF, Hsu CY, Chiu JH, Tseng LM. Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue for Early Breast Cancer. Cancers (Basel) 2023; 15:4475. [PMID: 37760445 PMCID: PMC10526508 DOI: 10.3390/cancers15184475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we evaluated the concordance of targeted sequencing between paired ctDNA and matched tumor samples from early breast cancers treated with curative intention. Molecular profiling was performed using the Oncomine Comprehensive Assay v3 and the Oncomine Breast cfDNA Assay v2. The liquid biopsy detection rate was 39% (all-stage breast cancers, n = 612). Among 246 early-stage patients assayed for both ctDNA and matched tumor, the cfDNA assay detected 73 (29.6%) and the comprehensive assay detected 201 (81.7%) breast cancers with at least one alteration (χ2 test, p = 0.001). In total, 67 (25.6%) cases tested positive on both platforms, while the cfDNA and comprehensive assays detected an additional 10 (4%) and 138 (56%) cases, respectively. The most prevalent mutant genes were TP53 (68.3%) and KRAS (53.5%), while the PIK3CA (39.4%), AKT1 (45.9%), and ERBB2 (17.1%) mutations constituted biomarkers for FDA-approved therapeutics. Our study showed that tumor tissue should be the source of actionable mutation detection for early breast cancers, considering that the concordance rate between tumor and liquid biopsy was only one-quarter.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Fang Tsai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Division of Chemotherapy, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Jen Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Jiun-I Lai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Han-Fang Cheng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Bo-Fang Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Yi Hsu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
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Sokolova AO, Marshall CH, Lozano R, Gulati R, Ledet EM, De Sarkar N, Grivas P, Higano CS, Montgomery B, Nelson PS, Olmos D, Sokolov V, Schweizer MT, Yezefski TA, Yu EY, Paller CJ, Sartor O, Castro E, Antonarakis ES, Cheng HH. Efficacy of systemic therapies in men with metastatic castration resistant prostate cancer harboring germline ATM versus BRCA2 mutations. Prostate 2021; 81:1382-1389. [PMID: 34516663 PMCID: PMC8563438 DOI: 10.1002/pros.24236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND Among men with metastatic prostate cancer, about 10% have germline alterations in DNA damage response genes. Most studies have examined BRCA2 alone or an aggregate of BRCA1/2 and ATM. Emerging data suggest that ATM mutations may have distinct biology and warrant individual evaluation. The objective of this study is to determine whether response to prostate cancer systemic therapies differs between men with germline mutations in ATM (gATM) and BRCA2 (gBRCA2). METHODS This is an international multicenter retrospective matched cohort study of men with prostate cancer harboring gATM or gBRCA2. PSA50 response (≥50% decline in prostate-specific antigen) was compared using Fisher's exact test. RESULTS AND LIMITATIONS The study included 45 gATM and 45 gBRCA2 patients, matched on stage and year of germline testing. Patients with gATM and gBRCA2 had similar age, Gleason grade, and PSA at diagnosis. We did not observe differences in PSA50 responses to abiraterone, enzalutamide, or docetaxel in metastatic castration resistant prostate cancer between the two groups; however, 0/7 with gATM and 12/14 with gBRCA2 achieved PSA50 response to PARPi (p < .001). Median (95% confidence interval) overall survival from diagnosis to death was 10.9 years (9.5-not reached) versus 9.9 years (7.1-not reached, p = .07) for the gATM and gBRCA2 cohorts, respectively. Limitations include the retrospective design and lack of mutation zygosity data. CONCLUSIONS Conventional therapies can be effective in gATM carriers and should be considered before PARPi, which shows limited efficacy in this group. Men with gATM mutations warrant prioritization for novel treatment strategies.
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Affiliation(s)
| | - Catherine H. Marshall
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebeca Lozano
- Prostate Cancer Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Genitourinary Cancer Traslational Research Group, Instituto de Investigación Biomédica de Málaga, Malaga, Spain
| | - Roman Gulati
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Petros Grivas
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Celestia S. Higano
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
| | - Peter S. Nelson
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Olmos
- Prostate Cancer Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Genitourinary Cancer Traslational Research Group, Instituto de Investigación Biomédica de Málaga, Malaga, Spain
| | | | - Michael T. Schweizer
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Todd A. Yezefski
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
| | - Evan Y. Yu
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Channing J. Paller
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Oliver Sartor
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Elena Castro
- Prostate Cancer Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Genitourinary Cancer Traslational Research Group, Instituto de Investigación Biomédica de Málaga, Malaga, Spain
- Hospital Universitario Virgen de la Victoria y Regional de Málaga, Spain
| | - Emmanuel S. Antonarakis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Heather H. Cheng
- University of Washington, Department of Medicine, Division of Medical Oncology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Huang CS, Liu CY, Lu TP, Huang CJ, Chiu JH, Tseng LM, Huang CC. Targeted Sequencing of Taiwanese Breast Cancer with Risk Stratification by the Concurrent Genes Signature: A Feasibility Study. J Pers Med 2021; 11:jpm11070613. [PMID: 34203389 PMCID: PMC8306786 DOI: 10.3390/jpm11070613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common female malignancy in Taiwan, while conventional clinical and pathological factors fail to provide full explanation for prognostic heterogeneity. The aim of the study was to evaluate the feasibility of targeted sequencing combined with concurrent genes signature to identify somatic mutations with clinical significance. The extended concurrent genes signature was based on the coherent patterns between genomic and transcriptional alterations. Targeted sequencing of 61 Taiwanese breast cancers revealed 1036 variants, including 76 pathogenic and 545 likely pathogenic variants based on the ACMG classification. The most frequently mutated genes were NOTCH, BRCA1, AR, ERBB2, FANCA, ATM, and BRCA2 and the most common pathogenic deletions were FGFR1, ATM, and WT1, while BRCA1 (rs1799965), FGFR2 (missense), and BRCA1 (rs1799949) were recurrent pathogenic SNPs. In addition, 38 breast cancers were predicted into 12 high-risk and 26 low-risk cases based on the extended concurrent genes signature, while the pathogenic PIK3CA variant (rs121913279) was significantly mutated between groups. Two deleterious SH3GLB2 mutations were further revealed by multivariate Cox’s regression (hazard ratios: 29.4 and 16.1). In addition, we identified several significantly mutated or pathogenic variants associated with differentially expressed signature genes. The feasibility of targeted sequencing in combination with concurrent genes risk stratification was ascertained. Future study to validate clinical applicability and evaluate potential actionability for Taiwanese breast cancers should be initiated.
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Affiliation(s)
- Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan;
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chih-Yi Liu
- Department of Pathology, Cathay General Hospital Sijhih, New Taipei 221, Taiwan;
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 110, Taiwan;
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 106, Taiwan;
- National Defense Medical Center, Department of Biochemistry, Taipei 114, Taiwan
| | - Jen-Hwey Chiu
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11121, Taiwan;
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Ling-Ming Tseng
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 1121, Taiwan
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 1121, Taiwan
- School of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
- Correspondence:
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