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Sassi F, Rekaya MB, Belarbi A, Chilla D, Mansouri N, Achouri L, Saied E, Kassa R, Kacem LB, Ouezani M, Debabeche N, Rebhi F, Rammeh S. Pathologically confirmed women's breast cancer: A descriptive study of Tunisian and Algerian series. Cancer Rep (Hoboken) 2023; 6 Suppl 1:e1818. [PMID: 37092543 PMCID: PMC10440841 DOI: 10.1002/cnr2.1818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is the most frequent malignancy among women in Tunisia and Algeria. Clinical and pathological characteristics of this cancer among these populations are not widely reported. The aim of the study was to report clinical and pathological characteristics of women's BC in a Tunisian and Algerian series. METHODS Pathologically confirmed 1089 BCs were gathered in the pathology departments of three Northern Tunisian hospitals: Tunis military, Charles Nicolle and Jendouba and in the pathology department of Alger Douera hospital between January 2015 and December 2020. Clinical and pathological findings of the two series: age, tumor size, histological type, grading according to Scarff-Bloom Richardson grading system, lymph node status at the time of diagnosis in axillary lymphadenectomy specimens and the immunohistochemical expression of estrogen and progesterone receptors (ER/PR), HER2 and Ki-67, were collected from the pathological reports. RESULTS The median age at diagnosis was 50 and 48 years in Tunisian and Algerian series, respectively (p = 0.016). The diagnosis of BC was made on surgical specimens (lumpectomy or mastectomy) in 373/491 (76%) cases of the Tunisian series and in 225/598 (37.6%) cases of the Algerian one. Median tumor size was 2.8 cm and 2.5 cm in Algerian and Tunisian series, respectively (p = 0.252). Invasive BCs not otherwise specified was observed in 440/481 (91.5%) BCs in Tunisian series and in 519/586 (88.6%) BCs in Algerian series. Axillary lymph node positive tumors were observed in 64.6% and 58.8% of Tunisian and Algerian women, respectively (p = 0.926). BCs were ER positive in 311/385 (80.8%) and 486/571 (85.1%) cases and HER2 positive in 86/283 (30.4%) and 60/385 (15.6%) cases of Tunisian and Algerian series, respectively. CONCLUSIONS In Tunisia and Algeria, BC has poor prognostic factors with large tumor sizes and high rates of lymph nodes involvement at diagnosis.
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Affiliation(s)
- Farah Sassi
- Department of Pathology, Charles Nicolle Hospital Tunis, UR17ES15, Faculté de Médecine de TunisUniversité de Tunis El ManarTunisTunisia
| | - Meriem Ben Rekaya
- Department of Pathology, Charles Nicolle Hospital Tunis, UR17ES15, Faculté de Médecine de TunisUniversité de Tunis El ManarTunisTunisia
| | - Ayed Belarbi
- Department of Pathology, Douéra Hospital, Laboratoire de Recherche polymorphisme génétique No. 18Université d'Alger 1Alger CentreAlgeria
| | - Dalia Chilla
- Department of Pathology, Douéra Hospital, Laboratoire de Recherche polymorphisme génétique No. 18Université d'Alger 1Alger CentreAlgeria
| | - Nada Mansouri
- Department of PathologyMilitary HospitalTunisTunisia
| | - Leila Achouri
- Department of Surgical OncologyRegional Hospital of JendoubaJendoubaTunisia
| | - Essia Saied
- Department of Pathology, Charles Nicolle Hospital Tunis, UR17ES15, Faculté de Médecine de TunisUniversité de Tunis El ManarTunisTunisia
| | - Reda Kassa
- Department of Pathology, Douéra Hospital, Laboratoire de Recherche polymorphisme génétique No. 18Université d'Alger 1Alger CentreAlgeria
| | - Linda Belhaj Kacem
- Department of Pathology, Charles Nicolle Hospital Tunis, UR17ES15, Faculté de Médecine de TunisUniversité de Tunis El ManarTunisTunisia
| | - Manel Ouezani
- Department of Pathology, Douéra Hospital, Laboratoire de Recherche polymorphisme génétique No. 18Université d'Alger 1Alger CentreAlgeria
| | - Nadjiba Debabeche
- Department of Pathology, Douéra Hospital, Laboratoire de Recherche polymorphisme génétique No. 18Université d'Alger 1Alger CentreAlgeria
| | - Fatima Rebhi
- Department of Pathology, Douéra Hospital, Laboratoire de Recherche polymorphisme génétique No. 18Université d'Alger 1Alger CentreAlgeria
| | - Soumaya Rammeh
- Department of Pathology, Charles Nicolle Hospital Tunis, UR17ES15, Faculté de Médecine de TunisUniversité de Tunis El ManarTunisTunisia
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Teng X, Yang T, Yuan B, Yang Y, Liu J, Wang X, Wang Y, Ma T, Yin X, Yu H, Wang S, Huang W. Prognostic analysis of patients with breast cancer based on tumor mutational burden and DNA damage repair genes. Front Oncol 2023; 13:1177133. [PMID: 37350936 PMCID: PMC10282748 DOI: 10.3389/fonc.2023.1177133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Background Breast cancer has a high tumor-specific death rate and poor prognosis. In this study, we aimed to provide a basis for the prognostic risk in patients with breast cancer using significant gene sets selected by analyzing tumor mutational burden (TMB) and DNA damage repair (DDR). Methods Breast cancer genomic and transcriptomic data were obtained from The Cancer Genome Atlas (TCGA). Breast cancer samples were dichotomized into high- and low-TMB groups according to TMB values. Differentially expressed DDR genes between high- and low-TMB groups were incorporated into univariate and multivariate cox regression model to build prognosis model. Performance of the prognosis model was validated in an independently new GEO dataset and evaluated by time-dependent ROC curves. Results Between high- and low-TMB groups, there were 6,424 differentially expressed genes, including 67 DDR genes. Ten genes associated with prognosis were selected by univariate cox regression analysis, among which seven genes constituted a panel to predict breast cancer prognosis. The seven-gene prognostic model, as well as the gene copy numbers are closely associated with tumor-infiltrating immune cells. Conclusion We established a seven-gene prognostic model comprising MDC1, PARP3, PSMB1, PSMB9, PSMD2, PSMD7, and PSMD14 genes, which provides a basis for further exploration of a population-based prediction of prognosis and immunotherapy response in patients with breast cancer.
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Affiliation(s)
- Xu Teng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Tianshu Yang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Baowen Yuan
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yunkai Yang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxiang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyu Ma
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Yin
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Hefen Yu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shuang Wang
- Department of Cardio Surgery Center, Shandong Second Provincial General Hospital, Jinan, China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Dutta R, Vallurupalli M, McVeigh Q, Huang FW, Rebbeck TR. Understanding inequities in precision oncology diagnostics. NATURE CANCER 2023; 4:787-794. [PMID: 37248397 DOI: 10.1038/s43018-023-00568-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/13/2023] [Indexed: 05/31/2023]
Abstract
Advances in molecular diagnostics have enabled the identification of targetable driver pathogenic variants, forming the basis of precision oncology care. However, the adoption of new technologies, such as next-generation sequencing (NGS) panels, can exacerbate healthcare disparities. Here, we summarize data on use patterns of advanced biomarker testing, highlight the disparities in both accessing NGS testing and using this data to match patients to appropriate personalized therapies and propose multidisciplinary strategies to address inequities looking forward.
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Affiliation(s)
- Ritika Dutta
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mounica Vallurupalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Quinn McVeigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Franklin W Huang
- Cancer Program, Broad Institute, Cambridge, MA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- San Francisco Veterans Health Care System, San Francisco, CA, USA.
| | - Timothy R Rebbeck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard TH Chan School of Public Health, Boston, MA, USA.
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Falcone R, Lombardi P, Filetti M, Fabi A, Altamura V, Scambia G, Daniele G. Molecular Profile and Matched Targeted Therapy for Advanced Breast Cancer Patients. Curr Oncol 2023; 30:2501-2509. [PMID: 36826152 PMCID: PMC9954949 DOI: 10.3390/curroncol30020191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
(1) Background: Precision oncology is opening new treatment opportunities for patients suffering from solid tumors. In the last two decades, the advent of CDK4/6 inhibitors, immunotherapy, and antibody-drug conjugates (ADC) improved survival outcomes for advanced or metastatic breast cancers (BC). Nevertheless, some patients progress to approved therapies and still maintain good clinical conditions. (2) Methods: With the aim to estimate the accrual rate to experimental precision oncology treatments, we collected molecular and clinical characteristics of BC patients evaluated at Phase 1 Unit of Fondazione Policlinico Gemelli. Clinical data were retrieved from hospital records. Molecular analysis was performed using Next-Generation Sequencing (NGS) FoundationOne CDx on tissue or blood. (3) Results: Among the 38 BC patients referred to our unit, 35 completed the genomic analysis. All patients were female with advanced (mean number of metastatic sites: 3, range 1-6) BC. Median age at our evaluation was 52 (IQR, 48-59). ECOG PS was good in 97% of the study population, although heavily pre-treated (median number of systemic treatments: 5, IQR 3-7). Half of referred patients were HR+/HER2- BC, with 39% triple negative breast cancer (TNBC). NGS testing was performed on relapsed disease among most (71%) participants, in particular lymph nodes and soft tissue. Liquid biopsy was requested in 23% of cases. The median time from sample collection to NGS testing was 1 month and from diagnosis 54 months. The median value of mutations, VUS, and TMB were 6, 11, and 5, respectively. TP53, PIK3CA, BRCA2, ESR1, and RAD21 were the genes with the highest number of molecular alterations. In 5 patients (14%), the molecular analysis was helpful to assign targeted therapy in the context of clinical trials with a median progression-free survival of 5 months. (4) Conclusions: HR+/HER2- and TNBC were the most frequent subtypes referred for NGS testing. Tissue biopsy of relapsed disease was feasible in 71% of cases. The molecular analysis offered a new treatment opportunity in 14% of patients. The real benefit of these treatments remains to be evaluated in larger cohorts.
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Affiliation(s)
- Rosa Falcone
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Correspondence:
| | - Pasquale Lombardi
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Marco Filetti
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessandra Fabi
- Unit of Precision Medicine in Breast Cancer, Scientific Directorate, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Valeria Altamura
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Giovanni Scambia
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gennaro Daniele
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Genes (Basel) 2022; 13:genes13091583. [PMID: 36140751 PMCID: PMC9498802 DOI: 10.3390/genes13091583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.
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Dissecting Molecular Heterogeneity of Circulating Tumor Cells (CTCs) from Metastatic Breast Cancer Patients through Copy Number Aberration (CNA) and Single Nucleotide Variant (SNV) Single Cell Analysis. Cancers (Basel) 2022; 14:cancers14163925. [PMID: 36010918 PMCID: PMC9405921 DOI: 10.3390/cancers14163925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 12/27/2022] Open
Abstract
Circulating tumor cells' (CTCs) heterogeneity contributes to counteract their introduction in clinical practice. Through single-cell sequencing we aim at exploring CTC heterogeneity in metastatic breast cancer (MBC) patients. Single CTCs were isolated using DEPArray NxT. After whole genome amplification, libraries were prepared for copy number aberration (CNA) and single nucleotide variant (SNV) analysis and sequenced using Ion GeneStudio S5 and Illumina MiSeq, respectively. CTCs demonstrate distinctive mutational signatures but retain molecular traces of their common origin. CNA profiling identifies frequent aberrations involving critical genes in pathogenesis: gains of 1q (CCND1) and 11q (WNT3A), loss of 22q (CHEK2). The longitudinal single-CTC analysis allows tracking of clonal selection and the emergence of resistance-associated aberrations, such as gain of a region in 12q (CDK4). A group composed of CTCs from different patients sharing common traits emerges. Further analyses identify losses of 15q and enrichment of terms associated with pseudopodium formation as frequent and exclusive events. CTCs from MBC patients are heterogeneous, especially concerning their mutational status. The single-cell analysis allows the identification of aberrations associated with resistance, and is a candidate tool to better address treatment strategy. The translational significance of the group populated by similar CTCs should be elucidated.
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Haynes RM, Sirintrapun SJ, Gao J, McKenzie AJ. Using Technology to Enhance Cancer Clinical Trial Participation. Am Soc Clin Oncol Educ Book 2022; 42:1-7. [PMID: 35486887 DOI: 10.1200/edbk_349671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The COVID-19 pandemic presented many challenges to health care systems, including oncology clinical research programs. There were substantial negative effects on oncology clinical trial screening, enrollment, and study activities that forced institutions and regulatory bodies to develop innovative solutions to maintain robust and equitable participation in these trials. Digital pathology innovations at Memorial Sloan Kettering Cancer Center have streamlined the diagnostic life cycle for patients with cancer, and the seamless integration of digital pathology services with next-generation sequencing and other molecular pathology services have accelerated the time to diagnosis and receipt of molecular results. Timely access to these results, coupled with Memorial Sloan Kettering Cancer Center's knowledge engine OncoKB, enhances patient clinical trial coordination precisely and efficiently. At the Sarah Cannon Research Institute, centralized remote clinical trial matching and screening, virtual molecular tumor boards, and centralized molecular interpretation support services have empowered clinic staff to identify more efficiently potential participants in clinical research, despite the COVID-19 pandemic. In addition, the U.S. Food and Drug Administration Oncology Center of Excellence has been involved in several efforts to address challenges for patients with cancer during the COVID-19 pandemic, including writing guidance documents and participating in efforts to modernize clinical trials. The enclosed personal experience of a patient with cancer currently participating in an oncology clinical trial emphasizes the need for continued decreasing of barriers to study participation. Clinical trial advances that were accelerated by the pandemic will ultimately help patients with cancer and the greater oncology health care community.
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Affiliation(s)
- Rudene Mercer Haynes
- Breast cancer survivor, clinical trial participant, and partner at Hunton Andrews Kurth LLP, Richmond, VA
| | | | - Jennifer Gao
- U.S. Food and Drug Administration, Oncology Center of Excellence, Silver Springs, MD
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Sturgill EG, Misch A, Jones CC, Luckett D, Fu X, Schlauch D, Jones SF, Burris HA, Spigel DR, McKenzie AJ. Discordance in Tumor Mutation Burden from Blood and Tissue Affects Association with Response to Immune Checkpoint Inhibition in Real-World Settings. Oncologist 2022; 27:175-182. [PMID: 35274716 PMCID: PMC8914506 DOI: 10.1093/oncolo/oyab064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/03/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tumor mutation burden (TMB), a biomarker for immune checkpoint inhibitor (CPI) response, is reported by both blood- and tissue-based next-generation sequencing (NGS) vendors. However, the agreement between TMB from blood (bTMB) and tissue (tTMB) in real-world settings, both in absolute value and association with CPI response, is not known. MATERIALS AND METHODS This study utilizes Sarah Cannon's precision medicine platform, Genospace, to harmonize clinico-genomic data from 17 206 patients with cancer with NGS results from September 2015 to August 2021. A subset of patients have both bTMB and tTMB results. Statistical analyses are performed in R and include (1) correlation (r) and concordance (ρ) between patient-matched bTMB-tTMB pairs, (2) distribution of total bTMB and tTMB values, and (3) association of bTMB and tTMB with time to CPI therapy failure. RESULTS In 410 patient-matched bTMB-tTMB pairs, the median bTMB (m = 10.5 mut/Mb) was significantly higher than the median tTMB (m = 6.0 mut/Mb, P < .001) leading to conflicting "high" and "low" statuses in over one-third of cases at a threshold of 10 mut/Mb (n = 410). Significant differences were observed in the distribution of bTMB values from blood-NGS vendors, with guardant health (GH) reporting higher (m = 10.5 mut/Mb, n = 2183) than Foundation Medicine (FMI, m = 3.8 mut/Mb, n = 462, P < .001). bTMB from GH required a higher threshold (≥40 mut/Mb) than bTMB from FMI (≥12 mut/Mb) in order to be associated with CPI response. CONCLUSIONS This study uncovers variability in bTMB reporting among commercial NGS platforms, thereby evidencing a need for assay-specific thresholds in identifying patients who may respond to CPI therapy.
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Affiliation(s)
| | - Amanda Misch
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | | | - Daniel Luckett
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | - Xiaotong Fu
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | - Dan Schlauch
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | | | - Howard A Burris
- Sarah Cannon Research Institute, Nashville, TN, USA
- Tennessee Oncology, Nashville, TN, USA
| | - David R Spigel
- Sarah Cannon Research Institute, Nashville, TN, USA
- Tennessee Oncology, Nashville, TN, USA
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