1
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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nat Commun 2024; 15:2790. [PMID: 38555308 PMCID: PMC10981715 DOI: 10.1038/s41467-024-47196-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH, 45229, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, 45229, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christopher Lo
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Atish D Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Samuel Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David W Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
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2
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Lynce F, Mainor C, Donahue RN, Geng X, Jones G, Schlam I, Wang H, Toney NJ, Jochems C, Schlom J, Zeck J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Tarantino P, Tolaney SM, Swain SM, Pohlmann P, Parsons HA, Isaacs C. Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study. Nat Commun 2024; 15:2691. [PMID: 38538574 PMCID: PMC10973408 DOI: 10.1038/s41467-024-46961-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints included the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that a combination of nivolumab plus capecitabine leads to a greater increase in PIS from baseline to week 6 (91%) compared with nivolumab (47%) or capecitabine (53%) alone (log-rank p = 0.08), meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) is associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.
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Affiliation(s)
- Filipa Lynce
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Candace Mainor
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Renee N Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue Geng
- Georgetown University, Washington, DC, USA
| | | | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC, USA
- Tufts Medical Center, Boston, MA, USA
| | | | - Nicole J Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Jochems
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Zeck
- MedStar Georgetown University Hospital, Washington, DC, USA
| | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ, USA
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC, USA
- AstraZeneca, Arlington, VA, USA
| | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Shruti Tiwari
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, USA
- AstraZeneca, Arlington, VA, USA
| | | | - Katia Khoury
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Paolo Tarantino
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara M Tolaney
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Paula Pohlmann
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Heather A Parsons
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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3
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Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Author Correction: Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2024; 30:907. [PMID: 38049623 PMCID: PMC10957463 DOI: 10.1038/s41591-023-02735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew P Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brad Fortunato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Shahabbedin Sotudian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ikenna Madueke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
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4
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Morganti S, Gibson CJ, Jin Q, Santos K, Patel A, Wilson A, Merrill M, Vincuilla J, Stokes S, Lipsyc-Sharf M, Parker T, King TA, Mittendorf EA, Curigliano G, Hughes ME, Stover DG, Tolaney SM, Weeks LD, Tayob N, Lin NU, Garber JE, Miller PG, Parsons HA. Prevalence, Dynamics, and Prognostic Role of Clonal Hematopoiesis of Indeterminate Potential in Patients With Breast Cancer. J Clin Oncol 2024:JCO2301071. [PMID: 38190580 DOI: 10.1200/jco.23.01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/15/2023] [Accepted: 10/18/2023] [Indexed: 01/10/2024] Open
Abstract
PURPOSE Clonal hematopoiesis of indeterminate potential (CHIP) is frequent in patients with solid tumors. Prospective data about CHIP prevalence at breast cancer diagnosis and its dynamic evolution under treatment selective pressure are limited. PATIENTS AND METHODS We performed targeted error-corrected sequencing on 614 samples from 380 patients with breast cancer. We investigated the dynamics of CHIP on prospectively collected paired samples from patients with early breast cancer (eBC) receiving chemotherapy (CT) or endocrine therapy (ET). We assessed the correlation of CHIP with survival in patients with metastatic triple-negative breast cancer (mTNBC). We estimated the risk of progression to treatment-related myeloid neoplasms (t-MN) according to the clonal hematopoiesis risk score (CHRS). In exploratory analyses, we considered clonal hematopoiesis (CH) with variant allele fraction (VAF) ≥0.005. RESULTS CHIP was identified in 15% of patients before treatment. Few CHIP emerged after treatment, and the risk of developing new mutations was similar for patients receiving CT versus ET (odds ratio [OR], 1.16; P = .820). However, CT increased the risk of developing new CH with VAF ≥0.005 (OR, 3.45; P = .002). Five TP53-mutant CH with VAF ≥0.005 emerged among patients receiving CT. Most patients had low risk of t-MN according to the CHRS score. CHIP did not correlate with survival in mTNBC. CONCLUSION CHIP is frequent in patients with breast cancer. In this study, CT did not lead to emergence of new CHIP, and most patients had low risk of developing t-MN. This finding is reassuring, given long life expectancy of patients with eBC and the association of CHIP with morbidity and mortality. However, TP53-mutant CH with VAF ≥0.005 emerged with CT, which carries high risk of t-MN. Evolution of these small clones and their clinical significance warrant further investigation.
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Affiliation(s)
- Stefania Morganti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Qingchun Jin
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Katheryn Santos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ashka Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Clinical Operations Department, Natera Inc, Austin, TX
| | - Alex Wilson
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Margaret Merrill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA
| | - Julie Vincuilla
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | | | - Marla Lipsyc-Sharf
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tonia Parker
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | - Tari A King
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | - Elizabeth A Mittendorf
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
| | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Lachelle D Weeks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Nabihah Tayob
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
- Center for Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA
| | - Peter G Miller
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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5
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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz D, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. bioRxiv 2024:2024.01.02.573710. [PMID: 38260558 PMCID: PMC10802291 DOI: 10.1101/2024.01.02.573710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from the existing dataset, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues-of-origin directly from plasma whole-genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow-coverage WGS and whole-genome bisulfite sequencing (WGBS) data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229
- University of Cincinnati Cancer Center, Cincinnati, OH 45229
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139
| | - Sarah C. Reed
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Atish D. Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | | | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - David Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | | | - Manolis Kellis
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229
- University of Cincinnati Cancer Center, Cincinnati, OH 45229
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6
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Lynce F, Mainor C, Donahue RN, Geng X, Jones G, Schlam I, Wang H, Toney NJ, Jochems C, Schlom J, Zeck J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Tarantino P, Tolaney SM, Swain SM, Pohlmann P, Parsons HA, Isaacs C. Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study. medRxiv 2023:2023.12.04.23297559. [PMID: 38105958 PMCID: PMC10723519 DOI: 10.1101/2023.12.04.23297559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints include the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that a combination of nivolumab plus capecitabine leads to a greater increase in PIS from baseline to week 6 (91%) compared with nivolumab (47%) or capecitabine (53%) alone (log-rank p = 0.08), meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) was associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.
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Affiliation(s)
- Filipa Lynce
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Candace Mainor
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Renee N. Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue Geng
- Georgetown University, Washington, DC
| | - Greg Jones
- NeoGenomics, Research Triangle Park, NC, USA
| | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC, USA
- Tufts Medical Center, Boston, MA, USA
| | | | - Nicole J. Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Jochems
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Zeck
- MedStar Georgetown University Hospital, Washington, DC, USA
| | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ, USA
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Shruti Tiwari
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | | | - Katia Khoury
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Paolo Tarantino
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara M. Tolaney
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Paula Pohlmann
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Heather A. Parsons
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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7
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Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2023; 29:2737-2741. [PMID: 37865722 PMCID: PMC10695830 DOI: 10.1038/s41591-023-02605-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling.
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Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew P Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brad Fortunato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Shahabbedin Sotudian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ikenna Madueke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
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8
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Parsons HA, Blewett T, Chu X, Sridhar S, Santos K, Xiong K, Abramson VG, Patel A, Cheng J, Brufsky A, Rhoades J, Force J, Liu R, Traina TA, Carey LA, Rimawi MF, Miller KD, Stearns V, Specht J, Falkson C, Burstein HJ, Wolff AC, Winer EP, Tayob N, Krop IE, Makrigiorgos GM, Golub TR, Mayer EL, Adalsteinsson VA. Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030. Ann Oncol 2023; 34:899-906. [PMID: 37597579 PMCID: PMC10898256 DOI: 10.1016/j.annonc.2023.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND We aimed to examine circulating tumor DNA (ctDNA) and its association with residual cancer burden (RCB) using an ultrasensitive assay in patients with triple-negative breast cancer (TNBC) receiving neoadjuvant chemotherapy. PATIENTS AND METHODS We identified responders (RCB 0/1) and matched non-responders (RCB 2/3) from the phase II TBCRC 030 prospective study of neoadjuvant paclitaxel versus cisplatin in TNBC. We collected plasma samples at baseline, 3 weeks and 12 weeks (end of therapy). We created personalized ctDNA assays utilizing MAESTRO mutation enrichment sequencing. We explored associations between ctDNA and RCB status and disease recurrence. RESULTS Of 139 patients, 68 had complete samples and no additional neoadjuvant chemotherapy. Twenty-two were responders and 19 of those had sufficient tissue for whole-genome sequencing. We identified an additional 19 non-responders for a matched case-control analysis of 38 patients using a MAESTRO ctDNA assay tracking 319-1000 variants (median 1000 variants) to 114 plasma samples from 3 timepoints. Overall, ctDNA positivity was 100% at baseline, 79% at week 3 and 55% at week 12. Median tumor fraction (TFx) was 3.7 × 10-4 (range 7.9 × 10-7-4.9 × 10-1). TFx decreased 285-fold from baseline to week 3 in responders and 24-fold in non-responders. Week 12 ctDNA clearance correlated with RCB: clearance was observed in 10 of 11 patients with RCB 0, 3 of 8 with RCB 1, 4 of 15 with RCB 2 and 0 of 4 with RCB 3. Among six patients with known recurrence, five had persistent ctDNA at week 12. CONCLUSIONS Neoadjuvant chemotherapy for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine whether ctDNA-guided approaches can improve outcomes.
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Affiliation(s)
- H A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston.
| | - T Blewett
- Broad Institute of MIT and Harvard, Cambridge
| | - X Chu
- Data Science, Dana-Farber Cancer Institute, Boston
| | - S Sridhar
- Broad Institute of MIT and Harvard, Cambridge
| | - K Santos
- Medical Oncology, Dana-Farber Cancer Institute, Boston
| | - K Xiong
- Broad Institute of MIT and Harvard, Cambridge
| | | | - A Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston
| | - J Cheng
- Broad Institute of MIT and Harvard, Cambridge
| | - A Brufsky
- University of Pittsburgh School of Medicine, Pittsburgh
| | - J Rhoades
- Broad Institute of MIT and Harvard, Cambridge
| | | | - R Liu
- Broad Institute of MIT and Harvard, Cambridge
| | - T A Traina
- Memorial Sloan Kettering Cancer Center, New York
| | - L A Carey
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill
| | - M F Rimawi
- Baylor College of Medicine Dan L. Duncan Comprehensive Cancer Center, Houston
| | - K D Miller
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis
| | - V Stearns
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore
| | - J Specht
- Seattle Cancer Care Alliance, Seattle
| | - C Falkson
- The University of Alabama at Birmingham, Birmingham
| | - H J Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston
| | - A C Wolff
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore
| | - E P Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston
| | - N Tayob
- Data Science, Dana-Farber Cancer Institute, Boston
| | - I E Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston
| | | | - T R Golub
- Broad Institute of MIT and Harvard, Cambridge
| | - E L Mayer
- Medical Oncology, Dana-Farber Cancer Institute, Boston; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston; Harvard Medical School, Boston.
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9
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Medford AJ, Denault EN, Moy B, Parsons HA, Bardia A. Circulating Tumor DNA in Breast Cancer: Current and Future Applications. Clin Breast Cancer 2023; 23:687-692. [PMID: 37438196 DOI: 10.1016/j.clbc.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/14/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
The assessment of plasma for circulating tumor DNA (ctDNA) via liquid biopsy has revolutionized our understanding of breast cancer pathogenesis and evolution. Historically, genotyping evaluation of breast cancer required invasive tissue biopsy, limiting potential for serial evaluation over the treatment course of advanced breast cancer, and not allowing for assessment for residual disease in early breast cancer after resection. However, technological advances over the years have led to an increase in the clinical use of ctDNA as a liquid biopsy for genotype-matched therapy selection and monitoring for patients undergoing treatment for advanced breast cancer. Furthermore, increasingly sensitive assays are being developed to facilitate detection of molecular evidence of residual or recurrent disease in localized breast cancer after definitive therapy. In this review, we discuss the current and future applications of ctDNA in breast cancer. Rational applications of ctDNA offer the potential to further refine patient-centered care and personalize treatment based on molecularly defined risk assessments for patients with breast cancer.
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Affiliation(s)
- Arielle J Medford
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA; Broad Institute of MIT & Harvard, Cambridge, MA.
| | - Elyssa N Denault
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Beverly Moy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | | | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
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10
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Mayerhofer C, Sedrak MS, Hopkins JO, Li T, Tayob N, Faggen MG, Sinclair NF, Chen WY, Parsons HA, Mayer EL, Lange PB, Basta AS, Perilla-Glen A, Lederman RI, Wong AR, Tiwari A, McAllister SS, Mittendorf EA, Gibson CJ, Burstein HJ, Kim AS, Freedman RA, Miller PG. Clonal hematopoiesis in older patients with breast cancer receiving chemotherapy. J Natl Cancer Inst 2023; 115:981-988. [PMID: 37042724 PMCID: PMC10407695 DOI: 10.1093/jnci/djad065] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The expansion of hematopoietic stem cells carrying recurrent somatic mutations, termed clonal hematopoiesis (CH), is common in elderly individuals and is associated with increased risk of myeloid malignancy and all-cause mortality. Though chemotherapy is a known risk factor for developing CH, how myelosuppressive therapies affect the short-term dynamics of CH remains incompletely understood. Most studies have been limited by retrospective design, heterogeneous patient populations, varied techniques to identifying CH, and analysis of single timepoints. METHODS We examined serial samples from 40 older women with triple-negative or hormone receptor-positive breast cancer treated on the prospective ADjuVANt Chemotherapy in the Elderly trial to evaluate the prevalence and dynamics of CH at baseline and throughout chemotherapy (6 and 12 weeks). RESULTS CH was detected in 44% of patients at baseline and in 53% at any timepoint. Baseline patient characteristics were not associated with CH. Over the course of treatment, mutations exhibited a variety of dynamics, including emergence, expansion, contraction, and disappearance. All mutations in TP53 (n = 3) and PPM1D (n = 4), genes that regulate the DNA damage response, either became detectable or expanded over the course of treatment. Neutropenia was more common in patients with CH, particularly when the mutations became detectable during treatment, and CH was significantly associated with cyclophosphamide dose reductions and holds (P = .02). CONCLUSIONS Our study shows that CH is common, dynamic, and of potential clinical significance in this population. Our results should stimulate larger efforts to understand the biological and clinical importance of CH in solid tumor malignancies. TRIAL REGISTRATION ClinicalTrials.gov (https://clinicaltrials.gov/ct2/show/NCT03858322). Clinical trial registration number: NCT03858322.
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Affiliation(s)
- Christina Mayerhofer
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mina S Sedrak
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Judith O Hopkins
- Novant Health Cancer Institute/SCOR NCORP, Winston Salem, NC, USA
| | - Tianyu Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nabihah Tayob
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Meredith G Faggen
- Dana-Farber Brigham Cancer Center at South Shore Hospital, South Weymouth, MA, USA
| | - Natalie F Sinclair
- Dana-Farber Brigham Cancer Center at Milford Regional Medical Center, Milford, MA, USA
| | - Wendy Y Chen
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Heather A Parsons
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Erica L Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Paulina B Lange
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ameer S Basta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ruth I Lederman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew R Wong
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Abhay Tiwari
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Sandra S McAllister
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Elizabeth A Mittendorf
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Christopher J Gibson
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Harold J Burstein
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Annette S Kim
- Brigham and Women’s Hospital, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Rachel A Freedman
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Peter G Miller
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
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11
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Morganti S, Parsons HA, Lin NU, Grinshpun A. Liquid biopsy for brain metastases and leptomeningeal disease in patients with breast cancer. NPJ Breast Cancer 2023; 9:43. [PMID: 37225714 DOI: 10.1038/s41523-023-00550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
A significant subset of patients with metastatic breast cancer develops brain metastasis. As efficacy of systemic therapies has improved and patients live longer with metastatic breast cancer, the incidence of breast cancer brain metastases has increased. Brain metastases pose a clinical challenge in diagnosis, treatment, and monitoring across all breast cancer subtypes, and better tools are needed. Liquid biopsy, which enables minimally invasive sampling of a patient's cancer, has the potential to shed light on intra-cranial tumor biology and to improve patient care by enabling therapy tailoring. Here we review current evidence for the clinical validity of liquid biopsy in patients with breast cancer brain metastases, with a focus on circulating tumor cells and circulating tumor DNA.
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Affiliation(s)
- Stefania Morganti
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Heather A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Albert Grinshpun
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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Bae JH, Liu R, Roberts E, Nguyen E, Tabrizi S, Rhoades J, Blewett T, Xiong K, Gydush G, Shea D, An Z, Patel S, Cheng J, Sridhar S, Liu MH, Lassen E, Skytte AB, Grońska-Pęski M, Shoag JE, Evrony GD, Parsons HA, Mayer EL, Makrigiorgos GM, Golub TR, Adalsteinsson VA. Single duplex DNA sequencing with CODEC detects mutations with high sensitivity. Nat Genet 2023; 55:871-879. [PMID: 37106072 PMCID: PMC10181940 DOI: 10.1038/s41588-023-01376-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
Detecting mutations from single DNA molecules is crucial in many fields but challenging. Next-generation sequencing (NGS) affords tremendous throughput but cannot directly sequence double-stranded DNA molecules ('single duplexes') to discern the true mutations on both strands. Here we present Concatenating Original Duplex for Error Correction (CODEC), which confers single duplex resolution to NGS. CODEC affords 1,000-fold higher accuracy than NGS, using up to 100-fold fewer reads than duplex sequencing. CODEC revealed mutation frequencies of 2.72 × 10-8 in sperm of a 39-year-old individual, and somatic mutations acquired with age in blood cells. CODEC detected genome-wide, clonal hematopoiesis mutations from single DNA molecules, single mutated duplexes from tumor genomes and liquid biopsies, microsatellite instability with 10-fold greater sensitivity and mutational signatures, and specific tumor mutations with up to 100-fold fewer reads. CODEC enables more precise genetic testing and reveals biologically significant mutations, which are commonly obscured by NGS errors.
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Affiliation(s)
- Jin H Bae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruolin Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Erica Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shervin Tabrizi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sahil Patel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Ju Cheng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Mei Hong Liu
- Center for Human Genetics and Genomics, Departments of Pediatrics and Neuroscience & Physiology, New York University Grossman School of Medicine, New York City, NY, USA
| | | | | | - Marta Grońska-Pęski
- Center for Human Genetics and Genomics, Departments of Pediatrics and Neuroscience & Physiology, New York University Grossman School of Medicine, New York City, NY, USA
| | - Jonathan E Shoag
- University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Gilad D Evrony
- Center for Human Genetics and Genomics, Departments of Pediatrics and Neuroscience & Physiology, New York University Grossman School of Medicine, New York City, NY, USA
| | | | | | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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13
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Parsons HA, Blewett T, Chu X, Sridhar S, Santos K, Xiong K, Abramson VG, Patel A, Cheng J, Brufsky A, Rhoades J, Force J, Liu R, Traina TA, Carey LA, Rimawi MF, Miller KD, Stearns V, Specht J, Falkson C, Burstein HJ, Wolff AC, Winer EP, Tayob N, Krop IE, Makrigiorgos GM, Golub TR, Mayer EL, Adalsteinsson VA. Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030. medRxiv 2023:2023.03.06.23286772. [PMID: 36945501 PMCID: PMC10029037 DOI: 10.1101/2023.03.06.23286772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Purpose To examine circulating tumor DNA (ctDNA) and its association with residual cancer burden (RCB) using an ultrasensitive assay in patients with triple-negative breast cancer (TNBC) receiving neoadjuvant chemotherapy (NAT). Patients and Methods We identified responders (RCB-0/1) and matched non-responders (RCB-2/3) from the phase II TBCRC 030 prospective study of neoadjuvant paclitaxel vs. cisplatin in TNBC. We collected plasma samples at baseline, three weeks, and twelve weeks (end of therapy). We created personalized ctDNA assays utilizing MAESTRO mutation enrichment sequencing. We explored associations between ctDNA and RCB status and disease recurrence. Results Of 139 patients, 68 had complete samples and no additional NAT. Twenty-two were responders and 19 of those had sufficient tissue for whole-genome sequencing. We identified an additional 19 non-responders for a matched case-control analysis of 38 patients using a MAESTRO ctDNA assay tracking 319-1000 variants (median 1000) to 114 plasma samples from 3 timepoints. Overall, ctDNA positivity was 100% at baseline, 79% at week 3, and 55% at week 12. Median tumor fraction (TFx) was 3.7 × 10 -4 (range: 7.9 × 10 -7 to 4.9 × 10 -1 ). TFx decreased 285-fold from baseline to week 3 in responders and 24-fold in non-responders. Week 12 ctDNA clearance correlated with RCB: clearance was observed in 10/11 patients with RCB-0, 3/8 with RCB-1, 4/15 with RCB-2, and 0/4 with RCB-3. Among 6 patients with known recurrence five had persistent ctDNA at week 12. Conclusion NAT for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine if ctDNA-guided approaches can improve outcomes.
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Affiliation(s)
- Heather A. Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Xiangying Chu
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Katheryn Santos
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Ashka Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ju Cheng
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Adam Brufsky
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | | | - Ruolin Liu
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Lisa A. Carey
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Mothaffar F. Rimawi
- Baylor College of Medicine Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Kathy D. Miller
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA; Birmingham, AB, USA
| | - Vered Stearns
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Carla Falkson
- The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Harold J. Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Antonio C. Wolff
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Eric P. Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nabihah Tayob
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ian E. Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Erica L. Mayer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Parsons HA, Blewett T, Chu X, Sridhar S, Santos K, Xiong K, Abramson V, Patel A, Cheng J, Brufsky AM, Rhoades J, Force J, Liu R, Traina TA, Carey L, Rimawi M, Elkhanany A, Stearns V, Specht JM, Burstein H, Wolff AC, Winer E, Tayob N, Krop I, Golub T, Mayer EL, Adalsteinsson V. Abstract PD11-06: PD11-06 Circulating tumor DNA association with residual cancer burden after neoadjuvant therapy in triple negative breast cancer in TBCRC 030. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd11-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background. Patients (pts) with early triple negative breast cancer (eTNBC) are at increased risk of breast cancer recurrence and death. Recent studies have focused on escalation of therapy, with current treatment standard of at least five drugs – and associated toxicities - for eTNBC. Though presence of residual disease after neoadjuvant therapy (NAT) as measured by residual cancer burden (RCB) helps guide addition of adjuvant treatment, more effective tools to tailor therapy are limited. Persistence of circulating tumor DNA (ctDNA) in the setting of residual disease is associated with high risk of distant recurrence. However, more sensitive minimal residual disease (MRD) assays are needed to potentially guide optimization of systemic therapy.
Methods. TBCRC 030 is a phase II randomized study of 12 weeks of NAT single agent cisplatin or paclitaxel for stage II-III TNBC, followed by surgery. The primary objective of the parent study was to correlate baseline biomarker for homologous recombination deficiency and RCB by study arm. From this group, responders (RCB 0/1) and non-responders (RCB 2/3) from both study arms who did not receive additional NAT prior to surgery were selected for analysis from the study cohort, matched on baseline nodal status and tumor size. As a post hoc study amendment, available pts were followed for event free survival (EFS). Plasma samples were collected prior to treatment initiation (W0), at three weeks (W3), and at twelve weeks, prior to surgery (W12). Whole genome sequencing (WGS) was performed on primary tumor tissue to identify somatic mutations and design for each pt a tumor-informed, ctDNA assay tracking up to 1000 mutations to detect MRD. Detection limit was computed for each tested sample as previously described. For each sample assayed, we report tumor fraction (TFx) when MRD was detected and the detection limit at 90% power when MRD was not detected.
Results. Of 139 study pts, 68 had complete tissue and plasma samples and no receipt of additional NAT. Of these, 22 were responders. These responders, and 22 matched non-responders were identified for analysis. Data from 22 pts – 11 responders, 11 non-responders - are described here; full analysis on all 44 pts will be presented at the meeting. Personalized ctDNA assays were designed targeting 434 to 1000 variants (median 1000) and applied to 66 plasma samples. At W0, 100% (22/22) were positive for ctDNA; 73% (16/22) and 55% (12/22) were positive at W3, and W12, respectively. In pts with T1-T2 tumors median TFx was 4.1e-3(7.8e-6, 3.4e-2) and 4.7e-1(4.3e-2, 9.0e-1) in pts with T3-T4 tumors. TFx decreased from W0 to W3 and from W0 to W12 in responders (Table 1). By W12, ctDNA had cleared in 7/8 pts with RCB 0, 1/3 with RCB 1, 2/8 with RCB 2, and 0/3 with RCB 3. Overall, ctDNA levels were broad with median TFx of 1.5e-3 (range 2.9e-6 to 0.90). Detection limit at 90% power for all tested samples was a median of 8.8e-6 (range 9.9e-7 to 6.8e-3).
To investigate whether ctDNA persistence after NAT was associated with BC recurrence, we analyzed a separate group of all 8 pts with known recurrence and with complete data and samples. All pts had persistent ctDNA at W12 (median TFx 6.8e-3, [2.9e-6 to 6.6e-2]).
Conclusions. After 3 weeks of NAT for eTNBC, ctDNA TFx decreased, with a 3900-fold change in responders and 18-fold change in non-responders. By W3, TFx for most pts with RCB 0/1 were below the 1 in 10,000 limit of detection for many currently available assays, emphasizing the need for sensitive tests to potentially guide therapy. Additional studies will determine if ctDNA-guided approaches in eTNBC can improve pt outcomes.
Table 1: Tumer Fraction and Tumer Fraction Fold Change by Response to Neoadjuvant Therapy
Citation Format: Heather A. Parsons, Timothy Blewett, Xiangying Chu, Sainetra Sridhar, Katheryn Santos, Kan Xiong, Vandana Abramson, Ashka Patel, Ju Cheng, Adam M. Brufsky, Justin Rhoades, Jeremy Force, Ruolin Liu, Tiffany A. Traina, Lisa Carey, Mothaffar Rimawi, Ahmed Elkhanany, Vered Stearns, Jennifer M. Specht, Harold Burstein, Antonio C. Wolff, Eric Winer, Nabihah Tayob, Ian Krop, Todd Golub, Erica L. Mayer, Viktor Adalsteinsson. PD11-06 Circulating tumor DNA association with residual cancer burden after neoadjuvant therapy in triple negative breast cancer in TBCRC 030 [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 PD11-06.
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Affiliation(s)
- Heather A. Parsons
- 1Dana Farber Cancer Institute; Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | | | | | - Ashka Patel
- 8Department of Pathology, Brigham and Women’s Hospital
| | | | - Adam M. Brufsky
- 10UPMC Hillman Cancer Center, University of Pittsburgh Medical Center
| | | | - Jeremy Force
- 12Duke University Medical Center/Duke Cancer Institute, Durham, NC, USA
| | - Ruolin Liu
- 13Broad Institute, Cambridge, Massachusetts
| | | | - Lisa Carey
- 15UNC-Lindberger Comprehensive Cancer Center, Chapel Hill, NC
| | | | | | | | | | | | | | | | | | - Ian Krop
- 24Yale School of Medicine, New Haven, Connecticut
| | - Todd Golub
- 25Broad Institute/Dana-Farber Cancer Institute
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Rosenberg S, Zheng Y, Santos K, Riley E, Meadows H, Snow C, Hughes ME, Frank E, Lin NU, Partridge A, Winer E, Parsons HA. Abstract P6-05-05: Patient-reported outcomes, perceptions, and knowledge about recurrence in women with high-risk hormone receptor-positive (HR+) breast cancer (BC). Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-05-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Over half of HR+ BC recurrences occur >5 years (y) from diagnosis (dx). While the risk of late recurrence is constant and extends for at least 20y, little is known about concerns, perceptions, knowledge, and interest in risk reduction in longer-term HR+ BC survivors.
Methods: From 1/2021-1/2022, we prospectively identified patients (pts) at Dana-Farber Cancer Institute with a history of stage II/III, HR+/HER2- BC, ≥5y from dx, without recurrence. Pts were invited to participate in a study investigating circulating tumor DNA and risk of recurrence as well as a separate, 1-time survey that assessed physical/mental health (PROMIS), dx/treatment concerns (Brief Illness Perception Questionnaire), risk perceptions, knowledge, and interest in risk reduction. “Overestimation” was defined as estimating ≥20% risk based on the response to the question: “If 100 women with HR+ BC are treated according to recommended guidelines, about how many will have BC come back in the 5-10y following completion of active treatment.” Descriptive statistics included medians and proportions. Logistic regression identified factors associated with overestimation of 5-10y metastatic recurrence risk.
Results: Among 166 women (of 209 sent surveys, 79%), median age at dx was 51 (range 21-76), 4% were Hispanic and/or Black; 19% did not have a college degree. Approximately 30% had stage III disease, most received chemotherapy (72%) and radiation (81%) and over half (57%) a mastectomy. Median time from dx was 10 y (range: 5-23). Almost all (97%) reported prior (44%) or current hormonal therapy (14% tamoxifen, 39% AI). Median PROMIS anxiety (53; range: 37-73), physical (51, range: 32-68), and mental (51, range: 25-68) scores were similar to population norms (score of 50). On a 0 (not at all)-10 (extremely) scale, the median rating for concern about dx/treatment was 5; for emotional impact of dx/treatment, the median rating was 9. Regarding risk perceptions, participants estimated that on average, a median of 15 and 10 women (of 100 women) would develop a loco-regional or distant recurrence, respectively, in the 5-10y interval; 43% and 40% estimated the risk of loco-regional and distant recurrence as ≥20%, respectively, for this interval. Pts without a college degree were more likely to overestimate 5-10y distant recurrence risk (multivariable OR: 3.66, 95% CI: 1.56, 8.59); age, chemotherapy receipt, surgery type, stage, and grade were not associated with overestimation. When asked, on average, which women have a higher chance of BC returning after 5y, 17% correctly responded HR+; 42% responded triple negative and 41% responded the risk was the same for both. While >1/3 responded they believed alcohol in moderation may decrease the risk of BC coming back, most also responded that having a healthy weight, eating ≥5 fruits/vegetables a day, and exercise may decrease this risk, with over half reporting engagement in these behaviors (Table).
Conclusion: While most longer-term stage II/III HR+ BC survivors report mental and physical health commensurate to population norms, inaccurate knowledge and perceptions about recurrence are common. Strategies to effectively communicate risk (e.g., pictograms, decision/conversation aids) and risk reduction information can promote an accurate understanding of risk in the setting of longer-term HR+ BC survivorship, potentially mitigating emotional concerns which are prevalent ≥5y post-dx. The association between lower educational attainment underscores the importance of attention to literacy and numeracy when developing interventions to improve risk communication.
Table. Perceived impact of health behaviors on recurrence risk.
Citation Format: Shoshana Rosenberg, Yue Zheng, Katheryn Santos, Elizabeth Riley, Hugh Meadows, Craig Snow, Melissa E. Hughes, Elizabeth Frank, Nancy U. Lin, Ann Partridge, Eric Winer, Heather A. Parsons. Patient-reported outcomes, perceptions, and knowledge about recurrence in women with high-risk hormone receptor-positive (HR+) breast cancer (BC) [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 P6-05-05.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nancy U. Lin
- 9Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Heather A. Parsons
- 12Dana Farber Cancer Institute; Harvard Medical School, Boston, Massachusetts
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Freedman RA, Li T, Sedrak MS, Hopkins JO, Tayob N, Faggen MG, Sinclair NF, Chen WY, Parsons HA, Mayer EL, Lange PB, Basta AS, Perilla-Glen A, Lederman RI, Wong A, Tiwari A, McAllister SS, Mittendorf EA, Miller PG, Gibson CJ, Burstein HJ. 'ADVANCE' (a pilot trial) ADjuVANt chemotherapy in the elderly: Developing and evaluating lower-toxicity chemotherapy options for older patients with breast cancer. J Geriatr Oncol 2023; 14:101377. [PMID: 36163163 PMCID: PMC10080267 DOI: 10.1016/j.jgo.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
INTRODUCTION Older adults with breast cancer receiving neo/adjuvant chemotherapy are at high risk for poor outcomes and are underrepresented in clinical trials. The ADVANCE (ADjuVANt Chemotherapy in the Elderly) trial evaluated the feasibility of two neo/adjuvant chemotherapy regimens in parallel-enrolling cohorts of older patients with human epidermal growth factor receptor 2-negative breast cancer: cohort 1-triple-negative; cohort 2-hormone receptor-positive. MATERIALS AND METHODS Adults age ≥ 70 years with stage I-III breast cancer warranting neo/adjuvant chemotherapy were enrolled. Cohort 1 received weekly carboplatin (area under the curve 2) and weekly paclitaxel 80 mg/m2 for twelve weeks; cohort 2 received weekly paclitaxel 80 mg/m2 plus every-three-weekly cyclophosphamide 600 mg/m2 over twelve weeks. The primary study endpoint was feasibility, defined as ≥80% of patients receiving ≥80% of intended weeks/doses of therapy. All dose modifications were applied per clinician discretion. RESULTS Forty women (n = 20 per cohort) were enrolled from March 25, 2019 through August 3, 2020 from three centers; 45% and 35% of patients in cohorts 1 and 2 were age > 75, respectively. Neither cohort achieved targeted thresholds for feasibility. In cohort 1, eight (40.0%) met feasibility (95% confidence interval [CI] = 19.1-63.9%), while ten (50.0%) met feasibility in cohort 2 (95% CI = 27.2-72.8). Neutropenia was the most common grade 3-4 toxicity (cohort 1-65%, cohort 2-55%). In cohort 1, 80% and 85% required ≥1 dose holds of carboplatin and/or paclitaxel, respectively. In cohort 2, 10% required dose hold(s) for cyclophosphamide and/or 65% for paclitaxel. DISCUSSION In this pragmatic pilot examining chemotherapy regimens in older adults with breast cancer, neither regimen met target goals for feasibility. Developing efficacious and tolerable regimens for older patients with breast cancer who need chemotherapy remains an important goal. CLINICALTRIALS gov Identifier: NCT03858322.
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Affiliation(s)
- Rachel A Freedman
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Tianyu Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mina S Sedrak
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Judith O Hopkins
- Novant Health Cancer Institute / SCOR NCORP, Winston Salem, NC, USA
| | - Nabihah Tayob
- Harvard Medical School, Boston, MA, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Meredith G Faggen
- Dana-Farber Brigham Cancer Center at South Shore Hospital, South Weymouth, MA, USA
| | - Natalie F Sinclair
- Dana-Farber Brigham Cancer Center at Milford Regional Medical Center, Milford, MA, USA
| | - Wendy Y Chen
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Erica L Mayer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Paulina B Lange
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ameer S Basta
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ruth I Lederman
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Wong
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Abhay Tiwari
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Sandra S McAllister
- Harvard Medical School, Boston, MA, USA; Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Elizabeth A Mittendorf
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter G Miller
- Harvard Medical School, Boston, MA, USA; Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher J Gibson
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Harold J Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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Doebley AL, Ko M, Liao H, Cruikshank AE, Santos K, Kikawa C, Hiatt JB, Patton RD, De Sarkar N, Collier KA, Hoge ACH, Chen K, Zimmer A, Weber ZT, Adil M, Reichel JB, Polak P, Adalsteinsson VA, Nelson PS, MacPherson D, Parsons HA, Stover DG, Ha G. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. Nat Commun 2022; 13:7475. [PMID: 36463275 PMCID: PMC9719521 DOI: 10.1038/s41467-022-35076-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Cell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we develop Griffin, a framework for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing data. Griffin employs a GC correction procedure tailored to variable cfDNA fragment sizes, which generates a better representation of chromatin accessibility and improves the accuracy of cancer detection and tumor subtype classification. We demonstrate estrogen receptor subtyping from cfDNA in metastatic breast cancer. We predict estrogen receptor subtype in 139 patients with at least 5% detectable circulating tumor DNA with an area under the receive operator characteristic curve (AUC) of 0.89 and validate performance in independent cohorts (AUC = 0.96). In summary, Griffin is a framework for accurate tumor subtyping and can be generalizable to other cancer types for precision oncology applications.
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Affiliation(s)
- Anna-Lisa Doebley
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Minjeong Ko
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanna Liao
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - A Eden Cruikshank
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Caroline Kikawa
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Joseph B Hiatt
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert D Patton
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Anna C H Hoge
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katharine Chen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Anat Zimmer
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary T Weber
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mohamed Adil
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jonathan B Reichel
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | | | - Peter S Nelson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David MacPherson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gavin Ha
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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18
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Sella T, Exman P, Ren S, Freret TS, Economy KE, Chen WY, Parsons HA, Lin NU, Moy B, Tung NM, Partridge AH, Tayob N, Mayer EL. Outcomes after treatment of breast cancer during pregnancy including taxanes and/or granulocyte colony-stimulating factor use: findings from a multi-institutional retrospective analysis. Breast Cancer Res Treat 2022; 194:597-606. [PMID: 35715538 DOI: 10.1007/s10549-022-06621-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/30/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Guidelines support comparable treatment for women diagnosed with breast cancer during pregnancy (PrBC) and nonpregnant women with limited case-specific modifications to ensure maternal-fetal safety. Experience during pregnancy with modern agents, such as taxanes or granulocyte colony-stimulating factors (GCSF), is limited. PATIENTS AND METHODS We retrospectively identified a multi-institutional cohort of PrBC between 1996 and 2020. Propensity score analyses with multiple imputation for missing variables were applied to determine the associations between chemotherapy exposures during pregnancy, with or without taxanes or GCSF, and a compound maternal-fetal outcome including spontaneous preterm birth, preterm premature rupture of membranes, chorioamnionitis, small for gestational age newborns, congenital malformation, or 5-min Apgar score < 7. RESULTS Among 139 PrBC pregnancies, 82 (59.0%) were exposed to chemotherapy, including 26 (31.7%) to taxane and 18 (22.0%) to GCSF. Chemotherapy use, in general, and inclusion of taxane and/or GCSF, specifically, increased over time. Pregnancies resulting in live singleton births (n = 123) and exposed to chemotherapy were as likely to reach term as those that were not (59.5% vs. 63.6%, respectively, punadjusted = 0.85). Among women treated with chemotherapy, propensity score-matched odds ratios (OR) for the composite maternal-fetal outcome were not significantly increased with taxane (OR 1.24, 95% CI 0.27-5.72) or GCSF (OR 2.11, 95% confidence interval (CI) 0.48-9.22) with similar effects in multiple imputation and sensitivity models. CONCLUSION The judicious increased use of taxane chemotherapy and/or growth factor support during pregnancy was not associated with unfavorable short-term maternal-fetal outcomes. While these findings are reassuring, case numbers remain limited and continued surveillance of these patients and progeny is warranted.
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Affiliation(s)
- Tal Sella
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Pedro Exman
- Hospital Alemão Oswaldo Cruz, Sao Paulo, Brazil
| | - Siyang Ren
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Taylor S Freret
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine E Economy
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wendy Y Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Beverly Moy
- Medical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Nadine M Tung
- Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Nabihah Tayob
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Erica L Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA.
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19
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Affiliation(s)
- Paolo Tarantino
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Heather A Parsons
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sara M Tolaney
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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20
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Lin Z, Stewart C, Martin EE, Danysh BP, Jacobs RA, Slowik K, Lawton L, Lightbody E, Rhrissorrakrai K, Utro F, Levovitz C, Cibulskis C, Ghobrial IM, Shipp M, Corcoran RB, Juric D, Parida L, Parsons HA, Getz G. Abstract 5162: TuFEst: a sensitive and cost-effective pan-cancer detection approach with accurate tumor fraction estimation. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Detecting cancer at early stages or upon recurrence is critical to decreasing cancer morbidity and mortality. We developed TuFEst (Tumor Fraction Estimator), a cost-effective computational approach for pan-cancer detection and tumor burden estimation from ultra-low coverage whole genome sequencing (~0.1x, ULP-WGS) of minimally invasive cell-free DNA (cfDNA). Current state-of-the-art methods estimate tumor fraction (TF) from ULP-WGS depending exclusively on total copy number variation, which loses tumor signal in either copy number-quiet tumors or tumors with copy-neutral loss-of-heterozygosity. Additionally, it is difficult in many cases to distinguish clonal from sub-clonal copy-number events, therefore complicating the ability to estimate tumor fraction. On the other hand, fragments shed into the blood from cancer cells, i.e., circulating tumor DNA (ctDNA), of various cancer types show significantly different length distribution than that from normal cells in healthy donors. By synergistically integrating both (i) copy number variation and (ii) altered fragment length signals, TuFEst successfully achieved higher sensitivity and more accurate TF estimation than current methods in >200 cfDNA samples across different cancer types, even in low tumor-fraction cases (TF < 0.1%). Application of TuFEst to serial cfDNA samples from blood biopsies demonstrate its utility in accurately estimating TF in ~100 cfDNAs, suggesting that TuFEst can be used to detect early cancer recurrence during different treatments. In one breast cancer patient receiving CDK4/6 therapy, TuFEst indicated disease progression 262 days earlier than routine imaging. Altogether, our work suggests that accurate TF estimation from cfDNA can not only aid in detecting cancer at early stages but also provide evidence of disease progression during treatment. We believe that such a non-invasive, cost-effective, pan-cancer detection method will benefit both initial cancer screening and monitoring of resistance to therapy in clinical applications.
Citation Format: Ziao Lin, Chip Stewart, Elizabeth E. Martin, Brian P. Danysh, Raquel A. Jacobs, Kara Slowik, Lee Lawton, Elizabeth Lightbody, Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Carrie Cibulskis, Irene M. Ghobrial, Margaret Shipp, Ryan B. Corcoran, Dejan Juric, Laxmi Parida, Heather A. Parsons, Gad Getz. TuFEst: a sensitive and cost-effective pan-cancer detection approach with accurate tumor fraction estimation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5162.
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Affiliation(s)
| | | | | | | | | | | | - Lee Lawton
- 2Dana Farber Cancer Institute, Boston, MA
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21
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Lipsyc-Sharf M, de Bruin EC, Santos K, McEwen R, Stetson D, Patel A, Kirkner GJ, Hughes ME, Tolaney SM, Partridge AH, Krop IE, Knape C, Feger U, Marsico G, Howarth K, Winer EP, Lin NU, Parsons HA. Circulating Tumor DNA and Late Recurrence in High-Risk Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Breast Cancer. J Clin Oncol 2022; 40:2408-2419. [PMID: 35658506 PMCID: PMC9467679 DOI: 10.1200/jco.22.00908] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To examine the prevalence and dynamics of circulating tumor DNA (ctDNA) and its association with metastatic recurrence in patients with high-risk early-stage hormone receptor-positive breast cancer (HR+ BC) more than 5 years from diagnosis. METHODS We enrolled 103 patients with high-risk stage II-III HR+ BC diagnosed more than 5 years prior without clinical evidence of recurrence. We performed whole-exome sequencing (WES) on primary tumor tissue to identify somatic mutations tracked via a personalized, tumor-informed ctDNA test to detect minimal residual disease (MRD). We collected plasma at the time of consent and at routine visits every 6-12 months. Patients were followed for clinical recurrence. RESULTS In total, 85 of 103 patients had sufficient tumor tissue; of them, 83 of 85 (97.6%) patients had successful whole-exome sequencing. Personalized ctDNA assays were designed targeting a median of 36 variants to test 219 plasma samples. The median time from diagnosis to first sample was 8.4 years. The median follow-up was 10.4 years from diagnosis and 2.0 years from first sample. The median number of plasma samples per patient was two. Eight patients (10%) had positive MRD testing at any time point. Six patients (7.2%) developed distant metastatic recurrence, all of whom were MRD-positive before overt clinical recurrence, with median ctDNA lead time of 12.4 months. MRD was not identified in one patient (1.2%) with local recurrence. Two of eight MRD-positive patients had not had clinical recurrence at last follow-up. CONCLUSION In this prospective study, in patients with high-risk HR+ BC in the late adjuvant setting, ctDNA was identified a median of 1 year before all cases of distant metastasis. Future studies will determine if ctDNA-guided intervention in patients with HR+ BC can alter clinical outcomes.
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Affiliation(s)
- Marla Lipsyc-Sharf
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | | | | | | | | | - Ashka Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | - Ian E Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA.,Present affiliation: Yale University, New Haven, CT
| | | | - Ute Feger
- Inivata Inc, Research Triangle Park, NC
| | | | | | - Eric P Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA.,Present affiliation: Yale University, New Haven, CT
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | - Heather A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
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22
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Gydush G, Nguyen E, Bae JH, Blewett T, Rhoades J, Reed SC, Shea D, Xiong K, Liu R, Yu F, Leong KW, Choudhury AD, Stover DG, Tolaney SM, Krop IE, Christopher Love J, Parsons HA, Mike Makrigiorgos G, Golub TR, Adalsteinsson VA. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nat Biomed Eng 2022; 6:257-266. [PMID: 35301450 PMCID: PMC9089460 DOI: 10.1038/s41551-022-00855-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
The ability to assay large numbers of low-frequency mutations is useful in biomedicine, yet, the technical hurdles of sequencing multiple mutations at extremely high depth, with accuracy, limits their detection in clinical practice. Low-frequency mutations can typically be detected by increasing the sequencing depth, however this limits the number of loci that can be probed for simultaneously. Here, we report a technique to accurately track thousands of distinct mutations with minimal reads, termed MAESTRO (minor allele enriched sequencing through recognition oligonucleotides), which employs massively-parallel mutation enrichment to enable duplex sequencing to track up to 10,000 low-frequency mutations, yet requiring up to 100-fold less sequencing. We show that MAESTRO could inform the mutation validation of whole-exome sequencing and whole genome sequencing data from tumor samples, enable chimerism testing, and is suitable for the monitoring of minimal residual disease via liquid biopsies. MAESTRO may improve the breadth, depth, accuracy, and efficiency of sequencing-based mutational testing. Massively-parallel mutation enrichment enables the tracking of up to 10,000 low-frequency mutations, via duplex sequencing, requiring up to 100-fold less sequencing depth.
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Affiliation(s)
| | - Erica Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jin H Bae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruolin Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Atish D Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ian E Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Viktor A Adalsteinsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
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23
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Abstract
The Oncology Grand Rounds series is designed to place original reports published in the Journal into clinical context. A case presentation is followed by a description of diagnostic and management challenges, a review of the relevant literature, and a summary of the authors' suggested management approaches. The goal of this series is to help readers better understand how to apply the results of key studies, including those published in the Journal of Clinical Oncology, to patients seen in their own clinical practice.
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Affiliation(s)
- Alexandra Thomas
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC
| | | | - Karen Lisa Smith
- Women's Malignancies Disease Group, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
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24
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Cescon DW, Kalinsky K, Parsons HA, Smith KL, Spears PA, Thomas A, Zhao F, DeMichele A. Therapeutic Targeting of Minimal Residual Disease to Prevent Late Recurrence in Hormone-Receptor Positive Breast Cancer: Challenges and New Approaches. Front Oncol 2022; 11:667397. [PMID: 35223447 PMCID: PMC8867255 DOI: 10.3389/fonc.2021.667397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
Abstract
While the majority of breast cancers are diagnosed at a curable stage, approximately 20% of women will experience recurrence at a distant site during their lifetime. These metastatic recurrences are incurable with current therapeutic approaches. Over the past decade, the biologic mechanisms underlying these recurrences have been elucidated, establishing the existence of minimal residual disease in the form of circulating micrometastases and dormant disease, primarily in the bone marrow. Numerous technologies are now available to detect minimal residual disease (MRD) after breast cancer treatment, but it is yet unknown how to best target and eradicate these cells, and whether clearance of detectable disease prior to the formation of overt metastases can prevent ultimate progression and death. Clinical trials to test this hypothesis are challenging due to the rare nature of MRD in the blood and bone marrow, resulting in the need to screen a large number of survivors to identify those for study. Use of prognostic molecular tools may be able to direct screening to those patients most likely to harbor MRD, but the relationship between these predictors and MRD detection is as yet undefined. Further challenges include the lack of a definitive assay for MRD with established clinical utility, difficulty in selecting potential interventions due to limitations in understanding the biology of MRD, and the emotional impact of detecting MRD in patients who have completed definitive treatment and have no evidence of overt metastatic disease. This review provides a roadmap for tackling these challenges in the design and implementation of interventional clinical trials aimed at eliminating MRD and ultimately preventing metastatic disease to improve survival from this disease, with a specific focus on late recurrences in ER+ breast cancer.
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Affiliation(s)
- David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, CA, Canada
| | - Kevin Kalinsky
- Winship Cancer Institute at Emory University, Atlanta, GA, United States
| | - Heather A Parsons
- Department of Medical Oncology, Division of Breast Oncology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Karen Lisa Smith
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Patricia A Spears
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Alexandra Thomas
- Division of Hematology and Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University, Winston-Salem, NC, United States
| | - Fengmin Zhao
- Dana Farber Cancer Institute - ECOG-ACRIN Biostatistics Center, Boston, MA, United States
| | - Angela DeMichele
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
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25
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Fu A, Cui W, Ton MV, Wang K, Gu W, Li T, Parsons HA, Liu MC, Sledge GW. Abstract P2-01-15: Developing highly sensitive high NGS data efficient ctDNA detection assays for breast cancer surveillance. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-01-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Growing data established the importance of monitoring dynamic changes in circulating tumor DNA (ctDNA) to identify early signs of therapeutic responses, allowing for timely management of treatment to achieve more effective personalized therapy. Higher assay accuracy and consistency, and lower assay cost will support more clinical validation trials and benefit more cancer patients with non-invasive ctDNA NGS tests that can simultaneously map multiple genomic alterations at an affordable price. Method: The NVIGEN X - Precision Cancer Profiling test is a next generation sequencing (NGS) based circulating tumor DNA detection assay using the hybridization capture approach with customized gene panels. Our ctDNA NGS assay was developed with the use of high performance magnetic nanobeads, which enhances assay workflow at key steps including cfDNA extraction, NGS library preparation, and target enrichment. Experiments with individual plasma samples and DNA mutant fragments spiked in plasma samples were carried out to establish the assay performance such as sensitivity, specificity, consistency and data efficiency. NGS data QC metrics of the NVIGEN assay were compared with other assays in peer reviewed publications. Results: We developed a focus 32 gene panel that covers 144 kb of gene regions of clinical significance for breast cancer treatment monitoring and guidance, such as AKT1, ERBB2, PIK3CA, EGFR, ESR1, BRCA1/2, and CD274. Our results demonstrated the capability of NVIGEN X ctDNA NGS assay to detect rare copies (8 cp) of gene mutation at 0.07% MAF from DNA mutant fragments spiked into plasma samples. The NVIGEN X ctDNA NGS assays consistently presented 2-5% duplication rate, >80% on-target rate, <10% CV for key NGS data metrics, and on average required 1.36X paired reads per 1X unique coverage. Compared with the Roche Avenio assays (targeted, expanded and surveillance panels) as published in 2020 which on average required 9.36X paired reads per 1X unique coverage, the NVIGEN X -precision cancer profiling assays demonstrated 85% reduction in NGS data need to generate each unique coverage. Compared with the original Capp-seq data as published in the 2014 Nature Medicine paper which required in average 13.78 or 27.56 paired reads per unique coverage, the NVIGEN X assay demonstrated >90% reduction in NGS data need per unique coverage. Conclusion: The NVIGEN X - Precision Cancer Profiling assay provided high NGS assay performance with high sensitivity, specificity, and consistency, and significantly improved NGS data efficiency. This allows for dramatically reduced assay cost and will help support routine applications of ctDNA NGS tests to improve cancer patient treatment. Experiments of applying NVIGEN X assays for clinical research with patient samples are ongoing and will be presented.
Citation Format: Aihua Fu, Wenwu Cui, Minh V. Ton, Kevan Wang, Weiwei Gu, Tianhong Li, Heather A. Parsons, Minetta C. Liu, George W. Sledge. Developing highly sensitive high NGS data efficient ctDNA detection assays for breast cancer surveillance [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 P2-01-15.
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26
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Santos K, Jin Q, Miller PG, Patel A, Kirkner GJ, Files JL, Hughes ME, Stokes SM, Tayob N, Stover DG, Gibson CJ, Winer EP, Lin NU, Garber JE, Parsons HA. Abstract P3-08-01: Clonal hematopoiesis of indeterminate potential (CHIP) in metastatic triple negative breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-08-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background. Patients (pts) with metastatic triple negative breast cancer (mTNBC) receive serial cytotoxic chemotherapy regimens, often with cumulative myelosuppressive effects, impairing treatment tolerance. Clonal hematopoiesis of indeterminate potential (CHIP) refers to the detection of somatic mutations in genes recurrently mutated in hematologic malignancies in the blood of adults with no evident hematologic abnormalities. Little is known about the natural history of CHIP after breast cancer treatment. We sought to characterize CHIP in pts undergoing treatment for mTNBC. Methods. In this retrospective cohort study we identified 149 pts with biopsy-proven mTNBC at a single tertiary care institution with at least one blood sample collected within six months of metastatic diagnosis. We performed targeted sequencing of cryopreserved peripheral blood mononuclear cell (PBMC)-derived genomic DNA and defined CHIP as the presence of at least one pathogenic somatic mutation present at variant allelic fraction (VAF) of 0.02-0.35. We assessed the relationship between CHIP status and overall survival (OS), demographics, clinicopathologic features, germline mutation status, and type and timing of therapy. Results. We identified 27 unique CHIP variants across 22/149 pts (15%) within six months of metastatic diagnosis. Frequency of mutated genes were as follows: DNMT3A (n=15), PPM1D (n=4), TP53 (n=3), TET2 (n=2), SRCAP (n=1), ZBTB33 (n=1), ZNF318 (n=1). Median follow-up in the cohort was 37.9 months (IQR: 23.9-Not reached). The median age at time of blood draw was 55 years (IQR: 8.5) for pts with CHIP vs. 51 years (IQR: 16.5) for pts without CHIP. Ten (45%) pts with CHIP and 47 (37%) pts without CHIP were current or former smokers. Two (9%) pts with CHIP and 10 (7.9%) pts without CHIP were known germline mutation carriers of BRCA1, BRCA2 or PALB2. Twenty-two (100%) pts with CHIP and 124 (98%) pts without CHIP had received systemic chemotherapy for mTNBC prior to blood draw. There were no significant differences in type of chemotherapy regimen received between patients with or without CHIP. Twenty (90.9%) pts with CHIP vs. 96 (75.6%) of pts without CHIP had received radiation therapy prior to blood draw. Pts with CHIP had similar OS to those without CHIP (median OS 7.75 [2.20-31.7] vs. 9.33 [8.02-11.73] months). No pts developed therapy-related myeloid neoplasms (t-MN) or died of complications of cardiac disease. Conclusions. Pts with mTNBC had a higher frequency of CHIP than previously reported in age-matched healthy populations, but similar CHIP prevalence to what has been seen in cohorts of pts with solid tumors. Our study assessed for the presence of CHIP at only a single time point early in the metastatic course, but serial blood sampling later in treatment might reveal additional cases of CHIP. Though this cohort of patients with life-limiting mTNBC was small, presence of CHIP in the first six months of metastatic diagnosis was not associated with worse survival.
Citation Format: Katheryn Santos, Qingchun Jin, Peter G. Miller, Ashka Patel, Gregory J. Kirkner, Janet L. Files, Melissa E. Hughes, Samantha M. Stokes, Nabihah Tayob, Daniel G. Stover, Christopher J. Gibson, Eric P. Winer, Nancy U. Lin, Judy E. Garber, Heather A. Parsons. Clonal hematopoiesis of indeterminate potential (CHIP) in metastatic triple negative 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 P3-08-01.
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27
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Lynce F, Mainor C, Geng X, Jones G, Schlam I, Wang H, Feger U, Donahue R, Toney N, Jochems C, Schlom J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Dilawari AA, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Swain SM, Parsons HA, Pohlmann P, Isaacs C. Abstract PD9-02: Peripheral immune subsets and circulating tumor DNA (ctDNA) in patients (pts) with residual triple negative breast cancer (TNBC) treated with adjuvant immunotherapy and/or chemotherapy (chemo): The OXEL study. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-pd9-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Poor clinical outcomes are noted in pts with TNBC who do not achieve a pathologic complete response (pCR). We characterized peripheral immune subsets and the role of minimal residual disease (MRD) detection via ctDNA in pts who participated in the OXEL study. Methods: OXEL (Opdivo® -XELoda ®) is a recently completed phase II open-label 3-arm randomized study of nivolumab (nivo), capecitabine (cape) or the combination as adjuvant therapy (tx) for pts with residual TNBC after appropriate neoadjuvant chemo. Residual disease was defined as ≥ 1.0 cm of primary tumor and/or nodal involvement. Eligible pts had completed definitive local tx. Pts were randomly assigned to nivo 360 mg iv q3wks x 6 (arm A); cape 1250mg/m2 po bid D1-D14 q3 wks x 6 (arm B); nivo 360mg iv q3wks + cape 1250mg/m2 po bid D1-D14 q3 wks x 6 (arm C). Peripheral blood mononuclear cells (PBMCs) and ctDNA were assessed at baseline (D1 of cycle 1), 6, and 12 wks and at time of recurrence, if applicable. PBMCs were stained with 30 markers and analyzed by flow cytometry to identify changes in 158 immune cell subsets at 6 wks, as a percent of total PBMCs. RaDaRTM, a deep sequencing based, tumor-informed personalized assay was utilized to detect the presence of ctDNA in plasma. Distant disease-free survival (DDFS) and overall survival (OS) were analyzed by the Kaplan-Meier method and Log-Rank test was used to compare DDFS and OS according to baseline MRD results. All pts will be followed for distant recurrence and survival for 3 yrs. Here we report the translational endpoints of the OXEL study. Clinical endpoints according to treatment received will be reported in a future analysis. Results: 45 pts were enrolled between 8/2018 and 6/2021. 29 (64%) were Caucasian and 14 (31%) were African American. Mean age at enrollment was 51 [+/- 12]. 93% of pts received a taxane-anthracycline containing neoadjuvant tx. 15 pts were randomized to each arm. DDFS probability at 1-yr and 2-yrs was 0.71 (+/- 0.07) and 0.66 (+/- 0.08) respectively. At 12 mos of median follow up, 13/45 pts (29%) experienced distant recurrence, none had local recurrence. 43 pts were evaluated for PBMC subsets. Changes in PBMC subsets at 6 wks were different amongst the arms; in arm A, reductions in NK subsets, including a 33% reduction in CD56dimCD16- cells, were observed, while in arm B, increases in naïve CD4+ T cells (+45%) and CD73+CD8+ T cells (+12%) and reductions in ki67+CD8+ T cells (-48%) were noted. In arm C, increases were observed in conventional dendritic cells (+36%), effector memory ki67+CD4+ T cells (+46%), and CD56dimCD16- NK cells (+29%). 33 pts underwent successful MRD analysis. 12/33 (36%) pts were MRD+ at baseline. 2/12 pts MRD+ at baseline subsequently cleared MRD, with undetectable ctDNA on future time points; neither patient has had recurrence to date. The remaining 10/12 MRD+ pts (83%) have experienced distance recurrence. 21/33 (64%) pts were ctDNA negative at baseline; 20/33 remained negative for all follow up timepoints. 10/11 pts experiencing distant recurrence were MRD+ at baseline, compared to 1/11 pt who became MRD+ at wk 6 post initiation of tx. At 12 mos of median follow-up, baseline MRD+ testing was significantly associated with an inferior DDFS ( p<0.0001 Log-rank test, median DDFS 4.0 mos vs. not reached) and OS (p=0.02 Log-rank test, median OS not reached for both groups). Results will be updated at the time of abstract presentation. Conclusions: Changes in PBMC subsets were associated with receipt of chemo and/or immunotherapy. Our results suggest that baseline MRD+ in pts without pCR is a poor prognostic factor. Future trials aiming to optimize adjuvant treatment with chemo and/or immunotherapy in residual TNBC should consider incorporating ctDNA as a selection marker of pts at higher risk of recurrence.
Citation Format: Filipa Lynce, Candace Mainor, Xue Geng, Greg Jones, Ilana Schlam, Hongkun Wang, Ute Feger, Renee Donahue, Nicole Toney, Caroline Jochems, Jeffrey Schlom, Christopher Gallagher, Rita Nanda, Deena Graham, Erica M Stringer-Reasor, Neelima Denduluri, Julie Collins, Asma A Dilawari, Ami Chitalia, Shruti Tiwari, Raquel Nunes, Rebecca Kaltman, Katia Khoury, Margaret Gatti-Mays, Sandra M Swain, Heather A. Parsons, Paula Pohlmann, Claudine Isaacs. Peripheral immune subsets and circulating tumor DNA (ctDNA) in patients (pts) with residual triple negative breast cancer (TNBC) treated with adjuvant immunotherapy and/or chemotherapy (chemo): The OXEL study [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 PD9-02.
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Affiliation(s)
| | | | - Xue Geng
- Georgetown University, Washington, DC
| | | | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC
| | | | | | | | | | | | | | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC
| | | | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC
| | | | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD
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Tarantino P, Curigliano G, Parsons HA, Lin NU, Krop I, Mittendorf EA, Waks A, Winer EP, Tolaney SM. Aiming at a Tailored Cure for ERBB2-Positive Metastatic Breast Cancer: A Review. JAMA Oncol 2022; 8:629-635. [PMID: 35024766 DOI: 10.1001/jamaoncol.2021.6597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Metastatic breast cancer (MBC) has traditionally been considered incurable. Accordingly, current treatment algorithms are aimed at maintaining quality of life and improving overall survival, rather than at complete eradication of the disease. Attempts to achieve cure with high-dose chemotherapy were conducted in the 1990s, with no observed long-term benefit compared with conventional chemotherapy. Nonetheless, Erb-B2 receptor tyrosine kinase 2 (ERBB2, formerly HER2)-targeted biologic treatments, developed in the past 2 decades, are currently challenging this paradigm. Indeed, a fraction of patients with ERBB2-positive MBC achieve long-lasting responses to chemotherapy and ERBB2-blockade, resembling a cure. In this setting, the challenge of identifying the optimal curable population has emerged, including identifying populations in whom treatment escalation strategies may be beneficial, while avoiding overtreatment in patients with incurable disease. Observations A number of clinical and pathologic features allow physicians to identify patients with ERBB2-positive MBC who are more likely to experience a long-lasting response to chemotherapy and ERBB2-blockade. Long-term responders tend to be de novo metastatic, have a reduced disease burden, and tend to show deep responses to systemic treatment. In pathologic terms, features associated with long-term response are high ERBB2 expression, lack of detrimental genomic aberrations, and antitumor immune activation. This population of patients may potentially derive benefit from a tailored escalation of frontline treatment with novel anti-ERBB2 drugs, such as trastuzumab deruxtecan, tucatinib, or margetuximab. Additional recent therapeutic and diagnostic advancements could further aid in the path toward a cure for ERBB2-positive MBC. Conclusions and Relevance Careful implementation of novel diagnostic and treatment tools could potentially expand the population of patients with ERBB2-positive MBC experiencing long-lasting disease response. Trials are in preparation to confirm this paradigm, and hopefully lead to a new era of precision therapy for breast cancer.
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Affiliation(s)
- Paolo Tarantino
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Heather A Parsons
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Nancy U Lin
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Ian Krop
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A Mittendorf
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Adrienne Waks
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Eric P Winer
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sara M Tolaney
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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Collier KA, Asad S, Tallman D, Jenison J, Rajkovic A, Mardis ER, Parsons HA, Tolaney SM, Winer EP, Lin NU, Ha G, Adalsteinsson VA, Stover DG. Association of 17q22 Amplicon Via Cell-Free DNA With Platinum Chemotherapy Response in Metastatic Triple-Negative Breast Cancer. JCO Precis Oncol 2021; 5:PO.21.00104. [PMID: 34849445 PMCID: PMC8624042 DOI: 10.1200/po.21.00104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/11/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022] Open
Abstract
PURPOSE To determine whether specific somatic copy-number alterations detectable in circulating tumor DNA (ctDNA) from patients with metastatic triple-negative breast cancer (mTNBC) are associated with sensitivity to platinum chemotherapy. MATERIALS AND METHODS In this secondary analysis of a large cohort of patients with mTNBC whose ctDNA underwent ultralow-pass whole-genome sequencing, tumor fraction and somatic copy-number alterations were derived with the ichorCNA algorithm. Seventy-two patients were identified who had received a platinum-based chemotherapy regimen in the metastatic setting. Gene-level copy-number analyses were performed with GISTIC2.0. Cytobands were associated with progression-free survival (PFS) to platinum chemotherapy using Cox proportional hazards models. The Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium data sets were interrogated for frequency of significant cytobands in primary triple-negative breast cancer (pTNBC) tumors. RESULTS Among 71 evaluable patients, 17q21 and 17q22 amplifications were most strongly associated with improved PFS with platinum chemotherapy. There were no significant differences in clinicopathologic features or (neo)adjuvant chemotherapy among patients with 17q22 amplification. Patients with 17q22 amplification (n = 17) had longer median PFS with platinum (7.0 v 3.8 months; log-rank P = .015) than patients without 17q22 amplification (n = 54), an effect that remained significant in multivariable analyses (PFS hazard ratio 0.37; 95% CI, 0.16 to 0.84; P = .02). Among 39 patients who received the nonplatinum chemotherapy agent capecitabine, there was no association between 17q22 amplification and capecitabine PFS (log-rank P = .69). In The Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium, 17q22 amplification occurred in more than 20% of both pTNBC and mTNBC tumors, whereas 17q21 was more frequently amplified in mTNBC relative to pTNBC (16% v 8.1%, P = .015). CONCLUSION The 17q22 amplicon, detected by ctDNA, is associated with improved PFS with platinum chemotherapy in patients with mTNBC and warrants further investigation.
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Affiliation(s)
- Katharine A Collier
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, OH
| | - Sarah Asad
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - David Tallman
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Janet Jenison
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Andrei Rajkovic
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Gavin Ha
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Daniel G Stover
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, OH.,Ohio State University Comprehensive Cancer Center, Columbus, OH.,Stefanie Spielman Comprehensive Breast Center, Columbus, OH
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Doebley AL, Liao H, Kikawa C, Cruikshank E, Ko M, Hoge A, Hiatt J, De Sarkar N, Adalsteinsson VA, Polak P, MacPherson D, Nelson PS, Parsons HA, Stover D, Ha G. Abstract LB022: Griffin: A method for nucleosome profiling and breast cancer subtype prediction from ultra-low pass whole genome sequencing of cell-free DNA. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Cell-free DNA (cfDNA) is released from dying cells, including tumor cells, and can be isolated from peripheral blood for studying cancer. In the bloodstream, cfDNA is protected from degradation by nucleosomes and other DNA binding proteins, leading to a coverage pattern that reflects the genomic organization in the cells-of-origin. Recent work has shown that it is possible to use this pattern to predict gene and transcription factor activity in cancer cells. This is known as nucleosome profiling.
Breast cancer is among the most common causes of cancer, accounting for 23% of cancer diagnoses and 14% of cancer-related deaths among women worldwide. Targeted therapy is guided by tumor subtype, including the expression of three key receptors: ER, PR and HER2. Typically, subtyping involves a tumor biopsy and immunohistochemistry. However, in late-stage cancer, surgical biopsies for disease monitoring are difficult to obtain. Accurate subtype determination is critical to address hormone subtype switches during metastasis or treatment resistance. cfDNA offers an alternative, non-invasive method for identifying tumor subtypes through nucleosome profiling and, to the best of our knowledge, has not been shown for breast cancer.
Methods: We developed a method, called Griffin, to examine nucleosome protection and genome accessibility by quantifying cfDNA fragments around accessible sites. Unlike previous methods, Griffin uses fragment length-based GC correction to remove GC biases that obscure signals. We used ATAC-seq data from TCGA to identify differentially accessible sites between ER positive and negative breast cancers. We developed a machine learning classifier that predicts ER subtype based upon the signals at these differentially accessible sites.
Results: We then tested Griffin by examining differentially accessible sites in ultra-low pass sequencing (ULP-WGS, 0.1X) of several hundred cfDNA samples from patients with ER positive or negative breast cancer. We found that overall, differential sites were more accessible in the cfDNA of their respective subtypes. Additionally, we found that site accessibility within patient cfDNA samples was correlated to the cfDNA tumor fraction. We built and tested a prediction model with cross-validation, which revealed an accuracy of >80% for correctly classifying tumor status as ER positive or negative from this ULP-WGS dataset.
Conclusion: This study has several novel aspects compared to prior nucleosome profiling approaches. First, we use fragment-based GC correction which reduces sample variability and allows us to observe previously obscured signals. Second, we demonstrated that signals are correlated to tumor fraction. And finally, we applied this method to cost-effective and scalable ULP-WGS of breast cancer and demonstrated the ability to predict breast cancer ER subtype in these samples.
Citation Format: Anna-Lisa Doebley, Hanna Liao, Caroline Kikawa, Eden Cruikshank, Minjeong Ko, Anna Hoge, Joseph Hiatt, Navonil De Sarkar, Viktor A. Adalsteinsson, Paz Polak, David MacPherson, Peter S. Nelson, Heather A. Parsons, Daniel Stover, Gavin Ha. Griffin: A method for nucleosome profiling and breast cancer subtype prediction from ultra-low pass whole genome sequencing of cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB022.
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Affiliation(s)
| | - Hanna Liao
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Minjeong Ko
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Anna Hoge
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Joseph Hiatt
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Paz Polak
- 4Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Daniel Stover
- 6The James Comprehensive Cancer Center, Ohio State University, Columbus, OH
| | - Gavin Ha
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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Weber ZT, Collier KA, Tallman D, Forman J, Shukla S, Asad S, Rhoades J, Freeman S, Parsons HA, Williams NO, Barroso-Sousa R, Stover EH, Mahdi H, Cibulskis C, Lennon NJ, Ha G, Adalsteinsson VA, Tolaney SM, Stover DG. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer. Genome Med 2021; 13:89. [PMID: 34016182 PMCID: PMC8136103 DOI: 10.1186/s13073-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) offers minimally invasive means to repeatedly interrogate tumor genomes, providing opportunities to monitor clonal dynamics induced by metastasis and therapeutic selective pressures. In metastatic cancers, ctDNA profiling allows for simultaneous analysis of both local and distant sites of recurrence. Despite the promise of ctDNA sampling, its utility in real-time genetic monitoring remains largely unexplored. METHODS In this exploratory analysis, we characterize high-frequency ctDNA sample series collected over narrow time frames from seven patients with metastatic triple-negative breast cancer, each undergoing treatment with Cabozantinib, a multi-tyrosine kinase inhibitor (NCT01738438, https://clinicaltrials.gov/ct2/show/NCT01738438 ). Applying orthogonal whole exome sequencing, ultra-low pass whole genome sequencing, and 396-gene targeted panel sequencing, we analyzed 42 plasma-derived ctDNA libraries, representing 4-8 samples per patient with 6-42 days between samples. Integrating tumor fraction, copy number, and somatic variant information, we model tumor clonal dynamics, predict neoantigens, and evaluate consistency of genomic information from orthogonal assays. RESULTS We measured considerable variation in ctDNA tumor faction in each patient, often conflicting with RECIST imaging response metrics. In orthogonal sequencing, we found high concordance between targeted panel and whole exome sequencing in both variant detection and variant allele frequency estimation (specificity = 95.5%, VAF correlation, r = 0.949), Copy number remained generally stable, despite resolution limitations posed by low tumor fraction. Through modeling, we inferred and tracked distinct clonal populations specific to each patient and built phylogenetic trees revealing alterations in hallmark breast cancer drivers, including TP53, PIK3CA, CDK4, and PTEN. Our modeling revealed varied responses to therapy, with some individuals displaying stable clonal profiles, while others showed signs of substantial expansion or reduction in prevalence, with characteristic alterations of varied literature annotation in relation to the study drug. Finally, we predicted and tracked neoantigen-producing alterations across time, exposing translationally relevant detection patterns. CONCLUSIONS Despite technical challenges arising from low tumor content, metastatic ctDNA monitoring can aid our understanding of response and progression, while minimizing patient risk and discomfort. In this study, we demonstrate the potential for high-frequency monitoring of evolving genomic features, providing an important step toward scalable, translational genomics for clinical decision making.
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Affiliation(s)
- Zachary T Weber
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Katharine A Collier
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA
| | - David Tallman
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Juliet Forman
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sachet Shukla
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sarah Asad
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Justin Rhoades
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Samuel Freeman
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Nicole O Williams
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA
| | | | - Elizabeth H Stover
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Haider Mahdi
- Department of Obstetrics and Gynecology, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Surgery, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA
| | - Carrie Cibulskis
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Niall J Lennon
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | | | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Daniel G Stover
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA.
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA.
- Biomedical Research Tower, Room 984, Ohio State University Comprehensive Cancer Center, Stefanie Spielman Comprehensive Breast Center, Columbus, OH, 43210, USA.
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Parsons HA, Macrae ER, Guo H, Li T, Barry WT, Tayob N, Wulf GM, Isakoff SJ, Krop IE. Phase II Single-Arm Study to Assess Trastuzumab and Vinorelbine in Advanced Breast Cancer Patients With HER2-Negative Tumors and HER2-Positive Circulating Tumor Cells. JCO Precis Oncol 2021; 5:896-903. [PMID: 34994617 PMCID: PMC9848583 DOI: 10.1200/po.20.00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Human epidermal growth factor receptor 2 (HER2)-directed treatments improve outcomes for patients with HER2-positive metastatic breast cancer (MBC). Current identification of patients with HER2-positive disease relies on tumor tissue testing, which can be inaccurate because of tumor heterogeneity or tumor evolution. Circulating tumor cells (CTCs) are often present in patients with cancer. We hypothesized that HER2 assessment of CTCs in patients with HER2-negative breast cancer could identify a subset of patients with HER2-positive CTCs who could benefit from HER2-directed treatments. METHODS This was a single-arm, two-stage, phase II trial. Patients with HER2-negative progressive MBC with HER2-positive CTC (defined as HER2/CEP17 ratio ≥ 2.0 by fluorescence in situ hybridization), ≥ 1 prior chemotherapy regimen for MBC, and no prior vinorelbine received trastuzumab in combination with vinorelbine on days 1, 8, and 15 of a 21-day cycle. The primary end point was objective response rate. RESULTS From January 2013 to June 2014, we prospectively screened CTCs from patients with HER2-negative MBC. CTCs were detected in 201 of 311 patients (65%). The median number of CTCs was 10 (interquartile range, 3-57). Sixty-nine of 311 patients (22%) had HER2+ CTCs, with a median of three HER2+ CTCs (range 1-21). Twenty patients with HER2+ CTCs were treated on study. At data cutoff (January 13, 2017), no patients remained on study therapy. The objective response rate was 5% (95% CI, 0.1 to 24.9), with one of 20 patients experiencing a partial response. The clinical benefit rate was 20.0% (1 partial response and 3 stable diseases > 24 weeks, 95% CI, 5.7% to 43.7%). The median progression-free survival was 2.7 months. CONCLUSION CTC analysis of patients with HER2-negative MBC identifies a subset with HER2-amplified CTCs. However, clinical activity of an HER2-directed regimen in this population was low. The functional significance of HER2-positive CTCs remains uncertain.
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Affiliation(s)
- Heather A. Parsons
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC
| | - Erin R. Macrae
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC
| | - Hao Guo
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC
| | - Tianyu Li
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC
| | - William T. Barry
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC
| | - Nabihah Tayob
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC
| | | | | | - Ian E. Krop
- Dana-Farber Cancer Institute, Boston, MA.
Currently Hao Guo at IQVIA Biotech, Morrisville, NC; Currently William T. Barry
at Rho Inc, Durham, NC,Ian E. Krop, MD, PhD, Dana-Farber Cancer Institute, 450 Brookline
Ave, Boston, MA 02215; e-mail:
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Cheng ML, Pectasides E, Hanna GJ, Parsons HA, Choudhury AD, Oxnard GR. Circulating tumor DNA in advanced solid tumors: Clinical relevance and future directions. CA Cancer J Clin 2021; 71:176-190. [PMID: 33165928 DOI: 10.3322/caac.21650] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/21/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
The application of genomic profiling assays using plasma circulating tumor DNA (ctDNA) is rapidly evolving in the management of patients with advanced solid tumors. Diverse plasma ctDNA technologies in both commercial and academic laboratories are in routine or emerging use. The increasing integration of such testing to inform treatment decision making by oncology clinicians has complexities and challenges but holds significant potential to substantially improve patient outcomes. In this review, the authors discuss the current role of plasma ctDNA assays in oncology care and provide an overview of ongoing research that may inform real-world clinical applications in the near future.
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Affiliation(s)
- Michael L Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Eirini Pectasides
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Glenn J Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey R Oxnard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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Affiliation(s)
- Heather A Parsons
- Dana-Farber Cancer Institute, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Harold J Burstein
- Dana-Farber Cancer Institute, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson VA. Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer. Clin Cancer Res 2020; 26:2556-2564. [PMID: 32170028 DOI: 10.1158/1078-0432.ccr-19-3005] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/26/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing. EXPERIMENTAL DESIGN We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2- metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative. We performed whole-exome sequencing of tumors and designed individualized MRD tests, which we applied to serial cfDNA samples. RESULTS Our approach was 100-fold more sensitive than ddPCR when tracking 488 mutations, but most patients had fewer identifiable tumor mutations to track in cfDNA (median = 57; range = 2-346). Clinical sensitivity was 81% (n = 13/16) in newly diagnosed MBC, 23% (n = 7/30) at postoperative and 19% (n = 6/32) at 1 year in early-stage disease, and highest in patients with the most tumor mutations available to track. MRD detection at 1 year was strongly associated with distant recurrence [HR = 20.8; 95% confidence interval, 7.3-58.9]. Median lead time from first positive sample to recurrence was 18.9 months (range = 3.4-39.2 months). CONCLUSIONS Tracking large numbers of individualized tumor mutations in cfDNA can improve MRD detection, but its sensitivity is driven by the number of tumor mutations available to track.
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Affiliation(s)
- Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Priyanka Ram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pedro Exman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher C Lo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Boston University School of Public Health, Boston, Massachusetts
| | - Tianyu Li
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark Fleharty
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gregory J Kirkner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shoshana M Rosenberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura C Collins
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Kathy D Miller
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | | | - Lorenzo Trippa
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Donna S Neuberg
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gavin Ha
- Division of Public Health Services, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel G Stover
- Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ian Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
| | - G Mike Makrigiorgos
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Massachusetts
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Erica L Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Viktor A Adalsteinsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
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Exman P, Mallery RM, Lin NU, Parsons HA. Response to Olaparib in a Patient with Germline BRCA2 Mutation and Breast Cancer Leptomeningeal Carcinomatosis. NPJ Breast Cancer 2019; 5:46. [PMID: 31815182 PMCID: PMC6884546 DOI: 10.1038/s41523-019-0139-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/30/2019] [Indexed: 11/09/2022] Open
Abstract
Leptomeningeal carcinomatosis (LC) is a devastating complication of metastatic cancer that disproportionately affects patients with advanced breast cancer. Moreover, those with BRCA1/2-mutated disease more often experience leptomeningeal metastasis. Treatment options for LC are limited and often include significant toxicities. PARP inhibitors offer an important potential treatment for patients with BRCA1/2-mutated breast and ovarian cancers, but clinical studies excluded patients with central nervous system (CNS) metastases, including LC. Efficacy data in this area are therefore limited, although a phase I study of olaparib in glioblastoma did show CNS penetration. Here we report a case of a patient with BRCA2-mutated breast cancer and solitary recurrence in the leptomeninges with ongoing complete response to treatment with the PARP inhibitor olaparib. PARP inhibitors may be an important treatment option for patients with BRCA-mutated disease and LC, and warrant further study.
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Affiliation(s)
- Pedro Exman
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Robert M. Mallery
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA USA
| | - Nancy U. Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
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Singh J, Asad S, Zhang Y, Nock W, Adams E, Damicis A, Ramaswamy B, Williams N, Parsons HA, Adalsteinsson VA, Winer EP, Lin NU, Partridge AH, Overmoyer B, Stover DG. Aggressive Subsets of Metastatic Triple Negative Breast Cancer. Clin Breast Cancer 2019; 20:e20-e26. [PMID: 31631016 DOI: 10.1016/j.clbc.2019.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/22/2019] [Accepted: 06/22/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND Relative to other metastatic breast cancer subtypes, metastatic triple-negative breast cancer (mTNBC) has a shorter duration of response to therapy and worse overall survival. Among patients with mTNBC, it is hypothesized that inflammatory breast cancer (IBC) and young women have particularly aggressive phenotypes. We investigated clinical and cell-free DNA (cfDNA) characteristics of inflammatory-mTNBC and young-mTNBC. PATIENTS AND METHODS We evaluated 158 patients with mTNBC who were stratified into 3 groups: (1) IBC; (2) patients aged 45 years or younger at primary diagnosis without IBC (non-IBC young); and (3) patients over age 45 at diagnosis without IBC. We evaluated clinicopathologic characteristics, sites of metastasis, survival outcomes, and the fraction of DNA in circulation derived from tumor (TFx). RESULTS Analysis of metastatic sites revealed that young patients without IBC had the most frequent lung metastases (P = .002). cfDNA analyses of first sample showed that TFx was highest in the non-IBC young group but not elevated in the IBC group (analysis of variance P = .056 for first TFx). Individually, median overall survival from metastatic diagnosis for the IBC group was 15.2 months; for the non-IBC young group, 21.2 months, and for the non-IBC over 45 group, 31.2 months. Patients with IBC and young patients without IBC had worse prognosis relative to patients over 45 without IBC (log-rank P = .023). CONCLUSIONS Among patients with mTNBC in this single-institution cohort, patients with IBC and young patients without IBC had significantly worse overall survival compared with patients over 45 without IBC. Young patients without IBC had significantly higher cfDNA TFx, whereas patients with IBC did not have elevated TFx despite a poor prognosis. These findings demonstrate that further analyses of mTNBC subsets are warranted.
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Affiliation(s)
- Jasneet Singh
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH
| | - Sarah Asad
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Yiqing Zhang
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - William Nock
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Elizabeth Adams
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Adrienne Damicis
- College of Public Health, Division of Biostatistics, Ohio State University, Columbus, OH
| | - Bhuvaneswari Ramaswamy
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH; Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Nicole Williams
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH; Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Heather A Parsons
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | | | - Eric P Winer
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Nancy U Lin
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Ann H Partridge
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Beth Overmoyer
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel G Stover
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH; Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH.
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Freedman RA, Gelman RS, Anders CK, Melisko ME, Parsons HA, Cropp AM, Silvestri K, Cotter CM, Componeschi KP, Marte JM, Connolly RM, Moy B, Van Poznak CH, Blackwell KL, Puhalla SL, Jankowitz RC, Smith KL, Ibrahim N, Moynihan TJ, O'Sullivan CC, Nangia J, Niravath P, Tung N, Pohlmann PR, Burns R, Rimawi MF, Krop IE, Wolff AC, Winer EP, Lin NU. TBCRC 022: A Phase II Trial of Neratinib and Capecitabine for Patients With Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer and Brain Metastases. J Clin Oncol 2019; 37:1081-1089. [PMID: 30860945 PMCID: PMC6494354 DOI: 10.1200/jco.18.01511] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Evidence-based treatments for metastatic, human epidermal growth factor receptor 2 (HER2)-positive breast cancer to the CNS are limited. We previously reported modest activity of neratinib monotherapy for HER2-positive breast cancer brain metastases. Here we report the results from additional study cohorts. PATIENTS AND METHODS Patients with measurable, progressive, HER2-positive brain metastases (92% after receiving CNS surgery and/or radiotherapy) received neratinib 240 mg orally once per day plus capecitabine 750 mg/m2 twice per day for 14 days, then 7 days off. Lapatinib-naïve (cohort 3A) and lapatinib-treated (cohort 3B) patients were enrolled. If nine or more of 35 (cohort 3A) or three or more of 25 (cohort 3B) had CNS objective response rates (ORR), the drug combination would be deemed promising. The primary end point was composite CNS ORR in each cohort separately, requiring a reduction of 50% or more in the sum of target CNS lesion volumes without progression of nontarget lesions, new lesions, escalating steroids, progressive neurologic signs or symptoms, or non-CNS progression. RESULTS Forty-nine patients enrolled in cohorts 3A (n = 37) and 3B (n = 12; cohort closed for slow accrual). In cohort 3A, the composite CNS ORR = 49% (95% CI, 32% to 66%), and the CNS ORR in cohort 3B = 33% (95% CI, 10% to 65%). Median progression-free survival was 5.5 and 3.1 months in cohorts 3A and 3B, respectively; median survival was 13.3 and 15.1 months. Diarrhea was the most common grade 3 toxicity (29% in cohorts 3A and 3B). Neratinib plus capecitabine is active against refractory, HER2-positive breast cancer brain metastases, adding additional evidence that the efficacy of HER2-directed therapy in the brain is enhanced by chemotherapy. For optimal tolerance, efforts to minimize diarrhea are warranted.
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Affiliation(s)
| | | | - Carey K Anders
- 2 University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | | | | | | | | | | | - Beverly Moy
- 5 Massachusetts General Hospital, Boston, MA
| | | | | | | | | | | | - Nuhad Ibrahim
- 9 The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Nadine Tung
- 12 Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | - Ian E Krop
- 1 Dana-Farber Cancer Institute, Boston, MA
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Singh J, Asad S, Nock W, Zhang Y, Adams E, Damicis A, Parsons HA, Adalsteinsson VA, Winer EP, Lin NU, Partridge AH, Overmoyer B, Stover DG. Abstract P4-01-17: Aggressive subgroups of metastatic triple-negative breast cancer: Inflammatory breast cancer and young patients in the Dana-Farber cell-free DNA cohort. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-01-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Relative to other metastatic breast cancer subtypes, metastatic triple-negative breast cancer (mTNBC) has a shorter duration of response to therapy and worse overall survival. Within mTNBCs, there is a prevailing belief that inflammatory breast cancer and young women tend to have among the most aggressive phenotypes. We investigated clinical and cell-free DNA (cfDNA) characteristics of inflammatory-mTNBC and young-mTNBC. We hypothesized that inflammatory-mTNBC may have distinct clinical and cfDNA characteristics, offering potential novel biomarker and therapeutic strategies.
Methods: 164 patients from the Dana-Farber metastatic triple-negative cell-free DNA cohort (Stover DG, et al J Clin Oncol 2018) were included in this secondary analysis. Patients were stratified into three groups: 1) inflammatory breast cancer ('IBC'); 2) non-IBC patients aged 45 years (yr) or younger at primary diagnosis ('non-IBC young'); and 3) non-IBC patients over age 45 yr at diagnosis. For each subset population, we evaluated clinicopathologic characteristics, sites of metastasis, survival outcomes, and cfDNA 'tumor fraction' – the fraction of DNA in circulation derived from tumor. Those patients with adequate cfDNA tumor content for high confidence copy number calls (n=101) were included in an analysis of copy number alterations.
Results: Among 164 patients with metastatic TNBC, 13.4% (22/164) had IBC, 37.8% (62/164) were non-IBC young, and 48.8% (80/164) were non-IBC and over 45 yr. Race and primary receptor status were similar. IBC patients were diagnosed at a higher stage (Chi-square p=0.0009) while non-IBC young patients were significantly more likely to harbor a BRCA mutation (Chi-square p=0.03). Analysis of metastatic sites revealed that IBC patients had significantly greater frequency of ipsilateral and contralateral breast chest wall recurrences (p=0.04 and p=0.046, respectively) while non-IBC young patients had the most frequent lung metastases (p=0.002). There were no significant differences in frequency of bone, brain, or liver metastases. cfDNA analyses showed that cfDNA 'tumor fraction' was highest in non-IBC young patients (ANOVA p=0.03 for maximum tumor fraction). Median overall survival from metastatic diagnosis was 22.9 months. IBC and non-IBC young patients had a worse prognosis relative to non-IBC patients over 45 yr (hazard ratio IBC=1.97, 95% CI 1.09-3.57; HR non-IBC young=1.60 95% CI 1.07-2.41; log-rank p=0.023). By subgroup, median overall survival from metastatic diagnosis for IBC was 15.2 months, non-IBC young 21.2 months, and non-IBC over 45 yr 31.2 months. Analyses of genome-wide copy number alterations from cell-free DNA will be presented.
Conclusions: Among metastatic TNBCs, IBC patients and non-IBC young patients have a significantly worse overall survival compared with non-IBC patients over 45 yr of age. Young patients have more frequent lung metastases and higher 'tumor fraction' of cfDNA. Confirmation of the reported findings is limited due to cohort size and may reflect referral bias.
Citation Format: Singh J, Asad S, Nock W, Zhang Y, Adams E, Damicis A, Parsons HA, Adalsteinsson VA, Winer EP, Lin NU, Partridge AH, Overmoyer B, Stover DG. Aggressive subgroups of metastatic triple-negative breast cancer: Inflammatory breast cancer and young patients in the Dana-Farber cell-free DNA cohort [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-17.
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Affiliation(s)
- J Singh
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - S Asad
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - W Nock
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - Y Zhang
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - E Adams
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - A Damicis
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - HA Parsons
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - VA Adalsteinsson
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - EP Winer
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - NU Lin
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - AH Partridge
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - B Overmoyer
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
| | - DG Stover
- Ohio State University Stefanie Spielman Comprehensive Breast Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of MIT and Harvard, Boston, MA
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Exman P, Freret TS, Economy KE, Chen WY, Parsons HA, Lin NU, Moy B, Tung NM, Partridge AH, Mayer EL. Abstract P1-17-02: Outcomes and safety of paclitaxel and granulocyte-colony stimulating factor (GCSF) in breast cancer in pregnancy (BCP) - A multi-institutional retrospective analysis. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p1-17-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
BCP is uncommon; however, the frequency is increasing due to trends in delayed childbearing. Studies have suggested that some systemic therapies, including doxorubicin and cyclophosphamide, can be delivered safely during pregnancy after the first trimester, whereas agents such as trastuzumab and endocrine therapy are contraindicated due to risk to the fetus. Data remain limited on the efficacy and safety of administering taxane chemotherapy or growth factor support during pregnancy. We retrospectively evaluated the safety of systemic therapies, including paclitaxel and GCSF, as well as clinical outcomes, in a multi-institutional cohort of patients (pts) with BCP.
Methods
Pts treated for BCP from 1996-2018 from 3 large academic institutions were included. Demographic, oncologic treatment, and obstetric/neonatal outcomes data were obtained from medical records. Disease-free survival (DFS) and overall survival (OS) were estimated by Kaplan-Meier; Log-rank test were used to compare different groups/outcomes. Associations were calculated by Fisher's exact test.
Results
A total of 114 pts diagnosed with BCP were included. The median age was 35 years (range 25-44) and median gestational age at diagnosis was 18 weeks (range 2-38). BCP was predominantly early stage at diagnosis (stage I 28.0%, stage II 53.5%) and ER+/HER2- negative (48.2%). Sixty-three (55.2%) women received chemotherapy, 13 (11.4%) received paclitaxel and 11 (9.6%) GCSF (daily or depot injections) while pregnant. A total of 78% of pts with HER-2-positive BCP (28/36) received trastuzumab after delivery (11% were treated before 2005 and 5.5% were T1a). With median follow-up of 67.7 months, median DFS (stage I-III) was 212.8 months (CI 95% 108.4-317.1), and median OS (stage I-IV) was not reached. Subgroup analysis suggested a higher DFS for pts diagnosed in the 1sttrimester compared to the 3rdtrimester among women with stage II-III (HR 0.25 CI 95% 0.09-0.70, p= 0.03). Among women who received paclitaxel, there was no significant increase in adverse obstetrical/neonatal outcomes: preterm delivery (23.1% vs 13.1%, p 0.39), low weight newborn (7.7% vs 9.1 %, p 1.0), congenital malformations (0% vs 6.1%, p 1.0) or acute neonatal adverse outcomes (7.7% vs 4.0%, p 0.51), which include NICU need and Apgar 5'<7, compared to pts who did not receive paclitaxel. Among pts who received GCSF during pregnancy, adverse outcomes were numerically but not statistically higher than women who did not receive growth factor: preterm delivery (36.3% vs 11.0%, p 0.051), low weight newborn (27.3% vs 6.9%, p 0.058), congenital malformations (9.1% vs 1.0%, p 0.18) or acute neonatal adverse outcomes (18.2% vs 3.0%, p 0.07).
Conclusion
In this multi-institution cohort of BCP pts, despite a small number of pts, exposure to contemporary therapies including paclitaxel was not associated with unfavorable obstetrical/neonatal outcomes and these results suggest it is safe to administer during pregnancy under the care of a multidisciplinary team. Although not statistically significant, GCSF presented numerical worse outcomes and combining data from several cohorts would be helpful to provide confirmation of these findings.
Citation Format: Exman P, Freret TS, Economy KE, Chen WY, Parsons HA, Lin NU, Moy B, Tung NM, Partridge AH, Mayer EL. Outcomes and safety of paclitaxel and granulocyte-colony stimulating factor (GCSF) in breast cancer in pregnancy (BCP) - A multi-institutional retrospective analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-17-02.
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Affiliation(s)
- P Exman
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - TS Freret
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - KE Economy
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - WY Chen
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - HA Parsons
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - NU Lin
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - B Moy
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - NM Tung
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - AH Partridge
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - EL Mayer
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Massachusets General Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
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Choudhury AD, Werner L, Francini E, Wei XX, Ha G, Freeman SS, Rhoades J, Reed SC, Gydush G, Rotem D, Lo C, Taplin ME, Harshman LC, Zhang Z, O'Connor EP, Stover DG, Parsons HA, Getz G, Meyerson M, Love JC, Hahn WC, Adalsteinsson VA. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight 2018; 3:122109. [PMID: 30385733 DOI: 10.1172/jci.insight.122109] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tumor content in circulating cell-free DNA (cfDNA) is a promising biomarker, but longitudinal dynamics of tumor-derived and non-tumor-derived cfDNA through multiple courses of therapy have not been well described. METHODS CfDNA from 663 plasma samples from 140 patients with castration-resistant prostate cancer (CRPC) was subject to sparse whole genome sequencing. Tumor fraction (TFx) estimated using the computational tool ichorCNA was correlated with clinical features and responses to therapy. RESULTS TFx associated with the number of bone metastases (median TFx = 0.014 with no bone metastases, 0.047 with 1-3 bone metastases, 0.190 for 4+ bone metastases; P < 0.0001) and with visceral metastases (P < 0.0001). In multivariable analysis, TFx remained associated with metastasis location (P = 0.042); TFx was positively correlated with alkaline phosphatase (P = 0.0227) and negatively correlated with hemoglobin (Hgb) (P < 0.001), but it was not correlated with prostate specific antigen (PSA) (P = 0.75). Tumor-derived and non-tumor-derived cfDNA track together and do not increase with generalized tissue damage from chemotherapy or radiation at the time scales examined. All new treatments that led to ≥30% PSA decline at 6 weeks were associated with TFx decline when baseline TFx was >7%; however, TFx in patients being subsequently maintained on secondary hormonal therapy was quite dynamic. CONCLUSION TFx correlates with clinical features associated with overall survival in CRPC, and TFx decline is a promising biomarker for initial therapeutic response. TRIAL REGISTRATION Dana-Farber/Harvard Cancer Center (DF/HCC) protocol no. 18-135. FUNDING Wong Family Award in Translational Oncology, Dana Farber Cancer Institute Medical Oncology grant, Gerstner Family Foundation, Janssen Pharmaceuticals Inc., and Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute (NCI).
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Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lillian Werner
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Edoardo Francini
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Sapienza University of Rome, Rome, Italy
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samuel S Freeman
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justin Rhoades
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah C Reed
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory Gydush
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Denisse Rotem
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher Lo
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren C Harshman
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | - Heather A Parsons
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gad Getz
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - J Christopher Love
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Viktor A Adalsteinsson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Freeman SS, Lin Z, Ha G, Leshchiner I, Rhoades J, Livitz D, Rosebrock D, Reed SC, Gydush G, Lo C, Rotem D, Choudhury AD, Stover DG, Parsons HA, Boehm JS, Love JC, Meyerson M, Grandgenett P, Hollingsworth MA, Adalsteinsson VA, Getz G. Abstract LB-225: Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Precision medicine approaches to guide therapy selection require routine sampling of tumors. However, tumor biopsies are not always accessible and may be confounded by spatial heterogeneity. Liquid biopsies, including analysis of cell-free DNA (cfDNA), present a non-invasive alternative which may reflect multiple tumors in the body. Previous studies have demonstrated exome-wide concordance between single-site tumor biopsies and cfDNA, but little is known about how cfDNA reflects multiple lesions within a patient. Here we sought to determine how cfDNA reflects the body-wide tumor phylogeny, which will inform the use of cfDNA for cancer precision medicine.
Methods: We identified 20 patients with pancreatic cancer who had undergone rapid autopsy. We then screened cfDNA tumor fraction and performed whole-exome sequencing of cfDNA and multiple tumor biopsies for 3 patients with cfDNA tumor fraction >10%. We inferred the tumor phylogeny and then developed a statistical approach to deconvolute the contributions to cfDNA from tumor phylogenetic nodes. Finally, we determined whether shared trunk mutations could be detected in cfDNA and tumor biopsies.
Results: For each patient, we found mutations shared between all sites and cfDNA, including putative driver mutations. We found mutations which were clonal in multiple regions were detectable in cfDNA, whereas mutations private to individual sites were never clonal in cfDNA. Through our deconvolution analysis, we found that cfDNA could not be modeled as a simple linear combination of individual sites, but rather that cfDNA represented multiple nodes in the inferred phylogeny. For two pancreatic adenocarcinoma patients, the inferred ancestor of the metastases had high estimated contribution (>70%) to cfDNA, while the ancestors of the primaries had lower contributions (<10%). Next, we considered trunk mutations, which originate earliest in the tumor phylogenetic tree. When we analyzed precision for detection of trunk mutations, we found on average, 71% of clonal mutations in metastases were truncal, while only 55% of clonal mutations in primary tumors were truncal. Due to copy number deletions, not all trunk mutations were detected in metastases. Finally, on average, cfDNA had equal or better precision than 83% of primaries and 88% of metastases, suggesting cfDNA may provide more accurate trunk SSNV calls than tumor biopsies.
Conclusions: Through analyzing cfDNA and synchronous tumor biopsies from the same patient, we find trunk mutations are enriched in cfDNA as compared to the average single-site biopsy. We also predict that cfDNA represents multiple nodes in the inferred phylogeny. In cases where tumor biopsies are inaccessible, we demonstrate that cfDNA might be a promising alternative to detect trunk SSNVs. These results suggest that cfDNA may be complementary to tumor biopsies for disease monitoring and treatment selection in personalized medicine.
Citation Format: Samuel S. Freeman, Ziao Lin, Gavin Ha, Ignaty Leshchiner, Justin Rhoades, Dimitri Livitz, Daniel Rosebrock, Sarah C. Reed, Gregory Gydush, Christopher Lo, Denisse Rotem, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Jesse S. Boehm, J Christopher Love, Matthew Meyerson, Paul Grandgenett, Michael A. Hollingsworth, Viktor A. Adalsteinsson, Gad Getz. Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-225.
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Affiliation(s)
| | | | - Gavin Ha
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | | | - Daniel G. Stover
- 3Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | | | | | | | - Gad Getz
- 6Massachusetts General Hospital, Boston, MA
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Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol 2018; 36:543-553. [PMID: 29298117 PMCID: PMC5815405 DOI: 10.1200/jco.2017.76.0033] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.
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Affiliation(s)
- Daniel G. Stover
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Heather A. Parsons
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gavin Ha
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Samuel S. Freeman
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - William T. Barry
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Hao Guo
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Atish D. Choudhury
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gregory Gydush
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah C. Reed
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Justin Rhoades
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Denisse Rotem
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Melissa E. Hughes
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Deborah A. Dillon
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ann H. Partridge
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nikhil Wagle
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ian E. Krop
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gad Getz
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Todd R. Golub
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Christopher Love
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Eric P. Winer
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sara M. Tolaney
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nancy U. Lin
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Viktor A. Adalsteinsson
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
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Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Abstract GS3-07: Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-gs3-07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance.
Methods:
506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage whole genome sequencing to determine genome-wide copy number and estimate 'tumor fraction' of cfDNA (TFx) using our recently-developed approach, ichorCNA. In patient samples with TFx >10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of 20 paired primary-metastatic samples and also mTNBCs from cfDNA versus primary TNBCs from TCGA and METABRIC.
Results:
We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. TFx and copy number profiles were highly concordant with paired metastatic biopsy (n=10, range 0-7 days from biopsy to blood draw) with sensitivity of 0.86 and specificity of 0.90 and reproducible in independently-processed blood draws (TFx intraclass correlation coefficient 0.984). Median overall survival from time of first blood draw was 8 months, and TFx was highly correlated independent of primary stage, primary receptor status, age at primary diagnosis, BRCA status, and metastatic line of therapy: adjusted hazard ratio between 4th and 1st quartiles = 2.14 (95% CI 1.40-3.28; p=0.00049). 101/158 patients (63.9%) had at least one sample with TFx >10%, our threshold for high confidence CNA calls. Copy number profiles and percent genome altered were remarkably similar between mTNBCs and primary TNBCs in TCGA and METABRIC (n=433), suggesting that large-scale chromosomal events are infrequent in TNBC metastatic progression. We identified chromosomal gains that demonstrated significant enrichment in mTNBCs relative to paired primary TNBCs (n=20) and also TCGA/METABRIC, including driver genes (NOTCH2, AKT2, AKT3) and putative antibody-drug conjugate targets. Finally, we identify a novel association of gains of 18q11 and/or 19p13 with poor metastatic prognosis, independent of clinicopathologic factors and TFx.
Conclusions:
Here, we present the first large-scale genomic characterization of metastatic TNBC to our knowledge, derived exclusively from cfDNA. 'Tumor fraction' of cfDNA is an independent prognostic marker in mTNBC. Primary and metastatic TNBC have remarkably similar copy number profiles yet we identify alterations enriched and prognostic in mTNBC. Collectively, these data have potential implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets.
Citation Format: Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS3-07.
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Affiliation(s)
- DG Stover
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - HA Parsons
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - G Ha
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - S Freeman
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - B Barry
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - H Guo
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - A Choudhury
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - G Gydush
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - S Reed
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - J Rhoades
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - D Rotem
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - ME Hughes
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - DA Dillon
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - AH Partridge
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - N Wagle
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - IE Krop
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - G Getz
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - TA Golub
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - JC Love
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - EP Winer
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - SM Tolaney
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - NU Lin
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
| | - VA Adalsteinsson
- The Ohio State University Comprehensive Cancer Center, Columbus, OH; Dana-Farber Cancer Institute, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA; Massachusetts Institute of Technology, Cambridge, MA
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Ladas I, Fitarelli-Kiehl M, Song C, Adalsteinsson VA, Parsons HA, Lin NU, Wagle N, Makrigiorgos GM. Multiplexed Elimination of Wild-Type DNA and High-Resolution Melting Prior to Targeted Resequencing of Liquid Biopsies. Clin Chem 2017; 63:1605-1613. [PMID: 28679646 PMCID: PMC5914173 DOI: 10.1373/clinchem.2017.272849] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/12/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The use of clinical samples and circulating cell-free DNA (cfDNA) collected from liquid biopsies for diagnostic and prognostic applications in cancer is burgeoning, and improved methods that reduce the influence of excess wild-type (WT) portion of the sample are desirable. Here we present enrichment of mutation-containing sequences using enzymatic degradation of WT DNA. Mutation enrichment is combined with high-resolution melting (HRM) performed in multiplexed closed-tube reactions as a rapid, cost-effective screening tool before targeted resequencing. METHODS We developed a homogeneous, closed-tube approach to use a double-stranded DNA-specific nuclease for degradation of WT DNA at multiple targets simultaneously. The No Denaturation Nuclease-assisted Minor Allele Enrichment with Probe Overlap (ND-NaME-PrO) uses WT oligonucleotides overlapping both strands on putative DNA targets. Under conditions of partial denaturation (DNA breathing), the oligonucleotide probes enhance double-stranded DNA-specific nuclease digestion at the selected targets, with high preference toward WT over mutant DNA. To validate ND-NaME-PrO, we used multiplexed HRM, digital PCR, and MiSeq targeted resequencing of mutated genomic DNA and cfDNA. RESULTS Serial dilution of KRAS mutation-containing DNA shows mutation enrichment by 10- to 120-fold and detection of allelic fractions down to 0.01%. Multiplexed ND-NaME-PrO combined with multiplexed PCR-HRM showed mutation scanning of 10-20 DNA amplicons simultaneously. ND-NaME-PrO applied on cfDNA from clinical samples enables mutation enrichment and HRM scanning over 10 DNA targets. cfDNA mutations were enriched up to approximately 100-fold (average approximately 25-fold) and identified via targeted resequencing. CONCLUSIONS Closed-tube homogeneous ND-NaME-PrO combined with multiplexed HRM is a convenient approach to efficiently enrich for mutations on multiple DNA targets and to enable prescreening before targeted resequencing.
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Affiliation(s)
- Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | | | - Heather A. Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA,Correspondence: G. Mike Makrigiorgos, Ph.D., Brigham and Women’s Hospital, Level L2, Radiation Therapy, 75 Francis Street, Boston, MA 02115., Tel: 617-525-7122. Fax: 617-582-6037,
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Dalton WB, Forde PM, Kang H, Connolly RM, Stearns V, Gocke CD, Eshleman JR, Axilbund J, Petry D, Geoghegan C, Wolff AC, Loeb DM, Pratilas CA, Meyer CF, Christenson ES, Slater SA, Ensminger J, Parsons HA, Park BH, Lauring J. Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board. JCO Precis Oncol 2017; 2017. [PMID: 30003184 DOI: 10.1200/po.16.00046] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purpose Tumor genomic profiling for personalized oncology therapy is being widely applied in clinical practice even as it is being evaluated more formally in clinical trials. Given the complexities of genomic data and its application to clinical use, molecular tumor boards with diverse expertise can provide guidance to oncologists and patients seeking to implement personalized genetically targeted therapy in practice. Methods A multidisciplinary molecular tumor board reviewed tumor molecular profiling reports from consecutive referrals at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins over a 3-year period. The tumor board weighed evidence for actionability of genomic alterations identified by molecular profiling and provided recommendations including US Food and Drug Administration-approved drug therapy, clinical trials of matched targeted therapy, off-label use of such therapy, and additional tumor or germline genetic testing. Results One hundred fifty-five patients were reviewed. Actionable genomic alterations were identified in 132 patients (85%). Off-label therapies were recommended in 37 patients (24%). Eleven patients were treated off-label, and 13 patients were enrolled onto clinical trials of matched targeted therapies. Median progression-free survival of patients treated with matched therapies was 5 months (95% CI, 2.9 months to not reached), and the progression-free survival probability at 6 months was 43%(95% CI, 26% to 71%). Lack of locally available clinical trials was the major limitation on clinical actionability of tumor profiling reports. Conclusion The molecular tumor board recommended off-label targeted therapies for a quarter of all patients reviewed. Outcomes were heterogeneous, although 43% of patients receiving genomically matched therapy derived clinical benefit lasting at least 6 months. Until more data become available from precision oncology trials, molecular tumor boards can help guide appropriate use of tumor molecular testing to direct therapy.
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Affiliation(s)
- W Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Hyunseok Kang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Roisin M Connolly
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Vered Stearns
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Christopher D Gocke
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - James R Eshleman
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Dana Petry
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Antonio C Wolff
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - David M Loeb
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Christian F Meyer
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Shannon A Slater
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Jennifer Ensminger
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Heather A Parsons
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ben H Park
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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Parsons HA, Beaver JA, Cimino-Mathews A, Ali SM, Axilbund J, Chu D, Connolly RM, Cochran RL, Croessmann S, Clark TA, Gocke CD, Jeter SC, Kennedy MR, Lauring J, Lee J, Lipson D, Miller VA, Otto GA, Rosner GL, Ross JS, Slater S, Stephens PJ, VanDenBerg DA, Wolff AC, Young LE, Zabransky DJ, Zhang Z, Zorzi J, Stearns V, Park BH. Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling of Tissue and Blood in Metastatic Triple-Negative Breast Cancer. Clin Cancer Res 2017; 23:379-386. [PMID: 27489289 PMCID: PMC5241251 DOI: 10.1158/1078-0432.ccr-16-1543] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022]
Abstract
PURPOSE The clinical utility of next-generation sequencing (NGS) in breast cancer has not been demonstrated. We hypothesized that we could perform NGS of a new biopsy from patients with metastatic triple-negative breast cancer (TNBC) in a clinically actionable timeframe. EXPERIMENTAL DESIGN We planned to enroll 40 patients onto a prospective study, Individualized Molecular Analyses Guide Efforts (IMAGE), to evaluate the feasibility of obtaining a new biopsy of a metastatic site, perform NGS (FoundationOne), and convene a molecular tumor board to formulate treatment recommendations within 28 days. We collected blood at baseline and at time of restaging to assess cell-free circulating plasma tumor DNA (ptDNA). RESULTS We enrolled 26 women with metastatic TNBC who had received ≥1 line of prior chemotherapy, and 20 (77%) underwent NGS of a metastatic site biopsy. Twelve (60%) evaluable patients received treatment recommendations within 28 days of consent. The study closed after 20 patients underwent NGS, based on protocol-specified interim futility analysis. Three patients went on to receive genomically directed therapies. Twenty-four of 26 patients had genetic alterations successfully detected in ptDNA. Among 5 patients, 4 mutations found in tumor tissues were not identified in blood, and 4 mutations found in blood were not found in corresponding tumors. In 9 patients, NGS of follow-up blood samples showed 100% concordance with baseline blood samples. CONCLUSIONS This study demonstrates challenges of performing NGS on prospective tissue biopsies in patients with metastatic TNBC within 28 days, while also highlighting the potential use of blood as a more time-efficient and less invasive method of mutational assessment. Clin Cancer Res; 23(2); 379-86. ©2016 AACR.
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Affiliation(s)
- Heather A Parsons
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julia A Beaver
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley Cimino-Mathews
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Jennifer Axilbund
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Roisin M Connolly
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rory L Cochran
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah Croessmann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Christopher D Gocke
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stacie C Jeter
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Justin Lee
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Doron Lipson
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | - Geoff A Otto
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Gary L Rosner
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Shannon Slater
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Dustin A VanDenBerg
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Antonio C Wolff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Daniel J Zabransky
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhe Zhang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jane Zorzi
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vered Stearns
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Ben H Park
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Abstract
Circulating cell-free DNA (ccfDNA)--first identified in 1947--is "naked" DNA that is free-floating in the blood, and derived from both normal and diseased cells. In the 1970s, scientists observed that patients with cancer had elevated levels of ccfDNA as compared to their healthy, cancer-free counterparts. The maternal fetal medicine community first developed techniques to identify the small fraction of fetal-derived ccfDNA for diagnostic purposes. Similarly, due to the presence of tumor-specific (somatic) variations in all cancers, the fraction of circulating cell-free plasma tumor DNA (ptDNA) in the larger pool of ccfDNA derived from normal cells can serve as extremely specific blood-based biomarkers for a patient's cancer. In theory this "liquid biopsy" can provide a real-time assessment of molecular tumor genotype (qualitative) and existing tumor burden (quantitative). Historically, the major limitation for ptDNA as a biomarker has been related to a low detection rate; however, current and developing techniques have improved sensitivity dramatically. In this chapter, we discuss these methods, including digital polymerase chain reaction and various approaches to tagged next-generation sequencing.
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Affiliation(s)
- Heather A Parsons
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA
| | - Julia A Beaver
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA
| | - Ben H Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA.
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Adalsteinsson VA, Ha G, Freeman S, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed S, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Cohen O, Oh C, Kim J, Stewart C, Rosenberg M, Ding H, Lloyd MR, Mahmud S, Helvie KE, Merrill MS, Santiago RA, O’Connor EP, Jeong SH, Kramkowski JF, Lohr JG, Polacek L, Oliver N, Marini L, Francis J, Harshman LC, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Meyerson M, Love CJ. Abstract LB-136: High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Circulating cell-free DNA (cfDNA) has largely been used to monitor blood for specific tumor mutations, but genome-wide discovery from cfDNA has not been well established. Here, we establish a scalable approach for whole-exome sequencing (WES) of cfDNA, making it possible to perform comprehensive genomic characterization of metastatic cancer in a routine and minimally-invasive manner.
Comprehensive genomic characterization of metastatic cancer stands to uncover novel alterations of clinical significance. A major challenge is that metastatic tumors are infrequently biopsied. Cell-free DNA is shed abundantly into the bloodstream from metastatic tumors, presenting an opportunity for genomic discovery in advanced cancers that are rarely biopsied in routine clinical care. We report an efficient process to qualify and sequence whole-exomes from cfDNA at scale and systematically compare the somatic mutations, indels, and copy number alterations detected in WES of cfDNA to WES of matched tumor biopsies.
Methods: We consented 86 patients with metastatic breast or prostate cancers for blood collection. We isolated cfDNA and germline DNA from blood and performed low coverage sequencing to estimate tumor content based on genome-wide copy number. We screened patient blood samples and prioritized those with higher tumor fractions for WES. In parallel, we analyzed cfDNA and germline DNA from healthy donors to calibrate our methods and assess false positive rate for genomic alterations.
Results: We found the vast majority of patients with metastatic prostate or breast cancer to have detectable tumor-derived cfDNA. WES of cfDNA from healthy donors revealed very low false positive rates for somatic mutations, indels and copy number alterations (SCNAs). By analyzing WES of cfDNA and tumor biopsies from dozens of patients with metastatic breast or prostate cancers, we established guidelines for the coverage and tumor fraction required for mutation discovery in WES of cfDNA. We found WES of cfDNA to uncover 91% of the clonal mutations, 59% of the subclonal mutations, and 75% of the SCNAs detected in WES of matched tumor biopsies. In several cases, we observed mutations exclusive to cfDNA that were confirmed in later blood draws, suggesting that cfDNA-exclusive mutations may be derived from unsampled metastases. In some cases, cfDNA revealed clinically actionable mutations that were not detected in matched tumor biopsies.
Conclusions: WES of cfDNA uncovers the majority of somatic mutations, indels, and SCNAs found in matched tumor biopsies of metastatic cancer. The high degree of concordance suggests that comprehensive sequencing of cfDNA can be leveraged for genomic discovery in settings where conventional biopsies are difficult to access. Furthermore, the detection of mutations in cfDNA that are not detected in concurrent biopsies suggests that cfDNA may be complementary to tumor biopsies for both translational studies and precision cancer medicine.
Citation Format: Viktor A. Adalsteinsson, Gavin Ha, Sam Freeman, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Gregory Gydush, Sarah Reed, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignat Leshchiner, Ofir Cohen, Coyin Oh, Jaegil Kim, Chip Stewart, Mara Rosenberg, Huiming Ding, Maxwell R. Lloyd, Sairah Mahmud, Karla E. Helvie, Margaret S. Merrill, Rebecca A. Santiago, Edward P. O’Connor, Seong H. Jeong, Joseph F. Kramkowski, Jens G. Lohr, Laura Polacek, Nelly Oliver, Lori Marini, Joshua Francis, Lauren C. Harshman, Eliezer M. Van Allen, Eric P. Winer, Nancy U. Lin, Mari Nakabayashi, Mary-Ellen Taplin, Levi A. Garraway, Todd R. Golub, Jesse S. Boehm, Nikhil Wagle, Gad Getz, Matthew Meyerson, Christopher J. Love. High concordance of whole-exome sequencing of cell-free DNA and matched biopsies enables genomic discovery in metastatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-136.
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Affiliation(s)
| | - Gavin Ha
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Sarah Reed
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Ofir Cohen
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Coyin Oh
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jaegil Kim
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | - Chip Stewart
- 1Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Getz
- 1Broad Institute of MIT and Harvard, Cambridge, MA
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Parsons HA, Beaver JA, Cimino-Mathews A, Zorzi J, Slater S, Clark T, Lipson D, Ali SM, Kennedy M, Otto GA, Young LE, Jeter S, VanDenBerg DA, Rosner GL, Park BH, Stearns V. Abstract PD6-08: IMAGE: Individualized molecular analyses guide efforts in breast cancer with comprehensive genomic profiling of tissue and plasma tumor DNA. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-pd6-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Standard treatment options for patients with metastatic triple negative breast cancer (TNBC) are limited to chemotherapy. Molecular profiling of tumors may allow for novel treatment recommendations.
Methods: We initiated a prospective study designated IMAGE. Women with newly progressing metastatic TNBC who received at least one line of prior chemotherapy were eligible. New metastatic biopsies were obtained for molecular profiling at study entry. Archived metastatic biopsy specimens were allowed if patients had not commenced new systemic therapy. The specimens were reviewed by the study pathologist and stained for ER, PR, HER2, and androgen receptor (AR) by immunohistochemistry. Specimens underwent hybrid-capture based comprehensive genomic profiling (CGP) (Foundation Medicine Inc., Cambridge, MA). Clinical data and genomic profiling reports were reviewed by the GAITWAY (Genomic Alterations in Tumors with Actionable Yields) Molecular Profile Tumor Board. Recommendations were communicated to the treating oncologist and patients were followed for treatment decision and clinical outcomes. Peripheral blood was also analyzed by an investigational assay for circulating plasma tumor DNA (ptDNA) (Foundation Medicine Inc.) at study entry, and when obtainable, from serial blood draws at time of progression. The primary objective was to assess feasibility of completing the process from consent to GAITWAY recommendations within 28 days for at least 80% of patients.
Results: From September 2013 to April 2015, we enrolled 26 eligible women. Median age was 55 (range 25-67); patients identified as white 12 (46%), black 11 (42%), or other 3 (12%); median number of prior lines of treatment was 3; and 65.4% of patients had visceral disease. Twenty (77%) eligible patients received CGP of a metastatic site biopsy. Six patients did not undergo CGP due to either absence of a metastatic site amenable for biopsy or inadequate tissue for CGP. The study met the predefined statistical endpoint for futility and was closed after 20 patients had undergone CGP. Twelve (60%) evaluable patients received treatment recommendations within 28 days of study consent. Failure to meet this time frame was due to difficulties in accessing archival tumor tissue (N=5) and need for additional tissue for molecular analysis (N=3). Preliminary results demonstrate high concordance between mutations in metastatic biopsies and ptDNA in 15/17 patients.
Enrolled in IMAGE26Successful NGS20Potentially actionable mutation identified15GAITWAY recommended targeted therapy as possible next treatment13Received targeted therapy4
Conclusions: CGP of patients with metastatic TNBC can provide additional information that may help direct treatment. However, difficulties in obtaining adequate tumor tissue may hinder this approach. Use of a well-validated ptDNA profiling assay could be an alternative to overcome these limitations.
Citation Format: Parsons HA, Beaver JA, Cimino-Mathews A, Zorzi J, Slater S, Clark T, Lipson D, Ali SM, Kennedy M, Otto GA, Young LE, Jeter S, VanDenBerg DA, Rosner GL, Park BH, Stearns V. IMAGE: Individualized molecular analyses guide efforts in breast cancer with comprehensive genomic profiling of tissue and plasma tumor DNA. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD6-08.
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Affiliation(s)
- HA Parsons
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - JA Beaver
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - A Cimino-Mathews
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - J Zorzi
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - S Slater
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - T Clark
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - D Lipson
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - SM Ali
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - M Kennedy
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - GA Otto
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - LE Young
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - S Jeter
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - DA VanDenBerg
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - GL Rosner
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - BH Park
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
| | - V Stearns
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Foundation Medicine, Inc., Cambridge, MA
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