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Mata DA, Lee JK, Shanmugam V, Marcus CB, Schrock AB, Williams EA, Ritterhouse LL, Hickman RA, Janovitz T, Patel NR, Kroger BR, Ross JS, Mirza KM, Oxnard GR, Vergilio JA, Elvin JA, Benhamida JK, Decker B, Xu ML. Liquid biopsy-based circulating tumour (ct)DNA analysis of a spectrum of myeloid and lymphoid malignancies yields clinically actionable results. Histopathology 2024; 84:1224-1237. [PMID: 38422618 DOI: 10.1111/his.15168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
AIMS Liquid biopsy (LBx)-based next-generation sequencing (NGS) of circulating tumour DNA (ctDNA) can facilitate molecular profiling of haematopoietic neoplasms (HNs), particularly when tissue-based NGS is infeasible. METHODS AND RESULTS We studied HN LBx samples tested with FoundationOne Liquid CDx, FoundationOne Liquid, or FoundationACT between July 2016 and March 2022. We identified 271 samples: 89 non-Hodgkin lymphoma (NHL), 43 plasma-cell neoplasm (PCN), 41 histiocytoses, 27 myelodysplastic syndrome (MDS), 25 diffuse large B-cell lymphoma (DLBCL), 22 myeloproliferative neoplasm (MPN), 14 Hodgkin lymphoma (HL), and 10 acute myeloid leukaemia (AML). Among 73.4% with detectable pathogenic alterations, median maximum somatic allele frequency (MSAF) was 16.6%, with AML (36.2%), MDS (19.7%), and MPN (44.5%) having higher MSAFs than DLBCL (3.9%), NHL (8.4%), HL (1.5%), PCN (2.8%), and histiocytoses (1.8%) (P = 0.001). LBx detected characteristic alterations across HNs, including in TP53, KRAS, MYD88, and BTK in NHLs; TP53, KRAS, NRAS, and BRAF in PCNs; IGH in DLBCL; TP53, ATM, and PDCD1LG2 in HL; BRAF and MAP2K1 in histiocytoses; TP53, SF3B1, DNMT3A, TET2, and ASXL1 in MDS; JAK2 in MPNs; and FLT3, IDH2, and NPM1 in AML. Among 24 samples, the positive percent agreement by LBx was 75.7% for variants present in paired buffy coat, marrow, or tissues. Also, 75.0% of pairs exhibited alterations only present on LBx. These were predominantly subclonal (clonal fraction of 3.8%), reflecting the analytical sensitivity of LBx. CONCLUSION These data demonstrate that LBx can detect relevant genomic alterations across HNs, including at low clonal fractions, suggesting a potential clinical utility for identifying residual or emerging therapy-resistant clones that may be undetectable in site-specific tissue biopsies.
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Affiliation(s)
| | | | - Vignesh Shanmugam
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Erik A Williams
- Foundation Medicine, Inc., Cambridge, MA, USA
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | | | | | - Benjamin R Kroger
- Division of Hematology/Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Departments of Pathology, Urology, and Medicine (Oncology), State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Kamran M Mirza
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | | | | | | | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Mina L Xu
- Department of Pathology, Yale New-Haven Hospital, Yale School of Medicine, New Haven, CT, USA
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2
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Passaro A, Al Bakir M, Hamilton EG, Diehn M, André F, Roy-Chowdhuri S, Mountzios G, Wistuba II, Swanton C, Peters S. Cancer biomarkers: Emerging trends and clinical implications for personalized treatment. Cell 2024; 187:1617-1635. [PMID: 38552610 PMCID: PMC7616034 DOI: 10.1016/j.cell.2024.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
The integration of cancer biomarkers into oncology has revolutionized cancer treatment, yielding remarkable advancements in cancer therapeutics and the prognosis of cancer patients. The development of personalized medicine represents a turning point and a new paradigm in cancer management, as biomarkers enable oncologists to tailor treatments based on the unique molecular profile of each patient's tumor. In this review, we discuss the scientific milestones of cancer biomarkers and explore future possibilities to improve the management of patients with solid tumors. This progress is primarily attributed to the biological characterization of cancers, advancements in testing methodologies, elucidation of the immune microenvironment, and the ability to profile circulating tumor fractions. Integrating these insights promises to continually advance the precision oncology field, fostering better patient outcomes.
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Affiliation(s)
- Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emily G Hamilton
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabrice André
- Gustave-Roussy Cancer Center, Paris Saclay University, Villejuif, France
| | - Sinchita Roy-Chowdhuri
- Department of Anatomic Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, Athens, Greece
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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3
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Jin WH, Zhang L, Graf R, Raskina K, Tukachinsky H, Huang RSP, McGregor K, Alshalalfa M, Hougen HY, Khan A, Punnen S, Schrock AB, Venstrom J, Mahal BA. The Molecular, Immunologic, and Clinicodemographic Landscape of MYC-Amplified Advanced Prostate Cancer. Clin Genitourin Cancer 2024; 22:e163-e169.e1. [PMID: 37978032 DOI: 10.1016/j.clgc.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND MYC is a commonly amplified, potentially targetable gene in prostate cancer (PCa). We sought to define the molecular, immunologic, and clinicodemographic landscape of MYC amplification (MYCamp) in advanced PCa to establish a rationale for personalized treatment combinations. METHODS Hybrid capture-based comprehensive genomic profiling (CGP) was performed on PCa tumor samples. MYCamp = copy number ≥6 (CN). Patients treated between January 2011 and December 2020 were selected from a nationwide deidentified (280 clinics) EHR-derived clinicogenomic database (CGDB). RESULTS Of 12,528 hormone-sensitive and castrate-resistant (CRPC) samples, MYCamp was detected in 10.6% (median CN = 8). MYCamp was more frequent in men with African versus European ancestry (12.9% vs. 10.2% P = .002), in metastatic vs. primary tissue (15.7% vs. 6.2% P < .001), and enriched in metastatic liver lesions (20.2%), but inversely associated with high microsatellite-instability (0.8% vs. 2.4%, P < .001). MYC CN≥15 was associated with PD-L1 expression (26.1% vs. 9.8%, P = .025). Amplification of AR, RAD21, LYN, CCND1, ZNF703, FGF3/4/19, and FGFR1 was enriched in MYCamp vs. MYCwt (all P < .001). In liquid samples with tumor fraction [TF]>0, MYCamp was detected in 2.0% (28/1,402), and 4.5% (20/445) with TF>20%. In the CGDB, (67 MYCamp and 658 MYCwt), patients received similar treatments; most received hormone therapies (35.8% MYCamp vs. 31.5% MYCwt) or chemotherapy (37.3% MYCamp vs. 27.7% MYCwt) as first therapy after CGP report. CONCLUSION MYCamp defines a biologically distinct subset of PCa patients and is characterized with multiple proxies of advanced disease. These data suggest that MYCamp may be prognostic; independent cohorts are needed to validate these findings.
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Affiliation(s)
- Will H Jin
- Department of Radiation Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL.
| | | | | | | | | | | | | | - Mohamed Alshalalfa
- Department of Radiation Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Helen Y Hougen
- Department of Urology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Anwar Khan
- Department of Radiation Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Sanoj Punnen
- Department of Urology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | | | - Brandon A Mahal
- Department of Radiation Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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4
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Martínez-Herrera JF, Sánchez Domínguez G, Juárez-Vignon Whaley JJ, Carrasco-Cara Chards S, López Vrátný C, Guzmán Casta J, Riera Sala RF, Alatorre-Alexander JA, Seidman Sorsby A, Cruz Zermeño M, Conde Flores E, Flores-Mariñelarena RR, Sánchez-Ríos CP, Martínez-Barrera LM, Gerson-Cwilich R, Santillán-Doherty P, Jiménez López JC, López Hernández W, Rodríguez-Cid JR. Mutation profile in liquid biopsy tested by next generation sequencing in Mexican patients with non-small cell lung carcinoma and its impact on survival. J Thorac Dis 2024; 16:161-174. [PMID: 38410597 PMCID: PMC10894362 DOI: 10.21037/jtd-23-1029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/24/2023] [Indexed: 02/28/2024]
Abstract
Background Lung cancer represents a significant global health concern, often diagnosed in its advanced stages. The advent of massive DNA sequencing has revolutionized the landscape of cancer treatment by enabling the identification of target mutations and the development of tailored therapeutic approaches. Unfortunately, access to DNA sequencing technology remains limited in many developing countries. In this context, we emphasize the critical importance of integrating this advanced technology into healthcare systems in developing nations to improve treatment outcomes. Methods We conducted an analysis of electronic clinical records of patients with confirmed advanced non-small cell lung cancer (NSCLC) and a verified negative status for the epidermal growth factor receptor (EGFR) mutation. These patients underwent next-generation sequencing (NGS) for molecular analysis. We performed descriptive statistical analyses for each variable and conducted both univariate and multivariate statistical analyses to assess their impact on progression-free survival (PFS) and overall survival (OS). Additionally, we classified genetic mutations as actionable or non-actionable based on the European Society for Medical Oncology Scale of Clinical Actionability of Molecular Targets (ESCAT) guidelines. Results Our study included a total of 127 patients, revealing the presence of twenty-one distinct mutations. The most prevalent mutations were EGFR (18.9%) and Kirsten rat sarcoma viral oncogene homolog (KRAS) (15.7%). Notably, anaplastic lymphoma kinase (ALK) [hazard ratio (HR): 0.258, P<0.001], tumor mutation burden (TMB) (HR: 2.073, P=0.042) and brain magnetic resonance imaging (MRI) (HR: 0.470, P=0.032) demonstrated statistical significance in both the univariate and multivariate analyses with respect to PFS. In terms of OS, ALK (HR: 0.285, P<0.001) and EGFR (HR: 0.482, P=0.024) exhibited statistical significance in both analyses. Applying the ESCAT classification system, we identified actionable genomic variations (ESCAT level-1), including EGFR, ALK, breast cancer (BRAF) gene, c-ros oncogene 1 (ROS1), and rearranged during transfection (RET) gene, in 32.3% of the patients. Conclusions Our findings from massive DNA sequencing underscore that 32.3% of patients who test negative for the EGFR mutation possess other targetable mutations, enabling them to receive personalized, targeted therapies at an earlier stage of their disease. Implementing massive DNA sequencing in developing countries is crucial to enhance survival rates among NSCLC patients and guide more effective treatment strategies.
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Affiliation(s)
- José Fabián Martínez-Herrera
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
- Cancer Center, Medical Center American British Cowdray, Mexico City, Mexico
- Cancer Research Networking, Universidad Cientifica del Sur, Lima, Perú
| | - Gisela Sánchez Domínguez
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Juan J. Juárez-Vignon Whaley
- Centro de Investigación en Ciencias de la Salud (CICSA), FCS, Universidad Anáhuac México Campus Norte, Mexico City, Mexico
| | | | | | - Jordi Guzmán Casta
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Rodrigo F. Riera Sala
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Jorge A. Alatorre-Alexander
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | | | | | - Carla P. Sánchez-Ríos
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Luis M. Martínez-Barrera
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Patricio Santillán-Doherty
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
- Medical Direction, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | | | - William López Hernández
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Jerónimo R. Rodríguez-Cid
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
- Oncology Center, Medica Sur Hospital, Mexico City, Mexico
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5
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Dziadziuszko R, Peled N, Mok T, Peters S, Aix SP, Alatorre-Alexander J, Vicuna BD, Maclennan M, Bhagawati-Prasad V, Shagan SM, Schleifman E, Ruf T, Mathisen MS, Gadgeel SM. High-dose alectinib for RET fusion-positive non-small cell lung cancer in the Blood First Assay Screening Trial. Contemp Oncol (Pozn) 2024; 27:217-223. [PMID: 38405208 PMCID: PMC10883190 DOI: 10.5114/wo.2023.135246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/06/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction This paper presents results from Cohort B (rearranged during transfection [RET], fusion-positive) of the Blood First Assay Screening Trial in patients with advanced non-small cell lung cancer (NSCLC) screened for genetic alterations using blood-based next-generation sequencing. Material and methods Adults with advanced RET fusion-positive NSCLC received alectinib 900 mg twice daily (BID) in Phase I. Enrolment closed prematurely with Phase II uninitiated. Results Among eight treated patients, confirmed best overall responses in evaluable patients were stable disease (4/5) and progressive disease (1/5). One dose-limiting toxicity (death, unknown cause) was considered by the investigator to be related to treatment and underlying disease. Serious adverse events (SAEs) occurred in five patients, and SAEs that may be related to treatment occurred in two patients. Conclusions Alectinib showed limited activity in advanced RET fusion-positive NSCLC, and further investigation was not conducted due to the development of selective RET inhibitors pralsetinib and selpercatinib. No new safety signals were observed, and the safety profile of alectinib was in line with previous reports at the 600 mg BID dose.
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Affiliation(s)
- Rafal Dziadziuszko
- Department of Oncology and Radiotherapy and Early Clinical Trials Centre, Medical University of Gdańsk, Gdańsk, Poland
| | - Nir Peled
- Soroka Medical Centre and Ben-Gurion University, Beer-Sheeva, Israel
- Helmsley Cancer Centre, Shaare Zedek Medical Centre, Hebrew University, Jerusalem, Israel (currently)
| | - Tony Mok
- State Key Laboratory of Translational Oncology, Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong
| | - Solange Peters
- Lausanne University Hospital, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | | | | | | | | | | | | | | | | | | | - Shirish M. Gadgeel
- Department of Internal Medicine, Henry Ford Cancer Institute/Henry Ford Health System, Detroit, MI, USA
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6
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Harter J, Buth E, Johaenning J, Battke F, Kopp M, Zelba H, Schulze M, Koedding J, Biskup S. Analytical Performance Evaluation of a 523-Gene Circulating Tumor DNA Assay for Next-Generation Sequencing-Based Comprehensive Tumor Profiling in Liquid Biopsy Samples. J Mol Diagn 2024; 26:61-72. [PMID: 37865292 DOI: 10.1016/j.jmoldx.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
Next-generation sequencing (NGS)-based comprehensive tumor profiling from liquid biopsy samples can significantly improve diagnosis and monitoring of tumors when high-quality tissue material is difficult to obtain. In addition, it offers the potential to capture the entire complexity of the tumor, which is particularly important for highly heterogeneous or metastatic tumors. Here, we report the findings of an analytical performance evaluation of the TruSight Oncology 500 circulating tumor DNA (ctDNA) assay, a 523-gene NGS panel developed for ctDNA-based comprehensive genomic profiling of tumors, using reference and patient samples. Using 30 ng cell-free DNA, the assay showed high sensitivity and low variant detection variability for single-nucleotide variants, insertions and deletions, and fusions down to a variant allele frequency (VAF) of 0.5% in the reference samples and VAFs that were highly concordant with previous digital droplet PCR results in the patient samples. At reduced input amounts (20, 15, and 5 ng) and below VAFs of 0.5%, sensitivity was considerably lower and variant detection variability increased. Covering 523 tumor-associated genes, the assay demonstrated a convincing performance comparable to NGS-based ctDNA assays with smaller gene panels, highlighting its value to screen large numbers of different genes.
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Affiliation(s)
| | | | | | | | | | - Henning Zelba
- Center for Human Genetics Tuebingen, Tuebingen, Germany
| | | | | | - Saskia Biskup
- CeGaT GmbH, Tuebingen, Germany; Center for Human Genetics Tuebingen, Tuebingen, Germany
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7
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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8
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Fernandez SV, Tan YF, Rao S, Fittipaldi P, Sheriff F, Borghaei H, Dotan E, Winn JS, Edelman MJ, Treat J, Judd J, Alpaugh RK, Wang YL, Yu JQ, Wasik M, Baldwin DA. Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing. Int J Mol Sci 2023; 24:15779. [PMID: 37958763 PMCID: PMC10648112 DOI: 10.3390/ijms242115779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%.
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Affiliation(s)
- Sandra V. Fernandez
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Yin Fei Tan
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Shilpa Rao
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Patricia Fittipaldi
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (P.F.); (R.K.A.)
| | - Fathima Sheriff
- Office of Clinical Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Hossein Borghaei
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Efrat Dotan
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Jennifer S. Winn
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Martin J. Edelman
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Joseph Treat
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Julia Judd
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - R. Katherine Alpaugh
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (P.F.); (R.K.A.)
| | - Y. Lynn Wang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Jian Q. Yu
- Department of Radiology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
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9
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Mostufa S, Rezaei B, Yari P, Xu K, Gómez-Pastora J, Sun J, Shi Z, Wu K. Giant Magnetoresistance Based Biosensors for Cancer Screening and Detection. ACS APPLIED BIO MATERIALS 2023; 6:4042-4059. [PMID: 37725557 DOI: 10.1021/acsabm.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Early-stage screening of cancer is critical in preventing its development and therefore can improve the prognosis of the disease. One accurate and effective method of cancer screening is using high sensitivity biosensors to detect optically, chemically, or magnetically labeled cancer biomarkers. Among a wide range of biosensors, giant magnetoresistance (GMR) based devices offer high sensitivity, low background noise, robustness, and low cost. With state-of-the-art micro- and nanofabrication techniques, tens to hundreds of independently working GMR biosensors can be integrated into fingernail-sized chips for the simultaneous detection of multiple cancer biomarkers (i.e., multiplexed assay). Meanwhile, the miniaturization of GMR chips makes them able to be integrated into point-of-care (POC) devices. In this review, we first introduce three types of GMR biosensors in terms of their structures and physics, followed by a discussion on fabrication techniques for those sensors. In order to achieve target cancer biomarker detection, the GMR biosensor surface needs to be subjected to biological decoration. Thus, commonly used methods for surface functionalization are also reviewed. The robustness of GMR-based biosensors in cancer detection has been demonstrated by multiple research groups worldwide and we review some representative examples. At the end of this review, the challenges and future development prospects of GMR biosensor platforms are commented on. With all their benefits and opportunities, it can be foreseen that GMR biosensor platforms will transition from a promising candidate to a robust product for cancer screening in the near future.
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Affiliation(s)
- Shahriar Mostufa
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Bahareh Rezaei
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Parsa Yari
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Kanglin Xu
- Department of Computer Science, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jenifer Gómez-Pastora
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jiajia Sun
- State Key Laboratory of Electrical Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China
| | - Zongqian Shi
- State Key Laboratory of Electrical Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China
| | - Kai Wu
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
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10
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Chen JW, Jacot W, Cortés J, Krop IE, Dent S, Harbeck N, De Laurentiis M, Diéras V, Im Y, Stout TJ, Schimmoller F, Savage HM, Hutchinson KE, Wilson TR. ER+, HER2- advanced breast cancer treated with taselisib and fulvestrant: genomic landscape and associated clinical outcomes. Mol Oncol 2023; 17:2000-2016. [PMID: 36892268 PMCID: PMC10552898 DOI: 10.1002/1878-0261.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/10/2023] [Accepted: 03/07/2023] [Indexed: 03/10/2023] Open
Abstract
Taselisib is a potent β-sparing phosphatidylinositol 3-kinase (PI3K) inhibitor that, with endocrine therapy, improves outcomes in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA)-mutated (PIK3CAmut) advanced breast cancer. To understand alterations associated with response to PI3K inhibition, we analysed circulating tumour DNA (ctDNA) from participants enrolled in the SANDPIPER trial. Participants were designated as either PIK3CAmut or PIK3CA no mutation was detected (NMD) per baseline ctDNA. The top mutated genes and tumour fraction estimates identified were analysed for their association with outcomes. In participants with PIK3CAmut ctDNA treated with taselisib + fulvestrant, tumour protein p53 (TP53; encoding p53) and fibroblast growth factor receptor 1 (FGFR1) alterations were associated with shorter progression-free survival (PFS) compared to participants with NMD in these genes. Conversely, participants with PIK3CAmut ctDNA harbouring a neurofibromin 1 (NF1) alteration or high baseline tumour fraction estimate experienced improved PFS upon treatment with taselisib + fulvestrant compared to placebo + fulvestrant. Broadly, alterations in oestrogen receptor (ER), PI3K and p53 pathway genes were associated with resistance to taselisib + fulvestrant in participants with PIK3CAmut ctDNA. Altogether, we demonstrated the impact of genomic (co-)alterations on outcomes with one of the largest clinico-genomic datasets of ER+, HER2-, PIK3CAmut breast cancer patients treated with a PI3K inhibitor.
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Affiliation(s)
- Jessica W. Chen
- Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCAUSA
| | - William Jacot
- Institut du Cancer de Montpellier (ICM) Val d'AurelleMontpellier University, INSERM U1194France
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea OncologyQuironsalud GroupMadridSpain
- International Breast Cancer Center (IBCC), Pangaea OncologyQuironsalud GroupBarcelonaSpain
- Faculty of Biomedical and Health Sciences, Department of MedicineUniversidad Europea de MadridMadridSpain
| | | | - Susan Dent
- Duke Cancer InstituteDuke UniversityDurhamNCUSA
| | - Nadia Harbeck
- Breast Center, Department Gynecology and Obstetrics and Comprehensive Cancer Center (CCC) MunichLudwig‐Maximilians‐University (LMU) HospitalMunichGermany
| | | | | | - Young‐Hyuck Im
- Division of Hematology‐Oncology, Department of Medicine, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Thomas J. Stout
- Product Development OncologyGenentech, Inc.South San FranciscoCAUSA
| | | | - Heidi M. Savage
- Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCAUSA
| | | | - Timothy R. Wilson
- Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCAUSA
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11
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Abida W, Campbell D, Patnaik A, Bryce AH, Shapiro J, Bambury RM, Zhang J, Burke JM, Castellano D, Font A, Ganju V, Hardy-Bessard AC, McDermott R, Sautois B, Spaeth D, Voog E, Piulats JM, Pintus E, Ryan CJ, Merseburger AS, Daugaard G, Heidenreich A, Fizazi K, Loehr A, Despain D, Simmons AD, Dowson M, Go J, Watkins SP, Chowdhury S. Rucaparib for the Treatment of Metastatic Castration-resistant Prostate Cancer Associated with a DNA Damage Repair Gene Alteration: Final Results from the Phase 2 TRITON2 Study. Eur Urol 2023; 84:321-330. [PMID: 37277275 PMCID: PMC10527050 DOI: 10.1016/j.eururo.2023.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/20/2023] [Accepted: 05/17/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND Initial TRITON2 (NCT02952534) results demonstrated the efficacy of rucaparib 600 mg BID in patients with metastatic castration-resistant prostate cancer (mCRPC) associated with a BRCA1 or BRCA2 (BRCA) or other DNA damage repair (DDR) gene alteration. OBJECTIVE To present the final data from TRITON2. DESIGN, SETTING, AND PARTICIPANTS TRITON2 enrolled patients with mCRPC who had progressed on one or two lines of next-generation androgen receptor-directed therapy and one taxane-based chemotherapy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The primary endpoint was objective response rate (ORR; as per the modified Response Evaluation Criteria in Solid Tumor Version 1.1/Prostate Cancer Clinical Trials Working Group 3 criteria in patients with measurable disease by independent radiology review [IRR]); prostate-specific antigen (PSA) response rate (≥50% decrease from baseline [PSA50]) was a key secondary endpoint. RESULTS AND LIMITATIONS As of July 27, 2021 (study closure), TRITON2 had enrolled 277 patients, grouped by mutated gene: BRCA (n = 172), ATM (n = 59), CDK12 (n = 15), CHEK2 (n = 7), PALB2 (n = 11), or other DDR gene (Other; n = 13). ORR by IRR was 46% (37/81) in the BRCA subgroup (95% confidence interval [CI], 35-57%), 100% (4/4) in the PALB2 subgroup (95% CI, 40-100%), and 25% (3/12) in the Other subgroup (95% CI, 5.5-57%). No patients within the ATM, CDK12, or CHEK2 subgroups had an objective response by IRR. PSA50 response rates (95% CI) in the BRCA, PALB2, ATM, CDK12, CHEK2, and Other subgroups were 53% (46-61%), 55% (23-83%), 3.4% (0.4-12), 6.7% (0.2-32%), 14% (0.4-58%), and 23% (5.0-54%), respectively. CONCLUSIONS The final TRITON2 results confirm the clinical benefit and manageable safety profile of rucaparib in patients with mCRPC, including those with an alteration in BRCA or select non-BRCA DDR gene. PATIENT SUMMARY Almost half of TRITON2 patients with BRCA-mutated metastatic castration-resistant prostate cancer had a complete or partial tumor size reduction with rucaparib; clinical benefits were also observed with other DNA damage repair gene alterations.
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Affiliation(s)
- Wassim Abida
- Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - David Campbell
- Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia
| | - Akash Patnaik
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | | | | | | | | | - John M Burke
- Rocky Mountain Cancer Centers and US Oncology Research, Denver, CO, USA
| | | | - Albert Font
- Institut Català d'Oncologia, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Vinod Ganju
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | | | - Ray McDermott
- Adelaide and Meath Hospital (Incorporating the National Children's Hospital), Dublin, Ireland
| | - Brieuc Sautois
- Medical Oncology, University Hospital of Liège, CHU Sart Tilman, Liège, Belgium
| | | | - Eric Voog
- Clinique Victor Hugo Centre Jean Bernard, Le Mans, France
| | | | - Elias Pintus
- Guy's & St Thomas' NHS Foundation Trust Hospital, London, UK
| | | | - Axel S Merseburger
- University Lübeck, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Gedske Daugaard
- Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Axel Heidenreich
- Universitätsklinikum Köln, Cologne, Germany; Department of Urology, Medical University Vienna, Vienna, Austria
| | - Karim Fizazi
- Institut Gustave Roussy, University of Paris Saclay, Villejuif Cedex, France
| | | | | | | | | | - Jowell Go
- Clovis Oncology, Inc., Boulder, CO, USA
| | | | - Simon Chowdhury
- Guy's & St Thomas' NHS Foundation Trust Hospital, London, UK
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12
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Santini D, Botticelli A, Galvano A, Iuliani M, Incorvaia L, Gristina V, Taffon C, Foderaro S, Paccagnella E, Simonetti S, Fazio F, Scagnoli S, Pomati G, Pantano F, Perrone G, De Falco E, Russo A, Spinelli GP. Network approach in liquidomics landscape. J Exp Clin Cancer Res 2023; 42:193. [PMID: 37542343 PMCID: PMC10401883 DOI: 10.1186/s13046-023-02743-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/06/2023] Open
Abstract
Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence.Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response.By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients.In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
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Affiliation(s)
- Daniele Santini
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Andrea Botticelli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Antonio Galvano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Lorena Incorvaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Taffon
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Simone Foderaro
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Elisa Paccagnella
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
| | - Sonia Simonetti
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Federico Fazio
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy.
| | - Simone Scagnoli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | | | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Giuseppe Perrone
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Elena De Falco
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
- Mediterranea Cardiocentro, 80122, Naples, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Gian Paolo Spinelli
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy
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13
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Xin L, Yue Y, Zihan R, Youbin C, Tianyu L, Rui W. Clinical application of liquid biopsy based on circulating tumor DNA in non-small cell lung cancer. Front Physiol 2023; 14:1200124. [PMID: 37351260 PMCID: PMC10282751 DOI: 10.3389/fphys.2023.1200124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Lung cancer is a widely occurring and deadly malignancy, with high prevalence rates in China and across the globe. Specifically, non-small cell lung cancer (NSCLC) represents about 85% of all lung cancer cases. The 5-year disease-free survival rate after surgery for stage IB-IIIB NSCLC patients (disease-free survival, DFS) has notably declined from 73% to 13%. Early detection of abnormal cancer molecules and subsequent personalized treatment plans are the most effective ways to address this problem. Liquid biopsy, surprisingly, enables safe, accurate, non-invasive, and dynamic tracking of disease progression. Among the various modalities, circulating tumor DNA (ctDNA) is the most commonly used liquid biopsy modality. ctDNA serves as a credible "liquid biopsy" diagnostic tool that, to a certain extent, overcomes tumor heterogeneity and harbors genetic mutations in malignancies, thereby providing early information on tumor genetic alterations. Despite considerable academic interest in the clinical significance of ctDNA, consensus on its utility remains lacking. In this review, we assess the role of ctDNA testing in the diagnosis and management of NSCLC as a reference for clinical intervention in this disease. Lastly, we examine future directions to optimize ctDNA for personalized therapy.
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Affiliation(s)
| | | | | | | | - Lu Tianyu
- *Correspondence: Wang Rui, ; Lu Tianyu,
| | - Wang Rui
- *Correspondence: Wang Rui, ; Lu Tianyu,
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14
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Vlataki K, Antonouli S, Kalyvioti C, Lampri E, Kamina S, Mauri D, Harissis HV, Magklara A. Circulating Tumor DNA in the Management of Early-Stage Breast Cancer. Cells 2023; 12:1573. [PMID: 37371043 DOI: 10.3390/cells12121573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Liquid biopsies refer to the isolation and analysis of tumor-derived biological material from body fluids, most commonly blood, in order to provide clinically valuable information for the management of cancer patients. Their non-invasive nature allows to overcome the limitations of tissue biopsy and complement the latter in guiding therapeutic decision-making. In the past years, several studies have demonstrated that circulating tumor DNA (ctDNA) detection can be used in the clinical setting to improve patient prognosis and monitor therapy response, especially in metastatic cancers. With the advent of significant technological advances in assay development, ctDNA can now be accurately and reliably identified in early-stage cancers despite its low levels in the bloodstream. In this review, we discuss the most important studies that highlight the potential clinical utility of ctDNA in early-stage breast cancer focusing on early diagnosis, detection of minimal residual disease and prediction of metastatic relapse. We also offer a concise description of the most sensitive techniques that are deemed appropriate for ctDNA detection in early-stage cancer and we examine their advantages and disadvantages, as they have been employed in various studies. Finally, we discuss future perspectives on how ctDNA could be better integrated into the everyday oncology practice.
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Affiliation(s)
- Katerina Vlataki
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Sevastiani Antonouli
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Christina Kalyvioti
- Breast Unit, Department of Surgery, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Evangeli Lampri
- Department of Pathology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Sevasti Kamina
- Department of Pathology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Davide Mauri
- Department of Medical Oncology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Haralampos V Harissis
- Breast Unit, Department of Surgery, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Angeliki Magklara
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece
- Institute of Biosciences, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
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15
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Falchook GS, Sachdev J, Imedio ER, Kumar S, Mugundu GM, Jenkins S, Chmielecki J, Jones S, Spigel DR, Johnson M. A phase Ib study of adavosertib, a selective Wee1 inhibitor, in patients with locally advanced or metastatic solid tumors. Invest New Drugs 2023:10.1007/s10637-023-01371-6. [PMID: 37171722 DOI: 10.1007/s10637-023-01371-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Adavosertib selectively inhibits Wee1, which regulates intra-S and G2/M cell-cycle checkpoints. This study investigated dosing schedules for adavosertib monotherapy, determining the maximum tolerated dose (MTD) and recommended Phase II dose (RP2D) in patients with advanced solid tumors.Patients received oral adavosertib qd or bid on a 5/9 schedule (5 days on treatment, 9 days off) in 14-day cycles, or qd on one of two 5/2 schedules (weekly, or for 2 of 3 weeks) in 21-day cycles. Safety, efficacy, and pharmacokinetic analyses were performed.Sixty-two patients (female, 64.5%; median age, 61.5 years; most common primary tumors: lung [24.2%], ovary [21.0%]) received treatment (qd schedules, n = 50; bid schedules, n = 12) for 1.8 months (median). Median time to maximum adavosertib concentration was 2.2-4.1 h; mean half-life was 5-12 h. Adverse events (AEs) caused dose reductions, interruptions and discontinuations in 17 (27.4%), 25 (40.3%) and 4 (6.5%) patients, respectively. Most common grade ≥ 3 AEs were anemia, neutropenia (each n = 9, 14.5%) and diarrhea (n = 8, 12.9%). Seven (11.3%) patients experienced 10 treatment-related serious AEs (pneumonia n = 2 [3.2%], dehydration n = 2 [3.2%], anemia n = 1 [1.6%], febrile neutropenia n = 1 [1.6%], and thrombocytopenia n = 1 [1.6%]). Overall objective response rate was 3.4% (2/58); disease control rate was 48.4% (30/62); median progression-free survival was 2.7 months.MTDs were 125 mg (bid 5/9) and 300 mg (qd 5/9 and 5/2 for 2 of 3 weeks); RP2D was 300 mg (qd 5/2 for 2 of 3 weeks). The safety profile was manageable, acceptable, and generally concordant with the known safety profile.
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Affiliation(s)
| | | | | | | | - Ganesh M Mugundu
- Clinical Pharmacology and Quantitative Pharmacology, CPSS, AstraZeneca, Boston, MA, USA
| | | | - Juliann Chmielecki
- Translational Medicine, Early Research and Development, AstraZeneca, Boston, MA, USA
| | | | - David R Spigel
- Sarah Cannon Research Institute, Nashville, TN, USA
- Tennessee Oncology, Nashville, TN, USA
| | - Melissa Johnson
- Sarah Cannon Research Institute, Nashville, TN, USA
- Tennessee Oncology, Nashville, TN, USA
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16
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Berko ER, Witek GM, Matkar S, Petrova ZO, Wu MA, Smith CM, Daniels A, Kalna J, Kennedy A, Gostuski I, Casey C, Krytska K, Gerelus M, Pavlick D, Ghazarian S, Park JR, Marachelian A, Maris JM, Goldsmith KC, Radhakrishnan R, Lemmon MA, Mossé YP. Circulating tumor DNA reveals mechanisms of lorlatinib resistance in patients with relapsed/refractory ALK-driven neuroblastoma. Nat Commun 2023; 14:2601. [PMID: 37147298 PMCID: PMC10163008 DOI: 10.1038/s41467-023-38195-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Activating point mutations in Anaplastic Lymphoma Kinase (ALK) have positioned ALK as the only mutated oncogene tractable for targeted therapy in neuroblastoma. Cells with these mutations respond to lorlatinib in pre-clinical studies, providing the rationale for a first-in-child Phase 1 trial (NCT03107988) in patients with ALK-driven neuroblastoma. To track evolutionary dynamics and heterogeneity of tumors, and to detect early emergence of lorlatinib resistance, we collected serial circulating tumor DNA samples from patients enrolled on this trial. Here we report the discovery of off-target resistance mutations in 11 patients (27%), predominantly in the RAS-MAPK pathway. We also identify newly acquired secondary compound ALK mutations in 6 (15%) patients, all acquired at disease progression. Functional cellular and biochemical assays and computational studies elucidate lorlatinib resistance mechanisms. Our results establish the clinical utility of serial circulating tumor DNA sampling to track response and progression and to discover acquired resistance mechanisms that can be leveraged to develop therapeutic strategies to overcome lorlatinib resistance.
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Affiliation(s)
- Esther R Berko
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Hematology and Oncology, Schneider Children's Medical Center, Petach Tikva, Israel, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriela M Witek
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Smita Matkar
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zaritza O Petrova
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Megan A Wu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Courtney M Smith
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Alex Daniels
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua Kalna
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Annie Kennedy
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ivan Gostuski
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Colleen Casey
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kateryna Krytska
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark Gerelus
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Susan Ghazarian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julie R Park
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Araz Marachelian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly C Goldsmith
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
| | - Yaël P Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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17
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Wu J, Liu Z, Huang T, Wang Y, Song MM, Song T, Long G, Zhang X, Li X, Zhang L. Cerebrospinal fluid circulating tumor DNA depicts profiling of brain metastasis in NSCLC. Mol Oncol 2023; 17:810-824. [PMID: 36495130 PMCID: PMC10158766 DOI: 10.1002/1878-0261.13357] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Brain metastasis (BM) genetically diverges from the primary tumor in non-small-cell lung cancer (NSCLC). Hence, accurately capturing clinically relevant alterations is pivotal for the delivery of targeted therapies. Circulating tumor DNA (ctDNA) sequencing has emerged as a promising liquid biopsy in the biomarker-based clinical management of recurrent and extracranial metastatic NSCLC. However, the absence of simultaneous sequencing data from brain metastatic sites prevents the definitive evaluation of the efficacy of ctDNA in representing genetic profiles in BM. Here, we performed parallel genomic comparisons between matched BM and primary tumor DNA, plasma ctDNA, and cerebrospinal fluid (CSF) ctDNA. The results indicated that CSF ctDNA had a greater ability than plasma ctDNA to comprehensively represent the mutational landscape of BM, with CSF ctDNA detecting all BM mutations in 83.33% of patients, while plasma ctDNA was only 27.78%. Mutant allele frequency (MAF) in CSF ctDNA was highly correlated with the tumor size of BM (r = 0.95), and the mean MAF in CSF ctDNA was higher than that in plasma ctDNA (38.05% vs. 4.57%, respectively). MAF and tumor mutational burden in CSF ctDNA were strongly associated with those in BM (r = 0.96 and 0.97, respectively). Of note, CSF ctDNA had significantly higher concordance with BM than plasma ctDNA (99.33% vs. 67.44%), facilitating the identification of clinically relevant mutations. Moreover, we found that plasma ctDNA has stronger profiling performance, with a concordance of 93.01% in multiple brain metastases, equivalent to CSF ctDNA. Collectively, our study indicates that CSF ctDNA is superior to plasma ctDNA in accurately representing the profiling of single BM. Plasma ctDNA could be an alternative liquid biopsy material to be applied in multiple brain metastatic NSCLC.
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Affiliation(s)
- Jun Wu
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaChina
| | - Zhiqiang Liu
- Department of NeuroscienceErasmus Medical Center, Erasmus University RotterdamThe Netherlands
| | - Tianxiang Huang
- Department of NeurosurgeryYale School of MedicineNew HavenCTUSA
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
| | - Ying Wang
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaChina
| | | | - Tao Song
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaChina
| | - Gretchen Long
- Department of NeurosurgeryYale School of MedicineNew HavenCTUSA
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
| | - Xiaobing Zhang
- Department of PsychologyFlorida State UniversityTallahasseeFLUSA
| | - Xi Li
- Hunan Key Laboratory of PharmacogeneticsXiangya Hospital, Central South UniversityChangshaChina
| | - Longbo Zhang
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaChina
- Department of NeurosurgeryYale School of MedicineNew HavenCTUSA
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
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18
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Hutchinson KE, Chen JW, Savage HM, Stout TJ, Schimmoller F, Cortés J, Dent S, Harbeck N, Jacot W, Krop I, Trabucco SE, Sivakumar S, Sokol ES, Wilson TR. Multiple PIK3CA mutation clonality correlates with outcomes in taselisib + fulvestrant-treated ER+/HER2-, PIK3CA-mutated breast cancers. Genome Med 2023; 15:28. [PMID: 37101291 PMCID: PMC10131374 DOI: 10.1186/s13073-023-01181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Mutations in the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), encoded by the PIK3CA gene, cause dysregulation of the PI3K pathway in 35-40% of patients with HR+/HER2- breast cancer. Preclinically, cancer cells harboring double or multiple PIK3CA mutations (mut) elicit hyperactivation of the PI3K pathway leading to enhanced sensitivity to p110α inhibitors. METHODS To understand the role of multiple PIK3CAmut in predicting response to p110α inhibition, we estimated the clonality of multiple PIK3CAmut in circulating tumor DNA (ctDNA) from patients with HR+/HER2- metastatic breast cancer enrolled to a prospectively registered clinical trial of fulvestrant ± taselisib, and analyzed the subgroups against co-altered genes, pathways, and outcomes. RESULTS ctDNA samples with clonal multiple PIK3CAmut had fewer co-alterations in receptor tyrosine kinase (RTK) or non-PIK3CA PI3K pathway genes compared to samples with subclonal multiple PIK3CAmut indicating a strong reliance on the PI3K pathway. This was validated in an independent cohort of breast cancer tumor specimens that underwent comprehensive genomic profiling. Furthermore, patients whose ctDNA harbored clonal multiple PIK3CAmut exhibited a significantly higher response rate and longer progression-free survival vs subclonal multiple PIK3CAmut. CONCLUSIONS Our study establishes clonal multiple PIK3CAmut as an important molecular determinant of response to p110α inhibition and provides rationale for further clinical investigation of p110α inhibitors alone or with rationally-selected therapies in breast cancer and potentially other solid tumor types.
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Affiliation(s)
- Katherine E Hutchinson
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jessica W Chen
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Heidi M Savage
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Thomas J Stout
- Product Development Oncology, Genentech, Inc., South San Francisco, CA, USA
| | - Frauke Schimmoller
- Product Development Oncology, Genentech, Inc., South San Francisco, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quironsalud Group, Madrid & Barcelona, Spain
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Susan Dent
- Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Nadia Harbeck
- Breast Center, Department Gynecology and Obstetrics and Comprehensive Cancer Center (CCC) Munich, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - William Jacot
- Institut du Cancer de Montpellier (ICM) Val d'Aurelle, Montpellier University, INSERM U1194, Montpellier, France
| | - Ian Krop
- Yale Cancer Center, New Haven, CT, USA
| | | | | | | | - Timothy R Wilson
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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19
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Goldsmith KC, Park JR, Kayser K, Malvar J, Chi YY, Groshen SG, Villablanca JG, Krytska K, Lai LM, Acharya PT, Goodarzian F, Pawel B, Shimada H, Ghazarian S, States L, Marshall L, Chesler L, Granger M, Desai AV, Mody R, Morgenstern DA, Shusterman S, Macy ME, Pinto N, Schleiermacher G, Vo K, Thurm HC, Chen J, Liyanage M, Peltz G, Matthay KK, Berko ER, Maris JM, Marachelian A, Mossé YP. Lorlatinib with or without chemotherapy in ALK-driven refractory/relapsed neuroblastoma: phase 1 trial results. Nat Med 2023; 29:1092-1102. [PMID: 37012551 DOI: 10.1038/s41591-023-02297-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Neuroblastomas harbor ALK aberrations clinically resistant to crizotinib yet sensitive pre-clinically to the third-generation ALK inhibitor lorlatinib. We conducted a first-in-child study evaluating lorlatinib with and without chemotherapy in children and adults with relapsed or refractory ALK-driven neuroblastoma. The trial is ongoing, and we report here on three cohorts that have met pre-specified primary endpoints: lorlatinib as a single agent in children (12 months to <18 years); lorlatinib as a single agent in adults (≥18 years); and lorlatinib in combination with topotecan/cyclophosphamide in children (<18 years). Primary endpoints were safety, pharmacokinetics and recommended phase 2 dose (RP2D). Secondary endpoints were response rate and 123I-metaiodobenzylguanidine (MIBG) response. Lorlatinib was evaluated at 45-115 mg/m2/dose in children and 100-150 mg in adults. Common adverse events (AEs) were hypertriglyceridemia (90%), hypercholesterolemia (79%) and weight gain (87%). Neurobehavioral AEs occurred mainly in adults and resolved with dose hold/reduction. The RP2D of lorlatinib with and without chemotherapy in children was 115 mg/m2. The single-agent adult RP2D was 150 mg. The single-agent response rate (complete/partial/minor) for <18 years was 30%; for ≥18 years, 67%; and for chemotherapy combination in <18 years, 63%; and 13 of 27 (48%) responders achieved MIBG complete responses, supporting lorlatinib's rapid translation into active phase 3 trials for patients with newly diagnosed high-risk, ALK-driven neuroblastoma. ClinicalTrials.gov registration: NCT03107988 .
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Affiliation(s)
- Kelly C Goldsmith
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Julie R Park
- Seattle Children's Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Kimberly Kayser
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jemily Malvar
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Yueh-Yun Chi
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Susan G Groshen
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Judith G Villablanca
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kateryna Krytska
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lillian M Lai
- Department of Radiology, University of Iowa Hospital and Clinics, Iowa City, IA, USA
| | - Patricia T Acharya
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Fariba Goodarzian
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Bruce Pawel
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Hiroyuki Shimada
- Department of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Ghazarian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Lisa States
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Lynley Marshall
- The Royal Marsden Hospital, London, UK
- The Institute of Cancer Research, London, UK
| | - Louis Chesler
- The Royal Marsden Hospital, London, UK
- The Institute of Cancer Research, London, UK
| | | | - Ami V Desai
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation, University of Chicago, Chicago, IL, USA
| | - Rajen Mody
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Morgenstern
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Suzanne Shusterman
- Dana-Farber Cancer Institute, Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Margaret E Macy
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Navin Pinto
- Seattle Children's Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Gudrun Schleiermacher
- RTOP (Recherche Translationelle en Oncologie Pédiatrique), INSERM U830, Research Center, PSL Research University, Institut Curie, Paris, France
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), Institut Curie, Paris, France
| | - Kieuhoa Vo
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Holger C Thurm
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Joseph Chen
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Marlon Liyanage
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Gerson Peltz
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Katherine K Matthay
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Esther R Berko
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Hematology and Oncology, Schneider Children's Medical Center, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Araz Marachelian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yael P Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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20
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Assaf ZJF, Zou W, Fine AD, Socinski MA, Young A, Lipson D, Freidin JF, Kennedy M, Polisecki E, Nishio M, Fabrizio D, Oxnard GR, Cummings C, Rode A, Reck M, Patil NS, Lee M, Shames DS, Schulze K. A longitudinal circulating tumor DNA-based model associated with survival in metastatic non-small-cell lung cancer. Nat Med 2023; 29:859-868. [PMID: 36928816 PMCID: PMC10115641 DOI: 10.1038/s41591-023-02226-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/23/2023] [Indexed: 03/18/2023]
Abstract
One of the great challenges in therapeutic oncology is determining who might achieve survival benefits from a particular therapy. Studies on longitudinal circulating tumor DNA (ctDNA) dynamics for the prediction of survival have generally been small or nonrandomized. We assessed ctDNA across 5 time points in 466 non-small-cell lung cancer (NSCLC) patients from the randomized phase 3 IMpower150 study comparing chemotherapy-immune checkpoint inhibitor (chemo-ICI) combinations and used machine learning to jointly model multiple ctDNA metrics to predict overall survival (OS). ctDNA assessments through cycle 3 day 1 of treatment enabled risk stratification of patients with stable disease (hazard ratio (HR) = 3.2 (2.0-5.3), P < 0.001; median 7.1 versus 22.3 months for high- versus low-intermediate risk) and with partial response (HR = 3.3 (1.7-6.4), P < 0.001; median 8.8 versus 28.6 months). The model also identified high-risk patients in an external validation cohort from the randomized phase 3 OAK study of ICI versus chemo in NSCLC (OS HR = 3.73 (1.83-7.60), P = 0.00012). Simulations of clinical trial scenarios employing our ctDNA model suggested that early ctDNA testing outperforms early radiographic imaging for predicting trial outcomes. Overall, measuring ctDNA dynamics during treatment can improve patient risk stratification and may allow early differentiation between competing therapies during clinical trials.
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Affiliation(s)
| | - Wei Zou
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Makoto Nishio
- The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | | | | | - Anja Rode
- F. Hoffman-La Roche AG, Basel, Switzerland
| | - Martin Reck
- LungenClinic Grosshansdorf, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | | | - Mark Lee
- Genentech Inc., South San Francisco, CA, USA
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21
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Englmeier F, Bleckmann A, Brückl W, Griesinger F, Fleitz A, Nagels K. Clinical benefit and cost-effectiveness analysis of liquid biopsy application in patients with advanced non-small cell lung cancer (NSCLC): a modelling approach. J Cancer Res Clin Oncol 2023; 149:1495-1511. [PMID: 35532791 PMCID: PMC10020305 DOI: 10.1007/s00432-022-04034-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/19/2022] [Indexed: 12/25/2022]
Abstract
PURPOSE Targeted therapies are effective therapeutic approaches in advanced stages of NSCLC and require precise molecular profiling to identify oncogenic drivers. Differential diagnosis on a molecular level contributes to clinical decision making. Liquid biopsy (LB) use has demonstrated its potential to serve as an alternative to tissue biopsy (TB) particularly in cases where tissue sampling is not feasible or insufficient. We aimed at evaluating the cost-effectiveness of ctDNA-based LB use (molecular multigene testing) according to German care guidelines for metastatic NSCLC. METHODS A Markov model was developed to compare the costs and clinical benefits associated with the use of LB as an add-on to TB according to the guidelines for NSCLC patients. Usual care TB served as comparator. A microsimulation model was used to simulate a cohort of non-squamous NSCLC patients stage IV. The parameters used for modelling were obtained from the literature and from the prospective German CRISP registry ("Clinical Research platform Into molecular testing, treatment, and outcome of non-Small cell lung carcinoma Patients"). For each pathway, average direct medical costs, and QALYs gained per patient were used for calculating incremental cost-effectiveness ratios (ICER). RESULTS The use of LB as an add-on was costlier (€144,981 vs. €144,587) but more effective measured in QALYs (1.20 vs. 1.19) for the care pathway of NSCLC patients (ICER €53,909/QALY). Cost-effectiveness was shown for EGFR-mutated patients (ICER €-13,247/QALY). CONCLUSION Including LB as an add-on into the care pathway of advanced NSCLC has positive clinical effects in terms of QALYs accompanied by a moderate cost-effectiveness.
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Affiliation(s)
- Fabienne Englmeier
- Chair of Healthcare Management and Health Services Research, University of Bayreuth, Parsifalstraße 25, 95445, Bayreuth, Germany
| | - Annalen Bleckmann
- Medical Clinic A, Haematology, Haemostaseology, Oncology and Pulmonology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
- Department of Haematology and Medical Oncology, University of Medicine Goettingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Wolfgang Brückl
- Department of Respiratory Medicine, Allergology and Sleep Medicine, Nuremberg Lung Cancer Center, General Hospital Nuremberg, Paracelsus Medical University, Prof.-Ernst-Nathan-Straße 1, 90419, Nuremberg, Germany
| | - Frank Griesinger
- Pius-Hospital Oldenburg, University Clinic Internal Medicine, Georgstraße 12, 26121, Oldenburg, Germany
| | - Annette Fleitz
- Clinical Epidemiology and Health Economics, iOMEDICO, Ellen-Gottlieb-Straße 19, 79108, Freiburg, Germany
| | - Klaus Nagels
- Chair of Healthcare Management and Health Services Research, University of Bayreuth, Parsifalstraße 25, 95445, Bayreuth, Germany.
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22
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Filis P, Kyrochristos I, Korakaki E, Baltagiannis EG, Thanos D, Roukos DH. Longitudinal ctDNA profiling in precision oncology and immunο-oncology. Drug Discov Today 2023; 28:103540. [PMID: 36822363 DOI: 10.1016/j.drudis.2023.103540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Serial analysis of circulating tumor DNA (ctDNA) over the disease course is emerging as a prognostic, predictive and patient-monitoring biomarker. In the metastatic setting, several multigene ctDNA assays have been approved or recommended by regulatory organizations for personalized targeted therapy, especially for lung cancer. By contrast, in nonmetastatic disease, detection of ctDNA resulting from minimal residual disease (MRD) following multimodal treatment with curative intent presents major technical challenges. Several studies using tumor genotyping-informed serial ctDNA profiling have provided promising findings on the sensitivity and specificity of ctDNA in predicting the risk of recurrence. We discuss progress, limitations and future perspectives relating to the use of ctDNA as a biomarker to guide targeted therapy in metastatic disease, as well as the use of ctDNA MRD detection to guide adjuvant treatment in the nonmetastatic setting.
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Affiliation(s)
- Panagiotis Filis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Medical Oncology, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-80539 Munich, Germany
| | - Efterpi Korakaki
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Physiology, Medical School, University of Ioannina, Ioannina 45110, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Surgery, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Dimitris Thanos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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23
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Clinical utility of liquid biopsy and integrative genomic profiling in early-stage and oligometastatic cancer patients treated with radiotherapy. Br J Cancer 2023; 128:857-876. [PMID: 36550207 PMCID: PMC9977775 DOI: 10.1038/s41416-022-02102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Liquid biopsy and Integrative Genomic Profiling (IGP) are yet to be implemented into routine Radiation Oncology. Here we assess the utility of germline, tumour and circulating cell-free DNA-based genomic analyses for the clinical management of early-stage and oligometastatic cancer patients treated by precision radiotherapy. METHODS We performed germline, tissue- and liquid biopsy NGS panels on 50 early-stage/oligometastatic cancer patients undergoing radiotherapy. We also monitored ctDNA variants in serial liquid biopsies collected during radiotherapy and follow-up and evaluated the clinical utility of such comprehensive approach. RESULTS The integration of different genomic studies revealed that only 1/3 of the liquid biopsy variants are of tumour origin. Altogether, 55 tumour variants (affecting 3/4 of the patients) were considered potentially actionable (for treatment and prognosis), whereas potential follow-up biomarkers were identified in all cases. Germline cancer-predisposing variants were present in three patients, which would have not been eligible for hereditary cancer testing according to clinical guidelines. The presence of detectable ctDNA variants before radiotherapy was associated with progression-free survival both in oligometastatic patients and in those with early-stage. CONCLUSIONS IGP provides both valuable and actionable information for personalised decision-making in Radiation Oncology.
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24
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Expert consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the determination of biomarkers in pancreatic and biliary tract cancer. REVISTA ESPANOLA DE PATOLOGIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ANATOMIA PATOLOGICA Y DE LA SOCIEDAD ESPANOLA DE CITOLOGIA 2023; 56:32-44. [PMID: 36599598 DOI: 10.1016/j.patol.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 01/31/2023]
Abstract
Pancreatic cancer and biliary tract cancer have a poor prognosis. In recent years, the development of new diagnostic techniques has enabled the identification of the main genetic alterations involved in the development of these tumours. Multiple studies have assessed the ability to predict response to treatment of certain biomarkers, such as BRCA in pancreatic cancer, IDH1 or FGFR2 in biliary tract cancer and microsatellite instability or NTRK fusions in an agnostic tumour fashion. In this consensus, a group of experts selected by the Spanish Society of Medical Oncology (SEOM) and the Spanish Society of Pathology (SEAP) reviewed the role played by these mutations in the process of carcinogenesis and their clinical implications. Based on their results, a series of recommendations are made to optimize the determination of these biomarkers and thus help standardize the diagnosis and treatment of these tumours.
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25
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Li Y, Jiang X, Zhong M, Yu B, Yuan H. Whole Genome Sequencing of Single-Circulating Tumor Cell Ameliorates Unraveling Breast Cancer Heterogeneity. BREAST CANCER (DOVE MEDICAL PRESS) 2022; 14:505-513. [PMID: 36597488 PMCID: PMC9805725 DOI: 10.2147/bctt.s388653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022]
Abstract
Objective Because tumor tissues are most frequently heterogeneous and hard to characterize, the resulting therapeutic strategy could be misled. The most active and invasive tumor cells are circulating tumor cells (CTCs). In this study, we investigated the feasibility of individualized treatment of breast cancer patients based on whole genome sequencing (WGS) of single cell CTC. Methods Twenty-four CTCs were identified in three breast cancer patients. For each patient, one polyploid CTC was captured, and on which the WGS was performed. WGS was considered due to its sequencing robustness compared to conventional sequencing approaches. Based on the histopathological Her-2 status in tumor tissue and the HER2 gene status in WGS results of CTC, we adjusted treatment strategies and monitored disease progression. Results Patients ID1 and ID2 are found to be Her-2 positive in primary tumors and HER2 gene amplification in the DNA of CTCs. In-patient ID3, histopathological examination of the primary tumor and liver metastases revealed Her-2 negative, but the WGS analysis of CTC showed HER2 gene amplification. After adjusting treatment by adding Her-2 inhibitors according to the results of CTC sequencing, liver metastases and pleural effusion were significantly reduced two months later, CTC number and ctDNA burden were decreased, and 18-months progression-free survival (PFS) was recorded. In addition, some potential therapeutic targets and mutations in drug-resistant genes were detected. Conclusion The results of CTC sequencing effectively guided the treatment of a patient with HER2 gene amplification in CTC but with Her-2 negative on tumor tissue. Therefore, CTC sequencing could help resolve the heterogeneity of tumors and provide precision medicine for patients.
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Affiliation(s)
- Yongping Li
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China
| | - Xiaofei Jiang
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China
| | - Ming Zhong
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China
| | - Bo Yu
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China,Bo Yu, Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong New Area, Shanghai, 201399, People’s Republic of China, Tel +86 18918922698, Email
| | - Hao Yuan
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China,Correspondence: Hao Yuan, Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong New Area, Shanghai, 201399, People’s Republic of China, Tel +86 18918790382, Email
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Lee JK, Sivakumar S, Schrock AB, Madison R, Fabrizio D, Gjoerup O, Ross JS, Frampton GM, Napalkov P, Montesion M, Schutzman JL, Ye X, Hegde PS, Nagasaka M, Oxnard GR, Sokol ES, Ou SHI, Shi Z. Comprehensive pan-cancer genomic landscape of KRAS altered cancers and real-world outcomes in solid tumors. NPJ Precis Oncol 2022; 6:91. [PMID: 36494601 PMCID: PMC9734185 DOI: 10.1038/s41698-022-00334-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Recent clinical development of KRAS inhibitors has heightened interest in the genomic landscape of KRAS-altered cancers. We performed a pan-cancer analysis of KRAS-altered samples from 426,706 adult patients with solid or hematologic malignancies using comprehensive genomic profiling; additional analyses included 62,369 liquid biopsy and 7241 pediatric samples. 23% of adult pan-cancer samples had KRAS alterations; 88% were mutations, most commonly G12D/G12V/G12C/G13D/G12R, and prevalence was similar in liquid biopsies. Co-alteration landscapes were largely similar across KRAS mutations but distinct from KRAS wild-type, though differences were observed in some tumor types for tumor mutational burden, PD-L1 expression, microsatellite instability, and other mutational signatures. Prognosis of KRAS-mutant versus other genomic cohorts of lung, pancreatic, and colorectal cancer were assessed using a real-world clinicogenomic database. As specific KRAS inhibitors and combination therapeutic strategies are being developed, genomic profiling to understand co-alterations and other biomarkers that may modulate response to targeted or immunotherapies will be imperative.
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Affiliation(s)
- Jessica K. Lee
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Smruthy Sivakumar
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Alexa B. Schrock
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Russell Madison
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - David Fabrizio
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Ole Gjoerup
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Jeffrey S. Ross
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA ,grid.411023.50000 0000 9159 4457Upstate Medical University, Syracuse, NY USA
| | | | - Pavel Napalkov
- grid.418158.10000 0004 0534 4718Genentech, Inc., South San Francisco, CA USA
| | - Meagan Montesion
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | | | - Xin Ye
- grid.418158.10000 0004 0534 4718Genentech, Inc., South San Francisco, CA USA
| | - Priti S. Hegde
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Misako Nagasaka
- grid.516069.d0000 0004 0543 3315Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, CA USA
| | - Geoffrey R. Oxnard
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Ethan S. Sokol
- grid.418158.10000 0004 0534 4718Foundation Medicine Inc., Cambridge, MA USA
| | - Sai-Hong Ignatius Ou
- grid.516069.d0000 0004 0543 3315Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, CA USA
| | - Zhen Shi
- grid.418158.10000 0004 0534 4718Genentech, Inc., South San Francisco, CA USA
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27
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Tissue and liquid biopsy profiling reveal convergent tumor evolution and therapy evasion in breast cancer. Nat Commun 2022; 13:7495. [PMID: 36470901 PMCID: PMC9723105 DOI: 10.1038/s41467-022-35245-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Pathological and genomic profiling have transformed breast cancer care by matching patients to targeted treatments. However, tumors evolve and evade therapeutic interventions often through the acquisition of genomic mutations. Here we examine patients profiled with tissue (TBx) and liquid biopsy (LBx) as part of routine clinical care, to characterize the tumor evolutionary landscape and identify potential vulnerabilities in the relapsed setting. Real-world evidence demonstrates that LBx is utilized later in care and identifies associations with intervening therapy. While driver events are frequently shared, acquired LBx alterations are detected in a majority of patients, with the highest frequency in ER+ disease and in patients with longer biopsy intervals. Acquired mutations are often polyclonal and present at lower allelic fractions, suggesting multi-clonal convergent evolution. In addition to well-characterized resistance mutations (e.g., ESR1, NF1, RB1, ERBB2), we observe a diversity of rarer but potentially targetable mutations (e.g., PIK3CA, HRAS/NRAS/KRAS, FGFR1/2/3, BRAF) and fusions (e.g., FGFR1/2, ERBB2, RET), as well as BRCA1/2 reversions through a variety of mechanisms, including splice alterations and structural deletions. This study provides insights on treatment and selection-driven tumor evolution and identifies potential combinatorial treatment options in advanced breast cancer.
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28
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Bosse KR, Giudice AM, Lane MV, McIntyre B, Schürch PM, Pascual-Pasto G, Buongervino SN, Suresh S, Fitzsimmons A, Hyman A, Gemino-Borromeo M, Saggio J, Berko ER, Daniels AA, Stundon J, Friedrichsen M, Liu X, Margolis ML, Li MM, Tierno MB, Oxnard GR, Maris JM, Mossé YP. Serial Profiling of Circulating Tumor DNA Identifies Dynamic Evolution of Clinically Actionable Genomic Alterations in High-Risk Neuroblastoma. Cancer Discov 2022; 12:2800-2819. [PMID: 36108156 PMCID: PMC9722579 DOI: 10.1158/2159-8290.cd-22-0287] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/21/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
Neuroblastoma evolution, heterogeneity, and resistance remain inadequately defined, suggesting a role for circulating tumor DNA (ctDNA) sequencing. To define the utility of ctDNA profiling in neuroblastoma, 167 blood samples from 48 high-risk patients were evaluated for ctDNA using comprehensive genomic profiling. At least one pathogenic genomic alteration was identified in 56% of samples and 73% of evaluable patients, including clinically actionable ALK and RAS-MAPK pathway variants. Fifteen patients received ALK inhibition (ALKi), and ctDNA data revealed dynamic genomic evolution under ALKi therapeutic pressure. Serial ctDNA profiling detected disease evolution in 15 of 16 patients with a recurrently identified variant-in some cases confirming disease progression prior to standard surveillance methods. Finally, ctDNA-defined ERRFI1 loss-of-function variants were validated in neuroblastoma cellular models, with the mutant proteins exhibiting loss of wild-type ERRFI1's tumor-suppressive functions. Taken together, ctDNA is prevalent in children with high-risk neuroblastoma and should be followed throughout neuroblastoma treatment. SIGNIFICANCE ctDNA is prevalent in children with neuroblastoma. Serial ctDNA profiling in patients with neuroblastoma improves the detection of potentially clinically actionable and functionally relevant variants in cancer driver genes and delineates dynamic tumor evolution and disease progression beyond that of standard tumor sequencing and clinical surveillance practices. See related commentary by Deubzer et al., p. 2727. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Anna Maria Giudice
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria V. Lane
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Brendan McIntyre
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Patrick M. Schürch
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Guillem Pascual-Pasto
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Samantha N. Buongervino
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Sriyaa Suresh
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alana Fitzsimmons
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Adam Hyman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria Gemino-Borromeo
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Saggio
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Esther R. Berko
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alexander A. Daniels
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Stundon
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | - Xin Liu
- Foundation Medicine, Inc. Cambridge, MA 02141; USA
| | | | - Marilyn M. Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and the Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | | | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Yael P. Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
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Vera R, Ibarrola-de-Andrés C, Adeva J, Pérez-Rojas J, García-Alfonso P, Rodríguez-Gil Y, Macarulla T, Serrano-Piñol T, Mondéjar R, Madrigal-Rubiales B. Expert consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the determination of biomarkers in pancreatic and biliary tract cancer. Clin Transl Oncol 2022; 24:2107-2119. [PMID: 36008616 PMCID: PMC9522813 DOI: 10.1007/s12094-022-02873-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 10/26/2022]
Abstract
Pancreatic cancer and biliary tract cancer have a poor prognosis. In recent years, the development of new diagnostic techniques has enabled the identification of the main genetic alterations involved in the development of these tumours. Multiple studies have assessed the ability of certain biomarkers, such as BRCA in pancreatic cancer, IDH1 or FGFR2 in biliary tract cancer and microsatellite instability or NTRK fusions in an agnostic tumour fashion, to predict response to treatment.In this consensus, a group of experts selected by the Spanish Society of Medical Oncology (SEOM) and the Spanish Society of Pathology (SEAP) reviewed the role played by these mutations in the process of carcinogenesis and their clinical implications. As a result, this article proposes a series of recommendations to optimize the determination of these biomarkers to help standardize the diagnosis and treatment of these tumours.
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Affiliation(s)
- Ruth Vera
- Navarra University Hospital, Spanish Society of Medical Oncology (SEOM), Calle Irunlarrea, 3, Navarra, 31008, Pamplona, Spain.
| | | | - Jorge Adeva
- 12 de Octubre University Hospital, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
| | - Judith Pérez-Rojas
- La Fe University and Polytechnic Hospital, Spanish Society of Pathology (SEAP), Valencia, Spain
| | - Pilar García-Alfonso
- Gregorio Marañón University Hospital, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
| | - Yolanda Rodríguez-Gil
- 12 de Octubre University Hospital, Spanish Society of Pathology (SEAP), Madrid, Spain
| | - Teresa Macarulla
- Vall d'Hebron University Hospital, Spanish Society of Medical Oncology (SEOM), Barcelona, Spain
| | - Teresa Serrano-Piñol
- Bellvitge University Hospital, Spanish Society of Pathology (SEAP), Barcelona, Spain
| | - Rebeca Mondéjar
- La Princesa University Hospital, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
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30
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Marotta V, Cennamo M, La Civita E, Vitale M, Terracciano D. Cell-Free DNA Analysis within the Challenges of Thyroid Cancer Management. Cancers (Basel) 2022; 14:cancers14215370. [PMID: 36358788 PMCID: PMC9654679 DOI: 10.3390/cancers14215370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Liquid biopsy is a minimally invasive method that emerged as a new promising tool for improving diagnosis, risk stratification, follow-up, and treatment of cancer patients. To date, the majority of the research in the area of liquid biopsy has focused on plasma-based cell-free DNA as a potential surrogate for tumor DNA obtained from a tissue biopsy. In the last decades, breakthrough advancements have been performed in the knowledge of thyroid cancer genetics, and the role of molecular characterization in clinical decision-making is continuously rising, from diagnosis completion to the personalization of treatment approach. Hence, it is expectable for cell-free DNA to be applicable in thyroid cancer management. This review aims to investigate the cell-free DNA utility for thyroid cancer patients’ care. Abstract Thyroid cancer is the most frequent endocrine malignancy with an increasing incidence trend during the past forty years and a concomitant rise in cancer-related mortality. The circulating cell-free DNA (cfDNA) analysis is a patient’s friendly and repeatable procedure allowing to obtain surrogate information about the genetics and epigenetics of the tumor. The aim of the present review was to address the suitability of cfDNA testing in different forms of thyroid cancer, and the potential clinical applications, as referred to the clinical weaknesses. Despite being limited by the absence of standardization and by reproducibility and validity issues, cfDNA assessment has great potential for the improvement of thyroid cancer management. cfDNA may support the pre-surgical definition of thyroid nodules by complementing invasive thyroid fine needle aspiration cytology. In addition, it may empower risk stratification and could be used as a biomarker for monitoring the post-surgical disease status, both during active surveillance and in the case of anti-tumor treatment.
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Affiliation(s)
- Vincenzo Marotta
- UOC Clinica Endocrinologica e Diabetologica, AOU San Giovanni di Dio e Ruggi d’Aragona, 84131 Salerno, Italy
- Correspondence: ; Tel.: +39-333-852-1005
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Mario Vitale
- Dipartimento di Medicina, Chirurgia e Odontoiatria, Università di Salerno, 84081 Baronissi, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
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31
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Steiert TA, Fuß J, Juzenas S, Wittig M, Hoeppner M, Vollstedt M, Varkalaite G, ElAbd H, Brockmann C, Görg S, Gassner C, Forster M, Franke A. High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing. NAR Genom Bioinform 2022; 4:lqac051. [PMID: 35855323 PMCID: PMC9278042 DOI: 10.1093/nargab/lqac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/08/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Hybridisation-based targeted enrichment is a widely used and well-established technique in high-throughput second-generation short-read sequencing. Despite the high potential to genetically resolve highly repetitive and variable genomic sequences by, for example PacBio third-generation sequencing, targeted enrichment for long fragments has not yet established the same high-throughput due to currently existing complex workflows and technological dependencies. We here describe a scalable targeted enrichment protocol for fragment sizes of >7 kb. For demonstration purposes we developed a custom blood group panel of challenging loci. Test results achieved > 65% on-target rate, good coverage (142.7×) and sufficient coverage evenness for both non-paralogous and paralogous targets, and sufficient non-duplicate read counts (83.5%) per sample for a highly multiplexed enrichment pool of 16 samples. We genotyped the blood groups of nine patients employing highly accurate phased assemblies at an allelic resolution that match reference blood group allele calls determined by SNP array and NGS genotyping. Seven Genome-in-a-Bottle reference samples achieved high recall (96%) and precision (99%) rates. Mendelian error rates were 0.04% and 0.13% for the included Ashkenazim and Han Chinese trios, respectively. In summary, we provide a protocol and first example for accurate targeted long-read sequencing that can be used in a high-throughput fashion.
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Affiliation(s)
- Tim Alexander Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
- Institute of Biotechnology, Life Science Centre, Vilnius University, Vilnius 02241, Lithuania
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Marc Patrick Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Melanie Vollstedt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Greta Varkalaite
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Christian Brockmann
- Institute of Transfusion Medicine, University Hospital of Schleswig-Holstein, Kiel 24105, Germany
| | - Siegfried Görg
- Institute of Transfusion Medicine, University Hospital of Schleswig-Holstein, Kiel 24105, Germany
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen 9495, Liechtenstein
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
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32
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Schwartzberg LS, Li G, Tolba K, Bourla AB, Schulze K, Gadgil R, Fine A, Lofgren KT, Graf RP, Oxnard GR, Daniel D. Complementary Roles for Tissue- and Blood-Based Comprehensive Genomic Profiling for Detection of Actionable Driver Alterations in Advanced NSCLC. JTO Clin Res Rep 2022; 3:100386. [PMID: 36089920 PMCID: PMC9460153 DOI: 10.1016/j.jtocrr.2022.100386] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Whereas tumor biopsy is the reference standard for genomic profiling of advanced NSCLC, there are now multiple assays approved by the Food and Drug Administration for liquid biopsy testing of circulating tumor DNA. Here, we study the incremental value that liquid biopsy comprehensive genomic profiling (CGP) adds to tissue molecular testing. Methods Patients with metastatic NSCLC were enrolled in a prospective diagnostic study to receive circulating tumor DNA CGP; tissue CGP was optional in addition to their standard tissue testing. Focusing on nine genes listed per the National Comprehensive Cancer Network (NCCN) guidelines, liquid CGP was compared with available tissue testing results across three subcohorts: tissue CGP, standard-of-care testing of up to five biomarkers, or no tissue testing. Results A total of 515 patients with advanced nonsquamous NSCLC received liquid CGP. Among 131 with tissue CGP results, NCCN biomarkers were detected in 86 (66%) with tissue CGP and 56 (43%) with liquid CGP (p < 0.001). Adding liquid CGP to tissue CGP detected no additional patients with NCCN biomarkers, whereas tissue CGP detected NCCN biomarkers in 30 patients (23%) missed by liquid CGP. Studying 264 patients receiving tissue testing of up to five genes, 102 (39%) had NCCN biomarkers detected in tissue, with an additional 48 (18%) detected using liquid CGP, including 18 with RET, MET, or ERBB2 drivers not studied in tissue. Conclusions For the detection of patients with advanced nonsquamous NSCLC harboring 9 NCCN biomarkers, liquid CGP increases detection in patients with limited tissue results, but does not increase detection in patients with tissue CGP results available. In contrast, tissue CGP can add meaningfully to liquid CGP for detection of NCCN biomarkers and should be considered as a follow-up when an oncogenic driver is not identified by liquid biopsy.
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Affiliation(s)
| | - Gerald Li
- Foundation Medicine, Clinical Development, Cambridge, Massachusetts
| | - Khaled Tolba
- Foundation Medicine, Clinical Development, Cambridge, Massachusetts
| | | | - Katja Schulze
- Genentech, Inc., Oncology Biomarker Development & Medical Affairs, South San Francisco, California
| | - Rujuta Gadgil
- Foundation Medicine, Clinical Operations, Cambridge, Massachusetts
| | - Alexander Fine
- Foundation Medicine, Cancer Genomics Research, Cambridge, Massachusetts
| | | | - Ryon P. Graf
- Foundation Medicine, Clinical Development, Cambridge, Massachusetts
| | | | - Davey Daniel
- Tennessee Oncology, Medical Oncology, Chattanooga, Tennessee
- Corresponding author. Address for correspondence: Davey Daniel, MD, Tennessee Oncology, 605 Glenwood Drive, Suite 200, Chattanooga, TN.
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33
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Zingg D, Bhin J, Yemelyanenko J, Kas SM, Rolfs F, Lutz C, Lee JK, Klarenbeek S, Silverman IM, Annunziato S, Chan CS, Piersma SR, Eijkman T, Badoux M, Gogola E, Siteur B, Sprengers J, de Klein B, de Goeij-de Haas RR, Riedlinger GM, Ke H, Madison R, Drenth AP, van der Burg E, Schut E, Henneman L, van Miltenburg MH, Proost N, Zhen H, Wientjens E, de Bruijn R, de Ruiter JR, Boon U, de Korte-Grimmerink R, van Gerwen B, Féliz L, Abou-Alfa GK, Ross JS, van de Ven M, Rottenberg S, Cuppen E, Chessex AV, Ali SM, Burn TC, Jimenez CR, Ganesan S, Wessels LFA, Jonkers J. Truncated FGFR2 is a clinically actionable oncogene in multiple cancers. Nature 2022; 608:609-617. [PMID: 35948633 PMCID: PMC9436779 DOI: 10.1038/s41586-022-05066-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/03/2022] [Indexed: 12/13/2022]
Abstract
Somatic hotspot mutations and structural amplifications and fusions that affect fibroblast growth factor receptor 2 (encoded by FGFR2) occur in multiple types of cancer1. However, clinical responses to FGFR inhibitors have remained variable1–9, emphasizing the need to better understand which FGFR2 alterations are oncogenic and therapeutically targetable. Here we apply transposon-based screening10,11 and tumour modelling in mice12,13, and find that the truncation of exon 18 (E18) of Fgfr2 is a potent driver mutation. Human oncogenomic datasets revealed a diverse set of FGFR2 alterations, including rearrangements, E1–E17 partial amplifications, and E18 nonsense and frameshift mutations, each causing the transcription of E18-truncated FGFR2 (FGFR2ΔE18). Functional in vitro and in vivo examination of a compendium of FGFR2ΔE18 and full-length variants pinpointed FGFR2-E18 truncation as single-driver alteration in cancer. By contrast, the oncogenic competence of FGFR2 full-length amplifications depended on a distinct landscape of cooperating driver genes. This suggests that genomic alterations that generate stable FGFR2ΔE18 variants are actionable therapeutic targets, which we confirmed in preclinical mouse and human tumour models, and in a clinical trial. We propose that cancers containing any FGFR2 variant with a truncated E18 should be considered for FGFR-targeted therapies. Truncation of exon 18 of FGFR2 (FGFR2ΔE18) is a potent driver mutation in mice and humans, and FGFR-targeted therapy should be considered for patients with cancer expressing stable FGFR2ΔE18 variants.
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Affiliation(s)
- Daniel Zingg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Jinhyuk Bhin
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julia Yemelyanenko
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Sjors M Kas
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | - Sjoerd Klarenbeek
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Stefano Annunziato
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Chang S Chan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Timo Eijkman
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Madelon Badoux
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Justin Sprengers
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bim de Klein
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Richard R de Goeij-de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gregory M Riedlinger
- Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA.,Department of Pathology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Hua Ke
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA
| | | | - Anne Paulien Drenth
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Eva Schut
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Linda Henneman
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martine H van Miltenburg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Ellen Wientjens
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ute Boon
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | - Bastiaan van Gerwen
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Luis Féliz
- Incyte Biosciences International, Morges, Switzerland
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College at Cornell University, New York, NY, USA
| | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA, USA.,Upstate University Hospital, Upstate Medical University, Syracuse, NY, USA
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands.,Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shridar Ganesan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA.
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, The Netherlands. .,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Oncode Institute, Utrecht, The Netherlands.
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Lindeman GJ, Fernando TM, Bowen R, Jerzak KJ, Song X, Decker T, Boyle F, McCune S, Armstrong A, Shannon C, Bertelli G, Chang CW, Desai R, Gupta K, Wilson TR, Flechais A, Bardia A. VERONICA: Randomized Phase II Study of Fulvestrant and Venetoclax in ER-Positive Metastatic Breast Cancer Post-CDK4/6 Inhibitors - Efficacy, Safety, and Biomarker Results. Clin Cancer Res 2022; 28:3256-3267. [PMID: 35583555 PMCID: PMC9662928 DOI: 10.1158/1078-0432.ccr-21-3811] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/16/2021] [Accepted: 05/16/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Despite promising activity in hematopoietic malignancies, efficacy of the B-cell lymphoma 2 (BCL2) inhibitor venetoclax in solid tumors is unknown. We report the prespecified VERONICA primary results, a randomized phase II clinical trial evaluating venetoclax and fulvestrant in estrogen receptor (ER)-positive, HER2-negative metastatic breast cancer, post-cyclin-dependent kinase (CDK) 4/6 inhibitor progression. PATIENTS AND METHODS Pre-/postmenopausal females ≥18 years were randomized 1:1 to venetoclax (800 mg orally daily) plus fulvestrant (500 mg intramuscular; cycle 1: days 1 and 15; subsequent 28-day cycles: day 1) or fulvestrant alone. The primary endpoint was clinical benefit rate (CBR); secondary endpoints were progression-free survival (PFS), overall survival, and safety. Exploratory biomarker analyses included BCL2 and BCL extra-large (BCLXL) tumor expression, and PIK3CA circulating tumor DNA mutational status. RESULTS At primary analysis (cutoff: August 5, 2020; n = 103), venetoclax did not significantly improve CBR [venetoclax plus fulvestrant: 11.8% (n = 6/51; 95% confidence interval (CI), 4.44-23.87); fulvestrant: 13.7% (7/51; 5.70-26.26); risk difference -1.96% (95% CI, -16.86 to 12.94)]. Median PFS was 2.69 months (95% CI, 1.94-3.71) with venetoclax plus fulvestrant versus 1.94 months (1.84-3.55) with fulvestrant (stratified HR, 0.94; 95% CI, 0.61-1.45; P = 0.7853). Overall survival data were not mature. A nonsignificant improvement of CBR and PFS was observed in patients whose tumors had strong BCL2 expression (IHC 3+), a BCL2/BCLXL Histoscore ratio ≥1, or PIK3CA-wild-type status. CONCLUSIONS Our findings do not indicate clinical utility for venetoclax plus fulvestrant in endocrine therapy-resistant, CDK4/6 inhibitor-refractory metastatic breast tumors, but suggest possible increased dependence on BCLXL in this setting.
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Affiliation(s)
- Geoffrey J. Lindeman
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia.,Corresponding Author: Geoffrey J. Lindeman, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia. Phone: 61-3-9345-2611; Fax: 61-3-9347-0852; E-mail:
| | - Tharu M. Fernando
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Rebecca Bowen
- Medical Oncology, Royal United Hospitals Bath NHS Foundation Trust, Bath, United Kingdom
| | - Katarzyna J. Jerzak
- Medical Oncology, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, Canada
| | - Xinni Song
- Medical Oncology, The Ottawa Hospital Cancer Centre, Ottawa, Canada
| | - Thomas Decker
- Hematology and Oncology, Onkologie Ravensburg, Ravensburg, Germany
| | - Frances Boyle
- Patricia Ritchie Centre for Cancer Care and Research, Mater Hospital, Sydney, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Steve McCune
- Medical Oncology, Wellstar Health System, Marietta, Georgia
| | - Anne Armstrong
- Medical Oncology, The Christie NHS Foundation Trust and the University of Manchester, Manchester, United Kingdom
| | | | | | - Ching-Wei Chang
- PHC and Early Development Oncology Biostatistics, Genentech, Inc., South San Francisco, California
| | - Rupal Desai
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Kushagra Gupta
- Biostatistics, IQVIA RDS (India) Private Ltd, Bangalore, India
| | - Timothy R. Wilson
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Aulde Flechais
- Global PD Senior Clinical Scientist-Oncology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Aditya Bardia
- Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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35
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Petrylak DP, Watkins SP, Loehr A. What Plasma Can Tell Us When Tissue Cannot: A Case Report of Genomic Testing in mCRPC and Clinical Response to Treatment With the PARP Inhibitor Rucaparib. Front Oncol 2022; 12:951348. [PMID: 35978838 PMCID: PMC9377337 DOI: 10.3389/fonc.2022.951348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background The poly(ADP-ribose) polymerase (PARP) inhibitor rucaparib was approved in the United States based on the phase 2 TRITON2 study of patients with BRCA1 or BRCA2 (BRCA)-mutated metastatic castration-resistant prostate cancer (mCRPC). Although genomic screening is recommended as part of a comprehensive assessment of prostate cancer prognosis and treatment options, the best way to select patients with mCRPC for treatment with a PARP inhibitor depends on individual clinical circumstances. For example, assessment of tumor tissue may not always be feasible. Genomic testing of DNA from plasma has become more readily available, providing a minimally invasive option to evaluate DNA from primary and metastatic lesions simultaneously. Case Presentation A patient from TRITON2 with BRCA-mutated mCRPC had a response to the PARP inhibitor rucaparib and remained on treatment for 32 weeks, which was >2 times longer than the duration of each of his prior therapies (bicalutamide, docetaxel, abiraterone). The patient enrolled in TRITON2 based on results of local genomic testing of an archival biopsy that indicated the presence of a BRCA1 T1399I (allelic fraction, 19%) mutation. Local testing also identified an ATM G1663C mutation, a TP53 P191del mutation, and a BRAF K601E mutation. Analysis of a plasma sample obtained before the patient started rucaparib detected the same alterations as those in the archival biopsy, but it also revealed the presence of a BRCA2 homozygous loss (whole gene, 26 of 26 exons) and several other alterations of unknown functional impact. We hypothesize the response of the patient's tumor to rucaparib was likely driven by DNA damage repair deficiency caused by homozygous loss of all BRCA2 exons. Following discontinuation from rucaparib due to clinical disease progression, the patient received carboplatin and cabazitaxel for ≈3 weeks. The patient died due to progression of his disease. Conclusions A notable aspect of this case is the differences in alterations detected in the archival tumor sample and a more recent plasma sample. This highlights the advantages of plasma testing compared with tissue testing when selecting targeted therapies for treatment of mCRPC; however, physicians must determine which tool presents the best solution for each individual case.
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Affiliation(s)
- Daniel P. Petrylak
- Smilow Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Simon P. Watkins
- Clinical Science, Clovis Oncology UK, Ltd, Cambridge, United Kingdom
| | - Andrea Loehr
- Translational Medicine, Clovis Oncology, Inc., Boulder, CO, United States
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36
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Imai M, Nakamura Y, Sunami K, Kage H, Komine K, Koyama T, Amano T, Ennishi D, Kanai M, Kenmotsu H, Maeda T, Morita S, Sakai D, Bando H, Makiyama A, Suzuki T, Hirata M, Kohsaka S, Tsuchihara K, Naito Y, Yoshino T. Expert Panel Consensus Recommendations on the Use of Circulating Tumor DNA Assays for Patients with Advanced Solid Tumors. Cancer Sci 2022; 113:3646-3656. [PMID: 35876224 PMCID: PMC9633310 DOI: 10.1111/cas.15504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 12/01/2022] Open
Abstract
Comprehensive genomic profiling is increasingly used to facilitate precision oncology based on molecular stratification. In addition to conventional tissue comprehensive genomic profiling, comprehensive genomic profiling of circulating tumor DNA has become widely utilized in cancer care owing on its advantages, including less invasiveness, rapid turnaround time, and capturing heterogeneity. However, circulating tumor DNA comprehensive genomic profiling has some limitations, mainly false negatives due to low levels of plasma circulating tumor deoxyribonucleic acid and false positives caused by clonal hematopoiesis. Nevertheless, no guidelines and recommendations fully address these issues. Here, an expert panel committee involving representatives from 12 Designated Core Hospitals for Cancer Genomic Medicine in Japan was organized to develop expert consensus recommendations for the use of circulating tumor deoxyribonucleic acid‐based comprehensive genomic profiling. The aim was to generate guidelines for clinicians and allied healthcare professionals on the optimal use of the circulating tumor DNA assays in advanced solid tumors and to aid the design of future clinical trials that utilize and develop circulating tumor DNA assays to refine precision oncology. Fourteen clinical questions regarding circulating tumor deoxyribonucleic acid comprehensive genomic profiling including the timing of testing and considerations for interpreting results were established by searching and curating associated literatures, and corresponding recommendations were prepared based on the literature for each clinical question. Final consensus recommendations were developed by voting to determine the level of each recommendation by the Committee members.
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Affiliation(s)
- Mitsuho Imai
- Translational Research Support Section, National Cancer Center Hospital East.,Genomics Unit, Keio University School of Medicine
| | - Yoshiaki Nakamura
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital
| | - Hidenori Kage
- Department of Next-Generation Precision Medicine Development Laboratory, Graduate School of Medicine, The University of Tokyo
| | - Keigo Komine
- Department of Medical Oncology, Tohoku University Hospital
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital
| | - Toraji Amano
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital
| | - Daisuke Ennishi
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University
| | | | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences
| | - Sachi Morita
- Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital
| | - Daisuke Sakai
- Center for Cancer Genomics and Personalized Medicine, Osaka University Hospital
| | - Hideaki Bando
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
| | | | - Tatsuya Suzuki
- Department of Hematology, National Cancer Center Hospital
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Japan
| | - Yoichi Naito
- Department of General Internal medicine/Experimental Therapeutics/Medical Oncology, National Cancer Center Hospital East
| | - Takayuki Yoshino
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
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37
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Lee JY, Kannan B, Lim BY, Li Z, Lim AH, Loh JW, Ko TK, Ng CCY, Chan JY. The Multi-Dimensional Biomarker Landscape in Cancer Immunotherapy. Int J Mol Sci 2022; 23:7839. [PMID: 35887186 PMCID: PMC9323480 DOI: 10.3390/ijms23147839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
The field of immuno-oncology is now at the forefront of cancer care and is rapidly evolving. The immune checkpoint blockade has been demonstrated to restore antitumor responses in several cancer types. However, durable responses can be observed only in a subset of patients, highlighting the importance of investigating the tumor microenvironment (TME) and cellular heterogeneity to define the phenotypes that contribute to resistance as opposed to those that confer susceptibility to immune surveillance and immunotherapy. In this review, we summarize how some of the most widely used conventional technologies and biomarkers may be useful for the purpose of predicting immunotherapy outcomes in patients, and discuss their shortcomings. We also provide an overview of how emerging single-cell spatial omics may be applied to further advance our understanding of the interactions within the TME, and how these technologies help to deliver important new insights into biomarker discovery to improve the prediction of patient response.
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Affiliation(s)
- Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Zhimei Li
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Jui Wan Loh
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Cedric Chuan-Young Ng
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.L.); (B.K.); (B.Y.L.); (Z.L.); (A.H.L.); (J.W.L.); (T.K.K.); (C.C.-Y.N.)
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore 169857, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
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38
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Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12071539. [PMID: 35885445 PMCID: PMC9318977 DOI: 10.3390/diagnostics12071539] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.
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39
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Sautois B, Loehr A, Watkins SP, Schroeder H, Abida W. A Case Study of Clinical Response to Rucaparib in a Patient with Metastatic Castration-Resistant Prostate Cancer and a RAD51B Alteration. Curr Oncol 2022; 29:4178-4184. [PMID: 35735442 PMCID: PMC9221801 DOI: 10.3390/curroncol29060333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
PARP inhibitors, such as rucaparib, have been well characterized in metastatic castration-resistant prostate cancer (mCRPC) associated with BRCA alterations, and the clinical activity of these agents has also been evaluated in patients with mCRPC associated with alterations in other non-BRCA DNA damage repair (DDR) genes, including RAD51B. There is likely a differential sensitivity to PARP inhibition based on the specific DDR gene altered, but research in this area is limited because of the low frequency of alterations in these genes. Here, we describe a mCRPC patient with a truncating rearrangement of RAD51B who had a radiographic and PSA response when treated with the PARP inhibitor rucaparib within the TRITON2 trial. We investigated the patients’ response parameters, circulating tumor DNA (ctDNA) fraction and tumor genomics longitudinally, using next-generation sequencing (NGS) of tissue and plasma. ctDNA fraction correlates with radiographic and PSA response and is lower during times of response. NGS did not reveal any potential genomic mechanism of acquired drug resistance. This case shows evidence for rucaparib activity in a rare patient with mCRPC and a RAD51B truncation.
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Affiliation(s)
- Brieuc Sautois
- Medical Oncology, University Hospital of Liège, CHU Sart Tilman, 4000 Liège, Belgium;
- Correspondence:
| | - Andrea Loehr
- Translational Medicine, Clovis Oncology Inc., Boulder, CO 08006, USA;
| | - Simon P. Watkins
- Clinical Science, Clovis Oncology UK, Ltd., Cambridge CB21 6GP, UK;
| | - Hélène Schroeder
- Medical Oncology, University Hospital of Liège, CHU Sart Tilman, 4000 Liège, Belgium;
| | - Wassim Abida
- Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
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40
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Li CL, Yeh SH, Chen PJ. Circulating Virus–Host Chimera DNAs in the Clinical Monitoring of Virus-Related Cancers. Cancers (Basel) 2022; 14:cancers14102531. [PMID: 35626135 PMCID: PMC9139492 DOI: 10.3390/cancers14102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cell-free tumor DNA (ctDNA), the DNA released into circulation from tumors, is a promising tumor marker with versatile applications. The associations of the amount, somatic mutation frequency, and epigenetic modifications of ctDNA with the tumor burden, tumor behavior, and prognosis have been widely investigated in different types of tumors. However, there are still some challenging issues to be resolved before ctDNA can complement or even replace current serum tumor markers. We propose employing exogenous viral DNA integration that produces unique virus–host chimera DNA (vh-DNA) at junction sites. Cell-free vh-DNA may become a new biomarker because it overcomes background interference detection problems, takes advantage of virus tropism to localize the tumor, and acts as a universal marker for monitoring clonal expansion or tumor loads in tumors related to oncogenic viruses. Abstract The idea of using tumor-specific cell-free DNA (ctDNA) as a tumor biomarker has been widely tested and validated in various types of human cancers and different clinical settings. ctDNA can reflect the presence or size of tumors in a real-time manner and can enable longitudinal monitoring with minimal invasiveness, allowing it to be applied in treatment response assessment and recurrence monitoring for cancer therapies. However, tumor detection by ctDNA remains a great challenge due to the difficulty in enriching ctDNA from a large amount of homologous non-tumor cell-free DNA (cfDNA). Only ctDNA with nonhuman sequences (or rearrangements) can be selected from the background of cfDNA from nontumor DNAs. This is possible for several virus-related cancers, such as hepatitis B virus (HBV)-related HCC or human papillomavirus (HPV)-related cervical or head and neck cancers, which frequently harbor randomly integrated viral DNA. The junction fragments of the integrations, namely virus–host chimera DNA (vh-DNA), can represent the signatures of individual tumors and are released into the blood. Such ctDNA can be enriched by capture with virus-specific probes and therefore exploited as a circulating biomarker to track virus-related cancers in clinical settings. Here, we review virus integrations in virus-related cancers to evaluate the feasibility of vh-DNA as a cell-free tumor marker and update studies on the development of detection and applications. vh-DNA may be a solution to the development of specific markers to manage virus-related cancers in the future.
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Affiliation(s)
- Chiao-Ling Li
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
| | - Shiou-Hwei Yeh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
| | - Pei-Jer Chen
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
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41
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Caputo V, De Falco V, Ventriglia A, Famiglietti V, Martinelli E, Morgillo F, Martini G, Corte CMD, Ciardiello D, Poliero L, De Vita F, Orditura M, Fasano M, Franco R, Caraglia M, Avitabile A, Scalamogna R, Marchi B, Ciardiello F, Troiani T, Napolitano S. Comprehensive genome profiling by next generation sequencing of circulating tumor DNA in solid tumors: a single academic institution experience. Ther Adv Med Oncol 2022; 14:17588359221096878. [PMID: 35547096 PMCID: PMC9082754 DOI: 10.1177/17588359221096878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 04/07/2022] [Indexed: 01/18/2023] Open
Abstract
Background: Recently, new evidence of the next-generation sequencing (NGS) liquid biopsy utility in clinical practice has been developed. This assay is emerging as a new promising tool to use as a noninvasive biomarker for cancer mutation profiling. Additional data supporting the clinical validity of cell free DNA (cfDNA) based testing is necessary to inform optimal use of these assays in the clinic. Materials and methods: A total of 398 cancer patients were analyzed by FoundationOne Liquid Analysis (F1LA), a genomic profiling assay and by standard NGS diagnostic ThermoFisher platform. The association between diagnostic technique was evaluated using a Poisson regression model. FoundationOne Liquid (F1L) and FoundationOne Liquid CDx (F1LCDx) detect 70 and 324 cancer-related genes alterations, respectively, including genomic signatures tumor fraction, blood tumor mutational burden (only for the 324 genes version), and microsatellite instability high status. Both assays used a single DNA extraction method to obtain cfDNA. The real-life clinical impact and feasibility of F1L and F1LCDx were evaluated across different solid tumors in our department. Results: Between 1 January 2019 and 28 February 2021, 398 samples of different tumor types from 398 patients were analyzed (overall success rate: 92%, in FoundationOne Liquid CDx Analysis success rate: 97%). Most frequent molecular alterations were TP53 (74), APC (40), DNMT3A (39), KRAS (23). The comprehensive clinical impact of F1LA compared with standard diagnostic was 64.7% versus 22.1% [risk ratio (RR) = 2.94; p < 0.001] and the potential clinical impact was 58.6% versus 11.0% (RR = 5.32; p < 0.001), respectively. Furthermore, some clinical cases were selected, in which F1LA detected actionable alterations offering an unexpected therapeutic choice. Conclusions: Although additional studies are needed to better select patients and setting, NGS F1LA is a useful, noninvasive, and repeatable assay to guide therapeutic choice in oncology. It provides a snapshot of cancer heterogeneity profile that could be incorporated in routinely clinical practice.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Vincenzo De Falco
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Anna Ventriglia
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Vincenzo Famiglietti
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Erika Martinelli
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Davide Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
- Oncology Unit, Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Luca Poliero
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Ferdinando De Vita
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Michele Orditura
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Morena Fasano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Michele Caraglia
- Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | | | | | | | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Teresa Troiani
- Full Professor, Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Via S. Pansini 5, Napoli 80131, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Via S. Pansini 5, Napoli 80131, Italy
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Dziadziuszko R, Peters S, Mok T, Camidge DR, Gadgeel SM, Ou SHI, Konopa K, Noé J, Nowicka M, Bordogna W, Morcos PN, Smoljanovic V, Shaw AT. Circulating Cell-free DNA as a Prognostic Biomarker in Patients with Advanced ALK+ Non-small Cell Lung Cancer in the Global Phase III ALEX Trial. Clin Cancer Res 2022; 28:1800-1808. [PMID: 35275991 PMCID: PMC9365376 DOI: 10.1158/1078-0432.ccr-21-2840] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/11/2021] [Accepted: 02/21/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE We retrospectively assessed prognostic value of circulating cell-free DNA (cfDNA) using data from the phase III ALEX study in treatment-naïve, advanced ALK+ non-small cell lung cancer (NSCLC). PATIENTS AND METHODS Patients were randomized to receive twice-daily alectinib 600 mg (n = 152) or crizotinib 250 mg (n = 151). cfDNA was quantified from baseline plasma samples, with patients stratified into ≤median and >median cfDNA biomarker-evaluable populations (BEP). Effect of cfDNA concentration on outcomes was analyzed using a Cox regression model with treatment group as covariate, and in multivariate analyses. RESULTS Median cfDNA concentration in the BEP was 11.53 ng/mL (n = 276). A positive correlation was found between cfDNA concentration and number of lesions, organ lesion sites, and tumor size (sum of longest diameter; all P < 0.0001). In both treatment arms, patients in the >median BEP were more likely to experience disease progression than the ≤median BEP [alectinib adjusted HR = 2.04; 95% confidence interval (CI), 1.07-3.89; P = 0.0305 and crizotinib adjusted HR = 1.83; 95% CI, 1.11-3.00, P = 0.0169]. Median progression-free survival was longer with alectinib than crizotinib in both ≤median and >median BEPs (P < 0.0001). Overall survival data remain immature; survival probability was lower in the >median versus ≤median BEP in both treatment arms (alectinib HR = 2.52; 95% CI, 1.08-5.88; P = 0.0333 and crizotinib HR = 2.63; 95% CI, 1.27-5.47; P = 0.0096). CONCLUSIONS These data suggest that plasma cfDNA concentration may have prognostic value in advanced ALK+ NSCLC. Prospectively designed studies are warranted to investigate this finding.
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Affiliation(s)
- Rafal Dziadziuszko
- Medical University of Gdańsk, Gdańsk, Poland. ,Corresponding Author: Rafal Dziadziuszko, Medical University of Gdańsk, Marii Skłodowskiej-Curie 3a, 80-210 Gdańsk, Poland. Phone: 585-846-269; E-mail:
| | - Solange Peters
- Lausanne University Hospital, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Tony Mok
- State Key Laboratory of Translational Oncology, Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong, China
| | | | - Shirish M. Gadgeel
- Department of Internal Medicine, Henry Ford Cancer Institute/Henry Ford Health System, Detroit, Michigan
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | | | | | | | | | | | | | - Alice T. Shaw
- Massachusetts General Hospital, Boston, Massachsuetts
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43
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Poh J, Ngeow KC, Pek M, Tan KH, Lim JS, Chen H, Ong CK, Lim JQ, Lim ST, Lim CM, Goh BC, Choudhury Y. Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA. PLoS One 2022; 17:e0267389. [PMID: 35486650 PMCID: PMC9053827 DOI: 10.1371/journal.pone.0267389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA (cfDNA). The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (Epstein-Barr virus (EBV) and hepatitis B virus (HBV)) and microsatellite instability (MSI). Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF. In non-cancer samples, a high specificity (≥99.9999% per-base) was observed. The limit of detection for copy number alterations, EBV, HBV, and MSI were also empirically determined. Orthogonal comparison of epidermal growth factor receptor (EGFR) variant calls made by LiquidHALLMARK and a reference allele-specific polymerase chain reaction (AS-PCR) method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% circulating tumor DNA (ctDNA)-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.
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Affiliation(s)
- Jonathan Poh
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | | | - Michelle Pek
- Lucence Health Inc, Palo Alto, California, United States of America
| | - Kian-Hin Tan
- Lucence Health Inc, Palo Alto, California, United States of America
| | | | - Hao Chen
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | | | - Jing Quan Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Soon Thye Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Chwee Ming Lim
- Department of Otolaryngology-Head and Neck Surgery, Singapore General Hospital, Duke-NUS Medical School, Singapore, Singapore
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44
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Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus. Sci Rep 2022; 12:5362. [PMID: 35354850 PMCID: PMC8967894 DOI: 10.1038/s41598-022-08939-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 03/10/2022] [Indexed: 11/19/2022] Open
Abstract
The Alpine goat (Capra aegagrus hircus) is parasitized by the barber pole worm (Haemonchus contortus). Hematological parameters from transcript and metagenome analysis in the host are reflective of infestation. We explored comparisons between blood samples of control, infected, infected zoledronic acid-treated, and infected antibody (anti-γδ T cells) treated wethers under controlled conditions. Seven days post-inoculation (dpi), we identified 7,627 transcripts associated with the different treatment types. Microbiome measurements at 7 dpi revealed fewer raw read counts across all treatments and a less diverse microbial flora than at 21 dpi. This study identifies treatment specific transcripts and an increase in microflora abundance and diversity as wethers age. Further, F/B ratio reflect health, based on depression or elevation above thresholds defined by the baseline of non-infected controls. Forty Alpine wethers were studied where blood samples were collected from five goats in four treatment groups on 7 dpi and 21 dpi. Transcript and microbiome profiles were obtained using the Partek Flow (St. Louis, Missouri, USA) software suites pipelines. Inflammation comparisons were based on the Firmicutes/Bacteriodetes ratios that are calculated as well as the reduction of microbial diversity.
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45
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Maron SB, Moya S, Morano F, Emmett MJ, Chou JF, Sabwa S, Walch H, Peterson B, Schrock AB, Zhang L, Janjigian YY, Chalasani S, Ku GY, Disel U, Enzinger P, Uboha N, Kato S, Yoshino T, Shitara K, Nakamura Y, Saeed A, Kasi P, Chao J, Lee J, Capanu M, Wainberg Z, Petty R, Pietrantonio F, Klempner SJ, Catenacci DVT. Epidermal Growth Factor Receptor Inhibition in Epidermal Growth Factor Receptor-Amplified Gastroesophageal Cancer: Retrospective Global Experience. J Clin Oncol 2022; 40:2458-2467. [PMID: 35349370 PMCID: PMC9467681 DOI: 10.1200/jco.21.02453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Subset analyses from phase III evaluation of epidermal growth factor receptor inhibition (EGFRi) suggest improved outcomes in patients with EGFR-amplified gastroesophageal adenocarcinoma (GEA), but large-scale analyses are lacking. This multi-institutional analysis sought to determine the role of EGFRi in the largest cohort of patients with EGFR-amplified GEA to date. PATIENTS AND METHODS A total of 60 patients from 15 tertiary cancer centers in six countries met the inclusion criteria. These criteria required histologically confirmed GEA in the metastatic or unresectable setting with EGFR amplification identified by using a Clinical Laboratory Improvement Amendments-approved assay, and who received on- or off-protocol EGFRi. Testing could be by tissue next-generation sequencing, plasma circulating tumor DNA next-generation sequencing, and/or fluorescence in situ hybridization performed by a Clinical Laboratory Improvement Amendments approved laboratory. Treatment patterns and outcomes analysis was also performed using a deidentified clinicogenomic database (CGDB). RESULTS Sixty patients with EGFR-amplified GEA received EGFRi, including 31 of 60 patients (52%) with concurrent chemotherapy. Across treatment lines, patients achieved a 43% objective response rate with a median progression-free survival of 4.6 months (95% CI, 3.5 to 6.4). Patients receiving EGFRi in first-, second-, and third-line therapy achieved a median overall survival of 20.6 months (95% CI, 13.5 to not reached [NR]), 9 months (95% CI, 7.9 to NR), and 8.4 months (7.6 to NR), respectively. This survival far exceeded the 11.2-month (95% CI, 8.7 to 14.2) median overall survival from first-line initiation of non-EGFRi therapy in patients with EGFR-amplified GEA in the CGDB. Despite this benefit, analysis of the CGDB (January 2011-December 2020) suggests that only 5% of patients with EGFR-amplified GEA received EGFRi. CONCLUSION Patients with EGFR-amplified GEA derive significant benefit from EGFRi. Further prospective investigation of EGFRi in a well-selected patient population is ongoing in an upcoming trial of amivantamab in EGFR and/or MET amplified GEA.
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Affiliation(s)
- Steven B Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Stephanie Moya
- Department of Medicine, Division of Hematology-Oncology, University of Chicago School of Medicine, Chicago, IL
| | - Federica Morano
- Oncologia Medica, Instituto Nazionale dei Tumori di Milano, Milan, Italy
| | | | - Joanne F Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shalom Sabwa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Henry Walch
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bryan Peterson
- Department of Medicine, Division of Hematology-Oncology, University of Chicago School of Medicine, Chicago, IL
| | | | | | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Sree Chalasani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Umut Disel
- Department of Medical Oncology, Adana Acibadem Hospital, Adana, Turkey
| | - Peter Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Nataliya Uboha
- Department of Medicine, Section of Hematology & Oncology, Carbone Cancer Center, University of Wisconsin, Madison, WI
| | - Shumei Kato
- Department of Medicine, University of California San Diego Moores Cancer Center, La Jolla, CA
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Anwaar Saeed
- Department of Medicine, Division of Medical Oncology, Kansas University Cancer Center, Kansas City, KS
| | - Pashtoon Kasi
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Department of Medicine, University of Iowa, Iowa City, IA
| | - Joseph Chao
- Department of Developmental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zev Wainberg
- Division of Oncology, Department of Medicine, UCLA School of Medicine, Los Angeles, CA
| | - Russell Petty
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, United Kingdom
| | | | | | - Daniel V T Catenacci
- Department of Medicine, Division of Hematology-Oncology, University of Chicago School of Medicine, Chicago, IL
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Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6:232-245. [PMID: 35102279 PMCID: PMC9336539 DOI: 10.1038/s41551-021-00837-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia Ruojia Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tianqing Chu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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47
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Lee JK, Hazar-Rethinam M, Decker B, Gjoerup O, Madison RW, Lieber DS, Chung JH, Schrock AB, Creeden J, Venstrom J, Alexander B, Oxnard GR. The Pan-Tumor Landscape of Targetable Kinase Fusions in Circulating Tumor DNA. Clin Cancer Res 2022; 28:728-737. [PMID: 34753780 PMCID: PMC9377769 DOI: 10.1158/1078-0432.ccr-21-2136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/15/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Oncogenic kinase fusions are targetable with approved and investigational therapies and can also mediate acquired resistance (AR) to targeted therapy. We aimed to understand the clinical validity of liquid biopsy comprehensive genomic profiling (CGP) to detect kinase fusions pan tumor. EXPERIMENTAL DESIGN CGP was performed on plasma and tissue samples during clinical care. All exons plus selected introns of 16 kinases involved in oncogenic fusions (ALK, BRAF, EGFR, ERBB2, FGFR1/2/3, MET, NTRK1/2/3, PDGFRA/B, RAF1, RET, and ROS1) were sequenced to capture fusions, including well-characterized and novel breakpoints. Plasma circulating tumor DNA (ctDNA) fraction was estimated to inform sensitivity. RESULTS Of 36,916 plasma cases, 32,492 (88%) had detectable ctDNA. Kinase fusions were detected in 1.8% of ctDNA-positive cases (571/32,492) and were most prevalent in patients with cholangiocarcinoma (4.2%), bladder cancer (3.6%), and non-small cell lung cancer (NSCLC; 3.1%). Of the 63 paired patient samples that had tissue and ctDNA specimens collected within 1 year and with estimated plasma ctDNA fraction >1%, fusions were detected in 47 of 51 (92%) liquid specimens with a fusion in the tissue sample. In 32 patients with fusions detected in liquid but not in tissue, 21 (66%) had evidence of putative acquired resistance. CONCLUSIONS Targetable kinase fusions are identified in ctDNA across cancer types. In pairs with tissue-identified fusions, fusion detection in ctDNA is reliable with elevated ctDNA fraction. These data support the validity of CGP to enable ctDNA-based fusion detection for informing clinical care in patients with advanced cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Geoffrey R. Oxnard
- Corresponding Author: Geoffrey R. Oxnard, Clinical Development, Foundation Medicine, Cambridge, MA 02141. Phone: 617-418-2200; E-mail:
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Paz-Ares L, Gondos A, Saldana D, Thomas M, Mascaux C, Bubendorf L, Barlesi F. Genomic testing among patients with newly diagnosed advanced non-small cell lung cancer in the United States: A contemporary clinical practice patterns study. Lung Cancer 2022; 167:41-48. [DOI: 10.1016/j.lungcan.2022.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 12/25/2022]
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49
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Xu D, Li J, Wang D, Zhou L, Jin J, Wang Y. Prediction performance of twelve tumor mutation burden panels in melanoma and non-small cell lung cancer. Crit Rev Oncol Hematol 2021; 169:103573. [PMID: 34933103 DOI: 10.1016/j.critrevonc.2021.103573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/14/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
As a potential biomarker to predict the response to immunotherapy, tumor mutation burden (TMB) which can be estimated by the cancer gene panel (CGP) has received considerable attention. However, it is not clear which CGP is better in predicting the efficacy of immunotherapy. To evaluate the twelve CGPs, we compared them on 13 datasets of melanoma and non-small cell lung cancer (NSCLC) from the perspective of gene composition, reliability of measuring TMB and prediction performance of patient treatment benefits. The larger CGPs generally performed better, but their proportions of driver genes and function densities were smaller. The CGPs performed differently on melanoma and NSCLC patients treated with two blockades. Moreover, their ability to classify and predict patients with or without long-term clinical benefits was similar but not good enough, so it is necessary to explore a higher-performance biomarker.
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Affiliation(s)
- Dechen Xu
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, Heilongjiang Province, China.
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, Heilongjiang Province, China.
| | - Dong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, Heilongjiang Province, China.
| | - Li Zhou
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, Heilongjiang Province, China.
| | - Jiahuan Jin
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, Heilongjiang Province, China.
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, Heilongjiang Province, China.
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50
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Loehr A, Patnaik A, Campbell D, Shapiro J, Bryce AH, McDermott R, Sautois B, Vogelzang NJ, Bambury RM, Voog E, Zhang J, Piulats JM, Hussain A, Ryan CJ, Merseburger AS, Daugaard G, Heidenreich A, Fizazi K, Higano CS, Krieger LE, Sternberg CN, Watkins SP, Despain D, Simmons AD, Dowson M, Golsorkhi T, Chowdhury S, Abida W. Response to Rucaparib in BRCA-Mutant Metastatic Castration-Resistant Prostate Cancer Identified by Genomic Testing in the TRITON2 Study. Clin Cancer Res 2021; 27:6677-6686. [PMID: 34598946 PMCID: PMC8678310 DOI: 10.1158/1078-0432.ccr-21-2199] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/18/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The PARP inhibitor rucaparib is approved in the United States for patients with metastatic castration-resistant prostate cancer (mCRPC) and a deleterious germline and/or somatic BRCA1 or BRCA2 (BRCA) alteration. While sequencing of tumor tissue is considered the standard for identifying patients with BRCA alterations (BRCA+), plasma profiling may provide a minimally invasive option to select patients for rucaparib treatment. Here, we report clinical efficacy in patients with BRCA+ mCRPC identified through central plasma, central tissue, or local genomic testing and enrolled in TRITON2. PATIENTS AND METHODS Patients had progressed after next-generation androgen receptor-directed and taxane-based therapies for mCRPC and had BRCA alterations identified by central sequencing of plasma and/or tissue samples or local genomic testing. Concordance of plasma/tissue BRCA status and objective response rate and prostate-specific antigen (PSA) response rates were summarized. RESULTS TRITON2 enrolled 115 patients with BRCA+ identified by central plasma (n = 34), central tissue (n = 37), or local (n = 44) testing. Plasma/tissue concordance was determined in 38 patients with paired samples and was 47% in 19 patients with a somatic BRCA alteration. No statistically significant differences were observed between objective and PSA response rates to rucaparib across the 3 assay groups. Patients unable to provide tissue samples and tested solely by plasma assay responded at rates no different from patients identified as BRCA+ by tissue testing. CONCLUSIONS Plasma, tissue, and local testing of mCRPC patients can be used to identify men with BRCA+ mCRPC who can benefit from treatment with the PARP inhibitor rucaparib.
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Affiliation(s)
- Andrea Loehr
- Translational Medicine, Clovis Oncology, Inc., Boulder, Colorado
| | - Akash Patnaik
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - David Campbell
- Medical Oncology, Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia
| | - Jeremy Shapiro
- Medical Oncology, Cabrini Hospital, Malvern, Victoria, Australia
| | - Alan H Bryce
- Hematology and Medical Oncology, Mayo Clinic, Phoenix, Arizona
| | - Ray McDermott
- Genitourinary Oncology, Adelaide and Meath Hospital (Incorporating the National Children's Hospital), Dublin, Ireland
| | - Brieuc Sautois
- Department of Medical Oncology, University Hospital of Liège, CHU Sart Tilman, Liège, Belgium
| | | | | | - Eric Voog
- Medical Oncology, Clinique Victor Hugo Centre Jean Bernard, Le Mans, France
| | - Jingsong Zhang
- Genitourinary Oncology Program, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Josep M Piulats
- Medical Oncology, Institut Català d'Oncologia, Barcelona, Spain
| | - Arif Hussain
- Department of Medicine, Greenebaum Cancer Center, Baltimore, Maryland
| | - Charles J Ryan
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | | | - Gedske Daugaard
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Axel Heidenreich
- Department of Urology, Universitätsklinikum Köln, Cologne, Germany
| | - Karim Fizazi
- Department of Cancer Medicine, Institut Gustave Roussy, University of Paris Saclay, Villejuif Cedex, France
| | - Celestia S Higano
- Department of Medicine, Division of Oncology, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Laurence E Krieger
- Oncology, Genesis Care Integrative Cancer Centre, St Leonards, Sydney, New South Wales, Australia
| | - Cora N Sternberg
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York-Presbyterian, New York, New York
| | - Simon P Watkins
- Clinical Science, Clovis Oncology UK, Ltd., Cambridge, United Kingdom
| | | | - Andrew D Simmons
- Translational Medicine, Clovis Oncology, Inc., Boulder, Colorado
| | - Melanie Dowson
- Study Operations, Clovis Oncology UK, Ltd., Cambridge, United Kingdom
| | - Tony Golsorkhi
- Clinical Development, Clovis Oncology, Inc., Boulder, Colorado
| | - Simon Chowdhury
- Medical Oncology, Guy's Hospital and Sarah Cannon Research Institute, London, United Kingdom
| | - Wassim Abida
- Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.
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