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Chen C, Douglas MP, Ragavan MV, Phillips KA, Jansen JP. Clinical Validity and Utility of Circulating Tumor DNA (ctDNA) Testing in Advanced Non-small Cell Lung Cancer (aNSCLC): A Systematic Literature Review and Meta-analysis. Mol Diagn Ther 2024; 28:525-536. [PMID: 39093546 DOI: 10.1007/s40291-024-00725-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 08/04/2024]
Abstract
PURPOSE Circulating tumor DNA (ctDNA) testing has become a promising tool to guide first-line (1L) targeted treatment for advanced non-small cell lung cancer (aNSCLC). This study aims to estimate the clinical validity (CV) and clinical utility (CU) of ctDNA-based next-generation sequencing (NGS) for oncogenic driver mutations to inform 1L treatment decisions in aNSCLC through a systematic literature review and meta-analysis. METHODS A systematic literature search was conducted in PubMed/MEDLINE and Embase to identify randomized control trials or observational studies reporting CV/CU on ctDNA testing in patients with aNSCLC. Meta-analyses were performed using bivariate random-effects models to estimate pooled sensitivity and specificity. Progression-free/overall survival (PFS/OS) was summarized for CU studies. RESULTS A total of 20 studies were identified: 17 CV only, 2 CU only, and 1 both, and 13 studies were included for the meta-analysis on multi-gene detection. The overall sensitivity and specificity for ctDNA detection of any mutation were 0.69 (95% CI 0.63-0.74) and 0.99 (95% CI 0.97-1.00), respectively. However, sensitivity varied greatly by driver gene, ranging from 0.29 (95% CI 0.13-0.53) for ROS1 to 0.77 (95% CI 0.63-0.86) for KRAS. Two studies that compared PFS with ctDNA versus tissue-based testing followed by 1L targeted therapy found no significant differences. One study reported OS curves on ctDNA-matched and tissue-matched therapies but no hazard ratios were provided. CONCLUSIONS ctDNA testing demonstrated an overall acceptable diagnostic accuracy in patients with aNSCLC, however, sensitivity varied greatly by driver mutation. Further research is needed, especially for uncommon driver mutations, to better understand the CU of ctDNA testing in guiding targeted treatments for aNSCLC.
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Affiliation(s)
- Cheng Chen
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA, USA
| | - Michael P Douglas
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA, USA
| | - Meera V Ragavan
- Division of Hematology and Oncology, UCSF Department of Medicine, San Francisco, CA, USA
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- UCSF Philip R. Lee Institute for Health Policy, San Francisco, CA, USA
| | - Jeroen P Jansen
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- UCSF Philip R. Lee Institute for Health Policy, San Francisco, CA, USA.
- Department of Clinical Pharmacy, School of Pharmacy, University of California San Francisco, 490 Illinois St. Valley Tower, 3rd Floor, Box 0613, San Francisco, CA, 94143, USA.
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Liu SY, Erazo T, Jee J, Arfe A, Gupta A, Pike LRG, Santini FC, Daly B, Schoenfeld A, Eichholz J, Johnson K, Martinez A, Sui J, Riaz N, Chang J, Yang SR, Travis W, Arcila ME, Guo J, Gagne E, Garg K, Baehner F, Lee NY, Drilon A, Kris MG, Scher HI, Razavi P, Gomez DR, Jones DR, Rudin CM, Chandarlapaty S, Isbell JM, Li BT. Optimal systemic treatment and real-world clinical application of ctDNA in patients with metastatic HER2-mutant lung cancer. Eur J Cancer 2024; 210:114257. [PMID: 39151324 DOI: 10.1016/j.ejca.2024.114257] [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: 04/30/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/19/2024]
Abstract
INTRODUCTION No definitive answers currently exist regarding optimal first-line therapy for HER2-mutant NSCLC. Access to rapid tissue sequencing is a major barrier to precision drug development in the first-line setting. ctDNA analysis has the potential to overcome these obstacles and guide treatment. METHODS We retrospectively analyzed patients with metastatic HER2-mutant NSCLC who underwent prospective clinical ctDNA sequencing and received systemic therapy at Memorial Sloan Kettering Cancer Center (MSK) from January 2016 to September 2022. HER2 mutations were identified by next-generation sequencing through MSK-IMPACT, MSK-ACCESS or Resolution ctDx LungTM assay. Primary endpoints were time to the next treatment (TTNT) and overall survival (OS). RESULTS Sixty-three patients were included in the primary analysis. Chemoimmunotherapy (33/63, 52.4 %) was the predominant first-line treatment with a median TTNT of 5.1 months (95 %CI 4.1 - 6.1) whereas 55.0 % (22/40) of patients who received second-line T-DXd obtained a median TTNT of 9.2 m (95 % CI, 0-22.2). Plasma ctDNA was tested before first-line therapy in 40 patients with a median OS of 28.0 months (95 % CI 21-34), in whom 31 patients (78.0 %) had detectable ctDNA. HER2 mutations were detected on ctDNA with a median turnaround time of 13 days, occasionally co-occurred with EGFR and MET alterations and were tracked longitudinally correlating with treatment response. Patients with detectable baseline ctDNA had significantly shorter OS (hazard ratio (HR), 5.25; 95 % CI, 1.2-23.9; p = 0.019). CONCLUSION Chemoimmunotherapy remains a major treatment option for metastatic HER2-mutant NSCLC. ctDNA can rapidly detect HER2 and co-mutations, and it has the potential to guide and monitor optimal first-line therapy. As a negative prognostic biomarker, detectable ctDNA at baseline would need to be taken into account for patient selection in future studies.
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Affiliation(s)
- Si-Yang Liu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Chinese Thoracic Oncology Group, Guangzhou, China
| | - Tatiana Erazo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Arfe
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Avantika Gupta
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luke R G Pike
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fernando C Santini
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bobby Daly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Kaylie Johnson
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jane Sui
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Chang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William Travis
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiannan Guo
- Resolution Bioscience, Exact Sciences, Kirkland, WA, USA
| | - Eric Gagne
- Resolution Bioscience, Exact Sciences, Kirkland, WA, USA
| | - Kavita Garg
- Resolution Bioscience, Exact Sciences, Kirkland, WA, USA
| | | | - Nancy Y Lee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel R Gomez
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sarat Chandarlapaty
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - James M Isbell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medicine, Cornell University, New York, NY, USA.
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Casolino R, Beer PA, Chakravarty D, Davis MB, Malapelle U, Mazzarella L, Normanno N, Pauli C, Subbiah V, Turnbull C, Westphalen CB, Biankin AV. Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance. CA Cancer J Clin 2024; 74:264-285. [PMID: 38174605 DOI: 10.3322/caac.21825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The last decade has seen rapid progress in the use of genomic tests, including gene panels, whole-exome sequencing, and whole-genome sequencing, in research and clinical cancer care. These advances have created expansive opportunities to characterize the molecular attributes of cancer, revealing a subset of cancer-associated aberrations called driver mutations. The identification of these driver mutations can unearth vulnerabilities of cancer cells to targeted therapeutics, which has led to the development and approval of novel diagnostics and personalized interventions in various malignancies. The applications of this modern approach, often referred to as precision oncology or precision cancer medicine, are already becoming a staple in cancer care and will expand exponentially over the coming years. Although genomic tests can lead to better outcomes by informing cancer risk, prognosis, and therapeutic selection, they remain underutilized in routine cancer care. A contributing factor is a lack of understanding of their clinical utility and the difficulty of results interpretation by the broad oncology community. Practical guidelines on how to interpret and integrate genomic information in the clinical setting, addressed to clinicians without expertise in cancer genomics, are currently limited. Building upon the genomic foundations of cancer and the concept of precision oncology, the authors have developed practical guidance to aid the interpretation of genomic test results that help inform clinical decision making for patients with cancer. They also discuss the challenges that prevent the wider implementation of precision oncology.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Hull York Medical School, York, UK
| | | | - Melissa B Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Luca Mazzarella
- Laboratory of Translational Oncology and Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, Tennessee, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - C Benedikt Westphalen
- Department of Medicine III, Ludwig Maximilians University (LMU) Hospital Munich, Munich, Germany
- Comprehensive Cancer Center, LMU Hospital Munich, Munich, Germany
- German Cancer Consortium, LMU Hospital Munich, Munich, Germany
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Liverpool, New South Wales, Australia
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Li W, Fei K, Guo L, Wang Y, Shu C, Wang J, Ying J. CD74/SLC34A2-ROS1 Fusion Variants Involving the Transmembrane Region Predict Poor Response to Crizotinib in NSCLC Independent of TP53 Mutations. J Thorac Oncol 2024; 19:613-625. [PMID: 38070598 DOI: 10.1016/j.jtho.2023.12.009] [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: 07/12/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/31/2023]
Abstract
INTRODUCTION Variable partners and breakpoints have been reported in patients with ROS1-rearranged NSCLC. Here, we investigated the association of fusion partners and breakpoints with crizotinib efficacy in NSCLCs with common ROS1 fusions. METHODS DNA and RNA next-generation sequencing (NGS) and immunohistochemistry were performed to characterize ROS1 fusions. RESULTS Using DNA NGS, we identified ROS1 fusions in 210 cases, comprising 171 common (CD74/EZR/TPM3/SDC4/SLC34A2-ROS1) and 39 uncommon (variants identified in <5%) ROS1 fusion cases. DNA NGS detected variable ROS1 genomic breakpoints in common ROS1 fusions, whereas RNA NGS found ROS1 breakpoints mainly occurring in exons 32, 34 and 35, resulting in long (exon 32) and short (exon 34 or 35) ROS1 fusions. ROS1 immunohistochemistry revealed that membranous and cytoplasmic staining was predominant in long ROS1 fusions, whereas cytoplasmic staining was predominant in short ROS1 fusions (p = 0.006). For patients who received first-line crizotinib, median progression-free survival (mPFS) was lower in patients with long ROS1 fusions than those with short ROS1 fusions (8.0 versus 24.0 mo, p = 0.006). Moreover, mPFS for patients with and without TP53 mutations was 8.0 and 19.0 months, respectively (p = 0.159); mPFS for patients with and without BIM deletion polymorphism was 5.0 and 22.0 months, respectively (p = 0.003). When analyzing together with fusion partners, patients with long CD74/SLC34A2-ROS1 fusions were found to have shorter PFS than those with other ROS1, regardless of the presence or absence of TP53 mutations (p < 0.001 and p = 0.002, respectively). CONCLUSIONS Long CD74/SLC34A2-ROS1 fusions, which retain transmembrane regions in ROS1 and fusion partners, are associated with poor response to crizotinib independent of TP53 mutations.
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Affiliation(s)
- Weihua Li
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Kailun Fei
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Lei Guo
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Yulan Wang
- Beijing Novogene Bioinformatics Technology Co., Ltd., Beijing, People's Republic of China
| | - Chang Shu
- Beijing Novogene Bioinformatics Technology Co., Ltd., Beijing, People's Republic of China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jianming Ying
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
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Friedlaender A, Perol M, Banna GL, Parikh K, Addeo A. Oncogenic alterations in advanced NSCLC: a molecular super-highway. Biomark Res 2024; 12:24. [PMID: 38347643 PMCID: PMC10863183 DOI: 10.1186/s40364-024-00566-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024] Open
Abstract
Lung cancer ranks among the most common cancers world-wide and is the first cancer-related cause of death. The classification of lung cancer has evolved tremendously over the past two decades. Today, non-small cell lung cancer (NSCLC), particularly lung adenocarcinoma, comprises a multitude of molecular oncogenic subsets that change both the prognosis and management of disease.Since the first targeted oncogenic alteration identified in 2004, with the epidermal growth factor receptor (EGFR), there has been unprecedented progress in identifying and targeting new molecular alterations. Almost two decades of experience have allowed scientists to elucidate the biological function of oncogenic drivers and understand and often overcome the molecular basis of acquired resistance mechanisms. Today, targetable molecular alterations are identified in approximately 60% of lung adenocarcinoma patients in Western populations and 80% among Asian populations. Oncogenic drivers are largely enriched among non-smokers, east Asians, and younger patients, though each alteration has its own patient phenotype.The current landscape of druggable molecular targets includes EGFR, anaplastic lymphoma kinase (ALK), v-raf murine sarcoma viral oncogene homolog B (BRAF), ROS proto-oncogene 1 (ROS1), Kirstin rat sarcoma virus (KRAS), human epidermal receptor 2 (HER2), c-MET proto-oncogene (MET), neurotrophic receptor tyrosine kinase (NTRK), rearranged during transfection (RET), neuregulin 1 (NRG1). In addition to these known targets, others including Phosphoinositide 3-kinases (PI3K) and fibroblast growth factor receptor (FGFR) have garnered significant attention and are the subject of numerous ongoing trials.In this era of personalized, precision medicine, it is of paramount importance to identify known or potential oncogenic drivers in each patient. The development of targeted therapy is mirrored by diagnostic progress. Next generation sequencing offers high-throughput, speed and breadth to identify molecular alterations in entire genomes or targeted regions of DNA or RNA. It is the basis for the identification of the majority of current druggable alterations and offers a unique window into novel alterations, and de novo and acquired resistance mechanisms.In this review, we discuss the diagnostic approach in advanced NSCLC, focusing on current oncogenic driver alterations, through their pathophysiology, management, and future perspectives. We also explore the shortcomings and hurdles encountered in this rapidly evolving field.
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Affiliation(s)
- Alex Friedlaender
- Clinique Générale Beaulieu, Geneva, Switzerland
- Oncology Department, University Hospital Geneva, Rue Gentil Perret 4. 1205, Geneva, Switzerland
| | - Maurice Perol
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Giuseppe Luigi Banna
- Portsmouth Hospitals University NHS Trust, Portsmouth, UK
- Faculty of Science and Health, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | | | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Rue Gentil Perret 4. 1205, Geneva, Switzerland.
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Gray JE, Han JY, Telaranta-Keerie A, Huang X, Kohlmann A, Hodge R, Rukazenkov Y, Chmielecki J, Espenschied CR, Lefterova M, Wu YL, Ramalingam SS, Barrett JC, Odegaard JI. Pan-Tumor Analytical Validation and Osimertinib Clinical Validation in EGFR Mutant Non-Small-Cell Lung Cancer, Supporting the First Next-Generation Sequencing Liquid Biopsy in Vitro Diagnostic. J Mol Diagn 2024; 26:73-84. [PMID: 37981090 DOI: 10.1016/j.jmoldx.2023.10.002] [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: 12/21/2022] [Revised: 08/22/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
Comprehensive genotyping is necessary to identify therapy options for patients with advanced cancer; however, many cancers are not tested, partly because of tissue limitations. Next-generation sequencing (NGS) liquid biopsies overcome some limitations, but clinical validity is not established and adoption is limited. Herein, clinical bridging studies used pretreatment plasma samples and data from FLAURA (NCT02296125; n = 441) and AURA3 (NCT02151981; n = 450) pivotal studies to demonstrate clinical validity of Guardant360 CDx (NGS LBx) to identify patients with advanced EGFR mutant non-small-cell lung cancer who may benefit from osimertinib. The primary end point was progression-free survival (PFS). Patients with EGFR mutation as identified by NGS LBx had significant PFS benefit with first-line osimertinib over standard of care (15.2 versus 9.6 months; hazard ratio, 0.41; P < 0.0001) and with later-line osimertinib over chemotherapy (8.3 versus 4.2 months; hazard ratio, 0.34; P < 0.0001). PFS benefits were similar to the original trial cohorts selected by tissue-based EGFR testing. Analytical validation included accuracy, precision, limit of detection, and specificity. Analytical validity was established for EGFR mutation detection and pan-tumor profiling. Panel-wide limit of detection was 0.1% to 0.5%, with 98% to 100% per-sample specificity. Patients with EGFR mutant non-small-cell lung cancer by NGS LBx had improved PFS with osimertinib, confirming clinical validity. Analytical validity was established for guideline-recommended therapeutic targets across solid tumors. The resulting US Food and Drug Administration approval of NGS LBx demonstrated safety and effectiveness for its intended use and is expected to improve adherence to guideline-recommended targeted therapy use.
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Affiliation(s)
- Jhanelle E Gray
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Aino Telaranta-Keerie
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Melbourn Royston, United Kingdom
| | - Xiangning Huang
- Oncology Biometrics, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Alexander Kohlmann
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Gaithersburg, Maryland
| | - Rachel Hodge
- Oncology Biometrics, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Yuri Rukazenkov
- Global Medicines Development, AstraZeneca, Cambridge, United Kingdom
| | - Juliann Chmielecki
- Translational Medicine, Early Research and Development, AstraZeneca, Waltham, Massachusetts
| | | | | | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial Peoples Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Suresh S Ramalingam
- Emory University School of Medicine, Winship Cancer Institute, Atlanta, Georgia
| | - J Carl Barrett
- Translational Medicine, Early Research and Development, AstraZeneca, Waltham, Massachusetts
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Lin Y, Ho C, Hsu W, Liao W, Yang C, Yu C, Tsai T, Yang JC, Wu S, Hsu C, Hsieh M, Huang Y, Wu C, Shih J. Tissue or liquid rebiopsy? A prospective study for simultaneous tissue and liquid NGS after first-line EGFR inhibitor resistance in lung cancer. Cancer Med 2024; 13:e6870. [PMID: 38140788 PMCID: PMC10807591 DOI: 10.1002/cam4.6870] [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: 09/22/2023] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
INTRODUCTION According to current International Association for the Study of Lung Cancer guideline, physicians may first use plasma cell-free DNA (cfDNA) methods to identify epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI)-resistant mechanisms (liquid rebiopsy) for lung cancer. Tissue rebiopsy is recommended if the plasma result is negative. However, this approach has not been evaluated prospectively using next-generation sequencing (NGS). METHODS We prospectively enrolled patients with lung cancer with first-line EGFR-TKI resistance who underwent tissue rebiopsy. The rebiopsied tissues and cfDNA were sequenced using targeted NGS, ACTDrug®+, and ACTMonitor®Lung simultaneously. The clinicopathological characteristics and treatment outcomes were analyzed. RESULTS Totally, 86 patients were enrolled. Twenty-six (30%) underwent tissue biopsy but the specimens were inadequate for NGS. Among the 60 patients with paired tissue and liquid rebiopsies, two-thirds (40/60) may still be targetable. T790M mutations were found in 29, including 14 (48%) only from tissue and 5 (17%) only from cfDNA. Twenty-four of them were treated with osimertinib, and progression-free survival was longer in patients without detectable T790M in cfDNA than in patients with detectable T790M in cfDNA (p = 0.02). For the 31 T790M-negative patients, there were six with mesenchymal-epithelial transition factor (MET) amplifications, four with ERBB2 amplifications, and one with CCDC6-RET fusion. One with MET amplification and one with ERBB2 amplification responded to subsequent MET and ERBB2 targeting agents respectively. CONCLUSIONS NGS after EGFR-TKI resistance may detect targetable drivers besides T790M. To do either liquid or tissue NGS only could miss patients with T790M. To do tissue and liquid NGS in parallel after EGFR-TKI resistance may find more patients with targetable cancers.
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Affiliation(s)
- Yen‐Ting Lin
- Graduate Institute of Clinical MedicineNational Taiwan University College of MedicineTaipeiTaiwan
- Department of MedicineNational Taiwan University Cancer CenterTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Chao‐Chi Ho
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Wei‐Hsun Hsu
- Department of Medical ResearchNational Taiwan University HospitalTaipeiTaiwan
| | - Wei‐Yu Liao
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Ching‐Yao Yang
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Chong‐Jen Yu
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital Hsin‐Chu BranchHsin‐ChuTaiwan
| | - Tzu‐Hsiu Tsai
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - James Chih‐Hsin Yang
- Department of Medical OncologyNational Taiwan University Cancer CenterTaipeiTaiwan
- Department of OncologyNational Taiwan University HospitalTaipeiTaiwan
- Graduate Institute of OncologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Shang‐Gin Wu
- Department of MedicineNational Taiwan University Cancer CenterTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Chia‐Lin Hsu
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Min‐Shu Hsieh
- Department of PathologyNational Taiwan University HospitalTaipeiTaiwan
- Department of PathologyNational Taiwan University Cancer CenterTaipeiTaiwan
| | - Yen‐Lin Huang
- Department of PathologyNational Taiwan University Cancer CenterTaipeiTaiwan
| | | | - Jin‐Yuan Shih
- Graduate Institute of Clinical MedicineNational Taiwan University College of MedicineTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
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Mi J, Wang R, Han X, Ma R, Li H. Circulating tumor DNA predicts recurrence and assesses prognosis in operable gastric cancer: A systematic review and meta-analysis. Medicine (Baltimore) 2023; 102:e36228. [PMID: 38050202 PMCID: PMC10695564 DOI: 10.1097/md.0000000000036228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Selecting the appropriate patient for further treatment after surgery for gastric cancer can improve the patient prognosis. Circulating tumor DNA (ctDNA) has the potential to predict recurrence and prognosis after gastric cancer surgery, but the results are still inconclusive. As the completed studies had small sample sizes and were inconsistent, a meta-analysis was conducted to assess the effect of ctDNA on recurrence and prognosis after gastric cancer surgery. METHODS PubMed, Embase, Scopus, and the Web of Science were searched for potentially eligible studies published up to April 7, 2023. Pooled relative risk (RR) and pooled hazard ratio (HR) were calculated to evaluate recurrence, recurrence-free survival (RFS), and overall survival (OS) following gastric cancer surgery. RESULTS A pooled analysis revealed that patients who were ctDNA positive before and after surgery were at a high risk of gastric cancer recurrence (RR = 1.79, 95% CI: 1.19-2.71; RR = 3.17, 95% CI: 2.36-4.25). The pooled data revealed that ctDNA-positive patients had a poorer RFS and OS (HR = 6.37, 95% CI: 2.70-15.01; HR = 4.58, 95% CI: 1.68-12.49). CONCLUSIONS ctDNA-positive patients were at a high risk of recurrence after gastric cancer surgery and had a poorer prognosis. Hence, ctDNA-positive patients needed close follow-up and further treatment.
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Affiliation(s)
- Junjie Mi
- Department of Gastroenterology, Shanxi Provincial People’s Hospital (The Fifth Hospital of Shanxi Medical University), Taiyuan, China
| | - Rong Wang
- Department of Gastroenterology, Shanxi Provincial People’s Hospital (The Fifth Hospital of Shanxi Medical University), Taiyuan, China
| | - Xiaofang Han
- Core Laboratory, Shanxi Provincial People’s Hospital (The Fifth Hospital of Shanxi Medical University), Taiyuan, China
| | - Ruijun Ma
- Department of Gastroenterology, Shanxi Provincial People’s Hospital (The Fifth Hospital of Shanxi Medical University), Taiyuan, China
| | - Huiying Li
- Fenyang College of Shanxi Medical University, Fenyang, China
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Chen C, Douglas MP, Ragavan MV, Phillips KA, Jansen JP. Clinical validity and utility of circulating tumor DNA (ctDNA) testing in advanced non-small cell lung cancer (aNSCLC): a systematic literature review and meta-analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.27.23297657. [PMID: 37961510 PMCID: PMC10635208 DOI: 10.1101/2023.10.27.23297657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Purpose Circulating tumor DNA (ctDNA) testing has become a promising tool to guide first-line (1L) targeted treatment for advanced non-small cell lung cancer (aNSCLC). This study aims to estimate the clinical validity (CV) and clinical utility (CU) of ctDNA-based next-generation sequencing (NGS) for oncogenic driver mutations to inform 1L treatment decisions in aNSCLC through a systematic literature review and meta-analysis. Methods A systematic literature search was conducted in PubMed/MEDLINE and Embase to identify randomized control trials or observational studies reporting CV/CU on ctDNA testing in patients with aNSCLC. Meta-analyses were performed using bivariate random-effects models to estimate pooled sensitivity and specificity. Progression-free/overall survival (PFS/OS) was summarized for CU studies. Results Eighteen studies were identified: 17 CV only, 2 CU only, and 1 both. Thirteen studies were included for the meta-analysis on multi-gene detection. The overall sensitivity and specificity for ctDNA detection of any mutation were 0.69 (95% CI, 0.63-0.74) and 0.99 (95% CI, 0.97-1.00) respectively. However, sensitivity varied greatly by driver gene, ranging from 0.29 (95% CI, 0.13-0.53) for ROS 1 to 0.77 (95% CI, 0.63-0.86) for KRAS . Two studies compared PFS with ctDNA versus tissue-based testing followed by 1L targeted therapy found no significant differences. One study reported OS curves on ctDNA-matched and tissue-matched therapies but no hazard ratios were provided. Conclusion ctDNA testing demonstrated an overall acceptable diagnostic accuracy in aNSCLC patients, however, sensitivity varied greatly by driver mutation. Further research is needed, especially for uncommon driver mutations, to better understand the CU of ctDNA testing in guiding targeted treatments for aNSCLC.
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Farncombe KM, Wong D, Norman ML, Oldfield LE, Sobotka JA, Basik M, Bombard Y, Carile V, Dawson L, Foulkes WD, Malkin D, Karsan A, Parkin P, Penney LS, Pollett A, Schrader KA, Pugh TJ, Kim RH. Current and new frontiers in hereditary cancer surveillance: Opportunities for liquid biopsy. Am J Hum Genet 2023; 110:1616-1627. [PMID: 37802042 PMCID: PMC10577078 DOI: 10.1016/j.ajhg.2023.08.014] [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: 04/14/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 10/08/2023] Open
Abstract
At least 5% of cancer diagnoses are attributed to a causal pathogenic or likely pathogenic germline genetic variant (hereditary cancer syndrome-HCS). These individuals are burdened with lifelong surveillance monitoring organs for a wide spectrum of cancers. This is associated with substantial uncertainty and anxiety in the time between screening tests and while the individuals are awaiting results. Cell-free DNA (cfDNA) sequencing has recently shown potential as a non-invasive strategy for monitoring cancer. There is an opportunity for high-yield cancer early detection in HCS. To assess clinical validity of cfDNA in individuals with HCS, representatives from eight genetics centers from across Canada founded the CHARM (cfDNA in Hereditary and High-Risk Malignancies) Consortium in 2017. In this perspective, we discuss operationalization of this consortium and early data emerging from the most common and well-characterized HCSs: hereditary breast and ovarian cancer, Lynch syndrome, Li-Fraumeni syndrome, and Neurofibromatosis type 1. We identify opportunities for the incorporation of cfDNA sequencing into surveillance protocols; these opportunities are backed by examples of earlier cancer detection efficacy in HCSs from the CHARM Consortium. We seek to establish a paradigm shift in early cancer surveillance in individuals with HCSs, away from highly centralized, regimented medical screening visits and toward more accessible, frequent, and proactive care for these high-risk individuals.
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Affiliation(s)
- Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maia L Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Julia A Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mark Basik
- Department of Surgery, McGill University Medical School, Montreal, QC, Canada; Department of Oncology, McGill University Medical School, Montreal, QC, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada; Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Victoria Carile
- Jewish General Hospital Stroll Cancer Prevention Centre, Montreal, QC, Canada
| | - Lesa Dawson
- Memorial University, St. John's, NL, Canada; Eastern Health Authority, St. John's, NL, Canada
| | - William D Foulkes
- Jewish General Hospital Stroll Cancer Prevention Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - David Malkin
- Division of Hematology-Oncology, Hospital for Sick Children, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Patricia Parkin
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | | | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Raymond H Kim
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, ON, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada.
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11
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Fang L, Shi C, Wang Y, Xiong Z, Wang Y. Exploring the diverse biomedical applications of programmable and multifunctional DNA nanomaterials. J Nanobiotechnology 2023; 21:290. [PMID: 37612757 PMCID: PMC10464147 DOI: 10.1186/s12951-023-02071-2] [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: 04/10/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
DNA nanoparticles hold great promise for a range of biological applications, including the development of cutting-edge treatments and diagnostic tests. Their subnanometer-level addressability enables precise, specific modifications with a variety of chemical and biological entities, making them ideal as diagnostic instruments and carriers for targeted delivery. This paper focuses on the potential of DNA nanomaterials, which offer scalability, programmability, and functionality. For example, they can be engineered to provide highly specific biosensing and bioimaging capabilities and show promise as a platform for disease diagnosis and treatment. Successful operation of various biomedical nanomaterials has been demonstrated both in vitro and in vivo. However, there are still significant challenges to overcome, including the need to improve the scalability and reliability of the technology, and to ensure safety in clinical applications. We discuss these challenges and opportunities in detail and highlight the progress and prospects of DNA nanotechnology for biomedical applications.
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Affiliation(s)
- Liuru Fang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Chen Shi
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Yuhua Wang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China.
| | - Zuzhao Xiong
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Yumei Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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12
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Verner EL, Jackson JB, Severson E, Valkenburg KC, Greer AE, Riley DR, Sausen M, Maddox C, McGregor PM, Karandikar A, Hastings SB, Previs RA, Reddy VP, Jensen TJ, Ramkissoon SH. Validation of the Labcorp Plasma Focus Test to Facilitate Precision Oncology Through Cell-Free DNA Genomic Profiling of Solid Tumors. J Mol Diagn 2023; 25:477-489. [PMID: 37068734 DOI: 10.1016/j.jmoldx.2023.03.008] [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: 12/24/2022] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
Genomic profiling is critical for precision oncology to guide treatment decisions. Liquid biopsy testing is a complementary approach to tissue testing, particularly when tissue is not readily available. The Labcorp Plasma Focus test is a circulating cell-free DNA genomic profiling test that identifies actionable variants in solid cancers, including non-small-cell lung, colorectal, melanoma, breast, esophageal, gastroesophageal junction, and gastric cancers. This study highlights the analytical validation of the test, including accuracy compared with orthogonal methods, as well as sensitivity, specificity, precision, reproducibility, and repeatability. Concordance with orthogonal methods showed percent positive agreement of 98.7%, 89.3%, and 96.2% for single nucleotide variants (SNVs), insertion/deletions (indels), and copy number amplifications (CNAs), respectively, and 100.0% for translocations and microsatellite instability (MSI). Analytical sensitivity revealed a median limit of detection of 0.7% and 0.6% for SNVs and indels, 1.4-fold for CNAs, 0.5% variant allele frequency for translocations, and 0.6% for MSI. Specificity was >99% for SNVs/indels and 100% for CNAs, translocations, and MSI. Average positive agreement from precision, reproducibility, and repeatability experiments was 97.5% and 88.9% for SNVs/indels and CNAs, and 100% for translocations and MSI. Taken together, these data show that the Labcorp Plasma Focus test is a highly accurate, sensitive, and specific approach for cell-free DNA genomic profiling to supplement tissue testing and inform treatment decisions.
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Affiliation(s)
- Ellen L Verner
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland.
| | | | - Eric Severson
- Enterprise Oncology, Labcorp, Durham, North Carolina
| | | | - Amy E Greer
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland
| | - David R Riley
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland
| | - Mark Sausen
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland
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Lin Z, Li Y, Tang S, Deng Q, Jiang J, Zhou C. Comparative analysis of genomic profiles between tissue-based and plasma-based next-generation sequencing in patients with non-small cell lung cancer. Lung Cancer 2023; 182:107282. [PMID: 37392713 DOI: 10.1016/j.lungcan.2023.107282] [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: 04/25/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/03/2023]
Abstract
OBJECTIVES Genotype-guided personalized therapy has become an essential part of routine clinical care in non-small cell lung cancer (NSCLC) patients. However, small tissue specimens often yield inadequate molecular testing material. Plasma ctDNA-based liquid biopsy is an increasingly common non-invasive alternative to tissue biopsy. This study examined the similarities and differences in the molecular profiling of tissue and plasma samples to provide insight into sample selection in clinical practice. MATERIALS AND METHODS Sequencing data from 190 NSCLC patients who underwent concurrent tissue-based next-generation sequencing (tissue-NGS) and plasma-based NGS (plasma-NGS) using a 168-gene panel were analyzed. RESULTS Tissue-NGS identified genomic alterations in 97.4% (185/190) of the enrolled patients and plasma-NGS identified genomic alterations in 72.1% (137/190) of the enrolled patients. Considering all NSCLC guideline-recommended biomarkers in the entire cohort of 190 cases, 81 patients had positive concordant mutations detected in both tissue and plasma samples, while 69 patients had no predefined alterations detected in either tissue or plasma samples. Additional mutations were found in the tissues of 34 patients and the plasma of six patients. The overall concordance rate between tissue and plasma samples was 78.9% (150/190). The tissue-NGS and plasma-NGS sensitivities were 95.0% and 71.9%, respectively. In the 137 patients with detectable ctDNA in plasma samples, the concordance rate between tissue and plasma samples reached 91.2%, and the sensitivity of plasma-NGS reached 93.5%. CONCLUSION Our findings indicate that plasma-NGS is less capable of detecting genetic alterations than tissue-NGS, especially for copy number variations and gene fusions. Tissue-NGS remains the preferred method for evaluating the molecular profile of NSCLC patients when tumor tissue is available. We suggest that the concurrent use of liquid biopsy and tissue biopsy is the optimal approach in clinical practice; alternatively, plasma can be used as substitute material when tissue is unavailable.
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Affiliation(s)
- Zeyun Lin
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqin Li
- Department of Clinical Laboratory, Dongguan Eighth People's Hospital, Dongguan, China
| | - Shiqi Tang
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuhua Deng
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Juhong Jiang
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Chengzhi Zhou
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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14
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Douglas MP, Ragavan MV, Chen C, Kumar A, Gray SW, Blakely CM, Phillips KA. Private Payer and Medicare Coverage Policies for Use of Circulating Tumor DNA Tests in Cancer Diagnostics and Treatment. J Natl Compr Canc Netw 2023; 21:609-616.e4. [PMID: 37308126 PMCID: PMC10846388 DOI: 10.6004/jnccn.2023.7011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/07/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is used to select initial targeted therapy, identify mechanisms of therapeutic resistance, and measure minimal residual disease (MRD) after treatment. Our objective was to review private and Medicare coverage policies for ctDNA testing. METHODS Policy Reporter was used to identify coverage policies (as of February 2022) from private payers and Medicare Local Coverage Determinations (LCDs) for ctDNA tests. We abstracted data regarding policy existence, ctDNA test coverage, cancer types covered, and clinical indications. Descriptive analyses were performed by payer, clinical indication, and cancer type. RESULTS A total of 71 of 1,066 total policies met study inclusion criteria, of which 57 were private policies and 14 were Medicare LCDs; 70% of private policies and 100% of Medicare LCDs covered at least one indication. Among 57 private policies, 89% specified a policy for at least 1 clinical indication, with coverage for ctDNA for initial treatment selection most common (69%). Of 40 policies addressing progression, coverage was provided 28% of the time, and of 20 policies addressing MRD, coverage was provided 65% of the time. Non-small cell lung cancer (NSCLC) was the cancer type most frequently covered for initial treatment (47%) and progression (60%). Among policies with ctDNA coverage, coverage was restricted to patients without available tissue or in whom biopsy was contraindicated in 91% of policies. MRD was commonly covered for hematologic malignancies (30%) and NSCLC (25%). Of the 14 Medicare LCD policies, 64% provided coverage for initial treatment selection and progression, and 36% for MRD. CONCLUSIONS Some private payers and Medicare LCDs provide coverage for ctDNA testing. Private payers frequently cover testing for initial treatment, especially for NSCLC, when tissue is insufficient or biopsy is contraindicated. Coverage remains variable across payers, clinical indications, and cancer types despite inclusion in clinical guidelines, which could impact delivery of effective cancer care.
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Affiliation(s)
- Michael P. Douglas
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, California
| | - Meera V. Ragavan
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Cheng Chen
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, California
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, California
| | - Anika Kumar
- UCSF School of Medicine, San Francisco, California
| | - Stacy W. Gray
- Department of Population Science, City of Hope, Duarte, California
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, California
| | - Collin M. Blakely
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
- UCSF Thoracic Oncology Program, University of California San Francisco, San Francisco, California
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Kathryn A. Phillips
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, California
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, California
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- UCSF Philip R. Lee Institute for Health Policy, San Francisco, California
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15
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Semenkovich NP, Szymanski JJ, Earland N, Chauhan PS, Pellini B, Chaudhuri AA. Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA. J Immunother Cancer 2023; 11:e006284. [PMID: 37349125 PMCID: PMC10314661 DOI: 10.1136/jitc-2022-006284] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.
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Affiliation(s)
- Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey J Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pradeep S Chauhan
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Aadel A Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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Al-Obeidi E, Riess JW, Malapelle U, Rolfo C, Gandara DR. Convergence of Precision Oncology and Liquid Biopsy in Non-Small Cell Lung Cancer. Hematol Oncol Clin North Am 2023; 37:475-487. [PMID: 37024388 DOI: 10.1016/j.hoc.2023.02.005] [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: 04/08/2023]
Abstract
This review article illuminates the role of liquid biopsy in the continuum of care for non-small cell lung cancer (NSCLC). We discuss its current application in advanced-stage NSCLC at the time of diagnosis and at progression. We highlight research showing that concurrent testing of blood and tissue yields faster, more informative, and cheaper answers than the standard stepwise approach. We also describe future applications for liquid biopsy including treatment response monitoring and testing for minimal residual disease. Lastly, we discuss the emerging role of liquid biopsy for screening and early detection.
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Affiliation(s)
- Ebaa Al-Obeidi
- Division of Hematology-Oncology, University of California, Davis, 4501 X Street, Suite 3016, Sacramento, CA 95817, USA.
| | - Jonathan W Riess
- Division of Hematology-Oncology, University of California, Davis, 4501 X Street, Suite 3016, Sacramento, CA 95817, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy. https://twitter.com/UmbertoMalapel1
| | - Christian Rolfo
- Center for Thoracic Oncology at the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, Box 1079, New York, NY 10029, USA. https://twitter.com/ChristianRolfo
| | - David R Gandara
- Division of Hematology-Oncology, University of California, Davis, 4501 X Street, Suite 3016, Sacramento, CA 95817, USA. https://twitter.com/drgandara
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Moreira AL, Sabari JK. Seeing Beyond the Smoke: Reclassifying Lung Cancer by Smoking-Related Mutational Signatures. J Thorac Oncol 2023; 18:396-398. [PMID: 36990571 DOI: 10.1016/j.jtho.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 03/29/2023]
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Wang Z, Yan X, Tang P, Tang T, Wang Y, Peng S, Wang S, Lan W, Wang L, Zhang Y, Zhang J, Li K, Shu Z, Xu J, Qin J, Zhang D, Jiang J, Liu Q. Genetic profiling of hormone-sensitive and castration-resistant prostate cancers and identification of genetic mutations prone to castration-resistant prostate cancer. Prostate Cancer Prostatic Dis 2023; 26:180-187. [PMID: 36401126 DOI: 10.1038/s41391-022-00618-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Genetic profiling of patients with prostate cancer could potentially identify mutations prone to castration-resistant prostate cancer (CRPC). Here, we aimed to identify the differences in genetic profiles of patients with hormone-sensitive prostate cancer (HSPC) and CRPC and stratify HSPC patients to identify mutations associated with CRPC progression. METHODS A total of 103 samples were collected, including 62 DNA samples from the tumor tissues of 59 HSPC patients and 41 cell-free DNA (cfDNA) samples from prostate cancer patients at different cancer stages. Targeted sequence was conducted on both the tissue DNA and cfDNA. The associations between mutations and clinical outcomes (CRPC-free time) were analyzed using χ2 test, logistic regression analysis, Kaplan-Meier analysis, and Cox regression analysis. RESULTS By comparing to that of cfDNA sequencing, the results from DNA sequencing of 1-needle (80%) and mixed 12-needle (77.8%) biopsies are highly comparable. FOXA1 (30.5%), CDK12 (23.7%), and TP53 (22.0%) were the top 3 most frequently mutated genes in HSPC patients; 50.8% (30/59) and 44.1% (26/59) HSPC patients had mutations in DDR and HRR pathway, respectively. Mutations in AR and APC as well as the members involved in the regulation of stem cell pluripotency and EMT pathway were often observed in CRPC samples. We established a panel of four genetic mutations (MSH2, CDK12, TP53, and RB1) to predict the risk of CRPC early progression with concordance index = 0.609 and the area under curve of the ROC curve as 0.838. CONCLUSIONS In this study, we demonstrated that the cfDNA can be used in genetic profiling in prostate cancer and our newly established panel is capable of predicting which mHSPC patient has a high risk of early CRPC progression.
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Affiliation(s)
- Ze Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Xuzhi Yan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Peng Tang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Tang Tang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Yapeng Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Song Peng
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Shuo Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Weihua Lan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Luofu Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Yao Zhang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Jun Zhang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Ke Li
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Zehua Shu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Jing Xu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, USA
| | - Jun Jiang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China.
| | - Qiuli Liu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, PR China.
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19
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Kemper M, Krekeler C, Menck K, Lenz G, Evers G, Schulze AB, Bleckmann A. Liquid Biopsies in Lung Cancer. Cancers (Basel) 2023; 15:1430. [PMID: 36900221 PMCID: PMC10000706 DOI: 10.3390/cancers15051430] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
As lung cancer has the highest cancer-specific mortality rates worldwide, there is an urgent need for new therapeutic and diagnostic approaches to detect early-stage tumors and to monitor their response to the therapy. In addition to the well-established tissue biopsy analysis, liquid-biopsy-based assays may evolve as an important diagnostic tool. The analysis of circulating tumor DNA (ctDNA) is the most established method, followed by other methods such as the analysis of circulating tumor cells (CTCs), microRNAs (miRNAs), and extracellular vesicles (EVs). Both PCR- and NGS-based assays are used for the mutational assessment of lung cancer, including the most frequent driver mutations. However, ctDNA analysis might also play a role in monitoring the efficacy of immunotherapy and its recent accomplishments in the landscape of state-of-the-art lung cancer therapy. Despite the promising aspects of liquid-biopsy-based assays, there are some limitations regarding their sensitivity (risk of false-negative results) and specificity (interpretation of false-positive results). Hence, further studies are needed to evaluate the usefulness of liquid biopsies for lung cancer. Liquid-biopsy-based assays might be integrated into the diagnostic guidelines for lung cancer as a tool to complement conventional tissue sampling.
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Affiliation(s)
- Marcel Kemper
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Carolin Krekeler
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Kerstin Menck
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Lenz
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Evers
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Arik Bernard Schulze
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Annalen Bleckmann
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
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20
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Parseghian CM, Sun R, Woods M, Napolitano S, Lee HM, Alshenaifi J, Willis J, Nunez S, Raghav KP, Morris VK, Shen JP, Eluri M, Sorokin A, Kanikarla P, Vilar E, Rehn M, Ang A, Troiani T, Kopetz S. Resistance Mechanisms to Anti-Epidermal Growth Factor Receptor Therapy in RAS/RAF Wild-Type Colorectal Cancer Vary by Regimen and Line of Therapy. J Clin Oncol 2023; 41:460-471. [PMID: 36351210 PMCID: PMC9870238 DOI: 10.1200/jco.22.01423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Acquired resistance to anti-epidermal growth factor receptor (EGFR) inhibitor (EGFRi) therapy in colorectal cancer (CRC) has previously been explained by the model of acquiring new mutations in KRAS/NRAS/EGFR, among other MAPK-pathway members. However, this was primarily on the basis of single-agent EGFRi trials and little is known about the resistance mechanisms of EGFRi combined with effective cytotoxic chemotherapy in previously untreated patients. METHODS We analyzed paired plasma samples from patients with RAS/BRAF/EGFR wild-type metastatic CRC enrolled in three large randomized trials evaluating EGFRi in the first line in combination with chemotherapy and as a single agent in third line. The mutational signature of the alterations acquired with therapy was evaluated. CRC cell lines with resistance to cetuximab, infusional fluorouracil, leucovorin, and oxaliplatin, and SN38 were developed, and transcriptional changes profiled. RESULTS Patients whose tumors were treated with and responded to EGFRi alone were more likely to develop acquired mutations (46%) compared with those treated in combination with cytotoxic chemotherapy (9%). Furthermore, contrary to the generally accepted hypothesis of the clonal evolution of acquired resistance, we demonstrate that baseline resistant subclonal mutations rarely expanded to become clonal at progression, and most remained subclonal or disappeared. Consistent with this clinical finding, preclinical models with acquired resistance to either cetuximab or chemotherapy were cross-resistant to the alternate agents, with transcriptomic profiles consistent with epithelial-to-mesenchymal transition. By contrast, commonly acquired resistance alterations in the MAPK pathway do not affect sensitivity to cytotoxic chemotherapy. CONCLUSION These findings support a model of resistance whereby transcriptomic mechanisms of resistance predominate in the presence of active cytotoxic chemotherapy combined with EGFRi, with a greater predominance of acquired MAPK mutations after single-agent EGFRi. The proposed model has implications for prospective studies evaluating EGFRi rechallenge strategies guided by acquired MAPK mutations, and highlights the need to address transcriptional mechanisms of resistance.
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Affiliation(s)
- Christine M. Parseghian
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Melanie Woods
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stefania Napolitano
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Hey Min Lee
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jumanah Alshenaifi
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason Willis
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shakayla Nunez
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kanwal P. Raghav
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Van K. Morris
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John P. Shen
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Madhulika Eluri
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexey Sorokin
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Preeti Kanikarla
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Eduardo Vilar
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Cancer Prevention and Population Sciences, Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Teresa Troiani
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Scott Kopetz
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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21
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Desmeules P, Dusselier M, Bouffard C, Bafaro J, Fortin M, Labbé C, Joubert P. Retrospective Assessment of Complementary Liquid Biopsy on Tissue Single-Gene Testing for Tumor Genotyping in Advanced NSCLC. Curr Oncol 2023; 30:575-585. [PMID: 36661694 PMCID: PMC9858142 DOI: 10.3390/curroncol30010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Biomarker testing is key for non-small cell lung cancer (NSCLC) management and plasma based next-generation sequencing (NGS) is increasingly characterized as a non-invasive alternative. This study aimed to evaluate the value of complementary circulating tumor DNA (ctDNA) NGS on tissue single-gene testing (SGT). Ninety-one advanced stage NSCLC patients with tumor genotyping by tissue SGT (3 genes) followed by ctDNA (38 genes amplicon panel) were included. ctDNA was positive in 47% (n = 43) and identified a targetable biomarker in 19 patients (21%). The likelihood of positivity on ctDNA was higher if patients had extra-thoracic disease (59%) or were not under active treatment (59%). When compared to SGT, ctDNA provided additional information in 41% but missed a known alteration in 8%. Therapeutic change for targeted therapy based on ctDNA occurred in five patients (5%), while seven patients with missed alterations on ctDNA had EGFR mutations or ALK fusions. The median turnaround time of ctDNA was 10 days (range 6-25), shorter (p = 0.002) than the cumulative delays for the tissue testing trajectory until biomarker availability (13 d; range 7-1737). Overall, the results from this study recapitulate the potential and limitations of ctDNA when used complementarily to tissue testing with limited biomarker coverage.
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Affiliation(s)
- Patrice Desmeules
- Service of Anatomic Pathology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
| | - Matthieu Dusselier
- Service of Respirology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
| | - Cédrik Bouffard
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
| | - Josée Bafaro
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
| | - Marc Fortin
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
- Service of Respirology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
| | - Catherine Labbé
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
- Service of Respirology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
| | - Philippe Joubert
- Service of Anatomic Pathology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC G1V 4G5, Canada
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22
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Ossowski S, Neeman E, Borden C, Stram D, Giraldo L, Kotak D, Thomas S, Suga JM, Lin A, Liu R. Improving Time to Molecular Testing Results in Patients With Newly Diagnosed, Metastatic Non-Small-Cell Lung Cancer. JCO Oncol Pract 2022; 18:e1874-e1884. [PMID: 36191286 DOI: 10.1200/op.22.00260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PURPOSE Next-generation sequencing (NGS) is a crucial component of evaluation of patients with newly diagnosed metastatic non-small-cell lung cancer (NSCLC) to determine appropriate first-line treatment. This quality improvement project aimed to reduce time to NGS results in patients with metastatic NSCLC. METHODS We reviewed electronic medical records of patients with newly diagnosed, untreated metastatic NSCLC from December 2018 to August 2021 and determined the number of days from pathologic diagnosis to NGS results. We reviewed process maps for oncology, pathology, the Division of Research, and a NGS vendor to determine factors leading to preventable delays. Since November 2020, we created an automated, electronic weekly report to provide earlier identification of new pathologic diagnoses in patients with metastatic NSCLC. On June 2021, we worked with our NGS vendors to expand days of the week to accept specimens. RESULTS Our interventions reduced the median time from pathologic diagnosis to NGS results from 24 (standard deviation [SD] 9) to 16 (SD 6) days. The median time from biopsy results to NGS order was reduced from 7 days to 1 day. The time from the specimen being sent from pathology to the NGS vendor was a median of 6 days in both cohorts. The total time from pathologic diagnosis to appropriate treatment was reduced from 33 (SD 18) to 22 (SD 8) days. CONCLUSION NGS processing in a community setting can be complex. Using a systems focused approach to quality improvement is crucial in identifying the greatest barriers in an organization. We found that delays in time to NGS results can be reduced by improved communication and workflows among departments.
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Affiliation(s)
- Stephanie Ossowski
- Department of Hematology Oncology, The Permanente Medical Group, San Francisco, CA
| | - Elad Neeman
- Department of Hematology Oncology, The Permanente Medical Group, San Francisco, CA
| | | | | | - Lucy Giraldo
- Diagnostic Pathology Medical Group, Sacramento, CA
| | - Dinesh Kotak
- Department of Hematology Oncology, The Permanente Medical Group, San Rafael, CA
| | - Sachdev Thomas
- Department of Hematology Oncology, The Permanente Medical Group, Vallejo, CA
| | - J Marie Suga
- Department of Hematology Oncology, The Permanente Medical Group, Vallejo, CA
| | - Amy Lin
- Department of Hematology Oncology, The Permanente Medical Group, San Francisco, CA
| | - Raymond Liu
- Department of Hematology Oncology, The Permanente Medical Group, San Francisco, CA
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23
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Jee J, Lebow ES, Yeh R, Das JP, Namakydoust A, Paik PK, Chaft JE, Jayakumaran G, Rose Brannon A, Benayed R, Zehir A, Donoghue M, Schultz N, Chakravarty D, Kundra R, Madupuri R, Murciano-Goroff YR, Tu HY, Xu CR, Martinez A, Wilhelm C, Galle J, Daly B, Yu HA, Offin M, Hellmann MD, Lito P, Arbour KC, Zauderer MG, Kris MG, Ng KK, Eng J, Preeshagul I, Victoria Lai W, Fiore JJ, Iqbal A, Molena D, Rocco G, Park BJ, Lim LP, Li M, Tong-Li C, De Silva M, Chan DL, Diakos CI, Itchins M, Clarke S, Pavlakis N, Lee A, Rekhtman N, Chang J, Travis WD, Riely GJ, Solit DB, Gonen M, Rusch VW, Rimner A, Gomez D, Drilon A, Scher HI, Shah SP, Berger MF, Arcila ME, Ladanyi M, Levine RL, Shen R, Razavi P, Reis-Filho JS, Jones DR, Rudin CM, Isbell JM, Li BT. Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer. Nat Med 2022; 28:2353-2363. [PMID: 36357680 PMCID: PMC10338177 DOI: 10.1038/s41591-022-02047-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing guides therapy decisions but has been studied mostly in small cohorts without sufficient follow-up to determine its influence on overall survival. We prospectively followed an international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy. ctDNA detection was associated with shorter survival (hazard ratio (HR), 2.05; 95% confidence interval (CI), 1.74-2.42; P < 0.001) independently of clinicopathologic features and metabolic tumor volume. Among the 722 (64%) patients with detectable ctDNA, 255 (23%) matched to targeted therapy by ctDNA sequencing had longer survival than those not treated with targeted therapy (HR, 0.63; 95% CI, 0.52-0.76; P < 0.001). Genomic alterations in ctDNA not detected by time-matched tissue sequencing were found in 25% of the patients. These ctDNA-only alterations disproportionately featured subclonal drivers of resistance, including RICTOR and PIK3CA alterations, and were associated with short survival. Minimally invasive ctDNA profiling can identify heterogeneous drivers not captured in tissue sequencing and expand community access to life-prolonging therapy.
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Affiliation(s)
- Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S Lebow
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Randy Yeh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeeban P Das
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - A Rose Brannon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hai-Yan Tu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chong-Rui Xu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | | | - Clare Wilhelm
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bobby Daly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Helena A Yu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Michael Offin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Piro Lito
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kathryn C Arbour
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marjorie G Zauderer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kenneth K Ng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Juliana Eng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Isabel Preeshagul
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - W Victoria Lai
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - John J Fiore
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Afsheen Iqbal
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniela Molena
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gaetano Rocco
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bernard J Park
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Lee P Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Candace Tong-Li
- GenesisCare, University of Sydney, Sydney, Australia
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - David L Chan
- GenesisCare, University of Sydney, Sydney, Australia
| | | | | | | | - Nick Pavlakis
- GenesisCare, University of Sydney, Sydney, Australia
| | - Adrian Lee
- GenesisCare, University of Sydney, Sydney, Australia
| | - Natasha Rekhtman
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jason Chang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - William D Travis
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory J Riely
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mithat Gonen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valerie W Rusch
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Andreas Rimner
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniel Gomez
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sohrab P Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jorge S Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - James M Isbell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
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24
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Malapelle U, Pisapia P, Pepe F, Russo G, Buono M, Russo A, Gomez J, Khorshid O, Mack PC, Rolfo C, Troncone G. The evolving role of liquid biopsy in lung cancer. Lung Cancer 2022; 172:53-64. [PMID: 35998482 DOI: 10.1016/j.lungcan.2022.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 12/20/2022]
Abstract
Liquid biopsy has revolutionized the management of cancer patients. In particular, liquid biopsy-based testing has proven to be highly beneficial for identifying actionable cancer markers, especially when solid tissue biopsies are insufficient or unattainable. Beyond the predictive role, liquid biopsy may be a useful tool for comprehensive tumor genotyping, identification of emergent resistance mechanisms, monitoring of minimal residual disease, early detection, and cancer interception. The application of next generation sequencing to liquid biopsy has led to the "quantum leap" of predictive molecular pathology. Here, we review the evolving role of liquid biopsy in lung cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Buono
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Jorge Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Philip C Mack
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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25
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Haseltine JM, Offin M, Flynn JR, Zhang Z, Lebow ES, Aziz K, Makhnin A, Eichholz J, Lim LP, Li M, Isbell JM, Gomez DR, Li BT, Rimner A. Tumor volume as a predictor of cell free DNA mutation detection in advanced non-small cell lung cancer. Transl Lung Cancer Res 2022; 11:1578-1590. [PMID: 36090640 PMCID: PMC9459617 DOI: 10.21037/tlcr-22-164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 01/13/2023]
Abstract
Background Cell free DNA (cfDNA) is an exciting biomarker with applications across the cancer care continuum. Determinants of cfDNA shedding dynamics remain an active research area. We performed a detailed analysis of tumor volume and factors associated with detection of cfDNA mutations. Methods Patients with advanced non-small cell lung cancers (NSCLCs) were prospectively enrolled on a plasma biomarker protocol. Next generation sequencing (NGS) was performed using a validated, bias-corrected, hybrid-capture panel assay of lung cancer-associated genes. Volume of tumor in different subsites and total tumor volume were determined through manual volume delineation using PET/CT and brain magnetic resonance imaging (MRI) imaging. The primary endpoint was detection of cfDNA mutation; secondary endpoints were overall survival (OS) and variant allele frequency (VAF). Results There were 110 patients included, 78 of whom had at least one mutation detected. Median total tumor volume for the entire cohort, patients with mutation detected, and patients with no mutation detected were 66 mL (range, 2-1,383 mL), 76 mL (range, 5-1,383 mL), and 45 mL (range, 2-460 mL), respectively (P=0.002; mutation detected vs. not). The optimal total tumor volume threshold to predict increased probability of mutation detection was 65 mL (P=0.006). Total tumor volume greater than 65 mL was a significant predictor of mutation detection on multivariate analysis (OR: 4.30, P=0.003). Significant predictors of OS were age (HR: 1.04, P=0.002), detection of cfDNA mutation (HR: 2.11, P=0.024), and presence of bone metastases (HR: 1.66, P=0.047). Conclusions Total tumor volume greater than 65 mL was associated with cfDNA mutation detection in patients with advanced NSCLC.
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Affiliation(s)
- Justin M. Haseltine
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica R. Flynn
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhigang Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S. Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khaled Aziz
- Department of Radiation Oncology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Alex Makhnin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jordan Eichholz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lee P. Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - James M. Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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26
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Chan HT, Chin YM, Low SK. Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges. Cancers (Basel) 2022; 14:3275. [PMID: 35805046 PMCID: PMC9265547 DOI: 10.3390/cancers14133275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.
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Affiliation(s)
- Hiu Ting Chan
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| | - Yoon Ming Chin
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
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27
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Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy. Sci Rep 2022; 12:10447. [PMID: 35729208 PMCID: PMC9213477 DOI: 10.1038/s41598-022-14675-z] [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: 01/01/2022] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Dying tumor cells shed DNA fragments into the circulation that are known as circulating tumor DNA (ctDNA). Liquid biopsy tests aim to detect cancer using known markers, including genetic alterations and epigenetic profiles of ctDNA. Despite various advantages, the major limitation remains the low fraction of tumor-originating DNA fragments in a high background of normal blood-cell originating fragments in the cell-free DNA (cfDNA) pool in plasma. Deep targeted sequencing of cfDNA allows for enrichment of fragments in known cancer marker-associated regions of the genome, thus increasing the chances of detecting the low fraction variant harboring fragments. Most targeted sequencing panels are designed to include known recurrent mutations or methylation markers of cancer. Here, we propose the integration of cancer-specific chromatin accessibility states into panel designs for liquid biopsy. Using machine learning approaches, we first identify accessible and inaccessible chromatin regions specific to each major human cancer type. We then introduce a score that quantifies local chromatin accessibility in tumor relative to blood cells and show that this metric can be useful for prioritizing marker regions with higher chances of being detected in cfDNA for inclusion in future panel designs.
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28
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Sakurai E, Ishizawa H, Kiriyama Y, Michiba A, Hoshikawa Y, Tsukamoto T. γH2AX, a DNA Double-Strand Break Marker, Correlates with PD-L1 Expression in Smoking-Related Lung Adenocarcinoma. Int J Mol Sci 2022; 23:6679. [PMID: 35743122 PMCID: PMC9223793 DOI: 10.3390/ijms23126679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
In recent years, the choice of immune checkpoint inhibitors (ICIs) as a treatment based on high expression of programmed death-ligand 1 (PD-L1) in lung cancers has been increasing in prevalence. The high expression of PD-L1 could be a predictor of ICI efficacy as well as high tumor mutation burden (TMB), which is determined using next-generation sequencing (NGS). However, a great deal of effort is required to perform NGS to determine TMB. The present study focused on γH2AX, a double-strand DNA break marker, and the suspected positive relation between TMB and γH2AX was investigated. We assessed the possibility of γH2AX being an alternative marker of TMB or PD-L1. One hundred formalin-fixed, paraffin-embedded specimens of lung cancer were examined. All of the patients in the study received thoracic surgery, having been diagnosed with lung adenocarcinoma or squamous cell carcinoma. The expressions of γH2AX and PD-L1 (clone: SP142) were evaluated immunohistochemically. Other immunohistochemical indicators, p53 and Ki-67, were also used to estimate the relationships of γH2AX. Positive relationships between γH2AX and PD-L1 were proven, especially in lung adenocarcinoma. Tobacco consumption was associated with higher expression of γH2AX, PD-L1, Ki-67, and p53. In conclusion, the immunoexpression of γH2AX could be a predictor for the adaptation of ICIs as well of as PD-L1 and TMB.
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Affiliation(s)
- Eiko Sakurai
- Department of Diagnostic Pathology, Graduate School of Medicine, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake 470-1192, Japan; (E.S.); (Y.K.); (A.M.)
| | - Hisato Ishizawa
- Department of Thoracic Surgery, Graduate School of Medicine, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake 470-1192, Japan; (H.I.); (Y.H.)
| | - Yuka Kiriyama
- Department of Diagnostic Pathology, Graduate School of Medicine, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake 470-1192, Japan; (E.S.); (Y.K.); (A.M.)
- Department of Diagnostic Pathology, Narita Memorial Hospital, 134, Haneihonmachi, Toyohashi 441-8029, Japan
| | - Ayano Michiba
- Department of Diagnostic Pathology, Graduate School of Medicine, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake 470-1192, Japan; (E.S.); (Y.K.); (A.M.)
| | - Yasushi Hoshikawa
- Department of Thoracic Surgery, Graduate School of Medicine, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake 470-1192, Japan; (H.I.); (Y.H.)
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology, Graduate School of Medicine, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake 470-1192, Japan; (E.S.); (Y.K.); (A.M.)
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He J, Hu X, Chen L, Liu Q, Jiang Y. Characteristics of Genomic Alterations in Pericardial Effusion of Advanced Non-small Cell Lung Cancer. Front Genet 2022; 13:850290. [PMID: 35646096 PMCID: PMC9133843 DOI: 10.3389/fgene.2022.850290] [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: 01/07/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The feasibility and value of pericardial effusion as a liquid biopsy sample for actionable alteration detection in patients with non-small cell lung cancer (NSCLC) has not been adequately investigated. Here, we aim to reveal genomic alterations between pericardial effusion and paired tumor tissue, plasma (plasma cfDNA), and pleural effusion supernatant (PE-cfDNA) based on second-generation sequencing technology. Material and methods: A total of 26 advanced NSCLC patients were retrospectively studied. The following samples were collected and sequenced using two targeted next-generation sequencing panels: pericardial effusion (n = 26), matched tumor tissue (n = 6), plasma (n = 16), and pleural effusion supernatant (n = 5). Results: A total of 10 actionable alterations were identified in pericardial effusion of the NSCLC patients, including MET amplification, EGFR L858R, EGFR T790M, EGFR exon 19 deletion, EGFR L861Q, KRAS G12C, EML4-ALK (exon 18: exon 20) fusion, EML4-ALK (exon 20: exon 20) fusion, EML4-ALK (exon 6: exon 20) fusion, and ERBB2 exon 20 insertion. All these actionable alterations harbored multiple drug-sensitive targets as well as several drug-resistant targets, such as EGFR T790M. Compared to plasma cfDNA of 16 patients, paired pericardial effusion had higher number of actionable alterations (p = 0.08) as well as higher percentage of the population with actionable alterations (p = 0.16). Moreover, 8 out of 10 actionable alterations with single nucleotide variations (SNVs) or insertions/deletions (indels) had a higher variant allele frequency (VAF) in pericardial effusion than plasma cfDNA. In addition, we identified two actionable alterations in paired pericardial effusion, which were absence in PE-cfDNA. Clearly, 2 out of 3 actionable alterations with SNVs/indels in pericardial effusion had a higher VAF than those in PE-cfDNA. Our finding suggested the importance of pericardial effusion in the optimal selection of patients for targeted therapy. Conclusion: Among liquid biopsy specimens from the advanced NSCLC patients, pericardial effusion may be a better candidate for genomic profiling than plasma cfDNA, while it could serve as a supplement to PE-cfDNA in detecting actionable alterations. Therefore, pericardial effusion might provide a new alternative for selection of patients for better treatment management.
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Affiliation(s)
- Jiaxue He
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Xintong Hu
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Liguo Chen
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Qiaoliang Liu
- College of Communication Engineering, Jilin University, Changchun, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Yanfang Jiang,
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30
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Sturgill EG, Misch A, Jones CC, Luckett D, Fu X, Schlauch D, Jones SF, Burris HA, Spigel DR, McKenzie AJ. Discordance in Tumor Mutation Burden from Blood and Tissue Affects Association with Response to Immune Checkpoint Inhibition in Real-World Settings. Oncologist 2022; 27:175-182. [PMID: 35274716 PMCID: PMC8914506 DOI: 10.1093/oncolo/oyab064] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/03/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tumor mutation burden (TMB), a biomarker for immune checkpoint inhibitor (CPI) response, is reported by both blood- and tissue-based next-generation sequencing (NGS) vendors. However, the agreement between TMB from blood (bTMB) and tissue (tTMB) in real-world settings, both in absolute value and association with CPI response, is not known. MATERIALS AND METHODS This study utilizes Sarah Cannon's precision medicine platform, Genospace, to harmonize clinico-genomic data from 17 206 patients with cancer with NGS results from September 2015 to August 2021. A subset of patients have both bTMB and tTMB results. Statistical analyses are performed in R and include (1) correlation (r) and concordance (ρ) between patient-matched bTMB-tTMB pairs, (2) distribution of total bTMB and tTMB values, and (3) association of bTMB and tTMB with time to CPI therapy failure. RESULTS In 410 patient-matched bTMB-tTMB pairs, the median bTMB (m = 10.5 mut/Mb) was significantly higher than the median tTMB (m = 6.0 mut/Mb, P < .001) leading to conflicting "high" and "low" statuses in over one-third of cases at a threshold of 10 mut/Mb (n = 410). Significant differences were observed in the distribution of bTMB values from blood-NGS vendors, with guardant health (GH) reporting higher (m = 10.5 mut/Mb, n = 2183) than Foundation Medicine (FMI, m = 3.8 mut/Mb, n = 462, P < .001). bTMB from GH required a higher threshold (≥40 mut/Mb) than bTMB from FMI (≥12 mut/Mb) in order to be associated with CPI response. CONCLUSIONS This study uncovers variability in bTMB reporting among commercial NGS platforms, thereby evidencing a need for assay-specific thresholds in identifying patients who may respond to CPI therapy.
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Affiliation(s)
| | - Amanda Misch
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | | | - Daniel Luckett
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | - Xiaotong Fu
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | - Dan Schlauch
- Sarah Cannon Research Institute, Nashville, TN, USA
- Genospace, Boston, MA, USA
| | | | - Howard A Burris
- Sarah Cannon Research Institute, Nashville, TN, USA
- Tennessee Oncology, Nashville, TN, USA
| | - David R Spigel
- Sarah Cannon Research Institute, Nashville, TN, USA
- Tennessee Oncology, Nashville, TN, USA
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31
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Clinical Impact of High Throughput Sequencing on Liquid Biopsy in Advanced Solid Cancer. Curr Oncol 2022; 29:1902-1918. [PMID: 35323355 PMCID: PMC8947301 DOI: 10.3390/curroncol29030155] [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: 02/10/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022] Open
Abstract
Background: Cancer therapies targeting actionable molecular alterations (AMA) have developed, but the clinical routine impact of high-throughput molecular profiling remains unclear. We present a monocentric experience of molecular profiling based on liquid biopsy in patients with cancer. Methods: Patients included had solid cancer and underwent cfDNA genomic profiling with FoudationOne Liquid CDx (F1LCDx) test, analyzing 324 genes. Primary endpoint was to describe patients with an AMA for whom clinical decisions were impacted by F1LCDx test results. Results: 191 patients were included, mostly with lung cancer (46%). An AMA was found in 52%. The most common molecular alterations were: TP53 (52%), KRAS (14%) and DNMT3 (11%). The most common AMA were: CHEK2 (10%), PIK3CA (9%), ATM (7%). There was no difference in progression-free survival (2.66 months vs. 3.81 months, p = 0.17), overall survival (5.3 months vs. 7.1 months, p = 0.64), or PFS2/PFS1 ratio ≥ 1.3 (20% vs. 24%, p = 0.72) between patients receiving a molecularly matched therapy (MMT) or a non-MMT, respectively. Patients with a MMT had an overall response rate of 19% and a disease control of 32%. Conclusions: Routine cfDNA molecular profiling is feasible and can lead to the access of targeted therapies. However, no notable benefit in patient’s outcomes was shown in this unselected pan-cancer study.
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32
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Vargas DY, Tyagi S, Marras SA, Moerzinger P, Abin-Carriquiry JA, Cuello M, Rodriguez C, Martinez A, Makhnin A, Farina A, Patel C, Chuang TL, Li BT, Kramer FR. Multiplex SuperSelective PCR Assays for the Detection and Quantitation of Rare Somatic Mutations in Liquid Biopsies. J Mol Diagn 2022; 24:189-204. [PMID: 34954118 PMCID: PMC8961470 DOI: 10.1016/j.jmoldx.2021.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/11/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022] Open
Abstract
SuperSelective primers, by virtue of their unique design, enable the simultaneous identification and quantitation of inherited reference genes and rare somatic mutations in routine multiplex PCR assays, while virtually eliminating signals from abundant wild-type sequences closely related to the target mutations. These assays are sensitive, specific, rapid, and low cost, and can be performed in widely available spectrofluorometric thermal cyclers. Herein, we provide examples of SuperSelective PCR assays that target eight different somatic EGFR mutations, irrespective of whether they occur in the same codon, occur at separate sites within the same exon, or involve deletions. In addition, we provide examples of SuperSelective PCR assays that detect specific EGFR mutations in circulating tumor DNA present in the plasma of liquid biopsies obtained from patients with non-small-cell lung cancer. The results suggest that multiplex SuperSelective PCR assays may enable the choice, and subsequent modification, of effective targeted therapies for the treatment of an individual's cancer, utilizing frequent noninvasive liquid biopsies.
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Affiliation(s)
- Diana Y. Vargas
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Salvatore A.E. Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | | | | | - Mauricio Cuello
- Servicio de Oncología Clínica, Hospital de Clínicas, Montevideo, Uruguay
| | - Clara Rodriguez
- Servicio de Oncología Clínica, Hospital de Clínicas, Montevideo, Uruguay
| | | | - Alex Makhnin
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Farina
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chintan Patel
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tuan L. Chuang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bob T. Li
- Memorial Sloan Kettering Cancer Center, New York, New York,Weill-Cornell Medicine, New York, New York,Address correspondence to Fred R. Kramer, Ph.D., Public Health Research Institute, 225 Warren St., Newark, NJ 07103; or Bob T. Li, M.D., Thoracic Liquid Biopsy Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY 10065.
| | - Fred R. Kramer
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey,Address correspondence to Fred R. Kramer, Ph.D., Public Health Research Institute, 225 Warren St., Newark, NJ 07103; or Bob T. Li, M.D., Thoracic Liquid Biopsy Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY 10065.
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Choudhury Y, Tan MH, Shi JL, Tee A, Ngeow KC, Poh J, Goh RR, Mong J. Complementing Tissue Testing With Plasma Mutation Profiling Improves Therapeutic Decision-Making for Patients With Lung Cancer. Front Med (Lausanne) 2022; 9:758464. [PMID: 35223889 PMCID: PMC8873935 DOI: 10.3389/fmed.2022.758464] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundTissue biopsy is an integral part of the diagnostic approach to lung cancer. It is however invasive and limited by heterogeneity. Liquid biopsies may complement tissue testing by providing additional molecular information and may be particularly helpful in patients from whom obtaining sufficient tissue for genomic profiling is challenging.MethodsPatients with suspected lung cancer (n = 71) were prospectively recruited. Blood and diagnostic tissue samples were collected within 48 h of each other. Plasma cell-free DNA (cfDNA) testing was done using an ultrasensitive amplicon-based next-generation sequencing (NGS) panel (plasma NGS testing). For cases diagnosed as non-small cell lung carcinoma (NSCLC) via histology or cytology, targeted testing for epidermal growth factor receptor (EGFR) mutations was performed using tissue biopsy samples (tissue EGFR testing), where available. Concordance of clinically actionable mutations between methods and sample types was assessed.ResultsFor confirmed NSCLC cases (n = 54), tissue EGFR test results were available only for 70.3% (38/54) due to sample inadequacies, compared to blood samples for 98.1% (53/54) cases. Tissue EGFR testing identified sensitizing EGFR (L858R or exon 19 deletion) mutation in 31.6% (12/38) of cases. Plasma NGS identified clinically actionable mutations in 37.7% (20/53) of cases, including EGFR mutations in two cases with no tissue EGFR results, and mutations in KRAS, BRAF, and MET. The overall sensitivity of sensitizing EGFR mutation detection by plasma NGS was 75% (9/12), and specificity was 100% (25/25) in patients tested in both tissue EGFR and plasma NGS (n = 37). In this cohort of patients, tissue EGFR testing alone informed clinical decisions in 22.2% (12/54) of cases. Adding plasma NGS to tissue EGFR testing increased the detection rate of actionable mutations to 42.6% (23/54), representing a 1.9-fold increase in clinically relevant findings. The average turnaround time of plasma NGS was shorter than standard tissue testing (10 vs. 29.9 days, p < 0.05).ConclusionsIn the first-line setting, plasma NGS was highly concordant with tissue EGFR testing. Plasma NGS increases the detection of actionable findings with a shorter time to results. This study outlines the clinical utility of complementary plasma mutation profiling in the routine management of lung cancer patients.
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Affiliation(s)
| | - Min-Han Tan
- Lucence Health Inc, Palo Alto, CA, United States
| | - Jun Li Shi
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - Augustine Tee
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore
| | | | - Jonathan Poh
- Lucence Diagnostics Pte. Ltd., Singapore, Singapore
| | - Ruth Rosalyn Goh
- Lucence Diagnostics Pte. Ltd., Singapore, Singapore
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jamie Mong
- Institute of Bioengineering and Bioimaging, Singapore, Singapore
- *Correspondence: Jamie Mong
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Petranovic M, Raoof S, Digumarthy SR, Sharma A, Shepard JAO, Gainor JF, Pandharipande PV. Liquid Biopsy, Diagnostic Imaging, and Future Synergies. J Am Coll Radiol 2022; 19:336-343. [DOI: 10.1016/j.jacr.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/16/2022]
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Duffy MJ, Crown J. Use of Circulating Tumour DNA (ctDNA) for Measurement of Therapy Predictive Biomarkers in Patients with Cancer. J Pers Med 2022; 12:99. [PMID: 35055414 PMCID: PMC8779216 DOI: 10.3390/jpm12010099] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023] Open
Abstract
Biomarkers that predict likely response or resistance to specific therapies are critical in personalising treatment for cancer patients. Such biomarkers are now available for an increasing number of anti-cancer therapies, especially targeted therapy and immunotherapy. The gold-standard method for determining predictive biomarkers requires tumour tissue. Obtaining tissue, however, is not always possible and even if possible, the amount or quality of tissue obtained may be inadequate for biomarker analysis. Tumour DNA, however, can be released into the bloodstream, giving rise to what is referred to as circulating tumour DNA (ctDNA). In contrast to tissue, blood can be obtained from effectively all patients in a minimally invasive and safe manner. Other advantages of blood over tissue for biomarker testing include a shorter turn-around time and an ability to perform serial measurements. Furthermore, blood should provide a more complete profile of mutations present in heterogeneous tumours than a single-needle tissue biopsy. A limitation of blood vis-à-vis tissue, however, is lower sensitivity and, thus, the possibility of missing an actionable mutation. Despite this limitation, blood-based predictive biomarkers, such as mutant EGFR for predicting response to EGFR tyrosine kinase inhibitors in advanced non-small-cell lung cancer and mutant PIK3CA for predicting response to alpelisib in combination with fulvestrant in advanced breast cancer, may be used when tissue is unavailable. Although tissue remains the gold standard for detecting predictive biomarkers, it is likely that several further blood-based assays will soon be validated and used when tissue is unavailable or unsuitable for analysis.
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Affiliation(s)
- Michael J. Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W Dublin, Ireland
- UCD Clinical Research Centre, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent’s University Hospital, D04 T6F4 Dublin, Ireland;
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Zhang DY, Gould A, Happ HC, Youngblood MW, Dmello C, Kang SJ, Canney M, Stupp R, Carvill GL, Sonabend AM. Ultrasound-mediated blood-brain barrier opening increases cell-free DNA in a time-dependent manner. Neurooncol Adv 2022; 3:vdab165. [PMID: 34993480 PMCID: PMC8717890 DOI: 10.1093/noajnl/vdab165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniel Y Zhang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Rush Medical College, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Andrew Gould
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hannah C Happ
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Crismita Dmello
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Seong Jae Kang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Michael Canney
- CarThera, Institut du Cerveau et de la Moelle epiniere (ICM), Paris, France
| | - Roger Stupp
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Gemma L Carvill
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Adam M Sonabend
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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Harvey MJ, Cunningham R, Sawchyn B, Montesion M, Reddy P, McBride A, Chawla AJ. Budget Impact Analysis of Comprehensive Genomic Profiling in Patients With Advanced Non-Small-Cell Lung Cancer. JCO Precis Oncol 2022; 5:1611-1624. [PMID: 34994647 DOI: 10.1200/po.20.00540] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE This study assessed the economic impact of increased use of comprehensive genomic profiling (CGP) versus conventional testing strategies among patients with advanced non-small-cell lung cancer (aNSCLC) from a US commercial health plan perspective. METHODS A decision analytic model was developed to estimate the incremental benefits and costs across testing methodologies (CGP v non-CGP), as well as across sample types (tissue-based and liquid-based), for patients with newly diagnosed aNSCLC. Model outcomes included total direct costs, testing costs, and per member per month budget impact. Secondary model outcomes included the number of patients needed to test with CGP to add 1 life-year, and the number of patients needed to test with CGP to treat one individual with a biomarker-matched therapy. RESULTS In a hypothetical 2,000,000-member health plan, 790 members were estimated to have incident aNSCLC; 609 underwent molecular diagnostic testing with 122 (20%) tested with CGP (109 tissue-based and 13 liquid) in the base-case. An increase in CGP from 20% to 30% (an additional 61 patients tested with CGP) was associated with 3.11 additional life-years gained and a $0.01 in US dollars per member per month budget impact. Approximately 19.6 patients would need to be tested with CGP versus non-CGP to add one life-year and 5.9 patients would need to be tested with CGP to treat at least one patient with a biomarker-matched therapy. CONCLUSION An increase in CGP from 20% to 30% among patients with aNSCLC undergoing molecular diagnostic testing was associated with modest budget impact, most of which was attributable to prolonged survival associated with increased use of more effective treatments.
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Liang Q, Xu H, Liu Y, Zhang W, Sun C, Hu M, Zhu Y, Tan S, Xu X, Wang S, Liu L. Coexistence of a novel NBEA-ALK, EML4-ALK double-fusion in a lung adenocarcinoma patient and response to alectinib: A case report. Lung Cancer 2021; 162:86-89. [PMID: 34763158 DOI: 10.1016/j.lungcan.2021.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVES The echinoderm microtubule-associated protein-like 4 gene (EML4) and anaplastic lymphoma kinase gene (ALK) fusion is the most common ALK rearrangements in non-small cell lung cancer (NSCLC). Herein, we firstly report that coexistence of a novel Neurobeachin (NBEA)-ALK, EML4-ALK double-fusion is sensitive to alectinib. MATERIALS AND METHODS Hematoxylin-eosin staining (HE), fluorescent in situ hybridization (FISH), and next-generation sequencing (NGS) was performed on the biopsy sample. RESULTS The patient responded to alectinib as a second-line treatment and achieved stable disease for 11 months, without significant symptoms of toxicity. Significantly, the liquid biopsy also validated clinical benefit, with the disappearance of NBEA-ALK and EML4-ALK fusion variants. We also provided a comprehensive review of all 50 ALK fusion genes in NSCLC. CONCLUSION This is the first report on one patient with a novel NBEA-ALK, EML4-ALK double-ALK fusion beneficial from alectinib. Alectinib may be a viable therapeutic option for NSCLC patients with double-ALK fusion, and liquid biopsy could dynamically monitor clinical curative effect.
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Affiliation(s)
- Qi Liang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Huanhuan Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yiqian Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Weiming Zhang
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Chongqi Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Meng Hu
- Department of Oncology, Liyang People's Hospital, Liyang 213300, China
| | - Yizhi Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shanyue Tan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xian Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Sumeng Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lingxiang Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
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Jensen TJ, Goodman AM, Ellison CK, Holden KA, Kato S, Kim L, Daniels GA, Fitzgerald K, McCarthy E, Nakashe P, Mazloom AR, Almasri E, McLennan G, Grosu DS, Eisenberg M, Kurzrock R. Genome-wide Sequencing of Cell-free DNA Enables Detection of Copy-number Alterations in Patients with Cancer Where Tissue Biopsy is Not Feasible. Mol Cancer Ther 2021; 20:2274-2279. [PMID: 34465593 PMCID: PMC9398131 DOI: 10.1158/1535-7163.mct-20-1066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/03/2021] [Accepted: 08/20/2021] [Indexed: 01/07/2023]
Abstract
When tissue biopsy is not medically prudent or tissue is insufficient for molecular testing, alternative methods are needed. Because cell-free DNA (cfDNA) has been shown to provide a representative surrogate for tumor tissue, we sought to evaluate its utility in this clinical scenario. cfDNA was isolated from the plasma of patients and assayed with low-coverage (∼0.3×), genome-wide sequencing. Copy-number alterations (CNA) were identified and characterized using analytic methods originally developed for noninvasive prenatal testing (NIPT) and quantified using the genomic instability number (GIN), a metric that reflects the quantity and magnitude of CNAs across the genome. The technical variability of the GIN was first evaluated in an independent cohort comprising genome-wide sequencing results from 27,754 women who consented to have their samples used for research and whose NIPT results yielded no detected CNAs to establish a detection threshold. Subsequently, cfDNA sequencing data from 96 patients with known cancers but for whom a tissue biopsy could not be obtained are presented. An elevated GIN was detected in 35% of patients and detection rates varied by tumor origin. Collectively, CNAs covered 96.6% of all autosomes. Survival was significantly reduced in patients with an elevated GIN relative to those without. Overall, these data provide a proof of concept for the use of low-coverage, genome-wide sequencing of cfDNA from patients with cancer to obtain relevant molecular information in instances where tissue is difficult to access. These data may ultimately serve as an informative complement to other molecular tests.
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Affiliation(s)
- Taylor J. Jensen
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California.,Laboratory Corporation of America, Durham, North Carolina.,Corresponding Author: Taylor J. Jensen, Research and Development, Laboratory Corporation of America, 1912 TW Alexander, Durham, NC 27703. Phone: 858-242-6842; E-mail:
| | - Aaron M. Goodman
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, San Diego.,Department of Medicine, Division of Blood and Marrow Transplantation, Moores Cancer Center, University of California, San Diego
| | - Christopher K. Ellison
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Kimberly A. Holden
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Shumei Kato
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, San Diego.,Department of Medicine, Division of Precision Medicine, Moores Cancer Center, University of California, San Diego
| | - Lisa Kim
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, San Diego
| | - Gregory A. Daniels
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, San Diego
| | - Kerry Fitzgerald
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Erin McCarthy
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Prachi Nakashe
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Amin R. Mazloom
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Eyad Almasri
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Graham McLennan
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | - Daniel S. Grosu
- Sequenom, Inc, a wholly owned subsidiary of Laboratory Corporation of America Holdings, San Diego, California
| | | | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, San Diego.,Department of Medicine, Division of Precision Medicine, Moores Cancer Center, University of California, San Diego
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Jang BS, Kim IA. Machine-learning algorithms predict breast cancer patient survival from UK Biobank whole-exome sequencing data. Biomark Med 2021; 15:1529-1539. [PMID: 34651513 DOI: 10.2217/bmm-2021-0280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: We tested whether machine-learning algorithm could find biomarkers predicting overall survival in breast cancer patients using blood-based whole-exome sequencing data. Materials & methods: Whole-exome sequencing data derived from 1181 female breast cancer patients within the UK Biobank was collected. We found feature genes (n = 50) regarding total mutation burden using the long short-term memory model. Then, we developed the XGBoost survival model with selected feature genes. Results: The XGBoost survival model performed acceptably, with a concordance index of 0.75 and a scaled Brier score of 0.146 in terms of overall survival prediction. The high-mutation group exhibited inferior overall survival compared with the low-mutation group in patients ≥56 years (log-rank test, p = 0.042). Conclusion: We showed that machine-learning algorithms can be used to predict overall survival in breast cancer patients from blood-based whole-exome sequencing data.
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Affiliation(s)
- Bum-Sup Jang
- Department of Radiation Oncology, Seoul National University Bundang Hospital, Seongnam, 13620, Korea.,Department of Radiation Oncology, Seoul National University, College of Medicine, Seoul, Korea
| | - In Ah Kim
- Department of Radiation Oncology, Seoul National University Bundang Hospital, Seongnam, 13620, Korea.,Department of Radiation Oncology, Seoul National University, College of Medicine, Seoul, Korea.,Integrated Major in Innovative Medical Science, Seoul National University Graduate School, Seoul, Korea
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Reita D, Pabst L, Pencreach E, Guérin E, Dano L, Rimelen V, Voegeli AC, Vallat L, Mascaux C, Beau-Faller M. Molecular Mechanism of EGFR-TKI Resistance in EGFR-Mutated Non-Small Cell Lung Cancer: Application to Biological Diagnostic and Monitoring. Cancers (Basel) 2021; 13:4926. [PMID: 34638411 PMCID: PMC8507869 DOI: 10.3390/cancers13194926] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common cancer in the world. Activating epidermal growth factor receptor (EGFR) gene mutations are a positive predictive factor for EGFR tyrosine kinase inhibitors (TKIs). For common EGFR mutations (Del19, L858R), the standard first-line treatment is actually third-generation TKI, osimertinib. In the case of first-line treatment by first (erlotinib, gefitinib)- or second-generation (afatinib) TKIs, osimertinib is approved in second-line treatment for patients with T790M EGFR mutation. Despite the excellent disease control results with EGFR TKIs, acquired resistance inevitably occurs and remains a biological challenge. This leads to the discovery of novel biomarkers and possible drug targets, which vary among the generation/line of EGFR TKIs. Besides EGFR second/third mutations, alternative mechanisms could be involved, such as gene amplification or gene fusion, which could be detected by different molecular techniques on different types of biological samples. Histological transformation is another mechanism of resistance with some biological predictive factors that needs tumor biopsy. The place of liquid biopsy also depends on the generation/line of EGFR TKIs and should be a good candidate for molecular monitoring. This article is based on the literature and proposes actual and future directions in clinical and translational research.
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Affiliation(s)
- Damien Reita
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- Bio-imagery and Pathology (LBP), UMR CNRS 7021, Strasbourg University, 67400 Illkirch-Graffenstaden, France
| | - Lucile Pabst
- Department of Pneumology, Strasbourg University Hospital, CEDEX, 67091 Strasbourg, France; (L.P.); (C.M.)
| | - Erwan Pencreach
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- INSERM U1113, IRFAC, Strasbourg University, 67000 Strasbourg, France
| | - Eric Guérin
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- INSERM U1113, IRFAC, Strasbourg University, 67000 Strasbourg, France
| | - Laurent Dano
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Valérie Rimelen
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Anne-Claire Voegeli
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Laurent Vallat
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Céline Mascaux
- Department of Pneumology, Strasbourg University Hospital, CEDEX, 67091 Strasbourg, France; (L.P.); (C.M.)
- INSERM U1113, IRFAC, Strasbourg University, 67000 Strasbourg, France
| | - Michèle Beau-Faller
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- INSERM U1113, IRFAC, Strasbourg University, 67000 Strasbourg, France
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Tu HY, Li YS, Bai XY, Sun YL, Zheng MY, Ke EE, Liao RQ, Jiang BY, Lin JX, Huang J, Xu BF, Yang JJ, Zhang XC, Zhou Q, Wang BC, Chen HJ, Tong X, Yu R, Wu X, Zhu D, Wu YL. Genetic Profiling of Cell-Free DNA From Pleural Effusion in Advanced Lung Cancer as a Surrogate for Tumor Tissue and Revealed Additional Clinical Actionable Targets. Clin Lung Cancer 2021; 23:135-142. [PMID: 34645582 DOI: 10.1016/j.cllc.2021.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/31/2021] [Accepted: 09/05/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Pleural effusion (PE) has been one of the promising sources of liquid biopsy in advanced lung cancer patients. However, its clinical utility is not widely accepted due to the lack of full estimation of its potential versus routine clinical samples. METHOD A total of 164 advanced lung cancer patients were enrolled with 164 matched tumor tissue and PE-cfDNA, 153 accompanied plasma and 63 1PE-sDNA. RESULT PE-cfDNA displayed significantly higher median mutant allele frequency and an overall mutation concordance rate of 65% to tissue, which was higher than PE-sDNA (43%) and plasma-cfDNA (43%). The discrepancies between PE-cfDNA and tumor tissue were high in several genes, including SMARCA4, PIK3CA, ERBB2, KM T2A, ALK and NF1. For clinically actionable mutations, the concordance rate between PE-cfDNA and tumor tissue is 87%. Eleven patients were identified with actionable mutations in PE-cfDNA and four patients benefited from PE-cfDNA-guided targeted. Meanwhile, PE-cfDNA recapitulated mutations of diverse tissue origins and provided more mutational information under the circumstance that tumor tissue or tumor tissue of different origins were unavailable. The combination of tumor tissue and PE-cfDNA profiling increased positive detection rates of patients compared to tumor tissue alone. Our finding highlighted the importance of PE-cfDNA in the optimal selection of patients for targeted therapy. CONCLUSION The PE-cfDNA-based liquid biopsy displays better performance in the characterization of gene alterations than PE-sDNA and plasma-cfDNA. PE-cfDNA together with tumor tissue profiling optimizes comprehensively genomic profiling of lung cancer patients, which might be important for selecting patients for better treatment management.
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Affiliation(s)
- Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yang-Si Li
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiao-Yan Bai
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yue-Li Sun
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ming-Ying Zheng
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - E-E Ke
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ri-Qiang Liao
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ben-Yuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jia-Xin Lin
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jie Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Bing-Fei Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Bin-Chao Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoling Tong
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Ruoying Yu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Dongqin Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; School of Medicine, South China University of Technology, Guangzhou, China.
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43
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Magios N, Bozorgmehr F, Volckmar AL, Kazdal D, Kirchner M, Herth FJ, Heussel CP, Eichhorn F, Meister M, Muley T, Elshafie RA, Fischer JR, Faehling M, Kriegsmann M, Schirmacher P, Bischoff H, Stenzinger A, Thomas M, Christopoulos P. Real-world implementation of sequential targeted therapies for EGFR-mutated lung cancer. Ther Adv Med Oncol 2021; 13:1758835921996509. [PMID: 34408792 PMCID: PMC8366107 DOI: 10.1177/1758835921996509] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/27/2021] [Indexed: 11/15/2022] Open
Abstract
Background: Epidermal growth factor receptor-mutated (EGFR+) non-small-cell lung cancer (NSCLC) patients failing tyrosine kinase inhibitors (TKI) can benefit from next-line targeted therapies, but implementation is challenging. Methods: EGFR+ NSCLC patients treated with first/second-generation (1G/2G) TKI at our institution with a last follow-up after osimertinib approval (February 2016), were analyzed retrospectively, and the results compared with published data under osimertinib. Results: A total of 207 patients received erlotinib (37%), gefitinib (16%) or afatinib (47%). The median age was 66 years, with a predominance of female (70%), never/light-smokers (69%). T790M testing was performed in 174/202 progressive cases (86%), positive in 93/174 (53%), and followed by osimertinib in 87/93 (94%). Among the 135 deceased patients, 94 (70%) received subsequent systemic treatment (43% chemotherapy, 39% osimertinib), while 30% died without, either before (4%) or after progression, due to rapid clinical deterioration (22%), patient refusal of further therapy (2%), or severe competing illness (2%). Lack of subsequent treatment was significantly (4.5x, p < 0.001) associated with lack of T790M testing, whose most frequent cause (in approximately 50% of cases) was also rapid clinical decline. Among the 127 consecutive patients with failure of 1G/2G TKI started after November 2015, 47 (37%) received osimertinib, with a median overall survival of 36 months versus 24 and 21 months for patients with alternative and no subsequent therapies (p = 0.003). Conclusion: Osimertinib after 1G/2G TKI failure prolongs survival, but approximately 15% and 30% of patients forego molecular retesting and subsequent treatment, respectively, mainly due to rapid clinical deterioration. This is an important remediable obstacle to sequential TKI treatment for EGFR+ NSCLC. It pertains also to other actionable resistance mechanisms emerging under 1G/2G inhibitors or osimertinib, whose rate for lack of next-line therapy is similar (approximately 35% in the FLAURA/AURA3 trials), and highlights the need for closer monitoring alongside broader profiling of TKI-treated EGFR+ NSCLC in the future.
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Affiliation(s)
- Nikolaus Magios
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Farastuk Bozorgmehr
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix J Herth
- Department of Pneumology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Claus-Peter Heussel
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Florian Eichhorn
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Rami A Elshafie
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen R Fischer
- Department of Thoracic Oncology, Lungenklinik Löwenstein, Löwenstein, Germany
| | - Martin Faehling
- Department of Cardiology, Angiology and Pneumology, Klinikum Esslingen, Esslingen, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Helge Bischoff
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | | | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Röntgenstraße 1, Heidelberg, Baden-Württemberg 69126, Germany
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Thompson MK, Gale D, Brenton JD. Circulating tumour DNA for clinicians: current and future clinical applications. Clin Radiol 2021; 76:737-747. [PMID: 34389159 DOI: 10.1016/j.crad.2021.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022]
Abstract
This review introduces clinicians to the basic concepts of the biology of circulating tumour DNA (ctDNA), which is required to understand clinical use of ctDNA technology. We provide an overview of how new technology has improved the sensitivity of ctDNA detection over the last decade and the available techniques for ctDNA analysis including whole-genome sequencing (WGS), targeted cancer-associated gene panels, and methylation analysis. We discuss the most recent evidence from clinical trials for ctDNA in patient care including precision treatment of advanced cancers, disease monitoring, improving adjuvant treatment, and screening for early detection of cancer. Finally, we outline how ctDNA is likely to directly impact radiologists, and identify further research required for ctDNA to progress into routine clinical application.
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Affiliation(s)
- M K Thompson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - D Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - J D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
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Di Capua D, Bracken-Clarke D, Ronan K, Baird AM, Finn S. The Liquid Biopsy for Lung Cancer: State of the Art, Limitations and Future Developments. Cancers (Basel) 2021; 13:cancers13163923. [PMID: 34439082 PMCID: PMC8391249 DOI: 10.3390/cancers13163923] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary During the development and progression of lung tumors, processes such as necrosis and vascular invasion shed tumor cells or cellular components into various fluid compartments. Liquid biopsies consist of obtaining a bodily fluid, typically peripheral blood, in order to isolate and investigate these shed tumor constituents. Circulating tumor cells (CTCs) are one such constituent, which can be isolated from blood and can act as a diagnostic aid and provide valuable prognostic information. Liquid-based biopsies may also have a potential future role in lung cancer screening. Circulating tumor DNA (ctDNA) is found in small quantities in blood and, with the recent development of sensitive molecular and sequencing technologies, can be used to directly detect actionable genetic alterations or monitor for resistance mutations and guide clinical management. While potential benefits of liquid biopsies are promising, they are not without limitations. In this review, we summarize the current state and limitations of CTCs and ctDNA and possible future directions. Abstract Lung cancer is a leading cause of cancer-related deaths, contributing to 18.4% of cancer deaths globally. Treatment of non-small cell lung carcinoma has seen rapid progression with targeted therapies tailored to specific genetic drivers. However, identifying genetic alterations can be difficult due to lack of tissue, inaccessible tumors and the risk of complications for the patient with serial tissue sampling. The liquid biopsy provides a minimally invasive method which can obtain circulating biomarkers shed from the tumor and could be a safer alternative to tissue biopsy. While tissue biopsy remains the gold standard, liquid biopsies could be very beneficial where serial sampling is required, such as monitoring disease progression or development of resistance mutations to current targeted therapies. Liquid biopsies also have a potential role in identifying patients at risk of relapse post treatment and as a component of future lung cancer screening protocols. Rapid developments have led to multiple platforms for isolating circulating tumor cells (CTCs) and detecting circulating tumor DNA (ctDNA); however, standardization is lacking, especially in lung carcinoma. Additionally, clonal hematopoiesis of uncertain clinical significance must be taken into consideration in genetic sequencing, as it introduces the potential for false positives. Various biomarkers have been investigated in liquid biopsies; however, in this review, we will concentrate on the current use of ctDNA and CTCs, focusing on the clinical relevance, current and possible future applications and limitations of each.
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Affiliation(s)
- Daniel Di Capua
- Department of Histopathology, St. James’s Hospital, D08NHY1 Dublin, Ireland;
| | - Dara Bracken-Clarke
- Department of Medical Oncology, St. James’ Hospital, D08NHY1 Dublin, Ireland;
| | - Karine Ronan
- Faculty of Medicine, University College Dublin, D04V1W8 Dublin, Ireland;
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College, D02PN40 Dublin, Ireland;
| | - Stephen Finn
- Department of Histopathology, St. James’s Hospital, D08NHY1 Dublin, Ireland;
- Correspondence:
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The Emerging Importance of Tumor Genomics in Operable Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13153656. [PMID: 34359558 PMCID: PMC8345160 DOI: 10.3390/cancers13153656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
During the last two decades, next-generation sequencing (NGS) has played a key role in enhancing non-small cell lung cancer treatment paradigms through the application of "targeted therapy" in advanced and metastatic disease. The use of specific tyrosine kinase inhibitors in patients with oncogenic driver alterations, such as EGFR, ALK, ROS1, BRAF V600E, MET, and NTRK mutations, among others, has changed treatment approaches and improved outcomes in patients with late-stage disease. Although NGS technology has mostly been used in the setting of systemic therapy to identify targets, response to therapy, and mechanisms of resistance, it has multiple potential applications for patients with earlier-stage disease, as well. In this review, we discuss the emerging role of NGS technologies to better understand tumor biology in patients with non-small cell lung cancer who are undergoing surgery with curative intent. In this patient cohort, we examine tumor heterogeneity, the underlying tumor genomics associated with lung adenocarcinoma subtypes, the prediction of recurrence after complete surgical resection, the use of plasma circulating tumor DNA for detection of early cancers and monitoring for minimal residual disease, the differentiation of separate primaries from intrapulmonary metastases, and the use of NGS to guide induction and adjuvant therapies.
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Wang H, Zhou F, Qiao M, Li X, Zhao C, Cheng L, Chen X, Zhou C. The Role of Circulating Tumor DNA in Advanced Non-Small Cell Lung Cancer Patients Treated With Immune Checkpoint Inhibitors: A Systematic Review and Meta-Analysis. Front Oncol 2021; 11:671874. [PMID: 34367957 PMCID: PMC8335591 DOI: 10.3389/fonc.2021.671874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background The use of circulating tumor DNA (ctDNA) to reflect clinical benefits of advanced non-small cell lung cancer (NSCLC) patients during immune checkpoint inhibitor (ICI) therapy remains controversial. This study aimed to determine the association of pre-treatment and early dynamic changes of ctDNA with clinical outcomes in advanced NSCLC patients treated with ICIs. Methods Electronic databases (PubMed, Embase, Web of Science, and Cochrane) were systematically searched to include relevant studies published in English up to November 2020. The primary outcomes were overall survival (OS) and progression-free survival (PFS) and the secondary outcome was objective response rate (ORR) with RECIST criteria. Results A total of 1017 patients from 10 studies were identified. The baseline ctDNA levels (detected versus not detected) showed no significant association with clinical outcomes regarding OS (hazard ratio [HR], 1.18; 95% confidence interval [CI], 0.93-1.51), PFS (HR, 0.98; 95% CI, 0.80-1.21), and ORR (odds ratio [OR], 0.89; 95% CI, 0.54-1.46). Interestingly, when taken early longitudinal assessment of ctDNA into consideration, the early reduction of the concentration of ctDNA was associated with significant improvements of OS (HR, 0.19; 95% CI, 0.10-0.35), PFS (HR, 0.30; 95% CI, 0.22-0.41) and ORR (OR, 0.07; 95% CI, 0.03-0.18). Further subgroup analyses revealed that the reduction magnitude did not significantly impact the association between ctDNA and clinical outcomes, suggesting that both patients with decreased ctDNA or a ≥50% reduction of ctDNA was associated with improved OS, PFS and ORR. Conclusion Early reduction of ctDNA was associated with improved OS, PFS and ORR in advanced NSCLC patients treated with ICIs. Systematic Review Registration https://www.crd.york.ac.uk/PROSPERO, CRD42021226255.
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Affiliation(s)
- Haowei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Meng Qiao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lei Cheng
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Mondaca S, Lebow ES, Namakydoust A, Razavi P, Reis-Filho JS, Shen R, Offin M, Tu HY, Murciano-Goroff Y, Xu C, Makhnin A, Martinez A, Pavlakis N, Clarke S, Itchins M, Lee A, Rimner A, Gomez D, Rocco G, Chaft JE, Riely GJ, Rudin CM, Jones DR, Li M, Shaffer T, Hosseini SA, Bertucci C, Lim LP, Drilon A, Berger MF, Benayed R, Arcila ME, Isbell JM, Li BT. Clinical utility of next-generation sequencing-based ctDNA testing for common and novel ALK fusions. Lung Cancer 2021; 159:66-73. [PMID: 34311346 DOI: 10.1016/j.lungcan.2021.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Liquid biopsy for plasma circulating tumor DNA (ctDNA) next-generation sequencing (NGS) can detect ALK fusions, though data on clinical utility of this technology in the real world is limited. MATERIALS AND METHODS Patients with lung cancer without known oncogenic drivers or who had acquired resistance to therapy (n = 736) underwent prospective plasma ctDNA NGS. A subset of this cohort (n = 497) also had tissue NGS. We evaluated ALK fusion detection, turnaround time (TAT), plasma and tissue concordance, matching to therapy, and treatment response. RESULTS ctDNA identified an ALK fusion in 21 patients (3%) with a variety of breakpoints and fusion partners, including EML4, CLTC, and PON1, a novel ALK fusion partner. TAT for ctDNA NGS was shorter than tissue NGS (10 vs. 20 days; p < 0.001). Among ALK fusions identified by ctDNA, 93% (13/14, 95% CI 66%-99%) were concordant with tissue evaluation. Among ALK fusions detected by tissue NGS, 54% (13/24, 95% CI 33%-74%) were concordant with plasma ctDNA. ctDNA matched patients to ALK-directed therapy with subsequent clinical response, including four patients matched on the basis of ctDNA results alone due to inadequate or delayed tissue testing. Serial ctDNA analysis detected MET amplification (n = 2) and ALK G1202R mutation (n = 2) as mechanisms of acquired resistance to ALK-directed therapy. CONCLUSION Our findings support a complementary role for ctDNA in detection of ALK fusions and other alterations at diagnosis and therapeutic resistance settings.
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Affiliation(s)
- Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Department of Hematology and Oncology, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 6th Fl, Rm 609, Santiago, Chile.
| | - Emily S Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Azadeh Namakydoust
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, 1275 York Avenue, New York, NY, USA
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Hai-Yan Tu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, China
| | - Yonina Murciano-Goroff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Chongrui Xu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, China
| | - Alex Makhnin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Andres Martinez
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Nick Pavlakis
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Stephen Clarke
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Malinda Itchins
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Adrian Lee
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gaetano Rocco
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Mark Li
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | - Tristan Shaffer
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | | | | | - Lee P Lim
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - James M Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
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Zhang M, Qi C, Wang Z, Chen H, Zhao X, Zhang X, Zhou Y, Gao C, Bai Y, Jia S, Ji J. Molecular characterization of ctDNA from Chinese patients with advanced gastric adenocarcinoma reveals actionable alterations for targeted and immune therapy. J Mol Med (Berl) 2021; 99:1311-1321. [PMID: 34057552 DOI: 10.1007/s00109-021-02093-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 05/08/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA (ctDNA) is considered an ideal sample type for genotyping patients with advanced unresectable cancer to inform treatment decision. It may better capture tumor heterogeneity, especially in gastric adenocarcinoma (GAC). However, there exists little evidence regarding genomic profiling of Chinese advanced GAC patients from ctDNA. Blood samples were obtained from 200 advanced GAC patients. Next-generation sequencing (NGS) was performed on ctDNA using a validated 150-gene panel. Blood tumor mutation burden (bTMB) was calculated according to the NGS results. Blood microsatellite instability (bMSI) status was determined by targeted sequencing of 100 microsatellite loci. One hundred sixty-nine (84.5%) patients carried at least one genomic alteration and 138 (69%) patients had at least one deleterious or likely deleterious alteration (del-alteration). The clonal fraction of del-alterations was higher than that of non-del-alterations (80.1% vs 54.5%, P < 0.0001). The most frequently altered genes were TP53 (38%), LRP1B (20%), MYC (13.5%), ERBB2 (12.5%), and KRAS (11.5%). The alterations were most enriched in the TP53/cell cycle (52%) and the RTK-Ras-MAPK pathway (51.5%). The median bTMB was two (range 0 to 42). Eight patients were identified to be high bMSI, with higher median bTMB than the blood microsatellite stable (bMSS) patients (15 vs 2, P = 0.0062). Patients harboring del-alterations of the DDR pathway had significantly higher percentages of high bTMB and bMSI-H patients than the wild-type subgroup (61.1% vs 6.5%, P < 0.0001; 33.3% vs 1.7%, P = 0.0002). A total of 45.5% cases harbored at least one potentially actionable alteration and one patient achieved complete response after receiving matched targeted therapy. Our study uncovered the molecular characterization of Chinese patients with advanced GAC from ctDNA, including genomic alteration, bTMB, and bMSI status. The findings suggested that targeted NGS-based ctDNA analysis may help inform the clinical decision in advanced GAC. KEY MESSAGES: We report the molecular profiling of the largest Chinese advance stage GACs cohort using a CLIA-certified ctDNA assay. Potentially actionable genomic alterations were identified in 45.5% of patients, suggesting clinical utility for ctDNA NGS in advance stage GACs. There was evidence of clinical benefit in one GAC patient with MET amplification treated with MET inhibitor.
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Affiliation(s)
- Meng Zhang
- Department of Molecular Diagnostics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, No. 52 Fucheng Road, Haidian District, Beijing, China
| | - Changsong Qi
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhenghang Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Hui Chen
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Xiaochen Zhao
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Xueming Zhang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yifan Zhou
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Chan Gao
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yuezong Bai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Shuqin Jia
- Department of Molecular Diagnostics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, No. 52 Fucheng Road, Haidian District, Beijing, China.
| | - Jiafu Ji
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
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50
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Ma L, Li H, Wang D, Hu Y, Yu M, Zhang Q, Qin N, Zhang X, Li X, Zhang H, Wu Y, Lv J, Yang X, Yu R, Zhang S, Wang J. Dynamic cfDNA Analysis by NGS in EGFR T790M-Positive Advanced NSCLC Patients Failed to the First-Generation EGFR-TKIs. Front Oncol 2021; 11:643199. [PMID: 33842353 PMCID: PMC8030263 DOI: 10.3389/fonc.2021.643199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose Circulating cell-free DNA (cfDNA) level has been demonstrated to be associated with efficacy in first generation EGFR TKIs in non-small cell lung cancer (NSCLC). However, the role of dynamic cfDNA analysis using next-generation sequencing (NGS) in patients with subsequent third-generation EGFR TKIs remains unclear. Methods From 2016 to 2019, 81 NSCLC patients with EGFR T790M mutation either in tissue or plasma who received third-generation EGFR TKIs treatment were enrolled. CfDNA were sequenced by NGS with a 425-gene panel. The association of clinical characteristics, pretreatment, dynamic cfDNA and T790M level with outcomes in patients treated with the third-generation TKIs were analyzed. Results In univariate analysis, the median PFS of patients with undetectable cfDNA level during treatment was significantly longer than those with detectable cfDNA (16.97 vs. 6.10 months; HR 0.2109; P < 0.0001). The median PFS of patients with undetectable T790M level during treatment was significantly longer than those with detectable T790M (14.1 vs. 4.4 months; HR 0.2192; P < 0.001). Cox hazard proportion model showed that cfDNA clearance was an independent predictor for longer PFS (HR 0.3085; P < 0.001) and longer OS (HR 0.499; P = 0.034). The most common resistant mutations of the third-generation TKIs were EGFR C797S (24%). CDK6 CNV, GRIN2A, BRCA2, EGFR D761N, EGFR Q791H, EGFR V843I, and ERBB4 mutation genes may possibly be new resistant mechanisms. Conclusions Patients with undetectable cfDNA during the third-generation EGFR TKI treatment have superior clinical outcomes, and dynamic cfDNA analysis by NGS is valuable to explore potential resistant mechanisms.
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Affiliation(s)
- Li Ma
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Haoyang Li
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dongpo Wang
- Department of Radiology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ying Hu
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Mengjun Yu
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Quan Zhang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Na Qin
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xinyong Zhang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xi Li
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hui Zhang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yuhua Wu
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jialin Lv
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xinjie Yang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ruoying Yu
- Research and Development, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Shucai Zhang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinghui Wang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China.,Cancer Research Center, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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