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Deshwal A, Saxena K, Sharma G, Rajesh, Sheikh FA, Seth CS, Tripathi RM. Nanozymes: A comprehensive review on emerging applications in cancer diagnosis and therapeutics. Int J Biol Macromol 2024; 256:128272. [PMID: 38000568 DOI: 10.1016/j.ijbiomac.2023.128272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Nanozymes, a new class of nanomaterials-based artificial enzymes, have gained huge attraction due to their high operational stability, working efficiency in extreme conditions, and resistance towards protease digestion. Nowadays, they are effectively substituted for natural enzymes for catalysis by closely resembling the active sites found in natural enzymes. Nanozymes can compensate for natural enzymes' drawbacks, such as high cost, poor stability, low yield, and storage challenges. Due to their transforming nature, nanozymes are of utmost importance in the detection and treatment of cancer. They enable precise cancer detection, tailored drug delivery, and catalytic therapy. Through enhanced diagnosis, personalized therapies, and reduced side effects, their adaptability and biocompatibility can transform the management of cancer. The review focuses on metal and metal oxide-based nanozymes, highlighting their catalytic processes, and their applications in the prevention and treatment of cancer. It emphasizes their potential to alter diagnosis and therapy, particularly when it comes to controlling reactive oxygen species (ROS). The article reveals the game-changing importance of nanozymes in the future of cancer care and describes future research objectives, making it a useful resource for researchers, and scientists. Lastly, outlooks for future perspective areas in this rapidly emerging field have been provided in detail.
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Affiliation(s)
- Akanksha Deshwal
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh (AUUP), Noida 201313, India
| | - Kirti Saxena
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh (AUUP), Noida 201313, India
| | - Garima Sharma
- Department of Biomedical Science & Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Rajesh
- CSIR-National Physical Laboratory, New Delhi, India
| | - Faheem A Sheikh
- Nanostructured and Biomimetic Lab, Department of Nanotechnology, University of Kashmir Hazratbal, Srinagar, Jammu and Kashmir 190006, India
| | | | - Ravi Mani Tripathi
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh (AUUP), Noida 201313, India.
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Ben X, Tian D, Zhuang W, Chen R, Wang S, Zhou Z, Deng C, Shi R, Liu S, Zhang D, Tang J, Xie L, Zhou H, Zhang Z, Li M, Zhang X, Qiao G. Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison. Diagn Pathol 2022; 17:78. [PMID: 36224661 PMCID: PMC9554964 DOI: 10.1186/s13000-022-01255-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Background Successful practice of precision medicine in advanced lung cancers relies on therapeutic regimens tailored to individual molecular characteristics. The aim of this study was to investigate the accuracy of small specimens for molecular profiling using next-generation sequencing (NGS). Methods Genetic alternations, tumor mutational burden (TMB), status of microsatellite instability (MSI), and expression of programmed death ligand 1 (PD-L1) were compared side-by-side between the concurrently obtained core needle biopsy (CNB) and resection specimens in 17 patients with resectable non-small cell lung cancers. Results DNA yield and library complexity were significantly lower in CNB specimens (both p < 0.01), whereas the insert size, sequencing depth, and Q30 ratio were similar between the matched specimens (all p > 0.05). The total numbers of genetic alternations detected in resection and CNB specimens were 186 and 211, respectively, with 156 alternations in common, yielding a specific concordance rate of 83.9%. The prevalence of mutations in 8 major driver genes was 100% identical between surgical and CNB specimens, though the allele frequency was lower in CNB specimens, with a median underestimation of 57%. Results of TMB were similar (p = 0.547) and MSI status was 100% matched in all paired specimens. Conclusions Pulmonary CNB specimens were suitable for NGS given the satisfactory accuracy when compared to corresponding surgical specimens. NGS results yielding from CNB specimens should be deemed reliable to provide instructive information for the treatment of advanced lung cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13000-022-01255-y.
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Affiliation(s)
- Xiaosong Ben
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Dan Tian
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Weitao Zhuang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
| | - Rixin Chen
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China.,Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Sichao Wang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Zihao Zhou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Cheng Deng
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Ruiqing Shi
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Songlin Liu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Dongkun Zhang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Jiming Tang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Zhou Zhang
- Department of Data Science, Burning Rock Biotech, Guangzhou, China
| | - Min Li
- Department of Medicine, Burning Rock Biotech, Guangzhou, China
| | - Xuanye Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China.
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Behel V, Noronha V, Choughule A, Shetty O, Chandrani P, Kapoor A, Bondili SK, Bajpai J, Kumar R, Pai T, Bal M, Gurav M, Bapat P, Mittal N, Menon S, Patil V, Menon N, Dutt A, Prabhash K. Impact of Molecular Tumor Board on the Clinical Management of Patients With Cancer. JCO Glob Oncol 2022; 8:e2200030. [PMID: 35802838 PMCID: PMC9296182 DOI: 10.1200/go.22.00030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Multidisciplinary molecular tumor boards (MTBs) help in interpreting complex genomic data generated by molecular tumor profiling and improve patients' access to targeted therapies. The purpose of this study was to assess the impact of our institution's MTB on the clinical management of patients with cancer. METHODS This study was conducted at a tertiary cancer center in India. Cases to be discussed in the MTB were identified by molecular pathologists, scientists, or oncologists. On the basis of the clinical data and molecular test reports, a course of clinical management was recommended and made available to the treating oncologist. We determined the proportion of patients who were recommended a change in the clinical management. We also assessed compliance of the treating oncologists with MTB recommendations. RESULTS There were 339 discussions for 328 unique patients. The median age of the cohort was 54 years (range 17-87), and the majority of the patients were men (65.1%). Of 339 cases, 133 (39.2%) were recommended continuation of ongoing therapy while the remaining 206 (60.7%) were recommended a change in clinical management. Compliance with MTB recommendations for a change in clinical management was 58.5% (79 of 138 evaluable cases). Compliance and implementation for MTB's recommendation to start a new therapy in 104 evaluable cases were 60.5% and 44.2%, respectively. A total of 248 biopsies had at least one actionable mutation. A total of 646 mutations were identified in the cohort, with EGFR being the most frequently altered gene. CONCLUSION MTBs help in interpreting results of molecular tests, understanding the significance of molecular abnormalities, and assessing the benefits of available targeted therapies and clinical trials in the management of patients with targetable genetic alterations.
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Affiliation(s)
- Vichitra Behel
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Anuradha Choughule
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Omshree Shetty
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Pratik Chandrani
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Akhil Kapoor
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
- Homi Bhabha Cancer Hospital, Varanasi, India
| | - Suresh Kumar Bondili
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Jyoti Bajpai
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Rajiv Kumar
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Trupti Pai
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Munita Bal
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Mamta Gurav
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Prachi Bapat
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Neha Mittal
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Santosh Menon
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Vijay Patil
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Nandini Menon
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute, Mumbai, India
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
- Kumar Prabhash, Department of Medical Oncology, Tata Memorial Hospital, Dr. E Borges Road, Parel, Mumbai - 400 012, Maharashtra, India; e-mail:
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Dong OM, Poonnen PJ, Winski D, Reed SD, Vashistha V, Bates J, Kelley MJ, Voora D. Cost-Effectiveness of Tumor Genomic Profiling to Guide First-Line Targeted Therapy Selection in Patients With Metastatic Lung Adenocarcinoma. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2022; 25:582-594. [PMID: 35365302 PMCID: PMC8976872 DOI: 10.1016/j.jval.2021.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/18/2021] [Accepted: 09/30/2021] [Indexed: 06/04/2023]
Abstract
OBJECTIVES A cost-effectiveness analysis comparing comprehensive genomic profiling (CGP) of 10 oncogenes, targeted gene panel testing (TGPT) of 4 oncogenes, and no tumor profiling over the lifetime for patients with metastatic lung adenocarcinoma from the Centers for Medicare and Medicaid Services' perspective was conducted. METHODS A decision analytic model used 10 000 hypothetical Medicare beneficiaries with metastatic lung adenocarcinoma to simulate outcomes associated with CGP (ALK, BRAF, EGFR, ERBB2, MET, NTRK1, NTRK2, NTRK3, RET, ROS1), TGPT (ALK, BRAF, EGFR, ROS1), and no tumor profiling (no genes tested). First-line targeted cancer-directed therapies were assigned if actionable gene variants were detected; otherwise, nontargeted cancer-directed therapies were assigned. Model inputs were derived from randomized trials (progression-free survival, adverse events), the Veterans Health Administration and Medicare (drug costs), published studies (nondrug cancer-related management costs, health state utilities), and published databases (actionable variant prevalences). Costs (2019 US$) and quality-adjusted life-years (QALYs) were discounted at 3% per year. Probabilistic sensitivity analyses used 1000 Monte Carlo simulations. RESULTS No tumor profiling was the least costly/person ($122 613 vs $184 063 for TGPT and $188 425 for CGP) and yielded the least QALYs/person (0.53 vs 0.73 for TGPT and 0.74 for CGP). The costs per QALY gained and corresponding 95% confidence interval were $310 735 ($278 323-$347 952) for TGPT vs no tumor profiling and $445 545 ($322 297-$572 084) for CGP vs TGPT. All probabilistic sensitivity analysis simulations for both comparisons surpassed the willingness-to-pay threshold ($150 000 per QALY gained). CONCLUSION Compared with no tumor profiling in patients with metastatic lung adenocarcinoma, tumor profiling (TGPT, CGP) improves quality-adjusted survival but is not cost-effective.
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Affiliation(s)
- Olivia M Dong
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Veterans Affairs, Durham VA Medical Center, Durham, NC, USA
| | - Pradeep J Poonnen
- Department of Veterans Affairs, Durham VA Medical Center, Durham, NC, USA; Duke University Medical Center, Durham, NC, USA
| | - David Winski
- Department of Veterans Affairs, VA Boston Healthcare System, Boston, MA, USA
| | - Shelby D Reed
- Department of Veterans Affairs, Durham VA Medical Center, Durham, NC, USA; Duke Cancer Institute, Durham, NC, USA; Duke Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Vishal Vashistha
- Section of Hematology/Oncology, Raymond G. Murphy New Mexico Veterans Affairs Medical Center, Albuquerque, NM, USA
| | - Jill Bates
- Department of Veterans Affairs, Durham VA Medical Center, Durham, NC, USA; Division of Practice Advancement and Clinical Education, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Veterans Affairs, National Oncology Program, Durham, NC, USA
| | - Michael J Kelley
- Department of Veterans Affairs, Durham VA Medical Center, Durham, NC, USA; Duke University Medical Center, Durham, NC, USA; Duke Cancer Institute, Durham, NC, USA; Department of Veterans Affairs, National Oncology Program, Durham, NC, USA
| | - Deepak Voora
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Veterans Affairs, Durham VA Medical Center, Durham, NC, USA; Department of Veterans Affairs, National Oncology Program, Durham, NC, USA.
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5
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Bradbury AR, Lee JW, Gaieski JB, Li S, Gareen IF, Flaherty KT, Herman BA, Domchek SM, DeMichele AM, Maxwell KN, Onitilo AA, Virani S, Park S, Faller BA, Grant SC, Ramaekers RC, Behrens RJ, Nambudiri GS, Carlos RC, Wagner LI. A randomized study of genetic education versus usual care in tumor profiling for advanced cancer in the ECOG-ACRIN Cancer Research Group (EAQ152). Cancer 2021; 128:1381-1391. [PMID: 34890045 PMCID: PMC8917095 DOI: 10.1002/cncr.34063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 01/19/2023]
Abstract
Background Enthusiasm for precision oncology may obscure the psychosocial and ethical considerations associated with the implementation of tumor genetic sequencing. Methods Patients with advanced cancer undergoing tumor‐only genetic sequencing in the National Cancer Institute Molecular Analysis for Therapy Choice (MATCH) trial were randomized to a web‐based genetic education intervention or usual care. The primary outcomes were knowledge, anxiety, depression, and cancer‐specific distress collected at baseline (T0), posteducation (T1) and after results (T2). Two‐sided, 2‐sample t tests and univariate and multivariable generalized linear models were used. Results Five hundred ninety‐four patients (80% from NCI Community Oncology Research Program sites) were randomized to the web intervention (n = 293) or usual care (n = 301) before the receipt of results. Patients in the intervention arm had greater increases in knowledge (P for T1‐T0 < .0001; P for T2‐T0 = .003), but there were no significant differences in distress outcomes. In unadjusted moderator analyses, there was a decrease in cancer‐specific distress among women (T0‐T1) in the intervention arm but not among men. Patients with lower health literacy in the intervention arm had greater increases in cancer‐specific distress and less decline in general anxiety (T0‐T1) and greater increases in depression (T0‐T2) in comparison with those receiving usual care. Conclusions Web‐based genetic education before tumor‐only sequencing results increases patient understanding and reduces distress in women. Refinements to the intervention could benefit low‐literacy groups and men. In the Communication and Education in Tumor Profiling (COMET) study, patients with advanced cancer undergoing tumor genetic sequencing in the National Cancer Institute Molecular Analysis for Therapy Choice (MATCH) trial have been randomized to a web‐based genetic education intervention or usual care. Web‐based genetic education has resulted in increased patient understanding and reduced distress in female patients with cancer.
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Affiliation(s)
- Angela R Bradbury
- University of Pennsylvania/Abramson Cancer Center, Philadelphia, Pennsylvania
| | - Ju-Whei Lee
- ECOG-ACRIN Biostatistics Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Shuli Li
- ECOG-ACRIN Biostatistics Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ilana F Gareen
- ECOG-ACRIN Biostatistics Center, Brown University, Providence, Rhode Island
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Benjamin A Herman
- ECOG-ACRIN Biostatistics Center, Brown University, Providence, Rhode Island
| | - Susan M Domchek
- University of Pennsylvania/Abramson Cancer Center, Philadelphia, Pennsylvania
| | - Angela M DeMichele
- University of Pennsylvania/Abramson Cancer Center, Philadelphia, Pennsylvania
| | - Kara N Maxwell
- University of Pennsylvania/Abramson Cancer Center, Philadelphia, Pennsylvania
| | | | | | - SuJung Park
- Medical Oncology Hematology Consultants PA, Newark, Delaware
| | | | - Stefan C Grant
- Wake Forest University Health Sciences, Winston-Salem, North Carolina
| | | | | | | | - Ruth C Carlos
- University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
| | - Lynne I Wagner
- Wake Forest University Health Sciences, Winston-Salem, North Carolina
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Anderson EC, Hinton AC, Lary CW, Fenton ATHR, Antov A, Edelman E, Helbig P, Reed K, Miesfeldt S, Thomas CA, Hall MJ, Roberts JS, Rueter J, Han PKJ. Community oncologists' perceptions and utilization of large-panel genomic tumor testing. BMC Cancer 2021; 21:1273. [PMID: 34823486 PMCID: PMC8620967 DOI: 10.1186/s12885-021-08985-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/07/2021] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Large-panel genomic tumor testing (GTT) is an emerging technology with great promise but uncertain clinical value. Previous research has documented variability in academic oncologists' perceptions and use of GTT, but little is known about community oncologists' perceptions of GTT and how perceptions relate to clinicians' intentions to use GTT. METHODS Community oncology physicians (N = 58) participating in a statewide initiative aimed at improving access to large-panel GTT completed surveys assessing their confidence in using GTT, attitudes regarding the value of GTT, perceptions of barriers to GTT implementation, and future intentions to use GTTs. Descriptive and multivariable regression analyses were conducted to characterize these perceptions and to explore the relationships between them. RESULTS There was substantial variability in clinicians' perceptions of GTT. Clinicians generally had moderate confidence in their ability to use GTT, but lower confidence in patients' ability to understand test results and access targeted treatment. Clinicians had positive attitudes regarding the value of GTT. Clinicians' future intentions to use GTT were associated with greater confidence in using GTT and greater perceived barriers to implementing GTT, but not with attitudes about the value of GTT. CONCLUSIONS Community oncologists' perceptions of large-panel genomic tumor testing are variable, and their future intentions to use GTT are associated with both their confidence in and perceived barriers to its use, but not with their attitudes towards GTT. More research is needed to understand other factors that determine how oncologists perceive and use GTT in clinical practice.
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Affiliation(s)
- Eric C Anderson
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA.
- Tufts University School of Medicine, Boston, MA, USA.
| | - Alexandra C Hinton
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
| | - Christine W Lary
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
- Tufts University School of Medicine, Boston, MA, USA
| | - Anny T H R Fenton
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
| | | | | | | | - Kate Reed
- The Jackson Laboratory, Augusta, ME, USA
| | | | | | | | - J Scott Roberts
- University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | - Paul K J Han
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
- Tufts University School of Medicine, Boston, MA, USA
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Blee SM, Shah RP, Pinheiro APM, Switchenko J, Dixon M, Owonikoko TK, Hill CE, Szabo SM, Pentz RD. Physician Communication and Patient Understanding of Molecular Testing Terminology. Oncologist 2021; 26:934-940. [PMID: 34369626 DOI: 10.1002/onco.13930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The use of molecular testing in oncology is rapidly expanding. The aim of this study was to determine how oncologists describe molecular testing and whether patients understand the terminology being used. MATERIALS AND METHODS Sixty conversations between oncologists and patients about molecular testing were observed, and the used technical terms were noted by the researcher. Patients were interviewed post-conversation to assess their understanding of the noted technical terms. A patient understanding score was calculated for each participant. Comparisons of the terms were conducted using χ2 tests, Fisher's exact tests, or ANOVA when appropriate. RESULTS Sixty-one unique technical terms were used by oncologists, to describe seven topics. "Mutation" was a challenging term for patients to understand with 48.8% (21/43 mentions) of participants correctly defining the term. "Genetic testing" and "Gene" were understood a little more than half the time (53.3%; 8/15 and 56.4%; 22/39 respectively). "DNA" was well understood (80%; 12/15). There was no correlation between the terms being defined by the oncologist in the conversation, and the likelihood of the patient providing a correct definition. White participants were significantly more likely to understand both "mutation" and "genetic testing" than non-White participants. Forty-two percent (n = 25) of participants had an understanding score below 50%, and a higher family income was significantly correlated with a higher score. CONCLUSION Our results show that oncologists use variable terminology to describe molecular testing, which is often not understood. Because oncologists defining the terms did not correlate with understanding, it is imperative to develop new, improved methods to explain molecular testing. IMPLICATIONS FOR PRACTICE The use of molecular testing is expanding in oncology, yet little is known about how effectively clinicians are communicating information about molecular testing and whether patients understand the terminology used. The results of this study indicate that patients do not understand some of the terminology used by their clinicians and that clinicians tend to use highly variable terminology to describe molecular testing. These results highlight the need to develop and implement effective methods to explain molecular testing terminology to patients to ensure that patients have the tools to make autonomous and informed decisions about their treatment.
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Affiliation(s)
- Shannon M Blee
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | | | - Ana P M Pinheiro
- Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Jeffrey Switchenko
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Margie Dixon
- Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Taofeek K Owonikoko
- Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Charles E Hill
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephen M Szabo
- Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Rebecca D Pentz
- Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
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Qi H, Zhu L, Chen L, Zhang W, Wang T, Chen H, Wu Q, Zhan Q, Le T, Zhang L, Zhong M, Shi X, Li Q. Reduced emergency room visits and improved medication adherence of an integrated oncology pharmaceutical care practice in China. J Oncol Pharm Pract 2021; 27:1503-1515. [PMID: 34162249 DOI: 10.1177/10781552211027218] [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: 11/17/2022]
Abstract
OBJECTIVE We described our initial experience of a new integrated oncology phamaceutical care practice to enhance the quality of pharmacy service and patient care in Huashan hospital.Data sources: A retrospective study was performed from August 2019 to September 2020. Patients were described as integrated pharmacy service group and routine care group. Medication adherence of patients in integrated pharmacy service group was recorded by the online management system. Patient satisfaction and the cumulative incidence of emergency room (ER) and outpatient visit were evaluated between two groups.Data summary: In total, 323 patients received the integrating oncology pharmacy service. The percentage of the patients missing administration every day was reduced from 29.7% to 0.3% within a 40-day monitoring and intervention period. There was a significant difference on patient satisfaction with pharmacy service in two groups (P < 0.05). Fewer patients in the integrated pharmacy service group visited clinic and ER compared with routine care group (33.1% vs. 59.2%; P < 0.05). CONCLUSIONS As a new practice model, the integrated program is adopted to provide patient care and ongoing monitoring for cancer patients. The practice model delivers high continuity of care for cancer patients and improves communication and collaboration between healthcare professionals and oncology patients. The practice also provides the potential of developing hospital pharmaceutical service and optimizing disease prevention and treatment strategies.
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Affiliation(s)
- Huijie Qi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Lili Zhu
- Hospital Executive Office, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Chen
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenxin Zhang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Tianxiao Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Haifei Chen
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Qian Wu
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiong Zhan
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai, China
| | - Tianji Le
- Shanghai Fengrao Medical Technology Co., Ltd, Shanghai, China
| | - Liudi Zhang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Mingkang Zhong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaojin Shi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Qunyi Li
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
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9
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Tønnesen E, Lade-Keller J, Stougaard M. Frequently used quantitative polymerase chain reaction-based methods overlook potential clinically relevant genetic alterations in epidermal growth factor receptor compared with next-generation sequencing: a retrospective clinical comparison of 1839 lung adenocarcinomas. Hum Pathol 2021; 115:67-75. [PMID: 34153308 DOI: 10.1016/j.humpath.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
AIMS The aim of the study was to investigate the advantage of implementing next-generation sequencing (NGS) compared with quantitative polymerase chain reaction (qPCR) when performing routine molecular diagnostics in adenocarcinomas of the lung. METHODS The study is a retrospective cross-sectional observational study of 1839 cytological and histological adenocarcinoma biopsies investigated for gene mutations from 2016 to 2018 at the Department of Pathology at Aarhus University Hospital. A total of 1169 samples were analyzed by qPCR for the presence of EGFR hotspot mutations from 2016 to 2017. A total of 670 samples were analyzed with NGS for the presence of EGFR mutations and other gene mutations in 2018. RESULTS The average frequency of EGFR mutations in the study population was 11.5%, with the highest frequency found in 2018, where NGS was implemented (10.8% in 2016, 11.5% in 2017, and 12.2% in 2018). Possible therapy resistance markers such as EGFR exon 20 mutations were found more commonly after NGS implementation, the difference being statistically significant (P = .015). In addition, NGS (2018) showed that 40.6% of the samples had KRAS mutations and 6.0% had BRAF mutations, mutations not commonly investigated in lung adenocarcinomas when qPCR is the method of choice. Among the EGFR-mutated samples analyzed with NGS, 13 contained a concurrent EGFR mutation, whereas three and two contained a concurrent KRAS and BRAF mutations, respectively. CONCLUSIONS With the implementation in a clinical setting, NGS identifies more uncommon but potentially clinically important EGFR mutations, unique combinations of EGFR mutations, and concurrent mutations in KRAS and BRAF.
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Affiliation(s)
- Ea Tønnesen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark.
| | - Johanne Lade-Keller
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark
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10
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Choi YJ, Choi JY, Kim JW, Lim AR, Lee Y, Chang WJ, Lee S, Sung JS, Chung HJ, Lee JW, Kang EJ, Kim JS, Lim T, Kim HS, Kim YJ, Ahn MS, Kim YS, Park JH, Lim S, Cho SS, Cho JH, Shin SW, Park KH, Kim YH. Comparison of the Data of a Next-Generation Sequencing Panel from K-MASTER Project with that of Orthogonal Methods for Detecting Targetable Genetic Alterations. Cancer Res Treat 2021; 54:30-39. [PMID: 34015890 PMCID: PMC8756135 DOI: 10.4143/crt.2021.218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/18/2021] [Indexed: 11/21/2022] Open
Abstract
Purpose K-MASTER project is a Korean national precision medicine platform that screened actionable mutations by analyzing next-generation sequencing (NGS) of solid tumor patients. We compared gene analyses between NGS panel from the K-MASTER project and orthogonal methods. Materials and Methods Colorectal, breast, non–small cell lung, and gastric cancer patients were included. We compared NGS results from K-MASTER projects with those of non-NGS orthogonal methods (KRAS, NRAS, and BRAF mutations in colorectal cancer [CRC]; epidermal growth factor receptor [EGFR], anaplastic lymphoma kinase [ALK] fusion, and reactive oxygen species 1 [ROS1] fusion in non–small cell lung cancer [NSCLC], and Erb-B2 receptor tyrosine kinase 2 (ERBB2) positivity in breast and gastric cancers). Results In the CRC cohort (n=225), the sensitivity and specificity of NGS were 87.4% and 79.3% (KRAS); 88.9% and 98.9% (NRAS); and 77.8% and 100.0% (BRAF), respectively. In the NSCLC cohort (n=109), the sensitivity and specificity of NGS for EGFR were 86.2% and 97.5%, respectively. The concordance rate for ALK fusion was 100%, but ROS1 fusion was positive in only one of three cases that were positive in orthogonal tests. In the breast cancer cohort (n=260), ERBB2 amplification was detected in 45 by NGS. Compared with orthogonal methods that integrated immunohistochemistry and in situ hybridization, sensitivity and specificity were 53.7% and 99.4%, respectively. In the gastric cancer cohort (n=64), ERBB2 amplification was detected in six by NGS. Compared with orthogonal methods, sensitivity and specificity were 62.5% and 98.2%, respectively. Conclusion The results of the K-MASTER NGS panel and orthogonal methods showed a different degree of agreement for each genetic alteration, but generally showed a high agreement rate.
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Affiliation(s)
- Yoon Ji Choi
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Jung Yoon Choi
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Ju Won Kim
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Ah Reum Lim
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Youngwoo Lee
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Won Jin Chang
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Soohyeon Lee
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Jae Sook Sung
- Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Hee-Joon Chung
- Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Jong Won Lee
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, Korea
| | - Eun Joo Kang
- Division of Oncology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jung Sun Kim
- Division of Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Taekyu Lim
- Division of Hematology-Oncology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Korea
| | - Hye Sook Kim
- Department of Internal Medicine, Inje University Ilsan Hospital, Goyang, Korea
| | - Yu Jung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Mi Sun Ahn
- Ajou University Medical Center, Suwon, Korea
| | - Young Saing Kim
- Division of Medical Oncology, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Ji Hyun Park
- Department of Hemato-Oncology, Konkuk Medical Center, University of Konkuk College of Medicine, Seoul, Korea
| | - Seungtaek Lim
- Department of Oncology, Wonju Severance Christianity Hospital, Wonju, Korea
| | - Sung Shim Cho
- Division of Medical Oncology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Jang Ho Cho
- Division of Oncology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Sang Won Shin
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Kyong Hwa Park
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Yeul Hong Kim
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
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11
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Pfohl U, Pflaume A, Regenbrecht M, Finkler S, Graf Adelmann Q, Reinhard C, Regenbrecht CRA, Wedeken L. Precision Oncology Beyond Genomics: The Future Is Here-It Is Just Not Evenly Distributed. Cells 2021; 10:928. [PMID: 33920536 PMCID: PMC8072767 DOI: 10.3390/cells10040928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer is a multifactorial disease with increasing incidence. There are more than 100 different cancer types, defined by location, cell of origin, and genomic alterations that influence oncogenesis and therapeutic response. This heterogeneity between tumors of different patients and also the heterogeneity within the same patient's tumor pose an enormous challenge to cancer treatment. In this review, we explore tumor heterogeneity on the longitudinal and the latitudinal axis, reviewing current and future approaches to study this heterogeneity and their potential to support oncologists in tailoring a patient's treatment regimen. We highlight how the ideal of precision oncology is reaching far beyond the knowledge of genetic variants to inform clinical practice and discuss the technologies and strategies already available to improve our understanding and management of heterogeneity in cancer treatment. We will focus on integrating multi-omics technologies with suitable in vitro models and their proficiency in mimicking endogenous tumor heterogeneity.
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Affiliation(s)
- Ulrike Pfohl
- CELLphenomics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany; (U.P.); (A.P.); (C.R.); (Q.G.A.); (C.R.A.R.)
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
- Institut für Molekulare Biowissenschaften, Goethe Universität Frankfurt am Main, Theodor-W.-Adorno-Platz 1, 60323 Frankfurt am Main, Germany
| | - Alina Pflaume
- CELLphenomics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany; (U.P.); (A.P.); (C.R.); (Q.G.A.); (C.R.A.R.)
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
| | - Manuela Regenbrecht
- Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125 Berlin, Germany;
| | - Sabine Finkler
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
| | - Quirin Graf Adelmann
- CELLphenomics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany; (U.P.); (A.P.); (C.R.); (Q.G.A.); (C.R.A.R.)
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
| | - Christoph Reinhard
- CELLphenomics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany; (U.P.); (A.P.); (C.R.); (Q.G.A.); (C.R.A.R.)
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
| | - Christian R. A. Regenbrecht
- CELLphenomics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany; (U.P.); (A.P.); (C.R.); (Q.G.A.); (C.R.A.R.)
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
- Institut für Pathologie, Universitätsklinikum Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Lena Wedeken
- CELLphenomics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany; (U.P.); (A.P.); (C.R.); (Q.G.A.); (C.R.A.R.)
- ASC Oncology GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany;
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12
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Construction of liver hepatocellular carcinoma-specific lncRNA-miRNA-mRNA network based on bioinformatics analysis. PLoS One 2021; 16:e0249881. [PMID: 33861762 PMCID: PMC8051809 DOI: 10.1371/journal.pone.0249881] [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: 05/24/2020] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Liver hepatocellular carcinoma (LIHC) is one of the major causes of cancer-related death worldwide with increasing incidences, however there are very few studies about the underlying mechanisms and pathways in the development of LIHC. We obtained LIHC samples from The Cancer Genome Atlas (TCGA) to screen differentially expressed mRNAs, lncRNAs, miRNAs and driver mutations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene ontology enrichment analyses and protein–protein interaction (PPI) network were performed. Moreover, we constructed a competing endogenous lncRNAs-miRNAs-mRNAs network. Finally, cox proportional hazards regression analysis was used to identify important prognostic differentially expressed genes. Total of 1284 mRNAs, 123 lncRNAs, 47 miRNAs were identified within different tissues of LIHC patients. GO analysis indicated that upregulated and downregulated differentially expressed mRNAs (DEmRNAs) were mainly associated with cell division, DNA replication, mitotic sister chromatid segregation and complement activation respectively. Meanwhile, KEGG terms revealed that upregulated and downregulated DEmRNAs were primarily involved in DNA replication, Metabolic pathways, cell cycle and Metabolic pathways, chemical carcinogenesis, retinol metabolism pathway respectively. Among the DERNAs, 542 lncRNAs-miRNAs-mRNAs pairs were predicted to construct a ceRNA regulatory network including 35 DElncRNAs, 26 DEmiRNAs and 112 DEmRNAs. In the Kaplan‐Meier analysis, total of 43 mRNAs, 14 lncRNAs and 3 miRNAs were screened out to be significantly correlated with overall survival of LIHC. The mutation signatures were analyzed and its correlation with immune infiltrates were evaluated using the TIMER in LIHC. Among the mutation genes, TTN mutation is often associated with poor immune infiltration and a worse prognosis in LIHC. This work conducted a novel lncRNAs-miRNAs-mRNAs network and mutation signatures for finding potential molecular mechanisms underlying the development of LIHC. The biomarkers also can be used for predicting prognosis of LIHC.
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13
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Pandey R, Johnson N, Cooke L, Johnson B, Chen Y, Pandey M, Chandler J, Mahadevan D. TP53 Mutations as a Driver of Metastasis Signaling in Advanced Cancer Patients. Cancers (Basel) 2021; 13:597. [PMID: 33546249 PMCID: PMC7913278 DOI: 10.3390/cancers13040597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular profiling with next generation sequencing (NGS) delivers key information on mutant gene sequences, copy number alterations, gene-fusions, and with immunohistochemistry (IHC), is a valuable tool in clinical decision making for patients entering investigational agent trials. Our objective was to elucidate mutational profiles from primary versus metastatic sites from advanced cancer patients to guide rational therapy. All phase I patients (n = 203) with advanced cancer were profiled by commercially available NGS platforms. The samples were annotated by histology, primary and metastatic site, biopsy site, gene mutations, mutation count/gene, and mutant TP53. A molecular profile of each patient was categorized into common and unique mutations, signaling pathways for each profile and TP53 mutations mapped to 3D-structure of p53 bound to DNA and pre/post therapy molecular response. Of the 171 patients analyzed, 145 had genetic alterations from primary and metastatic sites. The predominant histology was adenocarcinoma followed by squamous cell carcinoma, carcinoma of unknown primary site (CUPS), and melanoma. Of 790 unique mutations, TP53 is the most common followed by APC, KRAS, PIK3CA, ATM, PTEN, NOTCH1, BRCA2, BRAF, KMT2D, LRP1B, and CDKN2A. TP53 was found in most metastatic sites and appears to be a key driver of acquired drug resistance. We highlight examples of acquired mutational profiles pre-/post- targeted therapy in multiple tumor types with a menu of potential targeted agents. Conclusion: The mutational profiling of primary and metastatic lesions in cancer patients provides an opportunity to identify TP53 driver 'pathways' that may predict for drug sensitivity/resistance and guide rational drug combinations in clinical trials.
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Affiliation(s)
- Ritu Pandey
- Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (L.C.); (Y.C.)
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Nathan Johnson
- School of Medicine, Vanderbilt University, Nashville, TN 37325, USA;
| | - Laurence Cooke
- Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (L.C.); (Y.C.)
| | | | - Yuliang Chen
- Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (L.C.); (Y.C.)
| | - Manjari Pandey
- West Cancer Center, 7945 Wolf River Blvd, Germantown, TN 38138, USA; (M.P.); (J.C.)
| | - Jason Chandler
- West Cancer Center, 7945 Wolf River Blvd, Germantown, TN 38138, USA; (M.P.); (J.C.)
| | - Daruka Mahadevan
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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14
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Gąsior-Perczak D, Kowalik A, Gruszczyński K, Walczyk A, Siołek M, Pałyga I, Trepka S, Mikina E, Trybek T, Kopczyński J, Suligowska A, Ślusarczyk R, Gonet A, Jaskulski J, Orłowski P, Chrapek M, Góźdź S, Kowalska A. Incidence of the CHEK2 Germline Mutation and Its Impact on Clinicopathological Features, Treatment Responses, and Disease Course in Patients with Papillary Thyroid Carcinoma. Cancers (Basel) 2021; 13:cancers13030470. [PMID: 33530461 PMCID: PMC7865996 DOI: 10.3390/cancers13030470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 01/23/2023] Open
Abstract
Simple Summary The aim of our study was to evaluate whether the CHEK2 mutation was a predictor of poorer clinical course in patients with papillary thyroid cancer. The study included 1547 patients from a single center in Poland, in whom the presence and variant of the CHEK2 mutation were determined. Two hundred and forty patients were found to carry this mutation. We found significant association of the CHEK2 truncating variant with vascular invasion and intermediate or high initial risk of recurrence/persistence, whereas this relationship was not found in case of the missense CHEK2 variant. Neither the truncating nor the missense mutations were associated with worse primary treatment response and outcome of the disease. Abstract The CHEK2 gene is involved in the repair of damaged DNA. CHEK2 germline mutations impair this repair mechanism, causing genomic instability and increasing the risk of various cancers, including papillary thyroid carcinoma (PTC). Here, we asked whether CHEK2 germline mutations predict a worse clinical course for PTC. The study included 1547 unselected PTC patients (1358 women and 189 men) treated at a single center. The relationship between mutation status and clinicopathological characteristics, treatment responses, and disease outcome was assessed. CHEK2 mutations were found in 240 (15.5%) of patients. A CHEK2 I157T missense mutation was found in 12.3%, and CHEK2 truncating mutations (IVS2 + 1G > A, del5395, 1100delC) were found in 2.8%. The truncating mutations were more common in women (p = 0.038), and were associated with vascular invasion (OR, 6.91; p < 0.0001) and intermediate or high initial risk (OR, 1.92; p = 0.0481) in multivariate analysis. No significant differences in these parameters were observed in patients with the I157T missense mutation. In conclusion, the CHEK2 truncating mutations were associated with vascular invasion and with intermediate and high initial risk of recurrence/persistence. Neither the truncating nor the missense mutations were associated with worse primary treatment response and outcome of the disease.
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Affiliation(s)
- Danuta Gąsior-Perczak
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
- Correspondence:
| | - Artur Kowalik
- Department of Molecular Diagnostics, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (A.K.); (K.G.)
- Division of Medical Biology, Institute of Biology Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland
| | - Krzysztof Gruszczyński
- Department of Molecular Diagnostics, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (A.K.); (K.G.)
| | - Agnieszka Walczyk
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
| | - Monika Siołek
- Genetic Clinic, Holycross Cancer Center, 25-734 Kielce, Poland;
| | - Iwona Pałyga
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
| | - Sławomir Trepka
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
- Department of Surgical Oncology, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland
| | - Estera Mikina
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
| | - Tomasz Trybek
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
| | - Janusz Kopczyński
- Surgical Pathology, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland;
| | - Agnieszka Suligowska
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
| | - Rafał Ślusarczyk
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
| | - Agnieszka Gonet
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
| | - Jarosław Jaskulski
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
| | - Paweł Orłowski
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
| | - Magdalena Chrapek
- Faculty of Natural Sciences, Jan Kochanowski University, 25-406 Kielce, Poland;
| | - Stanisław Góźdź
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
- Clinical Oncology, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland
| | - Aldona Kowalska
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (A.W.); (I.P.); (S.T.); (R.Ś.); (A.G.); (J.J.); (P.O.); (S.G.); (A.K.)
- Endocrinology Clinic, Holycross Cancer Center, Artwińskiego 3, 25-734 Kielce, Poland; (E.M.); (T.T.); (A.S.)
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15
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Fenton AT, Anderson EC, Scharnetzki E, Reed K, Edelman E, Antov A, Rueter J, Han PKJ. Differences in cancer patients' and clinicians' preferences for disclosure of uncertain genomic tumor testing results. PATIENT EDUCATION AND COUNSELING 2021; 104:3-11. [PMID: 32690398 DOI: 10.1016/j.pec.2020.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/02/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To compare clinicians' and patients' preferences for disclosure of genomic tumor testing (GTT) results; to determine the sensitivity of these disclosure preferences to uncertainty about the actionability of results; and to explore factors associated with disclosure preferences. METHODS Community-based oncology clinicians (n = 94) and patients (n = 1121) were surveyed about their preferences for disclosing GTT results with varying levels of uncertainty (Tiers 1, 2, 3). Descriptive and multivariable regression analyses were used to compare clinicians' and patients' disclosure preferences and their sensitivity to uncertainty, and to explore associations between disclosure preferences and sociodemographic, clinical, and psychological factors. RESULTS Relatively more patients than clinicians preferred disclosure, and their preferences were less sensitive to the uncertainty of GTT results. For patients and clinicians, lower uncertainty sensitivity was associated with positive GTT attitudes; for patients it was also associated with greater uncertainty tolerance and knowledge of uncertainty in GTT. CONCLUSION Relatively more cancer patients than clinicians prefer disclosure of GTT results, and their preferences are less sensitive to result uncertainty. Uncertainty sensitivity in disclosure preferences is associated with GTT-related attitudes and uncertainty tolerance. PRACTICE IMPLICATIONS Differences in cancer patients' and clinicians' preferences for disclosure of uncertain GTT results warrant greater attention in cancer care.
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Affiliation(s)
- Anny T Fenton
- Center for Outcomes, Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
| | - Eric C Anderson
- Center for Outcomes, Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
| | - Elizabeth Scharnetzki
- Center for Outcomes, Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA
| | - Kate Reed
- The Jackson Laboratory, Bar Harbor, ME, USA
| | | | | | | | - Paul K J Han
- Center for Outcomes, Research and Evaluation, Maine Medical Center Research Institute, Portland, ME, USA.
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Smith PAD, Waugh EM, Crichton C, Jarrett RF, Morris JS. The prevalence and characterisation of TRAF3 and POT1 mutations in canine B-cell lymphoma. Vet J 2020; 266:105575. [PMID: 33323169 DOI: 10.1016/j.tvjl.2020.105575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
The genetic and mutational basis of canine lymphoma remains poorly understood. Several genes, including TRAF3 and POT1, are mutated in canine B-cell lymphoma (cBCL), and are likely involved in the pathogenesis of this disease. The purpose of this study was to assess the prevalence of TRAF3 and POT1 mutations in a cohort of dogs with cBCL, compared to dogs with non-cBCL diseases (including four dogs with T-cell lymphoma [cTCL]). Forty-nine dogs were included (n = 24 cBCL; n = 25 non-cBCL). Eleven dogs had matched non-tumour DNA assessed to determine if mutations were germline or somatic. All dogs had TRAF3 and POT1 assessed by Sanger sequencing. The prevalence of deleterious TRAF3 and POT1 mutations in cBCL was 36% and 17%, respectively. A deleterious TRAF3 mutation was suspected to be germline in 1/5 cases with matched non-tumour DNA available for comparison. Deleterious mutations were not found in specimens from the non-cBCL group. Several synonymous variants were identified in both genes in cBCL and non-cBCL samples, which likely represent polymorphisms. These results indicate TRAF3 and POT1 mutations are common in cBCL. Deleterious TRAF3 and POT1 mutations were only identified in dogs with cBCL, and not in dogs with non-cBCL diseases, suggesting they are important in the pathogenesis of cBCL. Future studies to investigate the prognostic and therapeutic implications of these mutations are required.
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Affiliation(s)
- P A D Smith
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK.
| | - E M Waugh
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK
| | - C Crichton
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK
| | - R F Jarrett
- MRC-University of Glasgow Centre for Virus Research, G61 1QH, Glasgow, UK
| | - J S Morris
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK
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International liquid biopsy standardization alliance white paper. Crit Rev Oncol Hematol 2020; 156:103112. [PMID: 33035734 DOI: 10.1016/j.critrevonc.2020.103112] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 01/04/2023] Open
Abstract
The promise of precision medicine as a model to customize health care to the individual patient is heavily dependent upon new genetic tools to classify and characterize diseases and their hosts. Liquid biopsies serve as a safe alternative to solid biopsies and are thus a useful and critical component to fully realizing personalized medicine. The International Liquid Biopsy Standardization Alliance (ILSA) comprises organizations and foundations that recognize the importance of working towards the global use of liquid biopsy in oncology practice to support clinical decision making and regulatory considerations and seek to promote it in their communities. This manuscript provides an overview of the independent liquid biopsy- and standardization-based programs engaged with ILSA, their objectives and progress to date, and the tools and resources each is developing to contribute to the field. It also describes the unique areas of effort as well as synergy found within the group.
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18
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Wu Z, Wang L, Li C, Cai Y, Liang Y, Mo X, Lu Q, Dong L, Liu Y. DeepLRHE: A Deep Convolutional Neural Network Framework to Evaluate the Risk of Lung Cancer Recurrence and Metastasis From Histopathology Images. Front Genet 2020; 11:768. [PMID: 33193560 PMCID: PMC7477356 DOI: 10.3389/fgene.2020.00768] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
It is critical for patients who cannot undergo eradicable surgery to predict the risk of lung cancer recurrence and metastasis; therefore, the physicians can design the appropriate adjuvant therapy plan. However, traditional circulating tumor cell (CTC) detection or next-generation sequencing (NGS)-based methods are usually expensive and time-inefficient, which urge the need for more efficient computational models. In this study, we have established a convolutional neural network (CNN) framework called DeepLRHE to predict the recurrence risk of lung cancer by analyzing histopathological images of patients. The steps for using DeepLRHE include automatic tumor region identification, image normalization, biomarker identification, and sample classification. In practice, we used 110 lung cancer samples downloaded from The Cancer Genome Atlas (TCGA) database to train and validate our CNN model and 101 samples as independent test dataset. The area under the receiver operating characteristic (ROC) curve (AUC) for test dataset was 0.79, suggesting a relatively good prediction performance. Our study demonstrates that the features extracted from histopathological images could be well used to predict lung cancer recurrence after surgical resection and help classify patients who should receive additional adjuvant therapy.
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Affiliation(s)
- Zhijun Wu
- Department of Oncology, The First People's Hospital of Changde City, Changde, China
| | - Lin Wang
- Department of Oncology, Hainan General Hospital, Haikou, China
| | - Churong Li
- Sichuan Cancer Hospital and Institute, The Affiliated Cancer Hospital, School of Medicine, UESTC, Chengdu, China
| | | | | | - Xiaofei Mo
- Geneis (Beijing) Co., Ltd., Beijing, China
| | | | - Lixin Dong
- The First Hospital of Qinhuangdao, Qinhuangdao, China
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19
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Anderson EJ, Mollon LE, Dean JL, Warholak TL, Aizer A, Platt EA, Tang DH, Davis LE. A Systematic Review of the Prevalence and Diagnostic Workup of PIK3CA Mutations in HR+/HER2- Metastatic Breast Cancer. Int J Breast Cancer 2020; 2020:3759179. [PMID: 32637176 PMCID: PMC7322582 DOI: 10.1155/2020/3759179] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
PIK3CA mutation frequency varies among breast cancer (BC) subtypes. Recent evidence suggests combination therapy with the PI3K inhibitor (PI3Ki) alpelisib and endocrine therapy (ET) improves response rates and progression-free survival (PFS) in PIK3CA-mutant, hormone receptor positive (HR+) BC versus ET alone; thus, better understanding the clinical and epidemiologic elements of these mutations is warranted. This systematic review characterizes the PIK3CA mutation epidemiology, type of testing approaches (e.g., liquid or tissue tumor biopsy), and stability/concordance (e.g., consistency in results by liquid versus solid tumor sample, by the same method over time) in patients with HR+/HER2- advanced (locally unresectable) or metastatic disease (HR+/HER2- mBC) and explores performance (e.g., pairwise concordance, sensitivity, specificity, or predictive value) of respective mutation findings. A comprehensive search of PubMed/MEDLINE, EMBASE, Cochrane Central, and select conference abstracts (i.e., AACR, ASCO, SABCS, ECCO, and ESMO conferences between 2014 and 2017) identified 39 studies of patients with HR+, HER2- mBC. The median prevalence of PIK3CA mutation was 36% (range: 13.3% to 61.5%); identified testing approaches more commonly used tissue over liquid biopsies and primarily utilized next-generation sequencing (NGS), polymerase chain reaction (PCR), or Sanger sequencing. There was concordance and stability between tissues (range: 70.4% to 94%) based on limited data. Given the clinical benefit of the PI3Ki alpelisib in patients with PIK3CA mutant HR+/HER2- mBC, determination of tumor PIK3CA mutation status is of importance in managing patients with HR+/HER2- mBC. Prevalence of this mutation and utility of test methodologies likely warrants PIK3CA mutation testing in all patients with this breast cancer subtype via definitive assessment of PIK3CA mutational status.
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Affiliation(s)
| | - Lea E. Mollon
- University of Arizona College of Pharmacy, Tucson, AZ, USA
| | - Joni L. Dean
- University of Arizona College of Pharmacy, Tucson, AZ, USA
| | | | | | | | | | - Lisa E. Davis
- University of Arizona College of Pharmacy, Tucson, AZ, USA
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20
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Bieg‐Bourne CC, Okamura R, Kurzrock R. Concordance between TP53 alterations in blood and tissue: impact of time interval, biopsy site, cancer type and circulating tumor DNA burden. Mol Oncol 2020; 14:1242-1251. [PMID: 32187847 PMCID: PMC7266274 DOI: 10.1002/1878-0261.12672] [Citation(s) in RCA: 8] [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: 10/15/2019] [Revised: 01/13/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
We examined the impact of spatial, temporal, histologic, and quantitative factors on concordance between TP53 alterations in tissue DNA vs in circulating tumor DNA (ctDNA). Four hundred and thirty-three patients underwent next-generation sequencing (NGS) in which both tissue and blood samples were evaluated. TP53 was detected in 258 of 433 patients (59.6%); 215 had tissue TP53 alterations (49.7%); 159, ctDNA (36.7%); and 116, both tissue and ctDNA (27.8%). Overall concordance rate between ctDNA and tissue biopsies for TP53 alterations was 67.2%; positive concordance was 45.0%. Overall concordance for TP53 did not vary among patients with ≤ 2 months vs > 6 months between test samples; however, positive concordance trended higher when time intervals between test samples were shorter, suggesting that the lack of difference in overall concordance may be due to the large number of negative/negative tests. There was a trend toward higher overall concordance based on biopsy site (metastatic vs primary) (P = 0.07) and significantly higher positive concordance if the tissue biopsy site was a metastatic lesion (P = 0.03). Positive concordance significantly decreased in noncolorectal cancer patients vs colorectal cancer patients (P = 0.02). Finally, higher %ctDNA was associated with higher concordance rates between blood and tissue (P < 0.001). Taken together, these data indicate that both blood and tissue DNA sequencing are necessary to evaluate the full scope of TP53 alterations, and that concordance rates may be related to multiple factors including, but not limited to, amount of ctDNA, histologic context, and site of tissue biopsy.
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Affiliation(s)
- Cheyennedra C. Bieg‐Bourne
- Center for Personalized Cancer TherapyMoores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Ryosuke Okamura
- Center for Personalized Cancer TherapyMoores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Razelle Kurzrock
- Center for Personalized Cancer TherapyMoores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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21
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Anderson EC, Hinton A, Lary CW, Strout T, Antov A, Edelman E, Helbig P, Reed K, Rueter J, Han PK. The influence of uncertainty and uncertainty tolerance on attitudes and self-efficacy about genomic tumor testing. PSYCHOL HEALTH MED 2020; 26:805-817. [DOI: 10.1080/13548506.2020.1764989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Eric C. Anderson
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, Maine, USA
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alexandra Hinton
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, Maine, USA
| | - Christine W. Lary
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, Maine, USA
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Tania Strout
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, USA
- Department of Emergency Medicine, Maine Medical Center, Maine, USA
| | | | | | | | - Kate Reed
- The Jackson Laboratory, Augusta, Maine, USA
| | | | - Paul K.J. Han
- Center for Outcomes Research and Evaluation, Maine Medical Center Research Institute, Portland, Maine, USA
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, USA
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22
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Sinn M, Sinn BV, Treue D, Keilholz U, Damm F, Schmuck R, Lohneis P, Klauschen F, Striefler JK, Bahra M, Bläker H, Bischoff S, Pelzer U, Oettle H, Riess H, Budczies J, Denkert C. TP53 Mutations Predict Sensitivity to Adjuvant Gemcitabine in Patients with Pancreatic Ductal Adenocarcinoma: Next-Generation Sequencing Results from the CONKO-001 Trial. Clin Cancer Res 2020; 26:3732-3739. [PMID: 32234756 DOI: 10.1158/1078-0432.ccr-19-3034] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/14/2020] [Accepted: 03/27/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE We performed next-generation sequencing (NGS) in the CONKO-001 phase III trial to identify clinically relevant prognostic and predictive mutations and conducted a functional validation in The Cancer Genome Atlas (TCGA) sequencing data. EXPERIMENTAL DESIGN Patients of the CONKO-001 trial received curatively intended surgery for pancreatic adenocarcinoma (PDAC) followed by adjuvant chemotherapy with gemcitabine (Gem) or observation only (Obs). Tissue samples of 101 patients were evaluated by NGS of 37 genes. Cox proportional hazard models were applied for survival analysis. In addition, functional genomic analyses were performed in an NGS and RNA-sequencing dataset of 146 pancreatic tumors from TCGA. RESULTS The most common mutations in the CONKO cohort were KRAS (75%), TP53 (60%), SMAD4 (10%), CDKNA2 (9%), as well as SWI/SNF (12%) complex alterations. In untreated patients, TP53 mutations were a negative prognostic factor for disease-free survival (DFS; HR mut vs. WT 2.434, P = 0.005). With respect to gemcitabine treatment, TP53 mutations were a positive predictive factor for gemcitabine efficacy [TP53mut: HR for DFS Gem vs. Obs, 0.235 (0.130 - 0.423; P < 0.001); TP53wt: HR for DFS Gem vs. Obs, 0.794 (0.417 - 1.513; P = 0.483)] with a significant test for interaction (P = 0.003). In the TCGA dataset, TP53 mutations were associated with shortened DFS. CONCLUSIONS In CONKO-001, the benefit from adjuvant gemcitabine was confined to the TP53mut patient group. This potentially clinical relevant observation needs to be confirmed in independent prospective studies. The sensitivity of TP53mut PDAC to gemcitabine in CONKO-001 provides a lead for further mechanistic investigations.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/mortality
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/therapy
- Chemotherapy, Adjuvant/methods
- Clinical Trials, Phase III as Topic
- DNA Mutational Analysis
- Deoxycytidine/analogs & derivatives
- Deoxycytidine/pharmacology
- Deoxycytidine/therapeutic use
- Disease-Free Survival
- Drug Resistance, Neoplasm/genetics
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Middle Aged
- Mutation
- Neoplasm Recurrence, Local/epidemiology
- Neoplasm Recurrence, Local/genetics
- Pancreatectomy
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/mortality
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/therapy
- Prospective Studies
- Randomized Controlled Trials as Topic
- Tumor Suppressor Protein p53/genetics
- Gemcitabine
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Affiliation(s)
- Marianne Sinn
- Department of Medical Oncology and Haematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- University Medical Center Hamburg-Eppendorf, Department of Oncology, Hematology and BMT, Hamburg, Germany
| | - Bruno V Sinn
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Denise Treue
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Central Biomaterial Bank Charité, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frederik Damm
- Department of Medical Oncology and Haematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Rosa Schmuck
- Department of General, Visceral and Transplantation Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner site Berlin, Germany
| | - Philipp Lohneis
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner site Berlin, Germany
| | - Jana K Striefler
- Department of Medical Oncology and Haematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marcus Bahra
- Department of General, Visceral and Transplantation Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sven Bischoff
- Department of Medical Oncology and Haematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Uwe Pelzer
- Department of Medical Oncology and Haematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Helmut Oettle
- Outpatient Department of Hematology/Oncology, Friedrichshafen, Germany
| | - Hanno Riess
- Department of Medical Oncology and Haematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jan Budczies
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner site Berlin, Germany
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg (UKGM), Marburg, Germany
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23
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Raheem F, Kim P, Grove M, Kiel PJ. Precision Genomic Practice in Oncology: Pharmacist Role and Experience in an Ambulatory Care Clinic. PHARMACY 2020; 8:pharmacy8010032. [PMID: 32182657 PMCID: PMC7151676 DOI: 10.3390/pharmacy8010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Recent advancements in molecular testing, the availability of cost-effective technology, and novel approaches to clinical trial design have facilitated the implementation of tumor genome sequencing into standard of care oncology practices. Current models of precision oncology practice include specialized clinics or consultation services based on a molecular tumor board (MTB) approach. MTBs are comprised of interprofessional teams of clinicians and scientists who evaluate tumors at the molecular level to guide patient-specific targeted therapy. The practice of precision oncology utilizing MTB-based models is an emerging approach, transforming precision genomics from a novel concept into clinical practice. This rapid shift in practice from cytotoxic therapy to targeted medicine poses challenges, yet brings exciting opportunities to clinical pharmacists practicing in hematology and oncology. Only a few precision genomics programs in the United States have a strong pharmacy presence with oncology pharmacists serving in leadership roles in research, interpreting genomic sequencing, making treatment recommendations, and facilitating off-label drug procurement. This article describes the experience of the precision medicine clinic at the Indiana University Health Simon Cancer Center, with emphasis on the role of the pharmacist in the precision oncology initiative.
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Phase I studies of vorinostat with ixazomib or pazopanib imply a role of antiangiogenesis-based therapy for TP53 mutant malignancies. Sci Rep 2020; 10:3080. [PMID: 32080210 PMCID: PMC7033174 DOI: 10.1038/s41598-020-58366-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022] Open
Abstract
We performed two phase I trials of the histone deacetylase inhibitor vorinostat combined with either the vascular endothelial growth factor inhibitor pazopanib (NCT01339871) or the proteasome inhibitor ixazomib (NCT02042989) in patients with metastatic TP53 mutant solid tumors. Both trials followed a 3 + 3 dose-escalation design allowing for a dose expansion cohort of up to 14 additional patients with a specific tumor type. Patients had to have a confirmed TP53 mutation to be enrolled in NCT02042989. Among patients enrolled in NCT01339871, TP53 mutation status was determined for those for whom tumor specimens were available. The results of NCT01339871 were reported previously. Common treatment-related adverse events in NCT02042989 included anemia, thrombocytopenia, fatigue, nausea, vomiting, and diarrhea. Compared with patients with metastatic TP53 hotspot mutant solid tumors who were treated with ixazomib and vorinostat (n = 59), those who were treated with pazopanib and vorinostat (n = 11) had a significantly higher rate of clinical benefit, defined as stable disease lasting ≥6 months or an objective response (3.4% vs. 45%; p < 0.001), a significantly longer median progression-free survival duration (1.7 months [95% confidence interval (CI), 1.1–2.3] vs. 3.5 months [95% CI, 1.7–5.2]; p = 0.002), and a longer median overall survival duration (7.3 months [95% CI, 4.8–9.8] vs. 12.7 months [95% CI, 7.1–18.3]; p = 0.24). Our two phase I trials provide preliminary evidence supporting the use of antiangiogenisis-based therapy in patients with metastatic TP53 mutant solid tumors, especially in those with metastatic sarcoma or metastatic colorectal cancer.
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25
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Parikh DA, Walia G, Freeman-Daily J, Hennink M, Tomalia T, Buonanno L, Goldman L, Addario B, Patel MI. Characteristics of Patients With ROS1+ Cancers: Results From the First Patient-Designed, Global, Pan-Cancer ROS1 Data Repository. JCO Oncol Pract 2019; 16:e183-e189. [PMID: 31880972 DOI: 10.1200/jop.19.00135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE The discovery of driver oncogenes, such as ROS1, has led to the development of targeted therapies. Despite clinical advancements, gaps remain in our understanding of characteristics of patients with ROS1-positive (ROS1+) cancers. The purpose of this study was to comprehensively assess demographic, clinical, and environmental characteristics associated with ROS1+ cancers worldwide. METHODS In collaboration with a panel of patients with ROS1+ cancer, we designed and conducted a 204-question online assessment regarding the demographic, clinical, and environmental factors of patients with ROS1+ cancers. We invited patients with ROS1+ cancers to participate in the study from May 2016 to December 2018. RESULTS A total of 277 patients from 18 countries worldwide responded and completed at least 90% of the survey. The majority of respondents were female (n = 191; 69%), non-Hispanic white (n = 202; 73%), never-smokers (n = 180/240; 75%). Most were diagnosed with lung cancer (n = 261/277; 94%) and stage IV disease (n = 201/277; 76%). The majority received chemotherapy in first (n = 137/199; 69%) and second (n = 103/199; 52%) lines of therapy. For patients diagnosed with lung cancer after the availability of crizotinib (n = 199), only a minority (n = 55/199; 28%) reported receiving crizotinib in the first line of therapy. CONCLUSION This study is the first global, patient-designed approach, to our knowledge, to comprehensively assess demographic, clinical, and environmental characteristics associated with ROS1+ cancers. Future efforts include assessing these characteristics as well as patient-reported outcomes and treatment responses longitudinally.
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Affiliation(s)
- Divya A Parikh
- Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Guneet Walia
- Department of Oncology, Genentech, South San Francisco, CA
| | | | - Merel Hennink
- Bonnie J. Addario Lung Cancer Foundation, San Carlos, CA
| | - Tori Tomalia
- Bonnie J. Addario Lung Cancer Foundation, San Carlos, CA
| | - Lysa Buonanno
- Bonnie J. Addario Lung Cancer Foundation, San Carlos, CA
| | - Lisa Goldman
- Bonnie J. Addario Lung Cancer Foundation, San Carlos, CA
| | - Bonnie Addario
- Bonnie J. Addario Lung Cancer Foundation, San Carlos, CA
| | - Manali I Patel
- Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, CA.,Center for Health Policy/Primary Care Outcomes Research, Stanford University, Stanford, CA
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26
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Netanely D, Stern N, Laufer I, Shamir R. PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. BMC Bioinformatics 2019; 20:732. [PMID: 31878868 PMCID: PMC6933892 DOI: 10.1186/s12859-019-3142-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/09/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Analysis of large genomic datasets along with their accompanying clinical information has shown great promise in cancer research over the last decade. Such datasets typically include thousands of samples, each measured by one or several high-throughput technologies ('omics') and annotated with extensive clinical information. While instrumental for fulfilling the promise of personalized medicine, the analysis and visualization of such large datasets is challenging and necessitates programming skills and familiarity with a large array of software tools to be used for the various steps of the analysis. RESULTS We developed PROMO (Profiler of Multi-Omic data), a friendly, fully interactive stand-alone software for analyzing large genomic cancer datasets together with their associated clinical information. The tool provides an array of built-in methods and algorithms for importing, preprocessing, visualizing, clustering, clinical label enrichment testing, and survival analysis that can be performed on a single or multi-omic dataset. The tool can be used for quick exploration and stratification of tumor samples taken from patients into clinically significant molecular subtypes. Identification of prognostic biomarkers and generation of simple subtype classifiers are additional important features. We review PROMO's main features and demonstrate its analysis capabilities on a breast cancer cohort from TCGA. CONCLUSIONS PROMO provides a single integrated solution for swiftly performing a complete analysis of cancer genomic data for subtype discovery and biomarker identification without writing a single line of code, and can, therefore, make the analysis of these data much easier for cancer biologists and biomedical researchers. PROMO is freely available for download at http://acgt.cs.tau.ac.il/promo/.
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Affiliation(s)
- Dvir Netanely
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Neta Stern
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Itay Laufer
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
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Pediatric surgical oncology: A brief overview of where we have been and the challenges we face. Semin Pediatr Surg 2019; 28:150864. [PMID: 31931962 DOI: 10.1016/j.sempedsurg.2019.150864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The evolution of the treatment of pediatric solid tumors has been one of progressive improvements in survival. With the advent of pediatric cooperative groups, a systematic approach has brought integrated multidisciplinary care to childhood cancer patients. Improved medical regimens and advances in the basic understanding and characterization of molecular biology of individual tumors continues to bring new treatment options. As long term survival has improved, a greater appreciation of the late effects of treatment has led to increase awareness and intervention for things like infertility. The surgeon remains a critical member of the treatment team. Surgical treatment techniques continue to evolve and the role of surgery in each tumor type is continually redefined. It is incumbent on the treating surgeon to know the treatment guidelines for each case in order to provide the patient with the best opportunity for a successful outcome.
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Martorell S, Tortajada-Genaro LA, Maquieira Á. Magnetic concentration of allele-specific products from recombinase polymerase amplification. Anal Chim Acta 2019; 1092:49-56. [DOI: 10.1016/j.aca.2019.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/06/2019] [Indexed: 02/07/2023]
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Coexisting Germline CHEK2 and Somatic BRAFV600E Mutations in Papillary Thyroid Cancer and Their Association with Clinicopathological Features and Disease Course. Cancers (Basel) 2019; 11:cancers11111744. [PMID: 31703344 PMCID: PMC6896084 DOI: 10.3390/cancers11111744] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 01/26/2023] Open
Abstract
BRAFV600E is the most common somatic mutation in papillary thyroid carcinoma (PTC) and the majority of evidence indicates that it is associated with an aggressive clinical course. Germline mutations of the CHEK2 gene impair the DNA damage repair process and increase the risk of PTC. Coexistence of both mutations is expected to be associated with poorer clinical course. We evaluated the prevalence of concomitant CHEK2 and BRAFV600E mutations and their associations with clinicopathological features, treatment response, and disease course in PTC patients. The study included 427 unselected PTC patients (377 women and 50 men) from one center. Relationships among clinicopathological features, mutation status, treatment response, and disease outcomes were assessed. Mean follow-up was 10 years. CHEK2 mutations were detected in 15.2% and BRAFV600E mutations in 64.2% patients. Neither mutation was present in 31.4% cases and both BRAFV600E and CHEK2 mutations coexisted in 10.8% patients. No significant differences in clinicopathological features, initial risk, treatment response, or disease outcome were detected among these patient groups. CHEK2 mutations were significantly associated with older age, while BRAFV600E was significantly associated with older age and extrathyroidal extension. The coexistence of both mutations was not associated with more aggressive clinicopathological features of PTC, poorer treatment response, or disease outcome.
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Conway JR, Warner JL, Rubinstein WS, Miller RS. Next-Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action. JCO Precis Oncol 2019; 3:PO.19.00232. [PMID: 32923847 PMCID: PMC7446333 DOI: 10.1200/po.19.00232] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 02/04/2023] Open
Abstract
PURPOSE Next-generation sequencing (NGS) of tumor and germline DNA is foundational for precision oncology, with rapidly expanding diagnostic, prognostic, and therapeutic implications. Although few question the importance of NGS in modern oncology care, the process of gathering primary molecular data, integrating it into electronic health records, and optimally using it as part of a clinical workflow remains far from seamless. Numerous challenges persist around data standards and interoperability, and clinicians frequently face difficulties in managing the growing amount of genomic knowledge required to care for patients and keep up to date. METHODS This review provides a descriptive analysis of genomic data workflows for NGS data in clinical oncology and issues that arise from the inconsistent use of standards for sharing data across systems. Potential solutions are described. RESULTS NGS technology, especially for somatic genomics, is well established and widely used in routine patient care, quality measurement, and research. Available genomic knowledge bases play an evolving role in patient management but lack harmonization with one another. Questions about their provenance and timeliness of updating remain. Potentially useful standards for sharing genomic data, such as HL7 FHIR and mCODE, remain primarily in the research and/or development stage. Nonetheless, their impact will likely be seen as uptake increases across care settings and laboratories. The specific use case of ASCO CancerLinQ, as a clinicogenomic database, is discussed. CONCLUSION Because the electronic health records of today seem ill suited for managing genomic data, other solutions are required, including universal data standards and applications that use application programming interfaces, along with a commitment on the part of sequencing laboratories to consistently provide structured genomic data for clinical use.
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Affiliation(s)
- Jake R. Conway
- Harvard Medical School, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
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Cherukuri AR, Lubner MG, Zea R, Hinshaw JL, Lubner SJ, Matkowskyj KA, Foltz ML, Pickhardt PJ. Tissue sampling in the era of precision medicine: comparison of percutaneous biopsies performed for clinical trials or tumor genomics versus routine clinical care. Abdom Radiol (NY) 2019; 44:2074-2080. [PMID: 30032384 DOI: 10.1007/s00261-018-1702-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of the study was to determine if patients undergoing percutaneous biopsy for genetic profiling are undergoing more biopsies (procedures, passes per procedure), or experiencing more procedure-related complications. METHODS 60 patients undergoing biopsy procedures for genetic profiling were retrospectively compared with 60 consecutive control patients undergoing routine biopsies. Procedural details and related complications were collected. Results were analyzed using t-tests and logistic regression. RESULTS Biopsied organs included mainly lung (n = 31), liver (n = 50), and lymph nodes (n = 18). The average number of core biopsy passes was 3.45 in the study group and 2.18 in the control group (0.73, 1.81; p = 0.0001). The average study patient underwent 1.44 biopsy procedures by radiology from 2016 to 2017, whereas the average control patient underwent 1.08 (0.1657, 0.5010, p = 0.0002). Results were similar when looking at the subset of patients undergoing liver biopsies. In our cohort of 120 patients total, only 6 complications were noted. There were 4 complications in the control patients and 2 complications in the study patients, all of which were pneumothoraces in patients undergoing lung biopsy; only 2 of these required treatment. The odds ratio for a complication occurring from an increase in one core biopsy is 1.07 (0.601, 1.573; p = 0.775), suggesting no significant relationship among the number of biopsies taken and the probability of complication in this cohort. CONCLUSIONS Patients being biopsied for genetic profiling or clinical study enrollment are undergoing more biopsy procedures and more biopsy passes per procedure, but are not experiencing a detectable increased rate of complications in this small cohort, single-center study.
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Affiliation(s)
- Anjuli R Cherukuri
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Meghan G Lubner
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA.
| | - Ryan Zea
- Biostatistics, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - J Louis Hinshaw
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Sam J Lubner
- Internal Medicine - Division of Human Oncology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Kristina A Matkowskyj
- Pathology and Lab Medicine, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Marcia L Foltz
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Perry J Pickhardt
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
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Loibl S, Treue D, Budczies J, Weber K, Stenzinger A, Schmitt WD, Weichert W, Jank P, Furlanetto J, Klauschen F, Karn T, Pfarr N, von Minckwitz G, Möbs M, Jackisch C, Sers C, Schneeweiss A, Fasching PA, Schem C, Hummel M, van Mackelenbergh M, Nekljudova V, Untch M, Denkert C. Mutational Diversity and Therapy Response in Breast Cancer: A Sequencing Analysis in the Neoadjuvant GeparSepto Trial. Clin Cancer Res 2019; 25:3986-3995. [PMID: 30979740 DOI: 10.1158/1078-0432.ccr-18-3258] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/18/2019] [Accepted: 04/02/2019] [Indexed: 12/28/2022]
Abstract
PURPOSE Next-generation sequencing (NGS) can be used for comprehensive investigation of molecular events in breast cancer. We evaluated the relevance of genomic alterations for response to neoadjuvant chemotherapy (NACT) in the GeparSepto trial. EXPERIMENTAL DESIGN Eight hundred fifty-one pretherapeutic formalin-fixed paraffin-embedded (FFPE) core biopsies from GeparSepto study were sequenced. The panel included 16 genes for mutational (AKT1, BRAF, CDH1, EGFR, ERBB2, ESR1, FBXW7, FGFR2, HRAS, KRAS, NRAS, SF3B1, TP53, HNF1A, PIK3CA, and PTEN) and 8 genes for copy-number alteration analysis (CCND1, ERBB2, FGFR1, PAK1, PIK3CA, TOP2A, TP53, and ZNF703). RESULTS The most common genomic alterations were mutations of TP53 (38.4%) and PIK3CA (21.5%), and 8 different amplifications (TOP2A 34.9%; ERBB2 30.6%; ZNF703 30.1%; TP53 21.9%; PIK3CA 24.1%; CCND1 17.7%; PAK1 14.9%; FGFR 12.6%). All other alterations had a prevalence of less than 5%. The genetic heterogeneity in different breast cancer subtypes [lum/HER2neg vs. HER2pos vs. triple-negative breast cancer (TNBC)] was significantly linked to differences in NACT response. A significantly reduced pathologic complete response rate was observed in PIK3CA-mutated breast cancer [PIK3CAmut: 23.0% vs. wild-type (wt) 38.8%, P < 0.0001] in particular in the HER2pos subcohort [multivariate OR = 0.43 (95% CI, 0.24-0.79), P = 0.006]. An increased response to nab-paclitaxel was observed only in PIK3CAwt breast cancer, with univariate significance for the complete cohort (P = 0.009) and the TNBC (P = 0.013) and multivariate significance in the HER2pos subcohort (test for interaction P = 0.0074). CONCLUSIONS High genetic heterogeneity was observed in different breast cancer subtypes. Our study shows that FFPE-based NGS can be used to identify markers of therapy resistance in clinical study cohorts. PIK3CA mutations could be a major mediator of therapy resistance in breast cancer.
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Affiliation(s)
| | - Denise Treue
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Jan Budczies
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Munich, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), Partner Sites Berlin and Munich, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang D Schmitt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Partner Sites Berlin and Munich, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Paul Jank
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Frederick Klauschen
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Munich, Germany
| | - Thomas Karn
- Department of Gynecology and Obstetrics, University of Frankfurt, Frankfurt am Main, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | | | - Markus Möbs
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Christian Jackisch
- Department of Obstetrics and Gynecology and Breast Cancer Center, Sana Klinikum Offenbach, Offenbach, Germany
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Munich, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Christian Schem
- Mammazentrum Hamburg - Brustklinik am Krankenhaus Jerusalem, Hamburg, Germany
| | - Michael Hummel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | | | | | - Carsten Denkert
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Munich, Germany.,Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
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Starlinger J, Pallarz S, Ševa J, Rieke D, Sers C, Keilholz U, Leser U. Variant information systems for precision oncology. BMC Med Inform Decis Mak 2018; 18:107. [PMID: 30463544 PMCID: PMC6249891 DOI: 10.1186/s12911-018-0665-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/28/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The decreasing cost of obtaining high-quality calls of genomic variants and the increasing availability of clinically relevant data on such variants are important drivers for personalized oncology. To allow rational genome-based decisions in diagnosis and treatment, clinicians need intuitive access to up-to-date and comprehensive variant information, encompassing, for instance, prevalence in populations and diseases, functional impact at the molecular level, associations to druggable targets, or results from clinical trials. In practice, collecting such comprehensive information on genomic variants is difficult since the underlying data is dispersed over a multitude of distributed, heterogeneous, sometimes conflicting, and quickly evolving data sources. To work efficiently, clinicians require powerful Variant Information Systems (VIS) which automatically collect and aggregate available evidences from such data sources without suppressing existing uncertainty. METHODS We address the most important cornerstones of modeling a VIS: We take from emerging community standards regarding the necessary breadth of variant information and procedures for their clinical assessment, long standing experience in implementing biomedical databases and information systems, our own clinical record of diagnosis and treatment of cancer patients based on molecular profiles, and extensive literature review to derive a set of design principles along which we develop a relational data model for variant level data. In addition, we characterize a number of public variant data sources, and describe a data integration pipeline to integrate their data into a VIS. RESULTS We provide a number of contributions that are fundamental to the design and implementation of a comprehensive, operational VIS. In particular, we (a) present a relational data model to accurately reflect data extracted from public databases relevant for clinical variant interpretation, (b) introduce a fault tolerant and performant integration pipeline for public variant data sources, and (c) offer recommendations regarding a number of intricate challenges encountered when integrating variant data for clincal interpretation. CONCLUSION The analysis of requirements for representation of variant level data in an operational data model, together with the implementation-ready relational data model presented here, and the instructional description of methods to acquire comprehensive information to fill it, are an important step towards variant information systems for genomic medicine.
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Affiliation(s)
- Johannes Starlinger
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099 Germany
- Department of Anesthesiology and Operative Intensive Care Medicine (CCM/CVK), Charité Unviersitätsmedizin Berlin, Charitéplatz 1, Berlin, 10117 Germany
| | - Steffen Pallarz
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099 Germany
| | - Jurica Ševa
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099 Germany
| | - Damian Rieke
- Charité Conprehensive Cancer Center, Charité Unviersitätsmedizin Berlin, Charitéplatz 1, Berlin, 10117 Germany
- Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité Unviersitätsmedizin Berlin, Hindenburgdamm 30, Berlin, 12203 Germany
- Berlin Institute of Health (BIH), Kapelle-Ufer 2, Berlin, 10117 Germany
| | - Christine Sers
- Institute of Pathology Molecular Tumor Pathology, Charité Unviersitätsmedizin Berlin, Charitéplatz 1, Berlin, 10117 Germany
| | - Ulrich Keilholz
- Charité Conprehensive Cancer Center, Charité Unviersitätsmedizin Berlin, Charitéplatz 1, Berlin, 10117 Germany
| | - Ulf Leser
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099 Germany
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Abstract
New experimental breast cancer therapies directed against novel targets are currently in clinical These experimental agents are likely to be effective for a niche of breast cancers with specific "driver mutations". The ability to perform comprehensive molecular profiling of individual tumors has rapidly expanded over the last few years, and new DNA sequencing technologies require relatively limited quantities of fresh or archived paraffin-embedded or snap-frozen tumor tissue and provide rapid turnaround of sequencing results within a few weeks or less. All these technologies provide an unprecedented opportunity to identify patients with rare "driver" molecular alternations that are candidates for proof-of-concept clinical trials with matched targeted therapy, in the context of basket trials. The aim of this chapter on molecular profiling is to summarize the known recurrent molecular alterations in breast cancer that are potentially amenable to investigational targeted therapy, to provide an overview of the existing technological platforms for molecular profiling and ongoing or planned institutional/national screening initiatives and to outline a vision for molecular screening that may be integrated into the future activities of breast cancer research.
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Affiliation(s)
- Giuseppe Curigliano
- Division of Experimental Cancer Medicine, Istituto Europeo di Oncologia, Milano, Italy.
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35
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Shee K, Muller KE, Marotti J, Miller TW, Wells WA, Tsongalis GJ. Ductal Carcinoma in Situ Biomarkers in a Precision Medicine Era: Current and Future Molecular-Based Testing. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 189:956-965. [PMID: 30385093 DOI: 10.1016/j.ajpath.2018.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/09/2018] [Accepted: 08/30/2018] [Indexed: 12/18/2022]
Abstract
Historically, ductal carcinoma in situ (DCIS) of the breast has been managed aggressively with surgery and radiotherapy because of a risk of progression to invasive ductal carcinoma. However, this treatment paradigm has been challenged by overtreatment concerns and evidence that suggests that DCIS can be stratified according to risk of recurrence or risk of progression to invasive disease. Traditional methods of risk stratification include histologic grade and hormone receptor status. Recent technological advancements have enabled an era of precision medicine, where DCIS can be molecularly analyzed by tools, such as next-generation DNA and RNA sequencing, to identify molecular biomarkers for risk stratification. These findings have led to the development of tools such as the Oncotype DX Breast DCIS Score, a gene expression-based assay with the potential to prevent overtreatment in low-risk disease.
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Affiliation(s)
- Kevin Shee
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon
| | - Kristen E Muller
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Jonathan Marotti
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Todd W Miller
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon
| | - Wendy A Wells
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Gregory J Tsongalis
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire.
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Mathé E, Hays JL, Stover DG, Chen JL. The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources. Yearb Med Inform 2018; 27:211-222. [PMID: 30157526 PMCID: PMC6115204 DOI: 10.1055/s-0038-1667085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The aim is to provide a comprehensive review of state-of-the art omics approaches, including proteomics, metabolomics, cell-free DNA, and patient cohort matching algorithms in precision oncology. METHODS In the past several years, the cancer informatics revolution has been the beneficiary of a data explosion. Different complementary omics technologies have begun coming into their own to provide a more nuanced view of the patient-tumor interaction beyond that of DNA alterations. A combined approach is beneficial to the patient as nearly all new cancer therapeutics are designed with an omics biomarker in mind. Proteomics and metabolomics provide us with a means of assaying in real-time the response of the tumor to treatment. Circulating cell-free DNA may allow us to better understand tumor heterogeneity and interactions with the host genome. RESULTS Integration of increasingly available omics data increases our ability to segment patients into smaller and smaller cohorts, thereby prompting a shift in our thinking about how to use these omics data. With large repositories of patient omics-outcomes data being generated, patient cohort matching algorithms have become a dominant player. CONCLUSIONS The continued promise of precision oncology is to select patients who are most likely to benefit from treatment and to avoid toxicity for those who will not. The increased public availability of omics and outcomes data in patients, along with improved computational methods and resources, are making precision oncology a reality.
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Affiliation(s)
- Ewy Mathé
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - John L. Hays
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, USA
| | - Daniel G. Stover
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James L. Chen
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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Chawla A, Peeples M, Li N, Anhorn R, Ryan J, Signorovitch J. Real-world utilization of molecular diagnostic testing and matched drug therapies in the treatment of metastatic cancers. J Med Econ 2018; 21:543-552. [PMID: 29295635 DOI: 10.1080/13696998.2017.1423488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
AIMS To assess the frequency of biopsies and molecular diagnostic testing (human DNA/RNA analysis), anti-cancer drug use (genomically-matched targeted therapy [GMTT], unmatched targeted therapy [UTT], endocrine therapy [ET], and chemotherapy [CT]), and medical service costs among adults with metastatic cancer. METHODS Adults diagnosed with metastatic breast, non-small cell lung (NSCLC), colorectal, head and neck, ovarian, and uterine cancer (2010Q1-2015Q1) were identified in the OptumHealth Care Solutions claims database and followed from first metastatic diagnosis for ≥1 month and until the end of data availability. Utilization was assessed for each cancer cohort (all and patients aged ≥65 years); per-patient-per-month (PPPM) medical service costs were assessed for all patients. Testing frequency estimates were applied to Surveillance, Epidemiology, and End Results Program data to estimate the number of untested patients (2010-2014). RESULTS Patients with metastatic cancer (n = 8,193; breast [n = 3,414], NSCLC [n = 2,231], colorectal [n = 1,611], head and neck [n = 511], ovarian [n = 275], and uterine [n = 151]) were 63 years old (mean), with 11.1-22.2 months of observation. Biopsy and molecular diagnostic testing frequencies ranged from 7% (uterine) to 73% (ovarian), and from 34% (head and neck) to 52% (breast), respectively. Few were treated with GMTT (breast, 11%; NSCLC, 9%; colorectal, 6%). Treatment with UTT ranged from 0.7% (uterine) to 21% (colorectal). Biopsy, diagnostic testing, and anti-cancer drug therapy were less frequent for those ≥65 years. Medical service costs (PPPM, mean) ranged from $6,618 (head and neck) to $9,940 (ovarian). The estimated number of untested new patients with metastatic cancer was 636,369 (all) and 341,397 (≥65). LIMITATIONS In addition to the limitations of claims analyses, diagnostic testing frequency may be under-estimated if patients underwent testing prior to study inclusion. CONCLUSIONS The low frequency of molecular diagnostic testing suggests there are opportunities to better inform management of patients with advanced cancer, particularly decisions to treat with GMTT.
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Affiliation(s)
| | | | - Nanxin Li
- b Analysis Group, Inc. , Boston , MA , USA
| | | | - Jason Ryan
- c Foundation Medicine, Inc. , Cambridge , MA , USA
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van der Velden DL, van Herpen CML, van Laarhoven HWM, Smit EF, Groen HJM, Willems SM, Nederlof PM, Langenberg MHG, Cuppen E, Sleijfer S, Steeghs N, Voest EE. Molecular Tumor Boards: current practice and future needs. Ann Oncol 2018; 28:3070-3075. [PMID: 29045504 DOI: 10.1093/annonc/mdx528] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Due to rapid technical advances, steeply declining sequencing costs, and the ever-increasing number of targeted therapies, it can be expected that extensive tumor sequencing such as whole-exome and whole-genome sequencing will soon be applied in standard care. Clinicians will thus be confronted with increasingly complex genetic information and multiple test-platforms to choose from. General medical training, meanwhile, can hardly keep up with the pace of innovation. Consequently, there is a rapidly growing gap between clinical knowledge and genetic potential in cancer care. Multidisciplinary Molecular Tumor Boards (MTBs) have been suggested as a means to address this disparity, but shared experiences are scarce in literature and no quality requirements or guidelines have been published to date. Methods Based on literature review, a survey among hospitals in The Netherlands, and our own experience with the establishment of a nationally operating MTB, this article evaluates current knowledge and unmet needs and lays out a strategy for successful MTB implementation. Results Having access to an MTB can improve and increase the application of genetics-guided cancer care. In our survey, however, <50% of hospitals and only 5% of nonacademic hospitals had access to an MTB. In addition, current MTBs vary widely in terms of composition, tasks, tools, and workflow. This may not only lead to variation in quality of care but also hinders data sharing and thus creation of an effective learning community. Conclusions This article acknowledges a leading role for MTBs to govern (extensive) tumor sequencing into daily practice and proposes three basic necessities for successful MTB implementation: (i) global harmonization in cancer sequencing practices and procedures, (ii) minimal member and operational requirements, and (iii) an appropriate unsolicited findings policy. Meeting these prerequisites would not only optimize MTB functioning but also improve general interpretation and application of genomics-guided cancer care.
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Affiliation(s)
| | - C M L van Herpen
- Division of Medical Oncology, Radboud University Medical Center, Nijmegen
| | | | - E F Smit
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam
| | - H J M Groen
- Division of Medical Oncology, University Medical Center Groningen, Groningen
| | - S M Willems
- Division of Pathology, University Medical Center Utrecht, Utrecht
| | - P M Nederlof
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam
| | | | - E Cuppen
- Human Genetics, University Medical Center Utrecht, Utrecht
| | - S Sleijfer
- Division of Medical Oncology, Erasmus University Medical Center, Rotterdam
| | - N Steeghs
- Division of Medical Oncology and Clinical Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E E Voest
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam
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Walko C, Kiel PJ, Kolesar J. Precision medicine in oncology: New practice models and roles for oncology pharmacists. Am J Health Syst Pharm 2018; 73:1935-1942. [PMID: 27864201 DOI: 10.2146/ajhp160211] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Three different precision medicine practice models developed by oncology pharmacists are described, including strategies for implementation and recommendations for educating the next generation of oncology pharmacy practitioners. SUMMARY Oncology is unique in that somatic mutations can both drive the development of a tumor and serve as a therapeutic target for treating the cancer. Precision medicine practice models are a forum through which interprofessional teams, including pharmacists, discuss tumor somatic mutations to guide patient-specific treatment. The University of Wisconsin, Indiana University, and Moffit Cancer Center have implemented precision medicine practice models developed and led by oncology pharmacists. Different practice models, including a clinic, a clinical consultation service, and a molecular tumor board (MTB), were adopted to enhance integration into health systems and payment structures. Although the practice models vary, commonalities of three models include leadership by the clinical pharmacist, specific therapeutic recommendations, procurement of medications for off-label use, and a research component. These three practice models function as interprofessional training sites for pharmacy and medical students and residents, providing an important training resource at these institutions. Key implementation strategies include interprofessional involvement, institutional support, integration into clinical workflow, and selection of model by payer mix. CONCLUSION MTBs are a pathway for clinical implementation of genomic medicine in oncology and are an emerging practice model for oncology pharmacists. Because pharmacists must be prepared to participate fully in contemporary practice, oncology pharmacy residents must be trained in genomic oncology, schools of pharmacy should expand precision medicine and genomics education, and opportunities for continuing education in precision medicine should be made available to practicing pharmacists.
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Affiliation(s)
- Christine Walko
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL
| | - Patrick J Kiel
- Precision Genomics Program, Indiana University Simon Cancer Center-IU Health, Indianapolis, IN
| | - Jill Kolesar
- College of Pharmacy, University of Kentucky, Lexington, KY .,Molecular Tumor Board, Markey Cancer Center, Lexington, KY.
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Connon RE, Jeffries KM, Komoroske LM, Todgham AE, Fangue NA. The utility of transcriptomics in fish conservation. ACTA ACUST UNITED AC 2018; 221:221/2/jeb148833. [PMID: 29378879 DOI: 10.1242/jeb.148833] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.
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Affiliation(s)
- Richard E Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Lisa M Komoroske
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA.,Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne E Todgham
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nann A Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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41
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Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. PLoS One 2017; 12:e0189651. [PMID: 29281680 PMCID: PMC5744968 DOI: 10.1371/journal.pone.0189651] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022] Open
Abstract
Purpose Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results 153 patients were included (58.2% female, average age 59.5 years). The most common malignancy was lung cancer (40.5%), most common biopsied site was lung (36%), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9%. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy </ = 3 months (OR 3.24; p = 0.01) compared to systemic therapy >3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.
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Lalonde E, Wertheim G, Li MM. Clinical Impact of Genomic Information in Pediatric Leukemia. Front Pediatr 2017; 5:263. [PMID: 29312903 PMCID: PMC5735078 DOI: 10.3389/fped.2017.00263] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/24/2017] [Indexed: 12/21/2022] Open
Abstract
Pediatric leukemia remains a significant contributor to childhood lethality rates. However, recent development of new technologies including next-generation sequencing (NGS) has increased our understanding of the biological and genetic underpinnings of leukemia, resulting in novel diagnostic and treatment paradigms. The most prevalent pediatric leukemias include B-cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). These leukemias are highly heterogeneous, both clinically and genetically. There are multiple genetic subgroups defined by the World Health Organization, each with distinct clinical management. Clinical laboratories have started adopting genomic testing strategies to include high-throughput sequencing assays which, together with conventional cytogenetic techniques, enable optimal patient care. This review summarizes genetic and genomic techniques used in clinical laboratories to support management of pediatric leukemia, highlighting technical, biological, and clinical advances. We illustrate clinical utilities of comprehensive genomic evaluation of leukemia genomes through clinical case examples, which includes the interrogations of hundreds of genes and multiple mutation mechanisms using NGS technologies. Finally, we provide a future perspective on clinical genomics and precision medicine.
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Affiliation(s)
- Emilie Lalonde
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Marilyn M. Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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43
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Hayes DF, Vose JM. Delivery of Personalized Medicine With Precision. JCO Precis Oncol 2017; 1:1-3. [DOI: 10.1200/po.16.00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Daniel F. Hayes
- Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Julie Vose, University of Nebraska Medical Center, Omaha, NE
| | - Julie M. Vose
- Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Julie Vose, University of Nebraska Medical Center, Omaha, NE
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Zhang YC, Zhou Q, Wu YL. The emerging roles of NGS-based liquid biopsy in non-small cell lung cancer. J Hematol Oncol 2017; 10:167. [PMID: 29061113 PMCID: PMC5654124 DOI: 10.1186/s13045-017-0536-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/17/2017] [Indexed: 12/25/2022] Open
Abstract
The treatment paradigm of non-small cell lung cancer (NSCLC) has evolved into oncogene-directed precision medicine. Identifying actionable genomic alterations is the initial step towards precision medicine. An important scientific progress in molecular profiling of NSCLC over the past decade is the shift from the traditional piecemeal fashion to massively parallel sequencing with the use of next-generation sequencing (NGS). Another technical advance is the development of liquid biopsy with great potential in providing a dynamic and comprehensive genomic profiling of NSCLC in a minimally invasive manner. The integration of NGS with liquid biopsy has been demonstrated to play emerging roles in genomic profiling of NSCLC by increasing evidences. This review summarized the potential applications of NGS-based liquid biopsy in the diagnosis and treatment of NSCLC including identifying actionable genomic alterations, tracking spatiotemporal tumor evolution, dynamically monitoring response and resistance to targeted therapies, and diagnostic value in early-stage NSCLC, and discussed emerging challenges to overcome in order to facilitate clinical translation in future.
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Affiliation(s)
- Yi-Chen Zhang
- Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, People's Republic of China.
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45
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Cheng Q, Li X, Acharya CR, Hyslop T, Sosa JA. A novel integrative risk index of papillary thyroid cancer progression combining genomic alterations and clinical factors. Oncotarget 2017; 8:16690-16703. [PMID: 28187428 PMCID: PMC5369994 DOI: 10.18632/oncotarget.15128] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 12/14/2022] Open
Abstract
Although the majority of papillary thyroid cancer (PTC) is indolent, a subset of PTC behaves aggressively despite the best available treatment. A major clinical challenge is to reliably distinguish early on between those patients who need aggressive treatment from those who do not. Using a large cohort of PTC samples obtained from The Cancer Genome Atlas (TCGA), we analyzed the association between disease progression and multiple forms of genomic data, such as transcriptome, somatic mutations, and somatic copy number alterations, and found that genes related to FOXM1 signaling pathway were significantly associated with PTC progression. Integrative genomic modeling was performed, controlling for demographic and clinical characteristics, which included patient age, gender, TNM stages, histological subtypes, and history of other malignancy, using a leave-one-out elastic net model and 10-fold cross validation. For each subject, the model from the remaining subjects was used to determine the risk index, defined as a linear combination of the clinical and genomic variables from the elastic net model, and the stability of the risk index distribution was assessed through 2,000 bootstrap resampling. We developed a novel approach to combine genomic alterations and patient-related clinical factors that delineates the subset of patients who have more aggressive disease from those whose tumors are indolent and likely will require less aggressive treatment and surveillance (p = 4.62 × 10-10, log-rank test). Our results suggest that risk index modeling that combines genomic alterations with current staging systems provides an opportunity for more effective anticipation of disease prognosis and therefore enhanced precision management of PTC.
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Affiliation(s)
- Qing Cheng
- Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA.,Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Xuechan Li
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710 USA
| | | | - Terry Hyslop
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710 USA.,Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Julie Ann Sosa
- Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA.,Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710 USA
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Movassaghi M, Shabihkhani M, Hojat SA, Williams RR, Chung LK, Im K, Lucey GM, Wei B, Mareninov S, Wang MW, Ng DW, Tashjian RS, Magaki S, Perez-Rosendahl M, Yang I, Khanlou N, Vinters HV, Liau LM, Nghiemphu PL, Lai A, Cloughesy TF, Yong WH. Early experience with formalin-fixed paraffin-embedded (FFPE) based commercial clinical genomic profiling of gliomas-robust and informative with caveats. Exp Mol Pathol 2017; 103:87-93. [PMID: 28663030 DOI: 10.1016/j.yexmp.2017.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/24/2017] [Accepted: 06/24/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND Commercial targeted genomic profiling with next generation sequencing using formalin-fixed paraffin embedded (FFPE) tissue has recently entered into clinical use for diagnosis and for the guiding of therapy. However, there is limited independent data regarding the accuracy or robustness of commercial genomic profiling in gliomas. METHODS As part of patient care, FFPE samples of gliomas from 71 patients were submitted for targeted genomic profiling to one commonly used commercial vendor, Foundation Medicine. Genomic alterations were determined for the following grades or groups of gliomas; Grade I/II, Grade III, primary glioblastomas (GBMs), recurrent primary GBMs, and secondary GBMs. In addition, FFPE samples from the same patients were independently assessed with conventional methods such as immunohistochemistry (IHC), Quantitative real-time PCR (qRT-PCR), or Fluorescence in situ hybridization (FISH) for three genetic alterations: IDH1 mutations, EGFR amplification, and EGFRvIII expression. RESULTS A total of 100 altered genes were detected by the aforementioned targeted genomic profiling assay. The number of different genomic alterations was significantly different between the five groups of gliomas and consistent with the literature. CDKN2A/B, TP53, and TERT were the most common genomic alterations seen in primary GBMs, whereas IDH1, TP53, and PIK3CA were the most common in secondary GBMs. Targeted genomic profiling demonstrated 92.3%-100% concordance with conventional methods. The targeted genomic profiling report provided an average of 5.5 drugs, and listed an average of 8.4 clinical trials for the 71 glioma patients studied but only a third of the trials were appropriate for glioma patients. CONCLUSIONS In this limited comparison study, this commercial next generation sequencing based-targeted genomic profiling showed a high concordance rate with conventional methods for the 3 genetic alterations and identified mutations expected for the type of glioma. While it may not be feasible to exhaustively independently validate a commercial genomic profiling assay, examination of a few markers provides some reassurance of its robustness. While potential targeted drugs are recommended based on genetic alterations, to date most targeted therapies have failed in glioblasomas so the usefulness of such recommendations will increase with development of novel and efficacious drugs.
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Affiliation(s)
- Masoud Movassaghi
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Maryam Shabihkhani
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Seyed A Hojat
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Ryan R Williams
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Lawrance K Chung
- Department of Neurosurgery, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Kyuseok Im
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Gregory M Lucey
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Bowen Wei
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Sergey Mareninov
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Michael W Wang
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Denise W Ng
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Randy S Tashjian
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Shino Magaki
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Mari Perez-Rosendahl
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Isaac Yang
- Department of Neurosurgery, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, United States
| | - Negar Khanlou
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States
| | - Harry V Vinters
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Brain Research Institute, University of California-Los Angeles, Los Angeles, CA, United States
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Brain Research Institute, University of California-Los Angeles, Los Angeles, CA, United States; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, United States
| | - Phioanh L Nghiemphu
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, United States
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Brain Research Institute, University of California-Los Angeles, Los Angeles, CA, United States; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, United States
| | - Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, United States
| | - William H Yong
- Divison of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, United States; Brain Research Institute, University of California-Los Angeles, Los Angeles, CA, United States; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, United States.
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Kou T, Kanai M, Yamamoto Y, Kamada M, Nakatsui M, Sakuma T, Mochizuki H, Hiroshima A, Sugiyama A, Nakamura E, Miyake H, Minamiguchi S, Takaori K, Matsumoto S, Haga H, Seno H, Kosugi S, Okuno Y, Muto M. Clinical sequencing using a next-generation sequencing-based multiplex gene assay in patients with advanced solid tumors. Cancer Sci 2017; 108:1440-1446. [PMID: 28440963 PMCID: PMC5497931 DOI: 10.1111/cas.13265] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/12/2017] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
Advances in next‐generation sequencing (NGS) technologies have enabled physicians to test for genomic alterations in multiple cancer‐related genes at once in daily clinical practice. In April 2015, we introduced clinical sequencing using an NGS‐based multiplex gene assay (OncoPrime) certified by the Clinical Laboratory Improvement Amendment. This assay covers the entire coding regions of 215 genes and the rearrangement of 17 frequently rearranged genes with clinical relevance in human cancers. The principal indications for the assay were cancers of unknown primary site, rare tumors, and any solid tumors that were refractory to standard chemotherapy. A total of 85 patients underwent testing with multiplex gene assay between April 2015 and July 2016. The most common solid tumor types tested were pancreatic (n = 19; 22.4%), followed by biliary tract (n = 14; 16.5%), and tumors of unknown primary site (n = 13; 15.3%). Samples from 80 patients (94.1%) were successfully sequenced. The median turnaround time was 40 days (range, 18–70 days). Potentially actionable mutations were identified in 69 of 80 patients (86.3%) and were most commonly found in TP53 (46.3%), KRAS (23.8%), APC (18.8%), STK11 (7.5%), and ATR (7.5%). Nine patients (13.0%) received a subsequent therapy based on the NGS assay results. Implementation of clinical sequencing using an NGS‐based multiplex gene assay was feasible in the clinical setting and identified potentially actionable mutations in more than 80% of patients. Current challenges are to incorporate this genomic information into better therapeutic decision making.
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Affiliation(s)
- Tadayuki Kou
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiro Yamamoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mayumi Kamada
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Nakatsui
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Sakuma
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Hiroaki Mochizuki
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Akinori Hiroshima
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Aiko Sugiyama
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eijiro Nakamura
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidehiko Miyake
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan
| | | | - Kyoichi Takaori
- Division of Hepatobiliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigemi Matsumoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Kosugi
- Department of Medical Ethics and Medical Genetics, Kyoto University School of Public Health, Kyoto, Japan
| | - Yasushi Okuno
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Muto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Prawira A, Pugh T, Stockley T, Siu L. Data resources for the identification and interpretation of actionable mutations by clinicians. Ann Oncol 2017; 28:946-957. [DOI: 10.1093/annonc/mdx023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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49
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Dey N, Williams C, Leyland-Jones B, De P. Mutation matters in precision medicine: A future to believe in. Cancer Treat Rev 2017; 55:136-149. [DOI: 10.1016/j.ctrv.2017.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/04/2017] [Indexed: 12/12/2022]
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50
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Gao Q, Wang ZC, Duan M, Lin YH, Zhou XY, Worthley DL, Wang XY, Niu G, Xia Y, Deng M, Liu LZ, Shi JY, Yang LX, Zhang S, Ding ZB, Zhou J, Liang CM, Cao Y, Xiong L, Xi R, Shi YY, Fan J. Cell Culture System for Analysis of Genetic Heterogeneity Within Hepatocellular Carcinomas and Response to Pharmacologic Agents. Gastroenterology 2017; 152:232-242.e4. [PMID: 27639803 DOI: 10.1053/j.gastro.2016.09.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 08/28/2016] [Accepted: 09/04/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS No targeted therapies have been found to be effective against hepatocellular carcinoma (HCC), possibly due to the large degree of intratumor heterogeneity. We performed genetic analyses of different regions of HCCs to evaluate levels of intratumor heterogeneity and associate alterations with responses to different pharmacologic agents. METHODS We obtained samples of HCCs (associated with hepatitis B virus infection) from 10 patients undergoing curative resection, before adjuvant therapy, at hospitals in China. We collected 4-9 spatially distinct samples from each tumor (55 regions total), performed histologic analyses, isolated cancer cells, and carried them low-passage culture. We performed whole-exome sequencing, copy-number analysis, and high-throughput screening of the cultured primary cancer cells. We tested responses of an additional 105 liver cancer cell lines to a fibroblast growth factor receptor (FGFR) 4 inhibitor. RESULTS We identified a total of 3670 non-silent mutations (3192 missense, 94 splice-site variants, and 222 insertions or deletions) in the tumor samples. We observed considerable intratumor heterogeneity and branched evolution in all 10 tumors; the mean percentage of heterogeneous mutations in each tumor was 39.7% (range, 12.9%-68.5%). We found significant mutation shifts toward C>T and C>G substitutions in branches of phylogenetic trees among samples from each tumor (P < .0001). Of note, 14 of the 26 oncogenic alterations (53.8%) varied among subclones that mapped to different branches. Genetic alterations that can be targeted by existing pharmacologic agents (such as those in FGF19, DDR2, PDGFRA, and TOP1) were identified in intratumor subregions from 4 HCCs and were associated with sensitivity to these agents. However, cells from the remaining subregions, which did not have these alterations, were not sensitive to these drugs. High-throughput screening identified pharmacologic agents to which these cells were sensitive, however. Overexpression of FGF19 correlated with sensitivity of cells to an inhibitor of FGFR 4; this observation was validated in 105 liver cancer cell lines (P = .0024). CONCLUSIONS By analyzing genetic alterations in different tumor regions of 10 HCCs, we observed extensive intratumor heterogeneity. Our patient-derived cell line-based model, integrating genetic and pharmacologic data from multiregional cancer samples, provides a platform to elucidate how intratumor heterogeneity affects sensitivity to different therapeutic agents.
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Affiliation(s)
- Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Zhi-Chao Wang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Meng Duan
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Yi-Hui Lin
- Institute of Precision Medicine, 3D Medicines Inc., Shanghai, China
| | - Xue-Ya Zhou
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Daniel L Worthley
- Cancer Theme, South Australian Health and Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Xiao-Ying Wang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Gang Niu
- Institute of Precision Medicine, 3D Medicines Inc., Shanghai, China
| | - Yuchao Xia
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Minghua Deng
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Long-Zi Liu
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Jie-Yi Shi
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Liu-Xiao Yang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Shu Zhang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Zhen-Bin Ding
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China; Cancer Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chun-Min Liang
- Department of Anatomy and Histology and Embryology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Hunan, China
| | - Lei Xiong
- Institute of Precision Medicine, 3D Medicines Inc., Shanghai, China
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Yong-Yong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China; Cancer Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China.
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