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Hu X, Zhang H, Wang Y, Lin Y, Li Q, Li L, Zeng G, Ou R, Cheng X, Zhang Y, Jin X. Effects of blood-processing protocols on cell-free DNA fragmentomics in plasma: Comparisons of one- and two-step centrifugations. Clin Chim Acta 2024; 560:119729. [PMID: 38754575 DOI: 10.1016/j.cca.2024.119729] [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: 03/29/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Cell-free DNA (cfDNA) fragmentomic characteristics are promising analytes with abundant physiological signals for non-invasive disease diagnosis and monitoring. Previous studies on plasma cfDNA fragmentomics commonly employed a two-step centrifugation process for removing cell debris, involving a low-speed centrifugation followed by a high-speed centrifugation. However, the effects of centrifugation conditions on the analysis of cfDNA fragmentome remain uncertain. METHODS We collected blood samples from 10 healthy individuals and divided each sample into two aliquots for plasma preparation with one- and two-step centrifugation processes. We performed whole genome sequencing (WGS) of the plasma cfDNA in the two groups and comprehensively compared the cfDNA fragmentomic features. Additionally, we reanalyzed the fragmentomic features of cfDNA from 16 healthy individuals and 16 COVID-19 patients, processed through one- and two-step centrifugation in our previous study, to investigate the impact of centrifugation on disease signals. RESULTS Our results showed that there were no significant differences observed in the characteristics of nuclear cfDNA, including size, motif diversity score (MDS) of end motifs, and genome distribution, between plasma samples treated with one- and two-step centrifugation. The cfDNA size shortening in COVID-19 patients was observed in plasma samples with one- and two-step centrifugation methods. However, we observed a significantly higher relative abundance and longer size of cell-free mitochondrial DNA (mtDNA) in the one-step samples compared to the two-step samples. This difference in mtDNA caused by the one- and two-step centrifugation methods surpasses the pathological difference between COVID-19 patients and healthy individuals. CONCLUSIONS Our findings indicate that one-step low-speed centrifugation is a simple and potentially suitable method for analyzing nuclear cfDNA fragmentation characteristics. These results offer valuable guidance for cfDNA research in various clinical scenarios.
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Affiliation(s)
- Xintao Hu
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China; BGI Research, Shenzhen 518083, China
| | | | | | - Yu Lin
- BGI Research, Shenzhen 518083, China
| | - Qiuyan Li
- BGI Research, Shenzhen 518083, China
| | | | | | - Rijing Ou
- BGI Research, Shenzhen 518083, China
| | - Xinyu Cheng
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yan Zhang
- BGI Research, Shenzhen 518083, China.
| | - Xin Jin
- BGI Research, Shenzhen 518083, China; School of Medicine, South China University of Technology, Guangzhou 510006, China.
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2
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Rickles-Young M, Tinoco G, Tsuji J, Pollock S, Haynam M, Lefebvre H, Glover K, Owen DH, Collier KA, Ha G, Adalsteinsson VA, Cibulskis C, Lennon NJ, Stover DG. Assay Validation of Cell-Free DNA Shallow Whole-Genome Sequencing to Determine Tumor Fraction in Advanced Cancers. J Mol Diagn 2024; 26:413-422. [PMID: 38490303 PMCID: PMC11090203 DOI: 10.1016/j.jmoldx.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/21/2023] [Accepted: 01/18/2024] [Indexed: 03/17/2024] Open
Abstract
Blood-based liquid biopsy is increasingly used in clinical care of patients with cancer, and fraction of tumor-derived DNA in circulation (tumor fraction; TFx) has demonstrated clinical validity across multiple cancer types. To determine TFx, shallow whole-genome sequencing of cell-free DNA (cfDNA) can be performed from a single blood sample, using an established computational pipeline (ichorCNA), without prior knowledge of tumor mutations, in a highly cost-effective manner. We describe assay validation of this approach to facilitate broad clinical application, including evaluation of assay sensitivity, precision, repeatability, reproducibility, pre-analytic factors, and DNA quality/quantity. Sensitivity to detect TFx of 3% (lower limit of detection) was 97.2% to 100% at 1× and 0.1× mean sequencing depth, respectively. Precision was demonstrated on distinct sequencing instruments (HiSeqX and NovaSeq) with no observable differences. The assay achieved prespecified 95% agreement of TFx across replicates of the same specimen (repeatability) and duplicate samples in different batches (reproducibility). Comparison of samples collected in EDTA and Streck tubes from single venipuncture in 23 patients demonstrated that EDTA or Streck tubes were comparable if processed within 8 hours. On the basis of a range of DNA inputs (1 to 50 ng), 20 ng cfDNA is the preferred input, with 5 ng minimum acceptable. Overall, this shallow whole-genome sequencing of cfDNA and ichorCNA approach offers sensitive, precise, and reproducible quantitation of TFx, facilitating assay application in clinical cancer care.
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Affiliation(s)
- Micah Rickles-Young
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gabriel Tinoco
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Junko Tsuji
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sam Pollock
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Marcy Haynam
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Heather Lefebvre
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Kristyn Glover
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Dwight H Owen
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Katharine A Collier
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Viktor A Adalsteinsson
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Carrie Cibulskis
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Niall J Lennon
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Daniel G Stover
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio.
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3
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Allan Z, Liu DS, Lee MM, Tie J, Clemons NJ. A Practical Approach to Interpreting Circulating Tumor DNA in the Management of Gastrointestinal Cancers. Clin Chem 2024; 70:49-59. [PMID: 38175583 DOI: 10.1093/clinchem/hvad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND There is accumulating evidence supporting the clinical use of circulating tumor DNA (ctDNA) in solid tumors, especially in different types of gastrointestinal cancer. As such, appraisal of the current and potential clinical utility of ctDNA is needed to guide clinicians in decision-making to facilitate its general applicability. CONTENT In this review, we firstly discuss considerations surrounding specimen collection, processing, storage, and analysis, which affect reporting and interpretation of results. Secondly, we evaluate a selection of studies on colorectal, esophago-gastric, and pancreatic cancer to determine the level of evidence for the use of ctDNA in disease screening, detection of molecular residual disease (MRD) and disease recurrence during surveillance, assessment of therapy response, and guiding targeted therapy. Lastly, we highlight current limitations in the clinical utility of ctDNA and future directions. SUMMARY Current evidence of ctDNA in gastrointestinal cancer is promising but varies depending on its specific clinical role and cancer type. Larger prospective trials are needed to validate different aspects of ctDNA clinical utility, and standardization of collection protocols, analytical assays, and reporting guidelines should be considered to facilitate its wider applicability.
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Affiliation(s)
- Zexi Allan
- Division of Cancer Research, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - David S Liu
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
- Upper Gastrointestinal Surgery Unit, Division of Surgery, Anaesthesia, and Procedural Medicine, Austin Health, Heidelberg, Victoria, Australia
| | - Margaret M Lee
- Division of Personalised Oncology, the Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jeanne Tie
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Division of Personalised Oncology, the Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
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4
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Pettersson L, Westerling S, Talla V, Sendel A, Wennberg L, Olsson R, Hedrum A, Hauzenberger D. Development and performance of a next generation sequencing (NGS) assay for monitoring of dd-cfDNA post solid organ transplantation. Clin Chim Acta 2024; 552:117647. [PMID: 37951377 DOI: 10.1016/j.cca.2023.117647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
The aim of this study was to evaluate the analytical performance of a novel NGS assay, intended for monitoring of donor-derived cell-free DNA (dd-cfDNA), and describe its validity in clinical plasma samples from kidney transplanted patients. Artificial and clinical samples with increasing amounts of patient DNA were evaluated using NGS analysis of indel markers. Monitoring of dd-cfDNA with the NGS assay presented herein demonstrated a sensitivity of ≥0.1% dd-cfDNA and excellent accuracy (R2 0.99) throughout an extensive range of dd-cfDNA (0.1-30%). The precision of the test was determined for two levels (0.1% (LoD) and 1%) of dd-cfDNA. The between run precision (CV%) for the respective level was 16% and 9% and the corresponding result for the within run precision was 19% and 7%. To evaluate performance of the assay in clinical samples, 507 retrospective monitoring samples from 21 patients transplanted either with kidneys from living or deceased donors were analyzed. Monitoring samples were sampled at multiple time points from 24 h up to 90 days post-transplantation. We show that in one patient, increase of dd-cfDNA preceded increase of creatinine caused by acute cellular rejection by several days. In conclusion, the NGS assay displayed a combination of high sensitivity with good accuracy and precision in both artificial and clinical dd-cfDNA samples.
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Affiliation(s)
| | | | - Venkat Talla
- Devyser AB, Instrumentvägen 19, SE-12653 Stockholm, Sweden
| | - Anton Sendel
- Dept. Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Wennberg
- Clinic for Transplantation Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Olsson
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anders Hedrum
- Devyser AB, Instrumentvägen 19, SE-12653 Stockholm, Sweden
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5
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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6
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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7
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Facchinetti F, Jänne PA, Tiseo M. Chasing EGFR Mutations in the Plasma of Patients With Resected NSCLC: Lessons in the ADAURA Era. J Thorac Oncol 2023; 18:1118-1120. [PMID: 37599043 DOI: 10.1016/j.jtho.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 08/22/2023]
Affiliation(s)
- Francesco Facchinetti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marcello Tiseo
- Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy; Medical Oncology Unit, University Hospital of Parma, Parma, Italy
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8
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Chan SF, Cheng H, Goh KKR, Zou R. Preanalytic Methodological Considerations and Sample Quality Control of Circulating miRNAs. J Mol Diagn 2023; 25:438-453. [PMID: 37030398 DOI: 10.1016/j.jmoldx.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/24/2023] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
As miRNAs emerge as potential circulating biomarkers for the diagnosis or prognosis of a wide variety of diseases, the quantification of miRNA necessitates careful preanalytic considerations and sample quality control becomes crucial. This study comprehensively analyzed the profiles of 356 miRNAs by quantitative RT-PCR in various blood sample types, with various processing protocols. The comprehensive analysis investigated the correlations of individual miRNAs with certain confounding factors. On the basis of these profiles, a panel of 7 miRNAs was established for the quality control of samples corresponding to hemolysis and platelet contamination. The panel was used to investigate the confounding impacts based on the size of the blood collection tube, the centrifugation protocol, post-freeze-thaw spinning, and whole blood storage. A standard dual-spin workflow for the processing of blood had been established for optimal sample quality. The real-time stability of 356 miRNAs was also investigated with demonstration of the temperature and time-induced miRNA degradation profile. Stability-related miRNAs were identified from real-time stability study and further incorporated into the quality control panel. This quality control panel enables the assessment of sample quality for more robust and reliable detection of circulating miRNAs.
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Affiliation(s)
- Suit-Fong Chan
- Research and Development Lab, MiRXES Lab Pte. Ltd., Singapore.
| | - He Cheng
- Research and Development Lab, MiRXES Lab Pte. Ltd., Singapore
| | | | - Ruiyang Zou
- Research and Development Lab, MiRXES Lab Pte. Ltd., Singapore
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9
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Su S, Xuan Y, Fan X, Bao H, Tang H, Lv X, Ren W, Chen F, Shao Y, Wang T, Wang L. Testing the generalizability of cfDNA fragmentomic features across different studies for cancer early detection. Genomics 2023; 115:110662. [PMID: 37270068 DOI: 10.1016/j.ygeno.2023.110662] [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: 02/07/2023] [Revised: 05/12/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
cfDNA fragmentomic features have been used in cancer detection models; however, the generalizability of the models needs to be tested. We proposed a type of cfDNA fragmentomic feature named chromosomal arm-level fragment size distribution (ARM-FSD), evaluated and compared its performance and generalizability for lung cancer and pan-cancer detection with existing cfDNA fragmentomic features (as reference) by using cohorts from different institutions. The ARM-FSD lung cancer model outperformed the reference model by ∼10% when being tested by two external cohorts (AUC: 0.97 vs. 0.86; 0.87 vs. 0.76). For pan-cancer detection, the performance of the ARM-FSD based model is consistently higher than the reference (AUC: 0.88 vs. 0.75, 0.98 vs. 0.63) in a pan-cancer and a lung cancer external validation cohort, indicating that ARM-FSD model produces stable performance across multiple cohorts. Our study reveals ARM-FSD based models have a higher generalizability, and highlights the necessity of cross-study validation for predictive model development.
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Affiliation(s)
- Shu Su
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Medical School of Nanjing University & Clinical Center Institute of Nanjing University, Nanjing, China
| | - Yulong Xuan
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaojun Fan
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing 210032, Jiangsu, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing 210032, Jiangsu, China
| | - Haimeng Tang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing 210032, Jiangsu, China
| | - Xin Lv
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Medical School of Nanjing University & Clinical Center Institute of Nanjing University, Nanjing, China
| | - Wei Ren
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Medical School of Nanjing University & Clinical Center Institute of Nanjing University, Nanjing, China
| | - Fangjun Chen
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Medical School of Nanjing University & Clinical Center Institute of Nanjing University, Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing 210032, Jiangsu, China; School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
| | - Lifeng Wang
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Medical School of Nanjing University & Clinical Center Institute of Nanjing University, Nanjing, China.
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10
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Fernandes G, Rodrigues A, Matos C, Barata F, Cirnes L, Ferreira L, Lopes JA, Felizardo M, Fidalgo P, Brito U, Parente B. Liquid biopsy in the management of advanced lung cancer: Implementation and practical aspects. Cancer Treat Res Commun 2023; 36:100725. [PMID: 37321073 DOI: 10.1016/j.ctarc.2023.100725] [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: 03/13/2023] [Revised: 05/10/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023]
Abstract
Non-small-cell lung cancer (NSCLC) is a major cause of cancer-related death worldwide. In recent years, the discovery of actionable molecular alterations has changed the treatment paradigm of the disease. Tissue biopsies have been the gold standard for the identification of targetable alterations but present several limitations, calling for alternatives to detect driver and acquired resistance alterations. Liquid biopsies reveal great potential in this setting and also in the evaluation and monitoring of treatment response. However, several challenges currently hamper its widespread adoption in clinical practice. This perspective article evaluates the potential and challenges associated with liquid biopsy testing, considering a Portuguese expert panel dedicated to thoracic oncology point of view, and providing practical insights for its implementation based on the experience and applicability in the Portuguese context.
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Affiliation(s)
- Gabriela Fernandes
- Pulmonology Department, Centro Hospitalar e Universitário de São João, EPE, Porto, Portugal, Faculdade de Medicina da Universidade do Porto, Porto, Portugal, IBMC/i3S - Instituto de Biologia Molecular e Celular/Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
| | | | - Cláudia Matos
- Lung Unit, Champalimaud Foundation, Lisboa, Portugal
| | - Fernando Barata
- Pulmonology Department, Centro Hospitalar e Universitário de Coimbra, EPE - Hospitais da Universidade de Coimbra, Coimbra, Portugal
| | | | | | - José Albino Lopes
- Pulmonology Department, ULSAM, Viana do Castelo, Portugal; Unidade CUF de Oncologia, Hospital CUF Porto, Porto Portugal
| | | | - Paula Fidalgo
- Medical Oncology Department, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Ulisses Brito
- Pulmonology Department, Centro Hospitalar e Universitário do Algarve, Faro, Portugal
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11
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Khan SR, Scheffler M, Soomar SM, Rashid YA, Moosajee M, Ahmad A, Raza A, Uddin S. Role of circulating-tumor DNA in the early-stage non-small cell lung carcinoma as a predictive biomarker. Pathol Res Pract 2023; 245:154455. [PMID: 37054576 DOI: 10.1016/j.prp.2023.154455] [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: 03/15/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
Lung cancer is one of the most common solid malignancies. Tissue biopsy is the standard method for accurately diagnosing lung and many other malignancies over decades. However, molecular profiling of tumors leads to establishing a new horizon in the field of precision medicine, which has now entered the mainstream in clinical practice. In this context, a minimally invasive complementary method has been proposed as a liquid biopsy (LB) which is a blood-based test that is gaining popularity as it provides the opportunity to test genotypes in a unique, less invasive manner. Circulating tumor cells (CTC) captivating the Circulating-tumor DNA (Ct-DNA) are often present in the blood of lung cancer patients and are the fundamental concept behind LB. There are multiple clinical uses of Ct-DNA, including its role in prognostic and therapeutic purposes. The treatment of lung cancer has drastically evolved over time. Therefore, this review article mainly focuses on the current literature on circulating tumor DNA and its clinical implications and future goals in non-small cell lung cancer.
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Affiliation(s)
- Saqib Raza Khan
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan.
| | - Matthias Scheffler
- Internal Medicine Department, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Yasmin Abdul Rashid
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Munira Moosajee
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Aamir Ahmad
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar.
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12
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Diaz IM, Nocon A, Held SAE, Kobilay M, Skowasch D, Bronkhorst AJ, Ungerer V, Fredebohm J, Diehl F, Holdenrieder S, Holtrup F. Pre-Analytical Evaluation of Streck Cell-Free DNA Blood Collection Tubes for Liquid Profiling in Oncology. Diagnostics (Basel) 2023; 13:diagnostics13071288. [PMID: 37046506 PMCID: PMC10093569 DOI: 10.3390/diagnostics13071288] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Excellent pre-analytical stability is an essential precondition for reliable molecular profiling of circulating tumor DNA (ctDNA) in oncological diagnostics. Therefore, in vitro degradation of ctDNA and the additional release of contaminating genomic DNA from lysed blood cells must be prevented. Streck Cell-Free DNA blood collection tubes (cfDNA BCTs) have proposed advantages over standard K2EDTA tubes, but mainly have been tested in healthy individuals. Blood was collected from cancer patients (n = 53) suffering from colorectal (n = 21), pancreatic (n = 11), and non-small-cell lung cancer (n = 21) using cfDNA BCT tubes and K2EDTA tubes that were processed immediately or after 3 days (BCTs) or 6 hours (K2EDTA) at room temperature. The cfDNA isolated from these samples was characterized in terms of yield using LINE-1 qPCR; the level of gDNA contamination; and the mutation status of KRAS, NRAS, and EGFR genes using BEAMing ddPCR. CfDNA yield and gDNA levels were comparable in both tube types and were not affected by prolonged storage of blood samples for at least 3 days in cfDNA BCTs or 6 hours in K2EDTA tubes. In addition, biospecimens collected in K2EDTA tubes and cfDNA BCTs stored for up to 3 days demonstrated highly comparable levels of mutational load across all respective cancer patient cohorts and a wide range of concentrations. Our data support the applicability of clinical oncology specimens collected and stored in cfDNA BCTs for up to 3 days for reliable cfDNA and mutation analyses.
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13
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Slonim LB, Mangold KA, Alikhan MB, Joseph N, Reddy KS, Sabatini LM, Kaul KL. Cell-free Nucleic Acids in Cancer: Current Approaches, Challenges, and Future Directions. Clin Lab Med 2022; 42:669-686. [PMID: 36368789 DOI: 10.1016/j.cll.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liron Barnea Slonim
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Kathy A Mangold
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Mir B Alikhan
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Nora Joseph
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Kalpana S Reddy
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Linda M Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Karen L Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201.
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14
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Ruhen O, Lak NS, Stutterheim J, Danielli SG, Chicard M, Iddir Y, Saint-Charles A, Di Paolo V, Tombolan L, Gatz SA, Aladowicz E, Proszek P, Jamal S, Stankunaite R, Hughes D, Carter P, Izquierdo E, Wasti A, Chisholm JC, George SL, Pace E, Chesler L, Aerts I, Pierron G, Zaidi S, Delattre O, Surdez D, Kelsey A, Hubank M, Bonvini P, Bisogno G, Di Giannatale A, Schleiermacher G, Schäfer BW, Tytgat GA, Shipley J. Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study. JCO Precis Oncol 2022; 6:e2100534. [PMID: 36265118 PMCID: PMC9616639 DOI: 10.1200/po.21.00534] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/17/2022] [Accepted: 08/26/2022] [Indexed: 05/24/2023] Open
Abstract
PURPOSE Rhabdomyosarcomas (RMS) are rare neoplasms affecting children and young adults. Efforts to improve patient survival have been undermined by a lack of suitable disease markers. Plasma circulating tumor DNA (ctDNA) has shown promise as a potential minimally invasive biomarker and monitoring tool in other cancers; however, it remains underexplored in RMS. We aimed to determine the feasibility of identifying and quantifying ctDNA in plasma as a marker of disease burden and/or treatment response using blood samples from RMS mouse models and patients. METHODS We established mouse models of RMS and applied quantitative polymerase chain reaction (PCR) and droplet digital PCR (ddPCR) to detect ctDNA within the mouse plasma. Potential driver mutations, copy-number alterations, and DNA breakpoints associated with PAX3/7-FOXO1 gene fusions were identified in the RMS samples collected at diagnosis. Patient-matched plasma samples collected from 28 patients with RMS before, during, and after treatment were analyzed for the presence of ctDNA via ddPCR, panel sequencing, and/or whole-exome sequencing. RESULTS Human tumor-derived DNA was detectable in plasma samples from mouse models of RMS and correlated with tumor burden. In patients, ctDNA was detected in 14/18 pretreatment plasma samples with ddPCR and 7/7 cases assessed by sequencing. Levels of ctDNA at diagnosis were significantly higher in patients with unfavorable tumor sites, positive nodal status, and metastasis. In patients with serial plasma samples (n = 18), fluctuations in ctDNA levels corresponded to treatment response. CONCLUSION Comprehensive ctDNA analysis combining high sensitivity and throughput can identify key molecular drivers in RMS models and patients, suggesting potential as a minimally invasive biomarker. Preclinical assessment of treatments using mouse models and further patient testing through prospective clinical trials are now warranted.
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Affiliation(s)
- Olivia Ruhen
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Nathalie S.M. Lak
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Experimental Immunohematology, Sanquin, Amsterdam, the Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Experimental Immunohematology, Sanquin, Amsterdam, the Netherlands
| | - Sara G. Danielli
- Department of Oncology and Children's Research Centre, University Children's Hospital, Zurich, Switzerland
| | - Mathieu Chicard
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Yasmine Iddir
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Alexandra Saint-Charles
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Virginia Di Paolo
- Department of Pediatric Haematology/Oncology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lucia Tombolan
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy
| | - Susanne A. Gatz
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ewa Aladowicz
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Paula Proszek
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sabri Jamal
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Reda Stankunaite
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Deborah Hughes
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Paul Carter
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Elisa Izquierdo
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ajla Wasti
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Julia C. Chisholm
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Sally L. George
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erika Pace
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Diagnostic Radiology, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Isabelle Aerts
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Gaelle Pierron
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, Paris, France
- Bone Sarcoma Research Laboratory, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Anna Kelsey
- Department of Pediatric Histopathology, Manchester University Foundation Trust, Manchester, United Kingdom
| | - Michael Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Paolo Bonvini
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy
| | - Gianni Bisogno
- Department of Woman's and Children's Health, Hematology and Oncology Unit, University of Padova, Padova, Italy
| | - Angela Di Giannatale
- Department of Pediatric Haematology/Oncology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Gudrun Schleiermacher
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
- Department of Pediatric Oncology, Hospital Group, Institut Curie, Paris, France
| | - Beat W. Schäfer
- Department of Oncology and Children's Research Centre, University Children's Hospital, Zurich, Switzerland
| | - Godelieve A.M. Tytgat
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Experimental Immunohematology, Sanquin, Amsterdam, the Netherlands
| | - Janet Shipley
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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15
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Abstract
Somatic mutations of genes involved in NF-κB, PI3K/AKT, NOTCH, and JAK/STAT signaling pathways play an important role in the pathogenesis of Hodgkin lymphoma (HL). HL tumor cells form only about 5% of the tumor mass; however, it was shown that HL tumor-derived DNA could be detected in the bloodstream. This circulating tumor DNA (ctDNA) reflects the genetic profile of HL tumor cells and can be used for qualitative and quantitative analysis of tumor-specific somatic DNA mutations within the concept of liquid biopsy. Overall, the most frequently mutated gene in HL is STAT6; however, the exact spectrum of mutations differs between individual HL histological subtypes. Importantly, reduction of ctDNA plasma levels after initial treatment is highly correlated with prognosis. Therefore, ctDNA shows great promise as a novel tool for non-invasive tumor genome analysis for biomarker driven therapy as well as for superior minimal residual disease monitoring and treatment resistance detection. Here, we summarize the recent advancements of ctDNA analysis in HL with focus on ctDNA detection methodologies, genetic profiling of HL and its clonal evolution, and the emerging prognostic value of ctDNA.
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16
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Zhang S, Zhou D, Li S, Bai Y, Huang B, Han J, Xu M, Wang S, Deng G. Performance of ImproGene cfDNA blood collection tubes for mutation analysis in cancer patients. Scandinavian Journal of Clinical and Laboratory Investigation 2022; 82:378-384. [PMID: 35861435 DOI: 10.1080/00365513.2022.2100272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
With the widely application of liquid biopsy and the development of detection technology, the standardization of pre-analysis procedures is necessary. For controlling pre-analysis variation of circulating tumor DNA (ctDNA) in blood samples, the blood collection tubes for ctDNA preservation particularly contribute a lot. The objective of this study was to investigate whether ImproGene® Cell Free DNA Tube (ImproGene tube) can be used in sample collection, preservation and NGS based mutation detection for ctDNA. We investigated hemolysis and cell free DNA (cfDNA) concentration of blood samples stored in ImproGene tubes and detected β-actin, LINE1 and exogenous gene level by qPCR. We compared cfDNA and RNA quantity between samples in ImproGene tube and Streck Cell-Free DNA BCT® (Streck tube). And 10 gene mutations and three fusion mutations analysis were compared by sequencing. When stored at room temperature within 7 days in ImproGene tubes, blood samples had no visible hemolysis and the cfDNA concentration, levels of β-actin, LINE1 and exogenous gene remained stable which means no genomic DNA release and cfDNA was protected. There was no significant difference in cfDNA and RNA quantity between ImproGene tubes and Streck tubes. Furthermore, based on this limited data set, ImproGene tubes showed increased detection rates of low-level mutations. Therefore, ImproGene Cell Free DNA Tubes may have promising applications in sample collection, preservation and NGS based mutation detection for ctDNA by its good preservation performance.
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Affiliation(s)
- Shu Zhang
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Dongyao Zhou
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Siyun Li
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Yingming Bai
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Bo Huang
- Department of Laboratory Medicine, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Jianhong Han
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Mingfei Xu
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Sina Wang
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
| | - Guanhua Deng
- Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Improve Medical Instruments Co., Ltd., Zhuhai, China
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17
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Igari F, Tanaka H, Giuliano AE. The applications of plasma cell-free DNA in cancer detection: Implications in the management of breast cancer patients. Crit Rev Oncol Hematol 2022; 175:103725. [PMID: 35618229 DOI: 10.1016/j.critrevonc.2022.103725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Liquid biopsy probes DNA, RNA, and proteins in body fluids for cancer detection and is one of the most rapidly developing areas in oncology. Tumor-derived DNA (circulating tumor DNA, ctDNA) in the context of cell-free DNA (cfDNA) in blood has been the main target for its potential utilities in cancer detection. Liquid biopsy can report tumor burden in real-time without invasive interventions, and would be feasible for screening tumor types that lack standard-of-care screening approaches. Two major approaches to interrogating ctDNA are genetic mutation and DNA methylation profiling. Mutation profiling can identify tumor driver mutations and guide precision therapy. Targeted genomic profiling of DNA methylation has become the main approach for cancer screening in the general population. Here we review the recent technological development and ongoing efforts in clinical applications. For clinical applications, we focus on breast cancer, in which subtype-specific biology demarcates the applications of ctDNA.
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Affiliation(s)
- Fumie Igari
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Breast Oncology, Juntendo University, Tokyo, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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18
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Galati L, Combes JD, Le Calvez-Kelm F, McKay-Chopin S, Forey N, Ratel M, McKay J, Waterboer T, Schroeder L, Clifford G, Tommasino M, Gheit T. Detection of Circulating HPV16 DNA as a Biomarker for Cervical Cancer by a Bead-Based HPV Genotyping Assay. Microbiol Spectr 2022; 10:e0148021. [PMID: 35225653 PMCID: PMC9045285 DOI: 10.1128/spectrum.01480-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Human papillomavirus (HPV) circulating tumor DNA (HPV ctDNA) was proposed as a biomarker for the detection and disease monitoring of HPV-related cancers. One hundred eighty plasma samples obtained from women diagnosed with HPV16-positive cervical cancer (CC) (n = 100), HPV16-positive premalignant lesions (cervical intraepithelial neoplasia grade 3 [CIN3]) (n = 20), and HPV DNA-negative controls (n = 60) were randomly selected from the archives for evaluating the performance of a bead-based HPV genotyping assay (E7 type-specific multiplex genotyping assay [E7-MPG]) in detecting HPV16 ctDNA. The performance of the E7-MPG was compared with those of DNA detection by droplet digital PCR (ddPCR) and detection of HPV16 E6 antibodies evaluated in an independent study. Internal controls to assess DNA quality were included in the molecular assays, i.e., beta-globin and ESR1, respectively. The sensitivity and specificity of E7-MPG and/or E6 antibodies to detect HPV16-positive CCs were evaluated. HPV16 ctDNA was detected using the E7-MPG in 42.3% of all plasma samples and in 74.7% of plasma samples from HPV16-positive CC cases. The validation of E7-MPG data by ddPCR showed that the sensitivity of the E7-MPG test for HPV16-positive CC detection was higher than that of ddPCR (74.7% versus 63.1%; P < 0.001). When both HPV16 ctDNA and E6 antibodies were considered, the sensitivity for HPV16-positive CC detection increased from 74.7% to 86.1%, while the specificity was unchanged at 97.8%. The performance of E7-MPG for the detection of HPV16 ctDNA appears to be at least as sensitive as that of ddPCR, offering an additional tool for ctDNA detection of HPV16-positive CC. The use of an additional blood marker of HPV infection, such as E6 antibodies, further improved the detection of CC. IMPORTANCE The validity of HPV ctDNA as a marker of HPV-driven cancers has been previously reported. Herein we validated an alternative to ddPCR for HPV16 ctDNA detection, using a bead-based HPV genotyping assay that offers the potential advantage of reducing the cost of clinical management due to the multiplex capability of the test, thus facilitating its use in clinical settings. In addition, we analyzed HPV ctDNA in the context of E6 antibodies as an additional HPV marker. The HPV16 ctDNA biomarker appeared to be highly specific and, to a lesser extent, sensitive for the detection of CC, mainly indicated for those at an advanced tumor stage. In this proof-of-principle study, E6 antibodies were mainly detected in early tumor stages of CC, while HPV ctDNA was mainly positive at advanced tumor stages.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer, Lyon, France
| | | | | | | | - Nathalie Forey
- International Agency for Research on Cancer, Lyon, France
| | - Mathis Ratel
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lea Schroeder
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gary Clifford
- International Agency for Research on Cancer, Lyon, France
| | | | - Tarik Gheit
- International Agency for Research on Cancer, Lyon, France
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19
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Alese OB, Cook N, Ortega-Franco A, Ulanja MB, Tan L, Tie J. Circulating Tumor DNA: An Emerging Tool in Gastrointestinal Cancers. Am Soc Clin Oncol Educ Book 2022; 42:1-20. [PMID: 35471832 DOI: 10.1200/edbk_349143] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Circulating tumor DNA (ctDNA) is tumor-derived fragmented DNA in the bloodstream that has come from primary or metastatic cancer sites. Neoplasm-specific genetic and epigenetic abnormalities are increasingly being identified through liquid biopsy: a novel, minimally invasive technique used to isolate and analyze ctDNA in the peripheral circulation. Liquid biopsy and other emerging ctDNA technologies represent a paradigm shift in cancer diagnostics because they allow for the detection of minimal residual disease in patients with early-stage disease, improve risk stratification, capture tumor heterogeneity and genomic evolution, and enhance ctDNA-guided adjuvant and palliative cancer therapy. Moreover, ctDNA can be used to monitor the tumor response to neoadjuvant and postoperative therapy in patients with metastatic disease. Using clearance of ctDNA as an endpoint for escalation/de-escalation of adjuvant chemotherapy for patients considered to have high-risk disease has become an important area of research. The possibility of using ctDNA as a surrogate for treatment response-including for overall survival, progression-free survival, and disease-free survival-is an attractive concept; this surrogate will arguably reduce study duration and expedite the development of new therapies. In this review, we summarize the current evidence on the applications of ctDNA for the diagnosis and management of gastrointestinal tumors. Gastrointestinal cancers-including tumors of the esophagus, stomach, colon, liver, and pancreas-account for one-quarter of global cancer diagnoses and contribute to more than one-third of cancer-related deaths. Given the prevalence of gastrointestinal malignancies, ctDNA technology represents a powerful tool to reduce the global burden of disease.
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Affiliation(s)
- Olatunji B Alese
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA
| | - Natalie Cook
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, United Kingdom.,Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Ana Ortega-Franco
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Mark B Ulanja
- Christus Ochsner St. Patrick Hospital, Lake Charles, LA
| | - Lavinia Tan
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Jeanne Tie
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Division of Personalized Oncology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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20
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Huang N, Lee KJ, Stark MS. Current Trends in Circulating Biomarkers for Melanoma Detection. Front Med (Lausanne) 2022; 9:873728. [PMID: 35492361 PMCID: PMC9038522 DOI: 10.3389/fmed.2022.873728] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Melanomas have increased in global incidence and are the leading cause of skin cancer deaths. Whilst the majority of early-stage, non-metastatic melanomas can be cured with surgical excision alone, ~5% of patients with early melanomas will experience recurrence following a variable disease-free interval and progression to metastatic melanoma and ultimately death. This is likely because of primary tumor heterogeneity and progressive clonal divergency resulting in the growth of more aggressive tumor populations. Liquid biomarkers have the advantage of real-time, non-invasive longitudinal monitoring of tumor burden and heterogeneity over tissue markers. Currently, the only serological marker used in the staging and monitoring of melanoma is serum lactate dehydrogenase, which is not sufficiently specific or sensitive, and is not used routinely in all centers. An ideal melanoma biomarker would be used to identify patients who are at high-risk of primary melanoma, screen for relapse, detect early-stage melanoma, provide treatment outcomes to personalize systemic treatment, follow tumor heterogeneity, provide prognostic data before, during and after treatment, and monitor response to treatment. This review provides a summary of the current research in this field with a specific focus on circulating tumor cells, circulating tumor DNA, microRNA, and extracellular vesicles which may serve to suit these goals.
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Affiliation(s)
| | | | - Mitchell S. Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
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21
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Haselmann V, Hedtke M, Neumaier M. Liquid Profiling for Cancer Patient Stratification in Precision Medicine—Current Status and Challenges for Successful Implementation in Standard Care. Diagnostics (Basel) 2022; 12:diagnostics12030748. [PMID: 35328301 PMCID: PMC8947441 DOI: 10.3390/diagnostics12030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.
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22
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Shin S, Woo HI, Kim JW, M D YK, Lee KA. Clinical Practice Guidelines for Pre-Analytical Procedures of Plasma Epidermal Growth Factor Receptor Variant Testing. Ann Lab Med 2022; 42:141-149. [PMID: 34635607 PMCID: PMC8548242 DOI: 10.3343/alm.2022.42.2.141] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/02/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
Standardization of cell-free DNA (cfDNA) testing processes is necessary to obtain clinically reliable results. The pre-analytical phase of cfDNA testing greatly influences the results because of the low proportion and stability of circulating tumor DNA (ctDNA). In this review, we provide evidence-based clinical practice guidelines for pre-analytical phase procedures of plasma epidermal growth factor receptor gene (EGFR) variant testing. Specific recommendations for pre-analytical procedures were proposed based on evidence from the literature and our experimental data. Standardization of pre-analytical procedures can improve the analytical performance of cfDNA testing.
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Affiliation(s)
- Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hye In Woo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonjung Kim M D
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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Kondratskaya VA, Pokrovskaya MS, Doludin YV, Borisova AL, Limonova AS, Meshkov АN, Drapkina OM. Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.
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Affiliation(s)
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - Yu. V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - А. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Sant M, Bernat-Peguera A, Felip E, Margelí M. Role of ctDNA in Breast Cancer. Cancers (Basel) 2022; 14:310. [PMID: 35053474 PMCID: PMC8773730 DOI: 10.3390/cancers14020310] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/01/2022] [Accepted: 01/06/2022] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is currently classified by immunohistochemistry. However, technological advances in the detection of circulating tumor DNA (ctDNA) have made new options available for diagnosis, classification, biological knowledge, and treatment selection. Breast cancer is a heterogeneous disease and ctDNA can accurately reflect this heterogeneity, allowing us to detect, monitor, and understand the evolution of the disease. Breast cancer patients have higher levels of circulating DNA than healthy subjects, and ctDNA can be used for different objectives at different timepoints of the disease, ranging from screening and early detection to monitoring for resistance mutations in advanced disease. In early breast cancer, ctDNA clearance has been associated with higher rates of complete pathological response after neoadjuvant treatment and with fewer recurrences after radical treatments. In metastatic disease, ctDNA can help select the optimal sequencing of treatments. In the future, thanks to new bioinformatics tools, the use of ctDNA in breast cancer will become more frequent, enhancing our knowledge of the biology of tumors. Moreover, deep learning algorithms may also be able to predict breast cancer evolution or treatment sensitivity. In the coming years, continued research and the improvement of liquid biopsy techniques will be key to the implementation of ctDNA analysis in routine clinical practice.
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Affiliation(s)
- Marta Sant
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
| | - Adrià Bernat-Peguera
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eudald Felip
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Mireia Margelí
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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Aberrant Methylation of SLIT2 Gene in Plasma Cell-Free DNA of Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2022; 14:cancers14020296. [PMID: 35053460 PMCID: PMC8773699 DOI: 10.3390/cancers14020296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Despite significant advances in the detection, prevention, and treatment of lung cancer, the prognosis of the patients is still very poor due in part to micrometastasis of cancer cells to surrounding tissues at the time of diagnosis. Therefore, identifying biomarkers for early detection of lung cancer is very important for prolonging the lifespan of patients with lung cancer. The methylation statuses of SLIT1, SLIT2, SLIT3 genes were analyzed in bronchial washing, bronchial biopsy, sputum, tumor and matched normal tissues, or plasma samples obtained from a total of 208 non-small cell lung cancer (NSCLC) patients and 121 cancer-free patients to understand the feasibility of the genes as biomarkers for early detection and survival prediction of NSCLC. The present study suggests that aberrant methylation of SLIT2 in plasma cell-free DNA might be a potential biomarker for the early detection and prognosis prediction of NSCLC patient. Abstract This study aimed to understand aberrant methylation of SLITs genes as a biomarker for the early detection and prognosis prediction of non-small cell lung cancer (NSCLC). Methylation levels of SLITs were determined using the Infinium HumanMethylation450 BeadChip or pyrosequencing. Five CpGs at the CpG island of SLIT1, SLIT2 or SLIT3 genes were significantly (Bonferroni corrected p < 0.05) hypermethylated in tumor tissues obtained from 42 NSCLC patients than in matched normal tissues. Methylation levels of these CpGs did not differ significantly between bronchial washings obtained from 76 NSCLC patients and 60 cancer-free patients. However, methylation levels of SLIT2 gene were significantly higher in plasma cell-free DNA of 72 NSCLC patients than in that of 61 cancer-free patients (p = 0.001, Wilcoxon rank sum test). Prediction of NSCLC using SLIT2 methylation was achieved with a sensitivity of 73.7% and a specificity of 61.9% in a plasma test dataset (N = 40). A Cox proportional hazards model showed that SLIT2 hypermethylation in plasma cell-free DNA was significantly associated with poor recurrence-free survival (hazards ratio = 2.19, 95% confidence interval = 1.21–4.36, p = 0.01). The present study suggests that aberrant methylation of SLIT2 in plasma cell-free DNA is a valuable biomarker for the early detection of NSCLC and prediction of recurrence-free survival. However, further research is needed with larger sample size to confirm results.
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Chan JA, Vercauteren SM. Processing and Cryopreservation of Blood, Cancer Tissues, and Cancer Cells for Viable Biobanking. Methods Mol Biol 2022; 2508:45-58. [PMID: 35737232 DOI: 10.1007/978-1-0716-2376-3_5] [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] [Indexed: 06/15/2023]
Abstract
Biorepositories of fresh frozen and formalin-fixed paraffin-embedded tissues have been foundational to many molecular cancer research studies. Collections of these materials, however, do not enable the establishment of short-term cultures, cell lines, or patient-derived xenograft models for functional studies. Also, intact dissociated cells that are required for some single-cell analyses cannot be obtained from these material types. Adding viable tumor banking to the repertoire of routine cancer biobanking would increase the value of samples collected. This chapter outlines procedures for processing and storing blood and tissue specimens viably in order to expand the future utility of the samples collected. We provide practical tips that can be used by banks and other researchers seeking to incorporate the cryopreservation of viable materials as part of their overall biobanking strategies.
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Affiliation(s)
- Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada.
| | - Suzanne M Vercauteren
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, BC, Canada
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Wan JCM, Mughal TI, Razavi P, Dawson SJ, Moss EL, Govindan R, Tan IB, Yap YS, Robinson WA, Morris CD, Besse B, Bardelli A, Tie J, Kopetz S, Rosenfeld N. Liquid biopsies for residual disease and recurrence. MED 2021; 2:1292-1313. [PMID: 35590147 DOI: 10.1016/j.medj.2021.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/27/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Detection of minimal residual disease in patients with cancer, who are in complete remission with no cancer cells detectable, has the potential to improve recurrence-free survival through treatment selection. Studies analyzing circulating tumor DNA (ctDNA) in patients with solid tumors suggest the potential to accurately predict and detect relapse, enabling treatment strategies that may improve clinical outcomes. Over the past decade, assays for ctDNA detection in plasma samples have steadily increased in sensitivity and specificity. These are applied for the detection of residual disease after treatment and for earlier detection of recurrence. Novel clinical trials are now assessing how assays for "residual disease and recurrence" (RDR) may influence current treatment paradigms and potentially change the landscape of risk classification for cancer recurrence. In this review, we appraise the progress of RDR detection using ctDNA and consider the emerging role of liquid biopsy in the monitoring and management of solid tumors.
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Affiliation(s)
| | - Tariq Imdadali Mughal
- Tufts University School of Medicine, Boston, MA 02111, USA; University of Buckingham, Buckingham MK18 1EG, UK
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Esther Louise Moss
- Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, Leicester LE1 7RH, UK; Department of Gynaecological Oncology, University Hospitals of Leicester NHS Trust, Leicester General Hospital, Leicester LE5 4PW, UK
| | | | - Iain Beehuat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 169610 Singapore, Singapore
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 169610 Singapore, Singapore
| | | | | | - Benjamin Besse
- Department of Cancer Medicine, Institut Gustave Roussy Cancer Center, 94805 Villejuif, France
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo TO, Italy; Department of Oncology, University of Turin, 10060 Candiolo TO, Italy
| | - Jeanne Tie
- Peter MacCallum Cancer Center, Melbourne, VIC 3000, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Scott Kopetz
- MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nitzan Rosenfeld
- Inivata, Cambridge CB22 3FH, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK.
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29
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Fox-Fisher I, Piyanzin S, Ochana BL, Klochendler A, Magenheim J, Peretz A, Loyfer N, Moss J, Cohen D, Drori Y, Friedman N, Mandelboim M, Rothenberg ME, Caldwell JM, Rochman M, Jamshidi A, Cann G, Lavi D, Kaplan T, Glaser B, Shemer R, Dor Y. Remote immune processes revealed by immune-derived circulating cell-free DNA. eLife 2021; 10:70520. [PMID: 34842142 PMCID: PMC8651286 DOI: 10.7554/elife.70520] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/24/2021] [Indexed: 01/08/2023] Open
Abstract
Blood cell counts often fail to report on immune processes occurring in remote tissues. Here, we use immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying human immune cell dynamics. We characterized cfDNA released from specific immune cell types in healthy individuals (N = 242), cross sectionally and longitudinally. Immune cfDNA levels had no individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza vaccination (N = 92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and predicted efficacy of antibody production. Patients with eosinophilic esophagitis (N = 21) and B-cell lymphoma (N = 27) showed selective elevation of eosinophil and B-cell cfDNA, respectively, which were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for monitoring immune responses to physiological and pathological processes that are not accessible using conventional methods.
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Affiliation(s)
- Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Bracha Lea Ochana
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Cohen
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yaron Drori
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Nehemya Friedman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | - Julie M Caldwell
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | | | | | - David Lavi
- Department of Hematology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Developmental Biology and Cancer Research, The Institute for Medical Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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Till JE, Black TA, Gentile C, Abdalla A, Wang Z, Sangha HK, Roth JJ, Sussman R, Yee SS, O'Hara MH, Thompson JC, Aggarwal C, Hwang WT, Elenitoba-Johnson KSJ, Carpenter EL. Optimization of Sources of Circulating Cell-Free DNA Variability for Downstream Molecular Analysis. J Mol Diagn 2021; 23:1545-1552. [PMID: 34454115 DOI: 10.1016/j.jmoldx.2021.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 06/10/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
Circulating cell-free DNA (ccfDNA) is used increasingly as a cancer biomarker for prognostication, as a correlate for tumor volume, or as input for downstream molecular analysis. Determining optimal blood processing and ccfDNA quantification are crucial for ccfDNA to serve as an accurate biomarker as it moves into the clinical realm. Whole blood was collected from 50 subjects, processed to plasma, and used immediately or frozen at -80°C. Plasma ccfDNA was extracted and concentration was assessed by real-time quantitative PCR (qPCR), fluorimetry, and droplet digital PCR (ddPCR). For the 24 plasma samples from metastatic pancreatic cancer patients, the variant allele fractions (VAF) of KRAS G12/13 pathogenic variants in circulating tumor DNA (ctDNA) were measured by ddPCR. Using a high-speed (16,000 × g) or slower-speed (4100 × g) second centrifugation step showed no difference in ccfDNA yield or ctDNA VAF. A two- versus three-spin centrifugation protocol also showed no difference in ccfDNA yield or ctDNA VAF. A higher yield was observed from fresh versus frozen plasma by qPCR and fluorimetry, whereas a higher yield was observed for frozen versus fresh plasma by ddPCR, however, no difference was observed in ctDNA VAF. Overall, our findings suggest factors to consider when implementing a ccfDNA extraction and quantification workflow in a research or clinical setting.
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Affiliation(s)
- Jacob E Till
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor A Black
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Caren Gentile
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aseel Abdalla
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhuoyang Wang
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hareena K Sangha
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacquelyn J Roth
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robyn Sussman
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark H O'Hara
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey C Thompson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charu Aggarwal
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kojo S J Elenitoba-Johnson
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Dama E, Colangelo T, Fina E, Cremonesi M, Kallikourdis M, Veronesi G, Bianchi F. Biomarkers and Lung Cancer Early Detection: State of the Art. Cancers (Basel) 2021; 13:cancers13153919. [PMID: 34359818 PMCID: PMC8345487 DOI: 10.3390/cancers13153919] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Lung cancer is the leading cause of cancer death worldwide. Detecting lung malignancies promptly is essential for any anticancer treatment to reduce mortality and morbidity, especially in high-risk individuals. The use of liquid biopsy to detect circulating biomarkers such as RNA, microRNA, DNA, proteins, autoantibodies in the blood, as well as circulating tumor cells (CTCs), can substantially change the way we manage lung cancer patients by improving disease stratification using intrinsic molecular characteristics, identification of therapeutic targets and monitoring molecular residual disease. Here, we made an update on recent developments in liquid biopsy-based biomarkers for lung cancer early diagnosis, and we propose guidelines for an accurate study design, execution, and data interpretation for biomarker development. Abstract Lung cancer burden is increasing, with 2 million deaths/year worldwide. Current limitations in early detection impede lung cancer diagnosis when the disease is still localized and thus more curable by surgery or multimodality treatment. Liquid biopsy is emerging as an important tool for lung cancer early detection and for monitoring therapy response. Here, we reviewed recent advances in liquid biopsy for early diagnosis of lung cancer. We summarized DNA- or RNA-based biomarkers, proteins, autoantibodies circulating in the blood, as well as circulating tumor cells (CTCs), and compared the most promising studies in terms of biomarkers prediction performance. While we observed an overall good performance for the proposed biomarkers, we noticed some critical aspects which may complicate the successful translation of these biomarkers into the clinical setting. We, therefore, proposed a roadmap for successful development of lung cancer biomarkers during the discovery, prioritization, and clinical validation phase. The integration of innovative minimally invasive biomarkers in screening programs is highly demanded to augment lung cancer early detection.
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Affiliation(s)
- Elisa Dama
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.); (T.C.)
| | - Tommaso Colangelo
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.); (T.C.)
| | - Emanuela Fina
- Humanitas Research Center, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy;
| | - Marco Cremonesi
- Adaptive Immunity Laboratory, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy; (M.C.); (M.K.)
| | - Marinos Kallikourdis
- Adaptive Immunity Laboratory, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy; (M.C.); (M.K.)
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy
| | - Giulia Veronesi
- Division of Thoracic Surgery, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Fabrizio Bianchi
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.); (T.C.)
- Correspondence: ; Tel.: +39-08-8241-0954; Fax: +39-08-8220-4004
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Tsui DWY, Cheng ML, Shady M, Yang JL, Stephens D, Won H, Srinivasan P, Huberman K, Meng F, Jing X, Patel J, Hasan M, Johnson I, Gedvilaite E, Houck-Loomis B, Socci ND, Selcuklu SD, Seshan VE, Zhang H, Chakravarty D, Zehir A, Benayed R, Arcila M, Ladanyi M, Funt SA, Feldman DR, Li BT, Razavi P, Rosenberg J, Bajorin D, Iyer G, Abida W, Scher HI, Rathkopf D, Viale A, Berger MF, Solit DB. Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients. Genome Med 2021; 13:96. [PMID: 34059130 PMCID: PMC8165771 DOI: 10.1186/s13073-021-00898-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth. METHODS Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES). RESULTS cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches. CONCLUSIONS cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
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Affiliation(s)
- Dana W Y Tsui
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Weill Cornell Medical College, Weill Cornell University, New York, USA.
- Present Address: PetDx, Inc., La Jolla, USA.
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
- Present Address: Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Maha Shady
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: Graduate School of Arts and Sciences, Harvard University, Cambridge, USA
| | - Julie L Yang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dennis Stephens
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Xiaohong Jing
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: NYU Langone Health, New York, USA
| | - Juber Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maysun Hasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Brian Houck-Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Samuel A Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jonathan Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dean Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Cornell Medical College, Weill Cornell University, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
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Cimadamore A, Cheng L, Massari F, Santoni M, Pepi L, Franzese C, Scarpelli M, Lopez-Beltran A, Galosi AB, Montironi R. Circulating Tumor DNA Testing for Homology Recombination Repair Genes in Prostate Cancer: From the Lab to the Clinic. Int J Mol Sci 2021; 22:5522. [PMID: 34073818 PMCID: PMC8197269 DOI: 10.3390/ijms22115522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022] Open
Abstract
Approximately 23% of metastatic castration-resistant prostate cancers (mCRPC) harbor deleterious aberrations in DNA repair genes. Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) therapy has shown improvements in overall survival in patients with mCRPC who harbor somatic and/or germline alterations of homology recombination repair (HRR) genes. Peripheral blood samples are typically used for the germline mutation analysis test using the DNA extracted from peripheral blood leucocytes. Somatic alterations can be assessed by extracting DNA from a tumor tissue sample or using circulating tumor DNA (ctDNA) extracted from a plasma sample. Each of these genetic tests has its own benefits and limitations. The main advantages compared to the tissue test are that liquid biopsy is a non-invasive and easily repeatable test with the value of better representing tumor heterogeneity than primary biopsy and of capturing changes and/or resistance mutations in the genetic tumor profile during disease progression. Furthermore, ctDNA can inform about mutation status and guide treatment options in patients with mCRPC. Clinical validation and test implementation into routine clinical practice are currently very limited. In this review, we discuss the state of the art of the ctDNA test in prostate cancer compared to blood and tissue testing. We also illustrate the ctDNA testing workflow, the available techniques for ctDNA extraction, sequencing, and analysis, describing advantages and limits of each techniques.
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Affiliation(s)
- Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
| | - Francesco Massari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy;
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Laura Pepi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Carmine Franzese
- Department of Specialist Clinical Science and Odontostomatology, Urology Division, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (C.F.); (A.B.G.)
| | - Marina Scarpelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Antonio Lopez-Beltran
- Department of Morphological Sciences, Cordoba University Medical School, 14071 Cordoba, Spain;
| | - Andrea Benedetto Galosi
- Department of Specialist Clinical Science and Odontostomatology, Urology Division, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (C.F.); (A.B.G.)
| | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
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35
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Morshneva A, Kozyulina P, Vashukova E, Tarasenko O, Dvoynova N, Chentsova A, Talantova O, Koroteev A, Ivanov D, Serebryakova E, Ivashchenko T, Sukhomyasova A, Maksimova N, Bespalova O, Kogan I, Baranov V, Glotov A. Pilot Screening of Cell-Free mtDNA in NIPT: Quality Control, Variant Calling, and Haplogroup Determination. Genes (Basel) 2021; 12:743. [PMID: 34069212 PMCID: PMC8156457 DOI: 10.3390/genes12050743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/31/2022] Open
Abstract
Clinical tests based on whole-genome sequencing are generally focused on a single task approach, testing one or several parameters, although whole-genome sequencing (WGS) provides us with large data sets that can be used for many supportive analyses. In spite of low genome coverage, data of WGS-based non-invasive prenatal testing (NIPT) contain fully sequenced mitochondrial DNA (mtDNA). This mtDNA can be used for variant calling, ancestry analysis, population studies and other approaches that extend NIPT functionality. In this study, we analyse mtDNA pool from 645 cell-free DNA (cfDNA) samples of pregnant women from different regions of Russia, explore the effects of transportation and storing conditions on mtDNA content, analyse effects, frequency and location of mitochondrial variants called from samples and perform haplogroup analysis, revealing the most common mitochondrial superclades. We have shown that, despite the relatively low sequencing depth of unamplified mtDNA from cfDNA samples, the mtDNA analysis in these samples is still an informative instrument suitable for research and screening purposes.
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Affiliation(s)
- Alisa Morshneva
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
| | - Polina Kozyulina
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
| | - Elena Vashukova
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
| | - Olga Tarasenko
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
| | - Natalia Dvoynova
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
| | - Anastasia Chentsova
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
| | - Olga Talantova
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
| | - Alexander Koroteev
- St. Petersburg State Pediatric Medical University, 2 Litovskaya Street, 194100 St. Petersburg, Russia; (A.K.); (D.I.)
- Center for Medical Genetics, Tobolskaya ul. 5, 194044 St. Petersburg, Russia
| | - Dmitrii Ivanov
- St. Petersburg State Pediatric Medical University, 2 Litovskaya Street, 194100 St. Petersburg, Russia; (A.K.); (D.I.)
| | - Elena Serebryakova
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
| | - Tatyana Ivashchenko
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
| | - Aitalina Sukhomyasova
- Molecular Medicine and Human Genetics, Research Laboratory, Medical Institute, M.K. Ammosov North-Eastern Federal University, 677007 Yakutsk, Russia;
- Republican Hospital No. 1, National Medical Centre, Ministry of Public Health of the Sakha Republic, 677008 Yakutsk, Russia;
| | - Nadezhda Maksimova
- Republican Hospital No. 1, National Medical Centre, Ministry of Public Health of the Sakha Republic, 677008 Yakutsk, Russia;
| | - Olesya Bespalova
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
| | - Igor Kogan
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
| | - Vladislav Baranov
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
| | - Andrey Glotov
- D.O. Ott Research Institute for Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (P.K.); (E.V.); (O.T.); (O.T.); (E.S.); (T.I.); (O.B.); (I.K.); (V.B.); (A.G.)
- Ltd NIPT, Bolshoi V.O. 90, Building 2 lit. 3, 199106 St. Petersburg, Russia; (N.D.); (A.C.)
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Liu H, Gao Y, Vafaei S, Gu X, Zhong X. The Prognostic Value of Plasma Cell-Free DNA Concentration in the Prostate Cancer: A Systematic Review and Meta-Analysis. Front Oncol 2021; 11:599602. [PMID: 33777743 PMCID: PMC7991303 DOI: 10.3389/fonc.2021.599602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/25/2021] [Indexed: 12/20/2022] Open
Abstract
Objective By virtue of largely disparate clinical outcomes of prostate cancer (PCA), there is a pressing need to search for useful biomarkers for PCA prognosis. Cell-free DNA (cfDNA) is a promising biomarker for detecting, monitoring, and predicting survival of prostate cancer (PCA). However, the utility of total cfDNA quantitation in PCA in clinical setting remains elusive. Here, we performed a thorough meta-analysis to assess the prognostic value of cfDNA concentration for patients with PCA. In addition, we tested the possibility of the combination of PSA and cfDNA test results to improve the prediction power in PCA prognosis. Method and Materials More than six databases, including PubMed, Web of Science, Medline, PMC, EMBASE and the Cochrane Library were searched. Results yielded all eligible articles from the date of inception to June 30, 2020. Continuous, diagnostic, and prognostic variables in cfDNA in PCA were included in the meta-analysis by STATA. Results A total of 23 articles were enrolled in our meta-analysis: 69.6% (16/23) were related to diagnosis, and 56.5% (13/23) were related to prognosis. The pooled concentration of cfDNA in PCA patients was significantly higher than in the control group (SMD = 0.89, 95%CI = 0.53, 1.26), mirroring results for the prostate-specific antigen (PSA). For the detection test variables, the SROC with 95%CI was 0.87 (0.84–0.90) for cfDNA concentration. In terms of prognostic variables, the concentrations of cfDNA were significantly related with progression-free survival (PFS, logHR = 0.84 (95%CI0.39, 1.28) and overall survival [OS, log HR = 0.60 (95%CI0.29, 0.90)]. Lastly, the test showed no significant publication bias in the present meta-analysis, excluding the diagnostic meta-analysis. Conclusions The concentration of cell-free DNA is high in the prostate cancer patients. The present study substantiates the prognostic value of the cfDNA concentration. High concentration cfDNA correlates with poor disease outcome of CRPC. The study cohort with large sample size is needed to evaluate the prognosis value of cfDNA in the future. We also emphasized that combination of PSA and cf DNA quantitation is important in future large individual meta study.
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Affiliation(s)
- Hongtao Liu
- Department of Graduate School, Dalian Medical University, Dalian City, China.,Department of Urology, Northern Jiangsu Hospital, Yangzhou University Clinical College, Yangzhou, China
| | - Yuzhen Gao
- Department of Molecular Diagnosis, Northern Jiangsu Hospital, Yangzhou University Clinical College, Yangzhou, China
| | - Somayeh Vafaei
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Xiao Gu
- Department of Urology, Northern Jiangsu Hospital, Yangzhou University Clinical College, Yangzhou, China.,Clinical Medical College, Yangzhou University, Yangzhou City, China
| | - Xiaoli Zhong
- Department of Molecular Diagnosis, Northern Jiangsu Hospital, Yangzhou University Clinical College, Yangzhou, China.,Clinical Medical College, Yangzhou University, Yangzhou City, China
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37
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Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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38
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Cell-free DNA Oncogene Copy Number as a Surrogate Molecular Biomarker in ALK/MYCN-coamplified Neuroblastoma. J Pediatr Hematol Oncol 2021; 43:e165-e168. [PMID: 32032241 DOI: 10.1097/mph.0000000000001720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/28/2019] [Indexed: 12/28/2022]
Abstract
Secondary expansion and/or evolution of aggressive subclones are associated with the disease progression and resistance to chemotherapy in neuroblastoma, and it is important to track the clonal changes during the treatment period. Cell-free (cf) DNA analysis, namely liquid biopsy, can detect the genomic change of tumor cells without surgical procedures. In this report, we showed that serial polymerase chain reaction-based cf DNA neuroblastoma proto-oncogene quantification is sensitive enough to evaluate the aggressive cellular characteristics of ALK/MYCN-coamplified neuroblastoma and stressed the promise of cf DNA analyses as a reliable molecular marker in advanced neuroblastoma.
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39
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Sivapalan L, Kocher H, Ross-Adams H, Chelala C. Molecular profiling of ctDNA in pancreatic cancer: Opportunities and challenges for clinical application. Pancreatology 2021; 21:363-378. [PMID: 33451936 PMCID: PMC7994018 DOI: 10.1016/j.pan.2020.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related mortality within the next decade, with limited effective treatment options and a dismal long-term prognosis for patients. Genomic profiling has not yet manifested clinical benefits for diagnosis, treatment or prognosis in PDAC, due to the lack of available tissues for sequencing and the confounding effects of low tumour cellularity in many biopsy specimens. Increasing focus is now turning to the use of minimally invasive liquid biopsies to enhance the characterisation of actionable PDAC tumour genomes. Circulating tumour DNA (ctDNA) is the most comprehensively studied liquid biopsy analyte in blood and can provide insight into the molecular profile and biological characteristics of individual PDAC tumours, in real-time and in advance of traditional imaging modalities. This can pave the way for identification of new therapeutic targets, novel risk variants and markers of tumour response, to supplement diagnostic screening and provide enhanced scrutiny in treatment stratification. In the roadmap towards the application of precision medicine for clinical management in PDAC, ctDNA analyses may serve a leading role in streamlining candidate biomarkers for clinical integration. In this review, we highlight recent developments in the use of ctDNA-based liquid biopsies for PDAC and provide new insights into the technical, analytical and biological challenges that must be overcome for this potential to be realised.
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Affiliation(s)
- L. Sivapalan
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - H.M. Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - H. Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - C. Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK,Corresponding author.
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Lim JK, Kuss B, Talaulikar D. Role of cell-free DNA in haematological malignancies. Pathology 2021; 53:416-426. [PMID: 33648721 DOI: 10.1016/j.pathol.2021.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/17/2021] [Indexed: 12/13/2022]
Abstract
Cell-free DNA (cfDNA) consists of fragments of double stranded DNA that are found in the circulation. They are released from the apoptosis of both normal haemopoietic cells and malignant cells. The use of cfDNA from easily accessible peripheral blood samples has created a new strategy in studying molecular genomics in haematological malignancies. Its use in diagnosis, prognosis and monitoring potentially precludes the need for repeated tissue samples, i.e., bone marrow biopsy or primary tissue biopsy. It also potentially provides a more comprehensive analysis of the disease as cfDNA are released from tumours from multiple sites of the body. While cfDNA research is still in its infancy, given its potential and the expansion in next generation sequencing (NGS) it has attracted a lot of attention in recent years. This review will focus on acute leukaemia, multiple myeloma and lymphoma and the potential diagnostic and prognostic implications of cfDNA, its role in response assessment and in detection of disease relapse.
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Affiliation(s)
- Jun K Lim
- Department of Haematology, The Canberra Hospital, Canberra, ACT, Australia
| | - Bryone Kuss
- Department of Molecular Medicine and Genetics, Flinders University/Flinders Medical Centre, SA Pathology Laboratories, Adelaide, SA, Australia
| | - Dipti Talaulikar
- Department of Haematology, The Canberra Hospital, Canberra, ACT, Australia; College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
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Sorber L, Zwaenepoel K, Jacobs J, De Winne K, Van Casteren K, Augustus E, Lardon F, Prenen H, Peeters M, Van Meerbeeck J, Roeyen G, Rolfo C, Pauwels P. Specialized Blood Collection Tubes for Liquid Biopsy: Improving the Pre-analytical Conditions. Mol Diagn Ther 2021; 24:113-124. [PMID: 31838654 DOI: 10.1007/s40291-019-00442-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The potential of circulating cell-free DNA (cfDNA) analysis as a liquid biopsy has led to the development of several specialized measuring tools. Interest in the (pre-)analytical conditions of the liquid biopsy workflow has increased over the past few years. METHODS In this study, we performed a systematic review of the cfDNA stabilizing efficacy in standard EDTA and specialized blood collection tubes (BCTs), namely CellSave, Norgen, PAXgene, Roche, and Streck tubes, and compared the efficacy of the latter three BCTs in a situation resembling the clinical setting. Blood samples were collected from ten KRAS-mutated metastatic cancer patients and stored for 72 h. During this time, samples were shaken and kept at either 6 °C or at room temperature for 24 h to mimic transport. RESULTS We demonstrated that while cfDNA levels in EDTA tubes are only stable for a couple of (≤ 6) hours, they could be sustained for at least 48-72 h in all three specialized BCTs, irrespective of temperature. This timespan enables a fast turnaround time, which is one of the advantages of liquid biopsy. CONCLUSIONS The choice between these specialized BCTs is less vital when they are processed correctly within a few days.
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Affiliation(s)
- Laure Sorber
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium. .,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium.
| | - Karen Zwaenepoel
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Julie Jacobs
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Koen De Winne
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Kaat Van Casteren
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium.,Biomedical Quality Assurance Research Unit, KU Leuven (KUL), 3000, Louvain, Belgium
| | - Elien Augustus
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Filip Lardon
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Hans Prenen
- Clinical Trials Unit, Department of Oncology and Phase 1, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Marc Peeters
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Department of Oncology, Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Jan Van Meerbeeck
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Department of Pulmonology and Thoracic Oncology, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Geert Roeyen
- Hepatobiliary Transplantation and Endocrine Surgery, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Christian Rolfo
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Thoracic Medical Oncology and Early Clinical Trials, Marlene and Steward Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 21201, Baltimore, MD, USA
| | - Patrick Pauwels
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium.,Biobank UZA/UAntwerpen, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
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Kahana-Edwin S, Cain LE, Karpelowsky J. Roadmap to Liquid Biopsy Biobanking from Pediatric Cancers-Challenges and Opportunities. Biopreserv Biobank 2021; 19:124-129. [PMID: 33493007 DOI: 10.1089/bio.2020.0117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is rapidly gaining traction for potentially revolutionizing cancer diagnosis and treatment through blood-based utilization of shed biomolecules. This approach can provide a global picture of the cancer in real time, at multiple time points, and with minimal invasiveness. In this review, we familiarize cancer biobanks with the principles used for liquid biopsy work and highlight unique aspects of applying liquid biopsy approaches to pediatric cancers to enable high-quality and efficient translational research.
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Affiliation(s)
- Smadar Kahana-Edwin
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | - Lucy E Cain
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | - Jonathan Karpelowsky
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
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Doludin YV, Limonova AS, Kozlova VA, Efimova AI, Borisova AL, Meshkov AN, Pokrovskaya MS, Drapkina OM. Collection and storage of DNA-containing biomaterial and isolated DNA. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2020. [DOI: 10.15829/1728-8800-2020-2730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advances of biomedicine include the new technologies, diagnosis and treatment techniques, as well as the practical use of new types of biological targets, in particular, nucleic acids. Genomic deoxyribonucleic acid (DNA), extracellular DNA (exDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. The use of new technologies for DNA analysis required the development of standardized methods for processing biological samples in order to obtain high-quality DNA samples. The research uses various methods for collecting, preparing samples and storing various DNA-containing biomaterials and isolated DNA, as well as methods for assessing the quality of samples and biobank standards. It is obvious that the use of uniform standards will allow large-scale genetic research on the basis of biobanks and research laboratories. Specialists from professional organizations such as International Society for Biological and Environmental Repositories (ISBER), Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), European, Middle Eastern & African Society for Biopreservationa and Biobanking (ESBB) and the Russian National Association of Biobanks and Biobanking Professionals.
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Affiliation(s)
- Yu. V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - V. A. Kozlova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. I. Efimova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Jaworski JJ, Morgan RD, Sivakumar S. Circulating Cell-Free Tumour DNA for Early Detection of Pancreatic Cancer. Cancers (Basel) 2020; 12:E3704. [PMID: 33317202 PMCID: PMC7763954 DOI: 10.3390/cancers12123704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/04/2020] [Indexed: 01/11/2023] Open
Abstract
Pancreatic cancer is a lethal disease, with mortality rates negatively associated with the stage at which the disease is detected. Early detection is therefore critical to improving survival outcomes. A recent focus of research for early detection is the use of circulating cell-free tumour DNA (ctDNA). The detection of ctDNA offers potential as a relatively non-invasive method of diagnosing pancreatic cancer by using genetic sequencing technology to detect tumour-specific mutational signatures in blood samples before symptoms manifest. These technologies are limited by a number of factors that lower sensitivity and specificity, including low levels of detectable ctDNA in early stage disease and contamination with non-cancer circulating cell-free DNA. However, genetic and epigenetic analysis of ctDNA in combination with other standard diagnostic tests may improve early detection rates. In this review, we evaluate the genetic and epigenetic methods under investigation in diagnosing pancreatic cancer and provide a perspective for future developments.
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Affiliation(s)
- Jedrzej J. Jaworski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK;
| | - Robert D. Morgan
- Department of Medical Oncology, Christie NHS Foundation Trust, Manchester M20 4BX, UK;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Shivan Sivakumar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Department of Medical Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
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Taylor C, Chacko S, Davey M, Lacroix J, MacPherson A, Finn N, Wajnberg G, Ghosh A, Crapoulet N, Lewis SM, Ouellette RJ. Peptide-Affinity Precipitation of Extracellular Vesicles and Cell-Free DNA Improves Sequencing Performance for the Detection of Pathogenic Mutations in Lung Cancer Patient Plasma. Int J Mol Sci 2020; 21:E9083. [PMID: 33260345 PMCID: PMC7730179 DOI: 10.3390/ijms21239083] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is a minimally-invasive diagnostic method that may improve access to molecular profiling for non-small cell lung cancer (NSCLC) patients. Although cell-free DNA (cf-DNA) isolation from plasma is the standard liquid biopsy method for detecting DNA mutations in cancer patients, the sensitivity can be highly variable. Vn96 is a peptide with an affinity for both extracellular vesicles (EVs) and circulating cf-DNA. In this study, we evaluated whether peptide-affinity (PA) precipitation of EVs and cf-DNA from NSCLC patient plasma improves the sensitivity of single nucleotide variants (SNVs) detection and compared observed SNVs with those reported in the matched tissue biopsy. NSCLC patient plasma was subjected to either PA precipitation or cell-free methods and total nucleic acid (TNA) was extracted; SNVs were then detected by next-generation sequencing (NGS). PA led to increased recovery of DNA as well as an improvement in NGS sequencing parameters when compared to cf-TNA. Reduced concordance with tissue was observed in PA-TNA (62%) compared to cf-TNA (81%), mainly due to identification of SNVs in PA-TNA that were not observed in tissue. EGFR mutations were detected in PA-TNA with 83% sensitivity and 100% specificity. In conclusion, PA-TNA may improve the detection limits of low-abundance alleles using NGS.
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Affiliation(s)
- Catherine Taylor
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Michelle Davey
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Jacynthe Lacroix
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Alexander MacPherson
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Nicholas Finn
- Dr Léon-Richard Oncology Center, Moncton, NB E1C 8X3, Canada;
| | - Gabriel Wajnberg
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Anirban Ghosh
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Nicolas Crapoulet
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Stephen M. Lewis
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
- Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Rodney J. Ouellette
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
- Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada
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Exploration of cell-free DNA (cfDNA) recovery for touch deposits. Forensic Sci Int Genet 2020; 51:102431. [PMID: 33260058 DOI: 10.1016/j.fsigen.2020.102431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/15/2022]
Abstract
Although touch deposit DNA is widely used in forensic casework, its cellular and acellular contents and their biological origins are poorly understood. There is evidence that the cell-free component of DNA deposited by handling may contribute substantial genetic information; however, most research into touch DNA recovery does not separate cellular and cell-free fractions or seek to characterize their contents. This work is an important early step in developing methods to isolate the cfDNA from biological material deposited by handling. Size-filtration as a separation technique was determined to be prone to DNA loss, even on optimized control samples of pure ladder DNA. Centrifugal separation was optimized to determine minimum speed and time required to reliably remove all cellular debris from the material collected by rinsing donor hands. To determine if the centrifugal force risked rupturing shed corneocyte cells and releasing cellular DNA into the supernatant, DNA levels were measured, and cells were visualized microscopically before and after centrifugation of hand rinses. Heated buccal cells were used as a positive control to demonstrate cell rupture would be detected with these methods. Following the determination of a suitable separation technique, an investigation into purification methods for cfDNA was conducted. DNA recovery using three kits for plasma cfDNA, one for PCR clean-up and one for genomic DNA were assessed on both ladder DNA to simulate cfDNA fragments and on collected hand deposit supernatants from both unwashed and washed hands. Purification methods designed for recovery of short DNA fragments from plasma yielded the highest recovery percentage across sample types, with BioChain cfPure performing the best. Donors' hands were shown to shed high levels of cfDNA, which were better recovered with a method for short fragments than with a traditional genomic technique often used on touch DNA samples.
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Cecchini MJ, Yi ES. Liquid biopsy is a valuable tool in the diagnosis and management of lung cancer. J Thorac Dis 2020; 12:7048-7056. [PMID: 33282410 PMCID: PMC7711358 DOI: 10.21037/jtd.2020.04.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the use of various body fluids to test for circulating biological elements derived from the tumor. Liquid biopsy has taken on an increasingly important role in lung cancer diagnosis, molecular characterization, surveillance, monitoring, and determining mechanisms of resistance. These assays can utilize various sources of cell-free DNA (cfDNA) including blood, pleural fluid, urine, and others to detect tumor associated alterations. With the increasing power of next-generation sequencing technologies and the development of assays such as digital droplet PCR, rare tumor alleles can be detected in cfDNA to determine key characteristics of the tumor. Current assays, while effective, are still challenged by limited sensitivity and capacity to single genes or small panels of genes, though this is rapidly expanding. Nevertheless, testing of cfDNA has been shown to be valuable in detecting resistance to targeted inhibitors, particularly for detection of T790M in EGFR and monitoring response to therapy. With the continued development of more powerful and sensitive assays, these techniques will empower clinicians to better characterize early stage disease and can be used in the screening of high-risk patients, which may eliminate the requirement for tissue diagnosis in some settings. That said, since the majority of these alterations are not specific to lung cancer, there will continue to be a need for tissue in at least the initial diagnosis. Used in conjugation with tissue sampling, these assays will assist the treating clinician and the pathologist to better characterize individual tumors, even in the setting of limited tissue.
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Affiliation(s)
- Matthew J Cecchini
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
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Garcia-Gisbert N, Fernández-Ibarrondo L, Fernández-Rodríguez C, Gibert J, Andrade-Campos M, Arenillas L, Camacho L, Angona A, Longarón R, Salar A, Calvo X, Besses C, Bellosillo B. Circulating cell-free DNA improves the molecular characterisation of Ph-negative myeloproliferative neoplasms. Br J Haematol 2020; 192:300-309. [PMID: 32945548 DOI: 10.1111/bjh.17087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022]
Abstract
Genetic studies in patients with Philadelphia-negative myeloproliferative neoplasms (MPNs) are essential to establish the correct diagnosis and to optimise their management. Recently, it has been demonstrated that it is possible to detect molecular alterations analysing cell-free DNA (cfDNA) in plasma samples, which is known as liquid biopsy. We have assessed the molecular profile of a cohort of 107 MPN patients [33 polycythaemia vera (PV), 56 essential thrombocythaemia (ET), 14 primary myelofibrosis (PMF) and 4 unclassifiable MPN] by next-generation sequencing (NGS) using cfDNA and paired granulocyte DNA. A high concentration of cfDNA in plasma was observed in patients with high molecular complexity, in MPL-mutated cases, and in PMF patients. Targeted sequencing of cfDNA showed a comparable mutational profile (100% accuracy) to the one obtained in granulocytic DNA and a strong correlation was observed between the variant allele frequency (VAF) of gene mutations in both DNA sources. The median VAF detected in cfDNA (29·0%; range: 0·95-91·73%) was significantly higher than the VAF detected in granulocytes (median 25·2%; range: 0·10-95·5%), especially for MPL mutations (44·3% vs. 22·5%). In conclusion, our data support the use of cfDNA as a fast, sensitive and accurate strategy for performing molecular characterisation of MPN patients.
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Affiliation(s)
- Nieves Garcia-Gisbert
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Pompeu Fabra University, Barcelona, Spain
| | - Lierni Fernández-Ibarrondo
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Pompeu Fabra University, Barcelona, Spain
| | - Concepcion Fernández-Rodríguez
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Joan Gibert
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Marcio Andrade-Campos
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Leonor Arenillas
- Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Laura Camacho
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Anna Angona
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Raquel Longarón
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Antonio Salar
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Xavier Calvo
- Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Carlos Besses
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Beatriz Bellosillo
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Pompeu Fabra University, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
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