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Tolmeijer SH, Boerrigter E, Van Erp NP, Mehra N. Using early on-treatment circulating tumor DNA measurements as response assessment in metastatic castration resistant prostate cancer. Oncotarget 2024; 15:421-423. [PMID: 38953903 DOI: 10.18632/oncotarget.28599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
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2
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Magbanua MJM, Ahmed Z, Sayaman RW, Brown Swigart L, Hirst GL, Yau C, Wolf DM, Li W, Delson AL, Perlmutter J, Pohlmann P, Symmans WF, Yee D, Hylton NM, Esserman LJ, DeMichele AM, Rugo HS, van 't Veer LJ. Cell-free DNA Concentration as a Biomarker of Response and Recurrence in HER2-Negative Breast Cancer Receiving Neoadjuvant Chemotherapy. Clin Cancer Res 2024; 30:2444-2451. [PMID: 38470545 PMCID: PMC11147708 DOI: 10.1158/1078-0432.ccr-23-2928] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE We previously demonstrated the clinical significance of circulating tumor DNA (ctDNA) in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy (NAC). Here, we compared its predictive and prognostic value with cell-free DNA (cfDNA) concentration measured in the same samples from the same patients. EXPERIMENTAL DESIGN 145 patients with hormone receptor (HR)-positive/HER2-negative and 138 triple-negative breast cancer (TNBC) with ctDNA data from a previous study were included in the analysis. Associations of serial cfDNA concentration with residual cancer burden (RCB) and distant recurrence-free survival (DRFS) were examined. RESULTS In TNBC, we observed a modest negative correlation between cfDNA concentration 3 weeks after treatment initiation and RCB, but none of the other timepoints showed significant correlation. In contrast, ctDNA was significantly positively correlated with RCB at all timepoints (all R > 0.3 and P < 0.05). In the HR-positive/HER2-negative group, cfDNA concentration did not associate with response to NAC, but survival analysis showed that high cfDNA shedders at pretreatment had a significantly worse DRFS than low shedders (hazard ratio, 2.12; P = 0.037). In TNBC, the difference in survival between high versus low cfDNA shedders at all timepoints was not statistically significant. In contrast, as previously reported, ctDNA at all timepoints was significantly correlated with DRFS in both subtypes. CONCLUSIONS In TNBC, cfDNA concentrations during therapy were not strongly correlated with response or prognosis. In the HR-positive/HER2-negative group, pretreatment cfDNA concentration was prognostic for DRFS. Overall, the predictive and prognostic value of cfDNA concentration was more limited than that of ctDNA.
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Affiliation(s)
- Mark Jesus M Magbanua
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Ziad Ahmed
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Rosalyn W Sayaman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Lamorna Brown Swigart
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Gillian L Hirst
- Department of Surgery, University of California San Francisco, San Francisco, California
| | - Christina Yau
- Department of Surgery, University of California San Francisco, San Francisco, California
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Wen Li
- Department of Radiology, University of California San Francisco, San Francisco, California
| | - Amy L Delson
- Breast Science Advocacy Core, University of California San Francisco, San Francisco, California
| | - Jane Perlmutter
- Breast Science Advocacy Core, University of California San Francisco, San Francisco, California
| | - Paula Pohlmann
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Douglas Yee
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Nola M Hylton
- Department of Radiology, University of California San Francisco, San Francisco, California
| | - Laura J Esserman
- Department of Surgery, University of California San Francisco, San Francisco, California
| | - Angela M DeMichele
- Division of Hematology/Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Laura J van 't Veer
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
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3
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Kim YJ, Min J. Hydrogel-based technologies in liquid biopsy for the detection of circulating clinical markers: challenges and prospects. Anal Bioanal Chem 2024; 416:2065-2078. [PMID: 37963993 DOI: 10.1007/s00216-023-05025-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023]
Abstract
Liquid biopsy, which promises noninvasive detection of tumor-derived material, has recently been highlighted because of its potential to lead us to an era of precision medicine. However, its development has encountered challenges owing to the extremely low frequency and low purity of circulating tumor markers, such as circulating tumor cells (CTCs), circulating exosomes, and circulating tumor nucleic acids (ctNAs). Much effort has been made to overcome this limitation over the last decade, and an increasing number of studies have shown interest in the special characteristics of hydrogels. This hydrophilic and biocompatible polymeric network, which absorbs a large amount of water, can aid in the isolation, protection, and analysis of these low-abundance and short-lived circulating biomarkers. The role of hydrogels in liquid biopsy is extensive and ranges from enrichment to encapsulation. This review provides an overview of hydrogel-based technologies to pave the way in liquid biopsy.
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Affiliation(s)
- Young Jun Kim
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul, 06974, Republic of Korea.
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Madsen AT, Kristiansen HP, Winther-Larsen A. Short-term biological variation of serum tryptase. Clin Chem Lab Med 2024; 62:713-719. [PMID: 37882699 DOI: 10.1515/cclm-2023-0606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
OBJECTIVES Serum tryptase is a biomarker of mast cell activation. Among others, it is used in the diagnosis of anaphylaxis where a significant increase during the acute phase supports the diagnosis. When evaluating changes in biomarker levels, it is of utmost importance to consider the biological variation of the marker. Therefore, the aim of this study was to evaluate the short-term biological variation of serum tryptase. METHODS Blood samples were drawn at 9 AM three days in a row from apparently healthy subjects. On day two, additional blood samples were drawn every third hour for 12 h. The tryptase concentration was measured in serum using a fluoroenzyme immunoassay (ImmunoCAP™, Thermo Fisher Scientific). Linear mixed-effects models were used to calculate components of biological variation. RESULTS In 32 subjects, the overall mean concentration of tryptase was 4.0 ng/mL (range, 1.3-8.0 ng/mL). The within-subject variation was 3.7 % (95 % confidence interval (CI) 3.0-4.4 %), the between-subject variation was 31.5 % (95 % CI 23.1-39.8 %), and the analytical variation was 3.4 % (95 % CI 2.9-4.1 %). The reference change value was 13.3 % for an increase in tryptase at a 95 % level of significance. No significant day-to-day variation was observed (p=0.77), while a minute decrease in the serum concentration was observed during the day (p<0.0001). CONCLUSIONS Serum tryptase is a tightly regulated biomarker with very low within-subject variation, no significant day-to-day variation, and only minor semidiurnal variation. In contrast, a considerable between-subject variation exists. This establishes serum tryptase as a well-suited biomarker for monitoring.
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Affiliation(s)
- Anne Tranberg Madsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
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5
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Balasubramanian S, Richert ME, Kong H, Fu S, Jang MK, Andargie TE, Keller MB, Alnababteh M, Park W, Apalara Z, Sun J, Redekar N, Orens J, Aryal S, Bush EL, Cantu E, Diamond J, Shah P, Yu K, Nathan SD, Agbor-Enoh S. Cell-Free DNA Maps Tissue Injury and Correlates with Disease Severity in Lung Transplant Candidates. Am J Respir Crit Care Med 2024; 209:727-737. [PMID: 38117233 PMCID: PMC10945061 DOI: 10.1164/rccm.202306-1064oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
Rationale: Plasma cell-free DNA levels correlate with disease severity in many conditions. Pretransplant cell-free DNA may risk stratify lung transplant candidates for post-transplant complications. Objectives: To evaluate if pretransplant cell-free DNA levels and tissue sources identify patients at high risk of primary graft dysfunction and other pre- and post-transplant outcomes. Methods: This multicenter, prospective cohort study recruited 186 lung transplant candidates. Pretransplant plasma samples were collected to measure cell-free DNA. Bisulfite sequencing was performed to identify the tissue sources of cell-free DNA. Multivariable regression models determined the association between cell-free DNA levels and the primary outcome of primary graft dysfunction and other transplant outcomes, including Lung Allocation Score, chronic lung allograft dysfunction, and death. Measurements and Main Results: Transplant candidates had twofold greater cell-free DNA levels than healthy control patients (median [interquartile range], 23.7 ng/ml [15.1-35.6] vs. 12.9 ng/ml [9.9-18.4]; P < 0.0001), primarily originating from inflammatory innate immune cells. Cell-free DNA levels and tissue sources differed by native lung disease category and correlated with the Lung Allocation Score (P < 0.001). High pretransplant cell-free DNA increased the risk of primary graft dysfunction (odds ratio, 1.60; 95% confidence interval [CI], 1.09-2.46; P = 0.0220), and death (hazard ratio, 1.43; 95% CI, 1.07-1.92; P = 0.0171) but not chronic lung allograft dysfunction (hazard ratio, 1.37; 95% CI, 0.97-1.94; P = 0.0767). Conclusions: Lung transplant candidates demonstrate a heightened degree of tissue injury with elevated cell-free DNA, primarily originating from innate immune cells. Pretransplant plasma cell-free DNA levels predict post-transplant complications.
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Affiliation(s)
- Shanti Balasubramanian
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Mary E. Richert
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sheng Fu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Department of Biology, Howard University, Washington, District of Columbia
| | - Michael B. Keller
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Muhtadi Alnababteh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Woojin Park
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jian Sun
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Neelam Redekar
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan Orens
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Shambhu Aryal
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Errol L. Bush
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland; and
| | - Edward Cantu
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joshua Diamond
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pali Shah
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven D. Nathan
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
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6
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Fonseca NM, Maurice-Dror C, Herberts C, Tu W, Fan W, Murtha AJ, Kollmannsberger C, Kwan EM, Parekh K, Schönlau E, Bernales CQ, Donnellan G, Ng SWS, Sumiyoshi T, Vergidis J, Noonan K, Finch DL, Zulfiqar M, Miller S, Parimi S, Lavoie JM, Hardy E, Soleimani M, Nappi L, Eigl BJ, Kollmannsberger C, Taavitsainen S, Nykter M, Tolmeijer SH, Boerrigter E, Mehra N, van Erp NP, De Laere B, Lindberg J, Grönberg H, Khalaf DJ, Annala M, Chi KN, Wyatt AW. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun 2024; 15:1828. [PMID: 38418825 PMCID: PMC10902374 DOI: 10.1038/s41467-024-45475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
No consensus strategies exist for prognosticating metastatic castration-resistant prostate cancer (mCRPC). Circulating tumor DNA fraction (ctDNA%) is increasingly reported by commercial and laboratory tests but its utility for risk stratification is unclear. Here, we intersect ctDNA%, treatment outcomes, and clinical characteristics across 738 plasma samples from 491 male mCRPC patients from two randomized multicentre phase II trials and a prospective province-wide blood biobanking program. ctDNA% correlates with serum and radiographic metrics of disease burden and is highest in patients with liver metastases. ctDNA% strongly predicts overall survival, progression-free survival, and treatment response independent of therapeutic context and outperformed established prognostic clinical factors. Recognizing that ctDNA-based biomarker genotyping is limited by low ctDNA% in some patients, we leverage the relationship between clinical prognostic factors and ctDNA% to develop a clinically-interpretable machine-learning tool that predicts whether a patient has sufficient ctDNA% for informative ctDNA genotyping (available online: https://www.ctDNA.org ). Our results affirm ctDNA% as an actionable tool for patient risk stratification and provide a practical framework for optimized biomarker testing.
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Affiliation(s)
- Nicolette M Fonseca
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wilson Tu
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - William Fan
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Murtha
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Department of Medicine, School of Clinical Sciences; Monash University, Melbourne, VIC, Australia
| | - Karan Parekh
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Gráinne Donnellan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Takayuki Sumiyoshi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Joanna Vergidis
- Department of Medical Oncology, BC Cancer, Victoria, BC, Canada
| | - Krista Noonan
- Department of Medical Oncology, BC Cancer, Surrey, BC, Canada
| | - Daygen L Finch
- Department of Medical Oncology, BC Cancer, Kelowna, BC, Canada
| | | | - Stacy Miller
- Department of Radiation Oncology, BC Cancer, Prince George, BC, Canada
| | - Sunil Parimi
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Edward Hardy
- Tom McMurtry & Peter Baerg Cancer Centre, Vernon Jubilee Hospital, Vernon, BC, Canada
| | - Maryam Soleimani
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Lucia Nappi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Bernhard J Eigl
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Sofie H Tolmeijer
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Emmy Boerrigter
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Nielka P van Erp
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Bram De Laere
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Daniel J Khalaf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
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7
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Sender R, Noor E, Milo R, Dor Y. What fraction of cellular DNA turnover becomes cfDNA? eLife 2024; 12:RP89321. [PMID: 38407214 PMCID: PMC10942627 DOI: 10.7554/elife.89321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Cell-free DNA (cfDNA) tests use small amounts of DNA in the bloodstream as biomarkers. While it is thought that cfDNA is largely released by dying cells, the proportion of dying cells' DNA that reaches the bloodstream is unknown. Here, we integrate estimates of cellular turnover rates to calculate the expected amount of cfDNA. By comparing this to the actual amount of cell type-specific cfDNA, we estimate the proportion of DNA reaching plasma as cfDNA. We demonstrate that <10% of the DNA from dying cells is detectable in plasma, and the ratios of measured to expected cfDNA levels vary a thousand-fold among cell types, often reaching well below 0.1%. The analysis suggests that local clearance, presumably via phagocytosis, takes up most of the dying cells' DNA. Insights into the underlying mechanism may help to understand the physiological significance of cfDNA and improve the sensitivity of liquid biopsies.
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Affiliation(s)
- Ron Sender
- Weizmann Institute of ScienceRehovotIsrael
| | - Elad Noor
- Weizmann Institute of ScienceRehovotIsrael
| | - Ron Milo
- Weizmann Institute of ScienceRehovotIsrael
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, the Hebrew University-Hadassah Medical SchoolJerusalemIsrael
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8
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Herzog C, Jones A, Evans I, Reisel D, Olaitan A, Doufekas K, MacDonald N, Rådestad AF, Gemzell-Danielsson K, Zikan M, Cibula D, Dostálek L, Paprotka T, Leimbach A, Schmitt M, Ryan A, Gentry-Maharaj A, Apostolidou S, Rosenthal AN, Menon U, Widschwendter M. Plasma cell-free DNA methylation analysis for ovarian cancer detection: Analysis of samples from a case-control study and an ovarian cancer screening trial. Int J Cancer 2024; 154:679-691. [PMID: 37861205 DOI: 10.1002/ijc.34757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Analysis of cell-free DNA methylation (cfDNAme), alone or combined with CA125, could help to detect ovarian cancers earlier and may reduce mortality. We assessed cfDNAme in regions of ZNF154, C2CD4D and WNT6 via targeted bisulfite sequencing in diagnostic and early detection (preceding diagnosis) settings. Diagnostic samples were obtained via prospective blood collection in cell-free DNA tubes in a convenience series of patients with a pelvic mass. Early detection samples were matched case-control samples derived from the UK Familial Ovarian Cancer Screening Study (UKFOCSS). In the diagnostic set (ncases = 27, ncontrols = 41), the specificity of cfDNAme was 97.6% (95% CI: 87.1%-99.9%). High-risk cancers were detected with a sensitivity of 80% (56.3%-94.3%). Combination of cfDNAme and CA125 resulted in a sensitivity of 94.4% (72.7%-99.9%) for high-risk cancers. Despite technical issues in the early detection set (ncases = 29, ncontrols = 29), the specificity of cfDNAme was 100% (88.1%-100.0%). We detected 27.3% (6.0%-61.0%) of high-risk cases with relatively lower genomic DNA (gDNA) contamination. The sensitivity rose to 33.3% (7.5%-70.1%) in samples taken <1 year before diagnosis. We detected ovarian cancer in several patients up to 1 year before diagnosis despite technical limitations associated with archival samples (UKFOCSS). Combined cfDNAme and CA125 assessment may improve ovarian cancer screening in high-risk populations, but future large-scale prospective studies will be required to validate current findings.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Adeola Olaitan
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Konstantinos Doufekas
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Nicola MacDonald
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Angelique Flöter Rådestad
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Gemzell-Danielsson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Charles University in Prague, First Faculty of Medicine and Hospital, Na Bulovce, Czech Republic
| | - David Cibula
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University, Prague and, General University Hospital, Prague, Czech Republic
| | - Lukáš Dostálek
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University, Prague and, General University Hospital, Prague, Czech Republic
| | | | | | - Markus Schmitt
- Eurofins Genomics Europe Sequencing GmbH, Konstanz, Germany
| | - Andy Ryan
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Sophia Apostolidou
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Adam N Rosenthal
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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9
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Shin S, Han S, Kim J, Shin Y, Song JJ, Hohng S. Fast, sensitive, and specific multiplexed single-molecule detection of circulating tumor DNA. Biosens Bioelectron 2023; 242:115694. [PMID: 37797531 DOI: 10.1016/j.bios.2023.115694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Circulating tumor DNA (ctDNA) analysis has emerged as a highly promising non-invasive assay for detection and monitoring of cancer. However, identification of multiple point-mutant ctDNAs, particularly at extremely low frequencies in early cancer stages, remains a significant challenge. To address this issue, we present a multiplexed ctDNA detection technique, SIMUL (single-molecule detection of multiple low-frequency mutations). SIMUL involves an unbiased preamplification of both wild-type and mutant DNAs, followed by the detection of mutant DNAs through single-molecule multicolor imaging. SIMUL enables highly sensitive and specific detection of multiple single-nucleotide mutations in a short span of time, even in the presence of 10,000-fold excess of wild-type DNA. Importantly, SIMUL can accurately measure mutant fractions due to its linear correlation between the number of single-molecule spots and the variant allele frequency. This breakthrough technique holds immense potential for clinical applications, offering significant improvements for example in early cancer detection and accurate evaluation of anticancer treatment responses.
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Affiliation(s)
- Soochul Shin
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea.
| | - Sun Han
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Juyoung Kim
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Yumi Shin
- Department of Biological Sciences, KI for BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, KI for BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea.
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10
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Berzero G, Pieri V, Mortini P, Filippi M, Finocchiaro G. The coming of age of liquid biopsy in neuro-oncology. Brain 2023; 146:4015-4024. [PMID: 37289981 PMCID: PMC10545511 DOI: 10.1093/brain/awad195] [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: 12/10/2022] [Revised: 04/05/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023] Open
Abstract
The clinical role of liquid biopsy in oncology is growing significantly. In gliomas and other brain tumours, targeted sequencing of cell-free DNA (cfDNA) from CSF may help differential diagnosis when surgery is not recommended and be more representative of tumour heterogeneity than surgical specimens, unveiling targetable genetic alterations. Given the invasive nature of lumbar puncture to obtain CSF, the quantitative analysis of cfDNA in plasma is a lively option for patient follow-up. Confounding factors may be represented by cfDNA variations due to concomitant pathologies (inflammatory diseases, seizures) or clonal haematopoiesis. Pilot studies suggest that methylome analysis of cfDNA from plasma and temporary opening of the blood-brain barrier by ultrasound have the potential to overcome some of these limitations. Together with this, an increased understanding of mechanisms modulating the shedding of cfDNA by the tumour may help to decrypt the meaning of cfDNA kinetics in blood or CSF.
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Affiliation(s)
- Giulia Berzero
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Valentina Pieri
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Pietro Mortini
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Filippi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Neurorehabilitation Unit; Neurophysiology Unit; Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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11
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Hoerres D, Dai Q, Elmore S, Sheth S, Gupta GP, Kumar S, Gulley ML. Calibration of cell-free DNA measurements by next-generation sequencing. Am J Clin Pathol 2023; 160:314-321. [PMID: 37244060 PMCID: PMC10472744 DOI: 10.1093/ajcp/aqad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVES Accurate monitoring of disease burden depends on accurate disease marker quantification. Although next-generation sequencing (NGS) is a promising technology for noninvasive monitoring, plasma cell-free DNA levels are often reported in misleading units that are confounded by non-disease-related factors. We proposed a novel strategy for calibrating NGS assays using spiked normalizers to improve precision and to promote standardization and harmonization of analyte concentrations. METHODS In this study, we refined our NGS protocol to calculate absolute analyte concentrations to (1) adjust for assay efficiency, as judged by recovery of spiked synthetic normalizer DNAs, and (2) calibrate NGS values against droplet digital polymerase chain reaction (ddPCR). As a model target, we chose the Epstein-Barr virus (EBV) genome. In patient (n = 12) and mock (n = 12) plasmas, NGS and 2 EBV ddPCR assays were used to report EBV load in copies per mL of plasma. RESULTS Next-generation sequencing was equally sensitive to ddPCR, with improved linearity when NGS values were normalized for spiked DNA read counts (R2 = 0.95 for normalized vs 0.91 for raw read concentrations). Linearity permitted NGS calibration to each ddPCR assay, achieving equivalent concentrations (copies/mL). CONCLUSIONS Our novel strategy for calibrating NGS assays suggests potential for a universal reference material to overcome biological and preanalytical variables hindering traditional NGS strategies for quantifying disease burden.
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Affiliation(s)
- Derek Hoerres
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Qunsheng Dai
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Sandra Elmore
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Sunil Kumar
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
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12
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Winther-Larsen A, Madsen AT, Nissen PH, Hoffmann-Lücke E, Greibe E. Short-term biological variation of plasma uracil in a Caucasian healthy population. Clin Chem Lab Med 2023; 61:1490-1496. [PMID: 36856054 DOI: 10.1515/cclm-2022-1167] [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: 11/16/2022] [Accepted: 02/22/2023] [Indexed: 03/02/2023]
Abstract
OBJECTIVES Plasma uracil is a new biomarker to assess the activity of dihydropyrimidine dehydrogenase before cancer treatment with fluoropyrimidine drugs. Knowledge on the biological variation of plasma uracil is important to assess the applicability of plasma uracil as a biomarker of drug tolerance and efficacy. METHODS A total of 33 apparently healthy individuals were submitted to sequential blood draws for three days. On the second day, blood draws were performed every third hour for 12 h. Plasma uracil was quantified by LC-MS/MS. The within-subject (CVI) and between-subject (CVG) biological variation estimates were calculated using linear mixed-effects models. RESULTS The overall median value of plasma uracil was 10.6 ng/mL (range 5.6-23.1 ng/mL). The CVI and CVG were 13.5 and 22.1%, respectively. Plasma uracil remained stable during the day, and there was no day-to-day variation observed. No differences in biological variation components were found between sex and no correlation to age was found. Four samples were calculated to be required to estimate the homeostatic set-point ±15% with 95% confidence. CONCLUSIONS Plasma uracil is subject to tight homeostatic regulation without semidiurnal and day-to-day variation, however between-subject variation exists. This emphasizes plasma uracil as a well-suited biomarker for evaluation of dihydropyrimidine dehydrogenase activity, but four samples are required to establish the homeostatic set-point in a patient.
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Affiliation(s)
- Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | - Anne Tranberg Madsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, USA
| | - Peter H Nissen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | - Elke Hoffmann-Lücke
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | - Eva Greibe
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
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13
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Heft Neal ME, Walline HM, Haring CT. Circulating Tumor DNA in Human Papillomavirus-Mediated Oropharynx Cancer: Leveraging Early Data to Inform Future Directions. Cancer J 2023; 29:215-219. [PMID: 37471611 DOI: 10.1097/ppo.0000000000000670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
ABSTRACT Circulating tumor DNA (ctDNA) has become an area of intense study in many solid malignancies including head and neck cancer. This is of particular interest for human papillomavirus-mediated oropharyngeal squamous cell carcinoma as this cohort of patients has excellent survival and is undergoing current clinical trials aimed at treatment de-escalation. Recent studies have demonstrated the prognostic implications of pretreatment ctDNA and the utility of monitoring ctDNA during and posttreatment; however, there is a need for a more critical understanding of ctDNA as it is beginning to be incorporated into clinical trials. This review discusses the current state of ctDNA in oropharynx cancer focusing on ctDNA kinetics and minimal residual disease detection and ends with a discussion of future applications.
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Affiliation(s)
| | - Heather M Walline
- From the Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI
| | - Catherine T Haring
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, OH
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14
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Meriranta L, Pitkänen E, Leppä S. Blood has never been thicker: Cell-free DNA fragmentomics in the liquid biopsy toolbox of B-cell lymphomas. Semin Hematol 2023; 60:132-141. [PMID: 37455222 DOI: 10.1053/j.seminhematol.2023.06.006] [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: 03/20/2023] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Liquid biopsies utilizing plasma circulating tumor DNA (ctDNA) are anticipated to revolutionize decision-making in cancer care. In the field of lymphomas, ctDNA-based blood tests represent the forefront of clinically applicable tools to harness decades of genomic research for disease profiling, quantification, and detection. More recently, the discovery of nonrandom fragmentation patterns in cell-free DNA (cfDNA) has opened another avenue of liquid biopsy research beyond mutational interrogation of ctDNA. Through examination of structural features, nucleotide content, and genomic distribution of massive numbers of plasma cfDNA molecules, the study of fragmentomics aims at identifying new tools that augment existing ctDNA-based analyses and discover new ways to profile cancer from blood tests. Indeed, the characterization of aberrant lymphoma ctDNA fragment patterns and harnessing them with powerful machine-learning techniques are expected to unleash the potential of nonmutant molecules for liquid biopsy purposes. In this article, we review cfDNA fragmentomics as an emerging approach in the ctDNA research of B-cell lymphomas. We summarize the biology behind the formation of cfDNA fragment patterns and discuss the preanalytical and technical limitations faced with current methodologies. Then we go through the advances in the field of lymphomas and envision what other noninvasive tools based on fragment characteristics could be explored. Last, we place fragmentomics as one of the facets of ctDNA analyses in emerging multiview and multiomics liquid biopsies. We pay attention to the unknowns in the field of cfDNA fragmentation biology that warrant further mechanistic investigation to provide rational background for the development of these precision oncology tools and understanding of their limitations.
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Affiliation(s)
- Leo Meriranta
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Esa Pitkänen
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), HILIFE, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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15
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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16
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Coskun A, Zarepour A, Zarrabi A. Physiological Rhythms and Biological Variation of Biomolecules: The Road to Personalized Laboratory Medicine. Int J Mol Sci 2023; 24:ijms24076275. [PMID: 37047252 PMCID: PMC10094461 DOI: 10.3390/ijms24076275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The concentration of biomolecules in living systems shows numerous systematic and random variations. Systematic variations can be classified based on the frequency of variations as ultradian (<24 h), circadian (approximately 24 h), and infradian (>24 h), which are partly predictable. Random biological variations are known as between-subject biological variations that are the variations among the set points of an analyte from different individuals and within-subject biological variation, which is the variation of the analyte around individuals’ set points. The random biological variation cannot be predicted but can be estimated using appropriate measurement and statistical procedures. Physiological rhythms and random biological variation of the analytes could be considered the essential elements of predictive, preventive, and particularly personalized laboratory medicine. This systematic review aims to summarize research that have been done about the types of physiological rhythms, biological variations, and their effects on laboratory tests. We have searched the PubMed and Web of Science databases for biological variation and physiological rhythm articles in English without time restrictions with the terms “Biological variation, Within-subject biological variation, Between-subject biological variation, Physiological rhythms, Ultradian rhythms, Circadian rhythm, Infradian rhythms”. It was concluded that, for effective management of predicting, preventing, and personalizing medicine, which is based on the safe and valid interpretation of patients’ laboratory test results, both physiological rhythms and biological variation of the measurands should be considered simultaneously.
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17
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Lorenzo-Lozano MC, Blázquez-Manzanera AL, Carnicero JA. How kidney clock works: circadian pattern of eGFR based on a population data group. J Physiol Biochem 2023:10.1007/s13105-023-00948-2. [PMID: 36808081 DOI: 10.1007/s13105-023-00948-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 02/03/2023] [Indexed: 02/20/2023]
Abstract
A circadian regulation of renal function it has been described in the last few years. An intradaily variation in glomerular filtration rate (eGFR) has also been discovered at the individual level. The aim of this study was to check if there exists a circadian pattern of eGFR at population data group level and to compare the population results with those described at individual level. We have studied a total of 446,441 samples analysed in the emergency laboratories of two Spanish hospitals between January 2015 and December 2019. We selected all the records of eGFR values between 60 and 140 mL/min/1.73 m2 using CKD-EPI formula from patients between 18 and 85 years. The intradaily intrinsic eGFR pattern was computed using the extraction time of day in four nested mixed linear and sinusoidal regression models. All models showed an intradaily eGFR pattern, but the estimated model coefficients differed depending on whether age was included. The inclusion of age improved the performance of the model. In this model, the acrophase occurred at 7:46 h. We describe the distribution of eGFR values depending on the time in two different populations. This distribution is adjusted to a circadian rhythm that behaves similarly to the individual rhythm. This pattern is similar in each of the years studied from each hospital as well as between both hospitals. The results found suggest the incorporation of the concept of "population circadian rhythm" into the scientific world.
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Affiliation(s)
- M C Lorenzo-Lozano
- Hospital Universitario de Toledo, Complejo Hospitalario Universitario de Toledo, Toledo, Spain. .,Spanish Research Group in Biological Rhythms and Laboratory Medicine, Toledo, Spain.
| | - A L Blázquez-Manzanera
- Spanish Research Group in Biological Rhythms and Laboratory Medicine, Toledo, Spain.,Hospital General Universitario Rafael Méndez, Lorca, Murcia, Spain.,Hospital General de Villarrobledo, Villarrobledo, Albacete, Spain
| | - J A Carnicero
- Spanish Research Group in Biological Rhythms and Laboratory Medicine, Toledo, Spain.,Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain.,Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
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18
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Kinetics of Plasma Cell-Free DNA under a Highly Standardized and Controlled Stress Induction. Cells 2023; 12:cells12040564. [PMID: 36831231 PMCID: PMC9954572 DOI: 10.3390/cells12040564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Psychological stress affects the immune system and activates peripheral inflammatory pathways. Circulating cell-free DNA (cfDNA) is associated with systemic inflammation, and recent research indicates that cfDNA is an inflammatory marker that is sensitive to psychological stress in humans. The present study investigated the effects of acute stress on the kinetics of cfDNA in a within-subjects design. Twenty-nine males (mean age: 24.34 ± 4.08 years) underwent both the Trier Social Stress Test (TSST) and a resting condition. Blood samples were collected at two time points before and at 9 time points up to 105 min after both conditions. The cfDNA immediately increased 2-fold after the TSST and returned to baseline levels after 30 min after the test, showing that a brief psychological stressor was sufficient to evoke a robust and rapid increase in cfDNA levels. No associations were detected between perceived stress, whereas subjects with higher basal cfDNA levels showed higher increases. The rapid cfDNA regulation might be attributed to the transient activation of immune cells caused by neuroendocrine-immune activation. Further research is required to evaluate the reliability of cfDNA as a marker of neuroendocrine-immune activation, which could be used for diagnostics purposes or monitoring of treatment progression.
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19
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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20
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Balla A, Bhak J, Biró O. The application of circulating tumor cell and cell-free DNA liquid biopsies in ovarian cancer. Mol Cell Probes 2022; 66:101871. [PMID: 36283501 DOI: 10.1016/j.mcp.2022.101871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Ovarian cancer is the deadliest gynecological cancer. 70% of the cases are diagnosed at late stages with already developed metastases due to the absence of easily noticeable symptoms. Early-stage ovarian cancer has a good prognosis with a 5-year survival rate reaching 95%, hence the identification of effective biomarkers for early diagnosis is important. Advances in liquid biopsy-based methods can have a significant impact not just on the development of an efficient screening strategy, but also in clinical decision-making with additional molecular profiling and genetic alterations linked to therapy resistance. Despite the well-known advantages of liquid biopsy, there are still challenges that need to be addressed before its routine use in clinical practice. Various liquid biopsy-based biomarkers have been investigated in ovarian cancer; however, in this review, we are concentrating on the current use of cell-free DNA (cfDNA) and circulating tumor cells (CTCs) in disease management, focusing on their emerging importance in clinical practice. We also discuss the technical aspects of these workflows. The analysis of cfDNA is often chosen for the detection of mutations, copy number aberrations, and DNA methylation changes, whereas CTC analysis provides a unique opportunity to study whole cells, thus allowing DNA, RNA, and protein-based molecular profiling as well as in vivo studies. Combined solutions which merge the strengths of cfDNA and CTC approaches should be developed to maximize the potential of liquid biopsy technology.
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Affiliation(s)
- Abigél Balla
- Clinomics Europe Ltd., Budapest, Hungary; Semmelweis University, Károly Rácz Doctoral School of Clinical Medicine, Budapest, Hungary
| | - Jong Bhak
- Clinomics Inc. UNIST, Ulsan, 44916, Republic of Korea
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21
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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22
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Shree R, Kolarova TR, MacKinnon HJ, Lockwood CM, Chandrasekaran S. Association of fetal fraction with hypertensive disorders of pregnancy incidence and disease severity. Am J Obstet Gynecol MFM 2022; 4:100671. [PMID: 35644526 PMCID: PMC9452472 DOI: 10.1016/j.ajogmf.2022.100671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hypertensive disorders of pregnancy contribute to maternal and offspring morbidity and mortality. Studies suggest that a lower early pregnancy fetal fraction is associated with an increased risk of hypertensive disorders of pregnancy. However, maternal obesity significantly affects fetal fraction and is a risk factor for hypertensive disorders of pregnancy. OBJECTIVE We determined the association between fetal fraction (using a standardized single-institution platform, including male and female fetuses) and hypertensive disorders of pregnancy, stratified by obesity status. Second, we evaluated differences in total cell-free DNA concentration and correlation of fetal fraction with clinical markers of hypertensive disorders of pregnancy severity. STUDY DESIGN This was a retrospective, single-institution study of a previously validated cell-free DNA-based noninvasive prenatal screening assay of 1058 samples. Maternal body mass index at the time of noninvasive prenatal screening was assessed, and hypertensive disorders of pregnancy were confirmed by a detailed medical record review. Differences in fetal fraction and total cell-free DNA concentration between the groups were assessed with univariate analyses. Multivariable regression was used to evaluate the association between fetal fraction and hypertensive disorders of pregnancy, adjusted for body mass index, maternal age, gestational age at noninvasive prenatal screening, and fetal sex. The association between fetal fraction and hypertensive disorders of pregnancy among individuals with obesity (body mass index, ≥30 kg/m2) and individuals without obesity (body mass index, <30 kg/m2) was investigated while controlling for the aforementioned covariates. Lastly, multivariable linear regression was used to evaluate the association between fetal fraction and clinical markers of hypertensive disorders of pregnancy severity. RESULTS We identified individuals with (n=117) and without (n=941) hypertensive disorders of pregnancy with noninvasive prenatal screening drawn before 20 weeks of gestation and with fetal fraction and body mass index data available. Those with hypertensive disorders of pregnancy had a lower fetal fraction (10.2%±4.2% vs 11.6%±4.7%; P<.01), without differences in total cell-free DNA concentration (P=.14). When groups were stratified by obesity status, this relationship was only valid for individuals without obesity (P=.02). Only when logistic regression analysis was restricted to individuals without obesity did the likelihood of hypertensive disorders of pregnancy rise with decreasing fetal fraction (odds ratio, 0.93; 95% confidence interval, 0.88-0.99; P=.02). In addition, fetal fraction was inversely associated with maximum systolic blood pressure at the time of hypertensive disorders of pregnancy only in the population without obesity (β, -0.08; 95% confidence interval, -0.147 to -0.01; P=.02). CONCLUSION Although a lower fetal fraction is associated with the development of hypertensive disorders of pregnancy, the use of this parameter for the prediction may be problematic in individuals with obesity, as obesity has such a profound effect on fetal fraction. However, we uniquely noted that among individuals without obesity, fetal fraction is lower for those that develop hypertensive disorders of pregnancy and lower fetal fraction increases the odds of hypertensive disorders of pregnancy development. Lastly, low fetal fraction in the population without obesity that developed hypertensive disorders of pregnancy was associated with higher systolic blood pressure at the time of hypertensive disorders of pregnancy, an important clinical marker of hypertensive disorders of pregnancy severity. As analytical approaches of cell-free DNA interrogation advance, the prediction of placental-mediated disorders with first-trimester sampling is likely to improve, although this may remain challenging in gravidas with obesity, a cohort at high risk of developing hypertensive disorders of pregnancy.
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Affiliation(s)
- Raj Shree
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran).
| | - Teodora R Kolarova
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran)
| | - Hayley J MacKinnon
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran)
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, WA (Dr Lockwood)
| | - Suchitra Chandrasekaran
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran); Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Emory University, Atlanta, GA (Dr Chandrasekaran)
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23
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Christensen SH, Hviid CVB, Madsen AT, Parkner T, Winther-Larsen A. Short-term biological variation of serum glial fibrillary acidic protein. Clin Chem Lab Med 2022; 60:1813-1819. [PMID: 35962632 DOI: 10.1515/cclm-2022-0480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/29/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Serum glial fibrillary acidic protein (GFAP) is an emerging biomarker for intracerebral diseases and is approved for clinical use in traumatic brain injury. GFAP is also being investigated for several other applications, where the GFAP changes are not always outstanding. It is thus essential for the interpretation of GFAP to distinguish clinical relevant changes from natural occurring biological variation. This study aimed at estimating the biological variation of serum GFAP. METHODS Apparently healthy subjects (n=33) had blood sampled for three consecutive days. On the second day, blood was also drawn every third hour from 9 AM to 9 PM. Serum GFAP was measured by Single Molecule Array (Simoa™). Components of biological variation were estimated in a linear mixed-effects model. RESULTS The overall median GFAP value was 92.5 pg/mL (range 34.4-260.3 pg/mL). The overall within- (CVI) and between-subject variations (CVG) were 9.7 and 39.5%. The reference change value was 36.9% for an increase. No day-to-day variation was observed, however semidiurnal variation was observed with increasing GFAP values between 9 AM and 12 PM (p<0.00001) and decreasing from 12 to 9 PM (p<0.001). CONCLUSIONS Serum GFAP exhibits a relatively low CVI but a considerable CVG and a marked semidiurnal variation. This implies caution on the timing of blood sampling and when interpreting GFAP in relation to reference intervals, especially in conditions where only small GFAP differences are observed.
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Affiliation(s)
| | - Claus Vinter Bødker Hviid
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anne Tranberg Madsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Tina Parkner
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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24
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Edwards RL, Menteer J, Lestz RM, Baxter-Lowe LA. Cell-free DNA as a solid-organ transplant biomarker: technologies and approaches. Biomark Med 2022; 16:401-415. [PMID: 35195028 DOI: 10.2217/bmm-2021-0968] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
High-quality biomarkers that detect emergent graft damage and/or rejection after solid-organ transplantation offer new opportunities to improve post-transplant monitoring, allow early therapeutic intervention and facilitate personalized patient management. Donor-derived cell-free DNA (DD-cfDNA) is a particularly exciting minimally invasive biomarker because it has the potential to be quantitative, time-sensitive and cost-effective. Increased DD-cfDNA has been associated with graft damage and rejection episodes. Efforts are underway to further improve sensitivity and specificity. This review summarizes the procedures used to process and detect DD-cfDNA, measurement of DD-cfDNA in clinical transplantation, approaches for improving sensitivity and specificity and long-term prospects as a transplant biomarker to supplement traditional organ monitoring and invasive biopsies.
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Affiliation(s)
- Rebecca L Edwards
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Cardiology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Rachel M Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Nephrology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Lee Ann Baxter-Lowe
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
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25
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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26
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Nidadavolu LS, Feger D, Wu Y, Grodstein F, Gross AL, Bennett DA, Walston JD, Oh ES, Abadir PM. Circulating Cell-Free Genomic DNA Is Associated with an Increased Risk of Dementia and with Change in Cognitive and Physical Function. J Alzheimers Dis 2022; 89:1233-1240. [PMID: 36031893 PMCID: PMC9969834 DOI: 10.3233/jad-220301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Altered cell homeostasis, seen in cognitive decline and frailty, leads to cell death and turnover, releasing circulating cell-free DNA (ccf-DNA). OBJECTIVE The goal of this study is to determine if serum genomic cell-free DNA (ccf-gDNA) is associated with physical and cognitive decline in older adults. METHODS We used serum from 631 community-dwelling individuals from the Religious Orders Study or Rush Memory and Aging Project who were without cognitive impairment at baseline. ccf-gDNA fragments in serum were quantified using digital PCR. An array of cognitive and physical traits, risk of dementia, global cognition, and frailty at or nearest the time of blood draw were regressed on ccf-DNA, with adjustment for age, sex, race, and education. RESULTS Cross-sectionally, higher ccf-gDNA levels were associated with lower global cognition score and slower gait speed at the evaluation nearest to blood draw. Higher ccf-gDNA levels were associated with increased odds of incident dementia (OR 1.27, 95% CI 1.05, 1.54). Longitudinally, higher levels of ccf-gDNA were associated with steeper general cognitive decline and worsening frailty over eight years of follow up. CONCLUSION This study demonstrates that ccf-gDNA fragments have utility for identifying persons at higher risk of developing dementia and worsening cognition and frailty.
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Affiliation(s)
- Lolita S. Nidadavolu
- Johns Hopkins University School of Medicine, Division of Geriatric Medicine and Gerontology, Baltimore, MD, USA
| | - Danielle Feger
- Johns Hopkins University Center on Aging and Health, Baltimore, MD, USA
| | - Yuqiong Wu
- Johns Hopkins University School of Medicine, Division of Geriatric Medicine and Gerontology, Baltimore, MD, USA
| | - Francine Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Alden L. Gross
- Johns Hopkins University School of Medicine, Division of Geriatric Medicine and Gerontology, Baltimore, MD, USA
- Johns Hopkins University Center on Aging and Health, Baltimore, MD, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Jeremy D. Walston
- Johns Hopkins University School of Medicine, Division of Geriatric Medicine and Gerontology, Baltimore, MD, USA
| | - Esther S. Oh
- Johns Hopkins University School of Medicine, Division of Geriatric Medicine and Gerontology, Baltimore, MD, USA
| | - Peter M. Abadir
- Johns Hopkins University School of Medicine, Division of Geriatric Medicine and Gerontology, Baltimore, MD, USA
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27
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Oversoe SK, Sorensen BS, Tabaksblat EM, Gronbaek H, Kelsen J. Cell-Free DNA and Clinical Characteristics in Patients with Small Intestinal or Pancreatic Neuroendocrine Tumors. Neuroendocrinology 2022; 112:43-50. [PMID: 33461190 DOI: 10.1159/000514457] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/15/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Neuroendocrine tumors (NETs) are rare and characterized by a heterogeneous clinical course and an unmet need for better prognostic markers. Plasma cell-free DNA (cfDNA) has prognostic value in other malignancies but is not previously investigated in NETs. We studied cfDNA levels in patients with mainly low-grade small intestinal NET -(siNET) or pancreatic NET (pNET) and evaluated the prognostic potential of cfDNA. MATERIALS AND METHODS We included 70 NET patients, siNET (n = 50) and pNET (n = 20). Plasma cfDNA levels were determined by droplet digital PCR for the beta-2-microglobulin gene every 6 months during a period of 3 years, including in a subgroup of 19 patients during peptide receptor radionuclide therapy (PRRT) therapy. RESULTS cfDNA levels were higher in both siNET and pNET compared to a previously established healthy cohort (p < 0.0001). -cfDNA levels did not predict overall survival (crude hazard ratio [HR] 0.95 [0.57-1.58], p = 0.837, adjusted for smoking status HR 0.77 [0.51-1.17], p = 0.22). The impact of cfDNA level on progression-free survival showed different trends in siNET and pNET. There was no effect of PRRT treatment on cfDNA levels and no difference in cfDNA levels between patients with and without progressive disease after PRRT (ANOVA p = 0.66). cfDNA levels were significantly higher in never-smokers and previous smokers than in current smokers (p = 0.029). DISCUSSION/CONCLUSION cfDNA levels are higher in NET patients than in healthy controls; however, there was no association with prognosis, and cfDNA levels were unaffected by PRRT. Our observations suggest that cfDNA levels are not associated with the disease course in low-grade NET in contrast to other malignancies.
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Affiliation(s)
- Stine Karlsen Oversoe
- Department of Hepatology and Gastroenterology, Denmark, Aarhus University Hospital, Aarhus, Denmark
- Department of Internal Medicine, Randers Regional Hospital, Randers, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | | | - Henning Gronbaek
- Department of Hepatology and Gastroenterology, Denmark, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Kelsen
- Department of Hepatology and Gastroenterology, Denmark, Aarhus University Hospital, Aarhus, Denmark
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28
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Yuwono NL, Warton K, Ford CE. The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma. eLife 2021; 10:e69679. [PMID: 34752217 PMCID: PMC8577835 DOI: 10.7554/elife.69679] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/23/2021] [Indexed: 01/02/2023] Open
Abstract
Research and clinical use of circulating cell-free DNA (cirDNA) is expanding rapidly; however, there remain large gaps in our understanding of the influence of lifestyle and biological factors on the amount of cirDNA present in blood. Here, we review 66 individual studies of cirDNA levels and lifestyle and biological factors, including exercise (acute and chronic), alcohol consumption, occupational hazard exposure, smoking, body mass index, menstruation, hypertension, circadian rhythm, stress, biological sex and age. Despite technical and methodological inconsistences across studies, we identify acute exercise as a significant influence on cirDNA levels. Given the large increase in cirDNA induced by acute exercise, we recommend that controlling for physical activity prior to blood collection is routinely incorporated into study design when total cirDNA levels are of interest. We also highlight appropriate selection and complete reporting of laboratory protocols as important for improving the reproducibility cirDNA studies and ability to critically evaluate the results.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
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29
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Bach S, Wever BMM, van de Wiel MA, Veltman JD, Hashemi SMS, Kazemier G, Bahce I, Steenbergen RDM. Dynamics of methylated cell-free DNA in the urine of non-small cell lung cancer patients. Epigenetics 2021; 17:1057-1069. [PMID: 34605346 PMCID: PMC9542718 DOI: 10.1080/15592294.2021.1982511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
High levels of methylated DNA in urine represent an emerging biomarker for non-small cell lung cancer (NSCLC) detection and are the subject of ongoing research. This study aimed to investigate the circadian variation of urinary cell-free DNA (cfDNA) abundance and methylation levels of cancer-associated genes in NSCLC patients. In this prospective study of 23 metastatic NSCLC patients with active disease, patients were asked to collect six urine samples during the morning, afternoon, and evening of two subsequent days. Urinary cfDNA concentrations and methylation levels of CDO1, SOX17, and TAC1 were measured at each time point. Circadian variation and between- and within-subject variability were assessed using linear mixed models. Variability was estimated using the Intraclass Correlation Coefficient (ICC), representing reproducibility. No clear circadian patterns could be recognized for cfDNA concentrations or methylation levels across the different sampling time points. Significantly lower cfDNA concentrations were found in males (p=0.034). For cfDNA levels, the between- and within-subject variability were comparable, rendering an ICC of 0.49. For the methylation markers, ICCs varied considerably, ranging from 0.14 to 0.74. Test reproducibility could be improved by collecting multiple samples per patient. In conclusion, there is no preferred collection time for NSCLC detection in urine using methylation markers, but single measurements should be interpreted carefully, and serial sampling may increase test performance. This study contributes to the limited understanding of cfDNA dynamics in urine and the continued interest in urine-based liquid biopsies for cancer diagnostics.
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Affiliation(s)
- Sander Bach
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Birgit M M Wever
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Mark A van de Wiel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Joris D Veltman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sayed M S Hashemi
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Geert Kazemier
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Idris Bahce
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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30
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van der Laan P, van Houdt WJ, van den Broek D, Steeghs N, van der Graaf WTA. Liquid Biopsies in Sarcoma Clinical Practice: Where Do We Stand? Biomedicines 2021; 9:1315. [PMID: 34680432 PMCID: PMC8533081 DOI: 10.3390/biomedicines9101315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Sarcomas are rare tumors of bone and soft tissue with a mesenchymal origin. This uncommon type of cancer is marked by a high heterogeneity, consisting of over 70 subtypes. Because of this broad spectrum, their treatment requires a subtype-specific therapeutic approach. Tissue biopsy is currently the golden standard for sarcoma diagnosis, but it has its limitations. Over the recent years, methods to detect, characterize, and monitor cancer through liquid biopsy have evolved rapidly. The analysis of circulating biomarkers in peripheral blood, such as circulating tumor cells (CTC) or circulating tumor DNA (ctDNA), could provide real-time information on tumor genetics, disease state, and resistance mechanisms. Furthermore, it traces tumor evolution and can assess tumor heterogeneity. Although the first results in sarcomas are encouraging, there are technical challenges that need to be addressed for implementation in clinical practice. Here, we summarize current knowledge about liquid biopsies in sarcomas and elaborate on different strategies to integrate liquid biopsy into sarcoma clinical care.
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Affiliation(s)
- Pia van der Laan
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winan J. van Houdt
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winette T. A. van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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31
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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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Vihinen M. Measuring and interpreting pervasive heterogeneity, poikilosis. FASEB Bioadv 2021; 3:611-625. [PMID: 34377957 PMCID: PMC8332472 DOI: 10.1096/fba.2021-00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 11/11/2022] Open
Abstract
Measurements are widely used in science, engineering, industry, and trade. They form the basis for experimental scientific research, approach, and progress; however, their foundations are seldom thought or questioned. Recently poikilosis, pervasive heterogeneity ranging from subatomic level to biosphere, was introduced. Poikilosis makes single point measurements and estimates obsolete and irrelevant as measurands display intervals of magnitudes. Consideration of poikilosis requires new lines of thinking in experimental design, conduction of studies, data analysis and interpretation. Measurements of poikilosis must consider lagom, normal, variation extent. Measurements, measures, and measurands as well as the measuring systems and uncertainties are discussed from the perspective of poikilosis. New systematics is introduced for description of uncertainty in measurements and for types of experimental designs. Poikilosis-aware experimenting, data analysis and interpretation are discussed. Instructions are provided for how to measure lagom and non-lagom effects of poikilosis. Consideration of poikilosis can solve scientific controversies and enigmas and can allow novel insight into systems, processes, mechanisms, and reactions and their interpretation, understanding, and manipulation. Furthermore, it will increase reproducibility of measurements and studies.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical ScienceLund UniversityLundSweden
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Shree R, Kolarova TR, MacKinnon HJ, Hedge JM, Vinopal E, Ma KK, Lockwood CM, Chandrasekaran S. Low fetal fraction in obese women at first trimester cell-free DNA based prenatal screening is not accompanied by differences in total cell-free DNA. Prenat Diagn 2021; 41:1277-1286. [PMID: 34297415 DOI: 10.1002/pd.6023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/26/2021] [Accepted: 07/10/2021] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Reasons for first trimester noninvasive prenatal screening (NIPS) test failure in obese women remain elusive. As dilution from maternal sources may be explanatory, we determined the relationship between obesity, fetal fraction (FF), and total cell-free DNA (cfDNA) using our NIPS platform. METHODS We assessed differences in first trimester (≤14 weeks) FF, indeterminate rate, and total cfDNA between obese (n = 518) and normal-weight women (n = 237) after exclusion of confounders (anticoagulation, autoimmunity, aneuploidy) and controlling for covariates. RESULTS Fetal fraction was lower, and the indeterminate rate higher, in obese compared to controls (9.2% ± 4.4 vs. 12.5% ± 4.5, p < 0.001 and 8.4 vs. 1.7%, p < 0.001, respectively), but total cfDNA was not different (92.0 vs. 82.1 pg/µl, p = 0.10). For each week, the FF remained lower in obese women (all p < 0.01) but did not increase across the first trimester for either group. Obesity increased the likelihood of indeterminate result (OR 6.1, 95% CI 2.5, 14.8; p < 0.001) and maternal body mass index correlated with FF (β -0.27, 95% CI -0.3, -0.22; p < 0.001), but not with total cfDNA (β 0.49, 95% CI -0.55, 1.53; p = 0.3). CONCLUSIONS First trimester obese women have persistently low FF and higher indeterminate rates, without differences in total cfDNA, suggesting placental-specific mechanisms versus dilution from maternal sources as a potential etiology.
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Affiliation(s)
- Raj Shree
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Teodora R Kolarova
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Hayley J MacKinnon
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Jaclynne M Hedge
- School of Medicine, University of Washington, Seattle, Washington, USA
| | - Elena Vinopal
- School of Medicine, University of Washington, Seattle, Washington, USA
| | - Kimberly K Ma
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Suchitra Chandrasekaran
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
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How to Obtain a High Quality ctDNA in Lymphoma Patients: Preanalytical Tips and Tricks. Pharmaceuticals (Basel) 2021; 14:ph14070617. [PMID: 34206947 PMCID: PMC8308879 DOI: 10.3390/ph14070617] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/20/2023] Open
Abstract
The analysis of circulating tumor DNA (ctDNA) released by tumor cells holds great promise for patients with lymphoma, to refine the diagnostic procedure, clarify the prognosis, monitor the response to treatment, and detect relapses earlier. One of the main challenges of the coming years is to adapt techniques from highly specialized translational teams to routine laboratories as this requires a careful technical and clinical validation, and we have to achieve this as fast as possible to transform a promising biomarker into a routine analysis to have a direct consequence on patient care. Whatever the analytical technology used, the prerequisite is to obtain high yields of ctDNA of optimal quality. In this review, we propose a step-by-step description of the preanalytical process to obtain high-quality ctDNA, emphasizing the technical choices that need to be made and the experimental data that can support these choices.
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Circulating biomarkers for monitoring therapy response and detection of disease progression in lung cancer patients. Cancer Treat Res Commun 2021; 28:100410. [PMID: 34107412 DOI: 10.1016/j.ctarc.2021.100410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023]
Abstract
Liquid biopsies have become of interest as minimally invasive ways to monitor treatment response in lung cancer patients. Circulating tumor DNA (ctDNA) and protein biomarkers are evaluated for their added value in monitoring therapy response and early detection of disease progression. Plasma and serum samples of non-small cell or small cell lung cancer patients were analyzed for driver mutations in ctDNA (EGFR, KRAS or BRAF) using droplet digital PCR and protein biomarkers (CA125, CEA, CA15.3, Cyfra 21-1, HE4, NSE, proGRP and SCCA) using electrochemiluminescence immunoassays. Biomarker concentration changes were compared with the outcome of CT-scans during therapy. The median difference of the concentration of ctDNA, CA125 and Cyfra21-1 was significantly lower in patients with partial response (PR) compared to patients with progressive disease (PD) on the first evaluation CT-scan (P<0.001, P=0.042 and P=0.020, respectively). A substantial agreement between ctDNA or CA125 response and radiographic response was observed (k=0.692 and k=0.792, respectively). The median difference of the concentration of ctDNA and Cyfra21-1 was also significantly lower in PR patients compared to PD patients at the last CT-scan during therapy (P<0.001 and P=0.026, respectively). An almost perfect agreement between ctDNA and radiographic response (k=0.827) and a moderate agreement between Cyfra21-1 response and radiographic response was observed (k=0.553). Serial testing of the concentration of ctDNA, Cyfra21-1, and possibly CA125 could be a useful added tool for monitoring therapy response and early detection of disease progression in lung cancer patients.
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Content of circulating tumor DNA depends on the tumor type and the dynamics of tumor size, but is not influenced significantly by physical exercise, time of the day or recent meal. Cancer Genet 2021; 256-257:165-178. [PMID: 34186498 DOI: 10.1016/j.cancergen.2021.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 01/20/2023]
Abstract
PURPOSE This study aimed to investigate factors, which influence the content of circulating tumor DNA (ctDNA). METHODS 398 serial plasma samples were collected within 1-7 consecutive days from patients with EGFR-mutated lung cancer (n = 13), RAS/RAF-mutated colorectal cancer (n = 54) and BRAF-mutated melanoma (n = 17), who presented with measurable tumor disease. The amount of ctDNA was determined by ddPCR. RESULTS Among 82 patients, who donated 2-6 serial plasma samples, 42 subjects were classified as ctDNA-positive; only 22% cases were mutation-positive across all consecutive tests, while 24/82 (29%) patients showed presence of mutated ctDNA in some but not all blood draws. Subjects with progressing tumors had higher probability of being detected ctDNA-positive as compared to patients, who responded to therapy or had stable disease (39/55 (71%) vs. 4/24 (17%); p = 0.0001). Our study failed to reveal the impact of the time of the day, recent meal or prior physical exercise on the results of ctDNA testing. CONCLUSIONS Presence of ctDNA in plasma is particularly characteristic for patients, who experience clinical progression of tumor disease. Consecutive plasma tests may occasionally provide discordant data; thus, the repetition of analysis may be advised in certain cases in order to ensure the validity of negative ctDNA result.
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Papaiakovou M, Littlewood DTJ, Gasser RB, Anderson RM. How qPCR complements the WHO roadmap (2021-2030) for soil-transmitted helminths. Trends Parasitol 2021; 37:698-708. [PMID: 33931342 DOI: 10.1016/j.pt.2021.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Complementing the launch of the World Health Organization (WHO) roadmap (2021-2030) we explore key elements needing attention before recruitment of qPCR as the main diagnostics tool to confirm reduction or elimination of soil-transmitted helminth (STH) transmission in both control and elimination programmes. Given the performance limitations of conventional methods, a proposed harmonised qPCR will provide a diagnostic tool, with the sensitivity and specificity required to monitor low-intensity infections, following mass drug administration (MDA). Technical and logistical challenges associated with introducing qPCR as a stand-alone tool are highlighted, and a decision-making scheme on how qPCR can support surveillance, resistance detection, and elimination is presented. An accurate point-of-care (POC) diagnostic test needs to be developed to support STH control in the field, and STH biorepositories need to be established and maintained to ensure that reference materials are available for research and validation.
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Affiliation(s)
- Marina Papaiakovou
- Department of Infectious Disease Epidemiology, St Mary's Campus, Imperial College London, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK.
| | - D Timothy J Littlewood
- Science Directorate, Natural History Museum, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Roy M Anderson
- Department of Infectious Disease Epidemiology, St Mary's Campus, Imperial College London, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK
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Yuwono NL, Henry CE, Ford CE, Warton K. Total and endothelial cell-derived cell-free DNA in blood plasma does not change during menstruation. PLoS One 2021; 16:e0250561. [PMID: 33901234 PMCID: PMC8075187 DOI: 10.1371/journal.pone.0250561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Assays measuring cell-free DNA (cfDNA) in blood have widespread potential in modern medicine. However, a comprehensive understanding of cfDNA dynamics in healthy individuals is required to assist in the design of assays that maximise the signal driven by pathological changes, while excluding fluctuations that are part of healthy physiological processes. The menstrual cycle involves major remodelling of endometrial tissue and associated apoptosis, yet there has been little investigation of the impact of the menstrual cycle on cfDNA levels. Paired plasma samples were collected from 40 healthy women on menstruating (M) and non-menstruating (NM) days of their cycle. We measured total cfDNA by targeting ALU repetitive sequences and measured endothelial-derived cfDNA by methylation-specific qPCR targeting an endothelium-unique unmethylated CDH5 DNA region. CfDNA integrity and endothelial cfDNA concentration, but not total cfDNA, are consistent across time between NM and M. No significant changes in total (ALU-115 p = 0.273; ALU-247 p = 0.385) or endothelial cell specific (p = 0.301) cfDNA were observed, leading to the conclusion that menstrual status at the time of diagnostic blood collection should not have a significant impact on the quantitation of total cfDNA and methylation-based cancer assays.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Claire Elizabeth Henry
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Andargie TE, Tsuji N, Seifuddin F, Jang MK, Yuen PS, Kong H, Tunc I, Singh K, Charya A, Wilkins K, Nathan S, Cox A, Pirooznia M, Star RA, Agbor-Enoh S. Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury. JCI Insight 2021; 6:147610. [PMID: 33651717 PMCID: PMC8119224 DOI: 10.1172/jci.insight.147610] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION The clinical course of coronavirus 2019 (COVID-19) is heterogeneous, ranging from mild to severe multiorgan failure and death. In this study, we analyzed cell-free DNA (cfDNA) as a biomarker of injury to define the sources of tissue injury that contribute to such different trajectories. METHODS We conducted a multicenter prospective cohort study to enroll patients with COVID-19 and collect plasma samples. Plasma cfDNA was subject to bisulfite sequencing. A library of tissue-specific DNA methylation signatures was used to analyze sequence reads to quantitate cfDNA from different tissue types. We then determined the correlation of tissue-specific cfDNA measures to COVID-19 outcomes. Similar analyses were performed for healthy controls and a comparator group of patients with respiratory syncytial virus and influenza. RESULTS We found markedly elevated levels and divergent tissue sources of cfDNA in COVID-19 patients compared with patients who had influenza and/or respiratory syncytial virus and with healthy controls. The major sources of cfDNA in COVID-19 were hematopoietic cells, vascular endothelium, hepatocytes, adipocytes, kidney, heart, and lung. cfDNA levels positively correlated with COVID-19 disease severity, C-reactive protein, and D-dimer. cfDNA profile at admission identified patients who subsequently required intensive care or died during hospitalization. Furthermore, the increased cfDNA in COVID-19 patients generated excessive mitochondrial ROS (mtROS) in renal tubular cells in a concentration-dependent manner. This mtROS production was inhibited by a TLR9-specific antagonist. CONCLUSION cfDNA maps tissue injury that predicts COVID-19 outcomes and may mechanistically propagate COVID-19–induced tissue injury. FUNDING Intramural Targeted Anti–COVID-19 grant, NIH.
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Affiliation(s)
- Temesgen E Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA.,Department of Biology, Howard University, Washington DC, USA
| | - Naoko Tsuji
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | | | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Peter St Yuen
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Ilker Tunc
- Bioinformatics and Computation Core, NHLBI, Maryland, USA
| | - Komudi Singh
- Bioinformatics and Computation Core, NHLBI, Maryland, USA
| | - Ananth Charya
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | | | - Steven Nathan
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia, USA
| | - Andrea Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Robert A Star
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Hviid CVB, Madsen AT, Winther-Larsen A. Biological variation of serum neurofilament light chain. Clin Chem Lab Med 2021; 60:569-575. [PMID: 33759425 DOI: 10.1515/cclm-2020-1276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023]
Abstract
OBJECTIVES The neurofilament light chain (NfL) has emerged as a versatile biomarker for CNS-diseases and is approaching clinical use. The observed changes in NfL levels are frequently of limited magnitude and in order to make clinical decisions based on NfL measurements, it is essential that biological variation is not confused with clinically relevant changes. The present study was designed to evaluate the biological variation of serum NfL. METHODS Apparently healthy individuals (n=33) were submitted to blood draws for three days in a row. On the second day, blood draws were performed every third hour for 12 h. NfL was quantified in serum using the Simoa™ HD-1 platform. The within-subject variation (CVI) and between-subject variation (CVG) were calculated using linear mixed-effects models. RESULTS The overall median value of NfL was 6.3 pg/mL (range 2.1-19.1). The CVI was 3.1% and the CVG was 35.6%. An increase in two serial measurements had to exceed 24.3% to be classified as significant at the 95% confidence level. Serum NfL levels remained stable during the day (p=0.40), whereas a minute variation (6.0-6.6 pg/mL) was observed from day-to-day (p=0.02). CONCLUSIONS Serum NfL is subject to tight homeostatic regulation with none or neglectable semidiurnal and day-to-day variation, but considerable between-subject variation exists. This emphasizes serum NfL as a well-suited biomarker for disease monitoring, but warrants caution when interpreting NfL levels in relation to reference intervals in a diagnosis setting. Furthermore, NfL's tight regulation requires that the analytical variation is kept at a minimum.
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Affiliation(s)
- Claus Vinter Bødker Hviid
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Biochemistry, Horsens Regional Hospital, Horsens, Denmark
| | - Anne Tranberg Madsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
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Ørntoft MBW, Jensen SØ, Øgaard N, Henriksen TV, Ferm L, Christensen IJ, Reinert T, Larsen OH, Nielsen HJ, Andersen CL. Age-stratified reference intervals unlock the clinical potential of circulating cell-free DNA as a biomarker of poor outcome for healthy individuals and patients with colorectal cancer. Int J Cancer 2020; 148:1665-1675. [PMID: 33320961 PMCID: PMC7898909 DOI: 10.1002/ijc.33434] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/17/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022]
Abstract
Circulating cell-free DNA (cfDNA) has spurred much interest as a biomarker in oncology. However, inter- and intra-individual cfDNA levels vary greatly. Consequently, in order to base clinical decisions on cfDNA measurements, normal reference intervals are essential to avoid that ordinary variation is confused with clinically relevant change. The lack of reference intervals may potentially explain the ambiguous results reported in the field. Our study aimed to establish reference intervals and to evaluate the association between cfDNA and demographic and clinical variables, including colorectal cancer (CRC). Plasma samples and clinical data from 2817 subjects were collected including 1930 noncancer individuals and 887 CRC patients. cfDNA was measured using droplet digital polymerase chain reaction (PCR). The large cohort combined with robust cfDNA quantification enabled establishment of reference intervals (<67 years: 775-4860 copies/mL; ≥67 years: 807-6561 copies/mL). A cfDNA level above the age-stratified 90% percentile was prognostic of reduced survival in both noncancer individuals and CRC patients, with HR values of 2.56 and 2.01, respectively. Moreover, cfDNA levels increased significantly with age, elevated BMI and chronic diseases. In CRC, the cfDNA level was increased for Stage IV, but not Stage I to Stage III cancer. In summary, the use of reference intervals revealed that high cfDNA levels were predictive of shorter survival in both noncancer individuals and CRC patients, and that CRC development did not affect the cfDNA level until metastatic dissemination. Furthermore, cfDNA levels were impacted by age and chronic diseases. Conclusively, our study presents reference intervals that will help pave the way for clinical utilization of cfDNA.
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Affiliation(s)
- Mai-Britt Worm Ørntoft
- Department of Surgery, Herning Regional Hospital, Herning, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Linnea Ferm
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
| | | | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Halfdan Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples. Sci Rep 2020; 10:16456. [PMID: 33020547 PMCID: PMC7536441 DOI: 10.1038/s41598-020-73350-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 11/08/2022] Open
Abstract
Many emerging technologies are reliant on circulating cell-free DNA (cfDNA) and cell-free RNA (cfRNA) applications in the clinic. However, the impact of diurnal cycles or daily meals on circulating analytes are poorly understood and may be confounding factors when developing diagnostic platforms. To begin addressing this knowledge gap, we obtained plasma from four healthy donors serially sampled five times during 12 h in a single day. For all samples, we measured concentrations of cfDNA and cfRNA using both bulk measurements and gene-specific digital droplet PCR. We found no significant variation attributed to blood draw number for the cfDNA or cfRNA. This indicated that natural diurnal cycles and meal consumption do not appear to significantly affect abundance of total cfDNA, total cfRNA, or our two selected cfRNA transcripts. Conversely, we observed significant variation between individual donors for cfDNA and one of the cfRNA transcripts. The results of this work suggest that it will be important to consider patient-specific baselines when designing reliable circulating cfDNA or cfRNA clinical assays.
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Eastley N, Sommer A, Ottolini B, Neumann R, Luo JL, Hastings RK, McCulloch T, Esler CP, Shaw JA, Ashford RU, Royle NJ. The Circulating Nucleic Acid Characteristics of Non-Metastatic Soft Tissue Sarcoma Patients. Int J Mol Sci 2020; 21:ijms21124483. [PMID: 32599895 PMCID: PMC7349923 DOI: 10.3390/ijms21124483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Soft tissue sarcomas (STS) are rare, malignant tumours with a generally poor prognosis. Our aim was to explore the potential of cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) analysis to track non-metastatic STS patients undergoing attempted curative treatment. The analysed cohort (n = 29) contained multiple STS subtypes including myxofibrosarcomas, undifferentiated pleomorphic sarcomas, leiomyosarcomas, and dedifferentiated liposarcomas amongst others. Perioperative cfDNA levels trended towards being elevated in patients (p = 0.07), although did not correlate with tumour size, grade, recurrence or subtype, suggesting a limited diagnostic or prognostic role. To characterise ctDNA, an amplicon panel covering three genes commonly mutated in STSs was first trialled on serial plasma collected from nine patients throughout follow-up. This approach only identified ctDNA in 2.5% (one in 40) of the analysed samples. Next custom-designed droplet digital PCR assays and Ion AmpliSeq™ panels were developed to track single nucleotide variants identified in patients’ STSs by whole exome sequencing (1–6 per patient). These approaches identified ctDNA in 17% of patients. Although ctDNA was identified before radiologically detectable recurrence in two cases, the absence of demonstrable ctDNA in 83% of cases highlights the need for much work before circulating nucleic acids can become a useful means to track STS patients.
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Affiliation(s)
- Nicholas Eastley
- Trauma and Orthopaedics, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK;
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
- Correspondence:
| | - Aurore Sommer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Barbara Ottolini
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Rita Neumann
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Jin-Li Luo
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Robert K. Hastings
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Thomas McCulloch
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; (T.M.); (C.P.E.)
| | - Claire P. Esler
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; (T.M.); (C.P.E.)
| | - Jacqueline A. Shaw
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
| | - Robert U. Ashford
- Trauma and Orthopaedics, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK;
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; (T.M.); (C.P.E.)
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (A.S.); (B.O.); (R.N.); (J.-L.L.); (R.K.H.); (JAS); (N.J.R.)
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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Madsen AT, Winther-Larsen A, McCulloch T, Meldgaard P, Sorensen BS. Genomic Profiling of Circulating Tumor DNA Predicts Outcome and Demonstrates Tumor Evolution in ALK-Positive Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2020; 12:E947. [PMID: 32290439 PMCID: PMC7226192 DOI: 10.3390/cancers12040947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/29/2022] Open
Abstract
With the rapid development of targeted therapies for the treatment of cancer, methods for predicting response and outcome are in high demand. Non-small cell lung cancer driven by genomic rearrangements of the anaplastic lymphoma kinase (ALK) gene can be successfully treated with ALK-targeted therapy. Unfortunately, a subset of patients does not respond, and all patients ultimately acquire resistance, highlighting the need for better clinical tools to manage these patients. Here, we performed targeted next-generation sequencing on plasma circulating tumor DNA (ctDNA) from 24 patients to assess the clinical utility of ctDNA genomic profiling. Patients with detectable ctDNA prior to treatment had worse progression-free survival (PFS) than those without (median 8.7 vs. 15.2 months, p = 0.028). In addition, the presence of ctDNA within two months after treatment initiation predicted inferior PFS (median 4.6 vs. 14.5 months, p = 0.028). Longitudinal monitoring of ctDNA with droplet digital PCR during treatment reflected the radiological response and revealed potential acquired resistance mutations. Interestingly, an increase in the ctDNA concentration was evident prior to the determination of progressive disease by conventional radiological imaging, with a median lead time of 69 days (range 30-113). Genomic profiling of ctDNA is a promising tool for predicting outcome and monitoring response to targeted therapy.
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Affiliation(s)
- Anne Tranberg Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark; (A.W.-L.); (B.S.S.)
| | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark; (A.W.-L.); (B.S.S.)
| | - Tine McCulloch
- Department of Oncology, Aalborg University Hospital, 9000 Aalborg, Denmark;
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus N, Denmark;
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark; (A.W.-L.); (B.S.S.)
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Lech Pedersen N, Mertz Petersen M, Ladd JJ, Lampe PD, Bresalier RS, Davis GJ, Demuth C, Jensen SØ, Andersen CL, Ferm L, Christensen IJ, Nielsen HJ. Development of blood-based biomarker tests for early detection of colorectal neoplasia: Influence of blood collection timing and handling procedures. Clin Chim Acta 2020; 507:39-53. [PMID: 32272156 DOI: 10.1016/j.cca.2020.03.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Blood-based, cancer-associated biomarkers are susceptible to a variety of well-known preanalytical factors. The influence of bowel preparation before a diagnostic colonoscopy on biomarker levels is, however, poorly investigated. The present study assessed the influence of bowel preparation on colorectal cancer-associated biomarkers. In addition, the effect of single versus double centrifugation of plasma biomarkers was assessed. METHODS Blood samples were collected pre- and post-bowel preparation from 125 subjects scheduled for first time diagnostic colonoscopy due to symptoms attributable to CRC. The samples were separated into serum and EDTA plasma, and analyzed by four independent collaborators for: 1) the proteins AFP, CA19-9, CEA, hs-CRP, CyFra21-1, Ferritin, Galectin-3 and TIMP-1, 2) the proteins BAG4, IL6ST, vWF, CD44 and EGFR, 3) the glycoprotein Galectin-3 ligand, and 4) cell-free DNA (cfDNA). Statistical analysis of biomarker data has been performed using mixed modelling, including repeated measures. RESULTS The biomarkers generally showed negligible variation between pre- and post-bowel preparation except for CyFra21-1, Ferritin, BAG4 and cfDNA. CyFra21-1 levels were systematically reduced with 29% (95% CI 21-36%) by bowel preparation (p ≤ 0.0001). Ferritin was not significantly different between pre- and post-bowel preparation (p = 0.07), however the estimated difference (increase) was 18%. BAG4 was systematically reduced by 12% (95% CI 1-22%, p = 0.04), while cfDNA showed a significant increase of 28% (95% CI 17-39%, p < 0.0001). Double centrifugation compared to single centrifugation showed reduced vWF (ratio 0.86, p ≤ 0.0001) and CD44 (ratio 0.85, p = 0.016), but increased IL6ST levels (ratio 1.18, p = 0.014). CONCLUSIONS Results of the present study demonstrated systematic, statistically significant differences between pre-bowel and post-bowel preparation levels for three independent blood-based biomarkers (BAG4, CyFra21-1, cfDNA), illustrating the importance of timing of sample collection for biomarker analyses.
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Affiliation(s)
- Niels Lech Pedersen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
| | - Mathias Mertz Petersen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark. http://www.colorectalcancer.dk
| | - Jon J Ladd
- Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul D Lampe
- Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert S Bresalier
- Department of Gastroenterology, Hepatology & Nutrition, MD Anderson Cancer Center, Houston, TX, USA
| | - Gerard J Davis
- Abbott Laboratories Inc., Cancer Core R&D, Abbott Park, IL, USA
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Denmark
| | - Sarah Ø Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Denmark
| | - Linnea Ferm
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
| | - Ib J Christensen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
| | - Hans J Nielsen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Use of Spiked Normalizers to More Precisely Quantify Tumor Markers and Viral Genomes by Massive Parallel Sequencing of Plasma DNA. J Mol Diagn 2020; 22:437-446. [PMID: 32036092 DOI: 10.1016/j.jmoldx.2020.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/19/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A problematic aspect of massive parallel sequencing is that somatic mutations and viral loads are typically quantified as a fraction relative to wild-type human DNA, yet wild-type levels vary with diverse biologic and preanalytic interferences. A novel strategy was devised to quantify target analytes in copies per mL of plasma after normalizing for read counts of spiked DNAs. Five synthetic DNAs (called EndoGenus spikes) were added to plasma before library preparation (modified ArcherDX LiquidPlex 28). By normalizing to the fractional recovery of EndoGenus spike reads, numerical values for each disease marker were reportable in units of copies per mL. To show how well this system operates, replicate assays were performed on 40 mock plasmas having 23 engineered mutations and on 21 natural plasmas. Reads for all five EndoGenus spikes were recovered (means, 313 and 376 copies/mL in mock and natural plasmas, respectively). Normalizing read counts for the proportional recovery of spikes helped control for variables in the multistep protocol, reducing the CV in replicate tests from 34% to 22% for mutations and from 25% to 7% for viral loads. In conclusion, the EndoGenus system is useful for evaluating efficiency of the total test system and for precisely quantifying target molecules. This system may benefit patients being monitored for disease burden while also tracking emerging subclones.
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Brodbeck K, Schick S, Bayer B, Anslinger K, Krüger K, Mayer Z, Holdenrieder S, Peldschus S. Biological variability of cell-free DNA in healthy females at rest within a short time course. Int J Legal Med 2020; 134:911-919. [DOI: 10.1007/s00414-019-02240-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022]
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Noncoding RNAs and Liquid Biopsy in Lung Cancer: A Literature Review. Diagnostics (Basel) 2019; 9:diagnostics9040216. [PMID: 31818027 PMCID: PMC6963838 DOI: 10.3390/diagnostics9040216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Lung cancer represents a genetically heterogeneous disease with low survival rates. Recent data have evidenced key roles of noncoding RNAs in lung cancer initiation and progression. These functional RNA molecules that can act as both oncogenes and tumor suppressors may become future biomarkers and more efficient therapeutic targets. In the precision medicine era, circulating nucleic acids have the potential to reshape the management and prognosis of cancer patients. Detecting genomic alterations and level variations of circulating nucleic acids in liquid biopsy samples represents a noninvasive method for portraying tumor burden. Research is currently trying to validate the potential role of liquid biopsy in lung cancer screening, prognosis, monitoring of disease progression, and treatment response. However, this method requires complex detection assays, and implementation of plasma genotyping in clinical practice continues to be hindered by discrepancies that arise when compared to tissue genotyping. Understanding the genomic landscape of lung cancer is essential in order to provide useful and innovative research in the age of patient-tailored therapy. In this landscape, the noncoding RNAs play a crucial role due to their target genes that dramatically influence the tumor microenvironment and the response to therapy. This article addresses present and future possible roles of liquid biopsy in lung cancer. It also discusses how the complex role of noncoding RNAs in lung tumorigenesis could influence the management of this pathology.
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