1
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Xian RR, Kinyera T, Otim I, Sampson JN, Nabalende H, Legason ID, Stone J, Ogwang MD, Reynolds SJ, Kerchan P, Bhatia K, Goedert JJ, Mbulaiteye SM, Ambinder RF. Plasma EBV DNA: A Promising Diagnostic Marker for Endemic Burkitt Lymphoma. Front Oncol 2022; 11:804083. [PMID: 34970500 PMCID: PMC8713969 DOI: 10.3389/fonc.2021.804083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Endemic Burkitt lymphoma (eBL) is the most common childhood cancer in regions of equatorial Africa where P. falciparum malaria is holoendemic. The tumor is consistently associated with Epstein-Barr virus (EBV). Screening for EBV DNA in plasma in a high-risk population in Hong Kong has been shown to be useful in facilitating the early diagnosis of nasopharyngeal carcinoma, another EBV-associated tumor. Here, we investigate plasma EBV as a diagnostic marker for eBL in children in Uganda. We studied plasma specimens from 25 children with eBL and 25 controls matched for age (<3-16 years), gender and geography, including many with asymptomatic P. falciparum infection. These specimens were previously collected under the auspices of the EMBLEM (Epidemiology of Burkitt lymphoma in East African children and minors) study. After cell-free DNA isolation, plasma EBV DNA was measured using a quantitative PCR assay that amplifies the large internal repeats of the EBV genome. All children with eBL had measurable plasma EBV, as compared to 84% of control children. The median plasma EBV DNA level was 5.23 log10 copies/mL (interquartile range 3.54-6.08 log10 copies/mL) in children with eBL. In contrast, the median plasma EBV DNA level was 0.37 log10 copies/mL (interquartile range 0.18-1.05 log10 copies/mL) in children without lymphoma. An EBV threshold of 2.52 log10 copies/mL yielded a sensitivity of.88 and a specificity of 1. The estimated AUC was 0.936 (95% CI: 0.8496 – 1.00) for the corresponding ROC curve. Plasma EBV copy number did not depend on age, gender, or malaria screening status. However, two control children with asymptomatic P. falciparum infection and parasitemia also had high plasma EBV copy number. Our analysis suggests that measurements of EBV copy number in plasma may be useful in identifying children with eBL versus control children. A promising area for future research is the differentiation of high copy number associated with tumor versus high copy number associated with asymptomatic parasitemia.
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Affiliation(s)
- Rena R Xian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Tobias Kinyera
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda.,Department of Pediatrics, St. Mary's Hospital Lacor, Gulu, Uganda
| | - Isaac Otim
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda.,Department of Pediatrics, St. Mary's Hospital Lacor, Gulu, Uganda
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Hadijah Nabalende
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda.,Department of Pediatrics, St. Mary's Hospital Lacor, Gulu, Uganda
| | - Ismail D Legason
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda.,Department of Pediatrics, St. Mary's Hospital Lacor, Gulu, Uganda
| | - Jennifer Stone
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Martin D Ogwang
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda.,Department of Pediatrics, St. Mary's Hospital Lacor, Gulu, Uganda
| | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda.,Children's Ward, Kuluva Hospital, Arua, Uganda
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Richard F Ambinder
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, United States
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2
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Foley JF, Elgart B, Alex Merrick B, Phadke DP, Cook ME, Malphurs JA, Solomon GG, Shah RR, Fessler MB, Miller FW, Gerrish KE. Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects. Physiol Rep 2021; 9:e14993. [PMID: 34350716 PMCID: PMC8339531 DOI: 10.14814/phy2.14993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
Cell-free DNA circulates in plasma at low levels as a normal by-product of cellular apoptosis. Multiple clinical pathologies, as well as environmental stressors can lead to increased circulating cell-free DNA (ccfDNA) levels. Plasma DNA studies frequently employ targeted amplicon deep sequencing platforms due to limited concentrations (ng/ml) of ccfDNA in the blood. Here, we report whole genome sequencing (WGS) and read distribution across chromosomes of ccfDNA extracted from two human plasma samples from normal, healthy subjects, representative of limited clinical samples at <1 ml. Amplification was sufficiently robust with ~90% of the reference genome (GRCh38.p2) exhibiting 10X coverage. Chromosome read coverage was uniform and directly proportional to the number of reads for each chromosome across both samples. Almost 99% of the identified genomic sequence variants were known annotated dbSNP variants in the hg38 reference genome. A high prevalence of C>T and T>C mutations was present along with a strong concordance of variants shared between the germline genome databases; gnomAD (81.1%) and the 1000 Genome Project (93.6%). This study demonstrates isolation and amplification procedures from low input ccfDNA samples that can detect sequence variants across the whole genome from amplified human plasma ccfDNA that can translate to multiple clinical research disciplines.
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Affiliation(s)
- Julie F. Foley
- Division of National Toxicology ProgramNIEHSDurhamNorth CarolinaUSA
| | | | - B. Alex Merrick
- Division of National Toxicology ProgramNIEHSDurhamNorth CarolinaUSA
| | | | - Molly E. Cook
- Division of Intramural ResearchNIEHSDurhamNorth CarolinaUSA
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3
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Chen X, Wu T, Li L, Lin Y, Ma Z, Xu J, Li H, Cheng F, Chen R, Sun K, Luo Y, Zhang C, Chen F, Wang J, Kuo T, Li X, Geng C, Lin F, Huang C, Hu J, Yin J, Liu M, Tao Y, Zhang J, Ou R, Zheng F, Jin Y, Yang H, Wang J, Xu X, Fu S, Jiang H, Jin X, Zhang H. Transcriptional Start Site Coverage Analysis in Plasma Cell-Free DNA Reveals Disease Severity and Tissue Specificity of COVID-19 Patients. Front Genet 2021; 12:663098. [PMID: 34122515 PMCID: PMC8194351 DOI: 10.3389/fgene.2021.663098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/14/2021] [Indexed: 01/10/2023] Open
Abstract
Symptoms of coronavirus disease 2019 (COVID-19) range from asymptomatic to severe pneumonia and death. A deep understanding of the variation of biological characteristics in severe COVID-19 patients is crucial for the detection of individuals at high risk of critical condition for the clinical management of the disease. Herein, by profiling the gene expression spectrum deduced from DNA coverage in regions surrounding transcriptional start site in plasma cell-free DNA (cfDNA) of COVID-19 patients, we deciphered the altered biological processes in the severe cases and demonstrated the feasibility of cfDNA in measuring the COVID-19 progression. The up- and downregulated genes in the plasma of severe patient were found to be closely related to the biological processes and functions affected by COVID-19 progression. More importantly, with the analysis of transcriptome data of blood cells and lung cells from control group and cases with severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, we revealed that the upregulated genes were predominantly involved in the viral and antiviral activity in blood cells, reflecting the intense viral replication and the active reaction of immune system in the severe patients. Pathway analysis of downregulated genes in plasma DNA and lung cells also demonstrated the diminished adenosine triphosphate synthesis function in lung cells, which was evidenced to correlate with the severe COVID-19 symptoms, such as a cytokine storm and acute respiratory distress. Overall, this study revealed tissue involvement, provided insights into the mechanism of COVID-19 progression, and highlighted the utility of cfDNA as a noninvasive biomarker for disease severity inspections.
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Affiliation(s)
- Xinping Chen
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Tao Wu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Lingguo Li
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen, China
| | - Zhichao Ma
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Hui Li
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Kun Sun
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Yuxue Luo
- BGI-Shenzhen, Shenzhen, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Chen Zhang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Jiao Wang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Tingyu Kuo
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xiaojuan Li
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Feng Lin
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Junjie Hu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Ming Liu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Ye Tao
- BGI-Shenzhen, Shenzhen, China
| | - Jiye Zhang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Jin
- Department of Emergency Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Shengmiao Fu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Hongyan Jiang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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4
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Kallionpää RA, Ahramo K, Aaltonen M, Pennanen P, Peltonen J, Peltonen S. Circulating free DNA in the plasma of individuals with neurofibromatosis type 1. Am J Med Genet A 2021; 185:1098-1104. [PMID: 33484105 DOI: 10.1002/ajmg.a.62081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant syndrome whose characteristic manifestations include benign neurofibromas, yet NF1 is also associated with a high risk of cancer. Measurements of circulating free plasma DNA (cfDNA) are gaining wider applicability in cancer diagnostics, targeting of therapy, and monitoring of therapeutic response. Individuals with NF1 are likely to be followed up using this method, but the effects of NF1 and neurofibromas on cfDNA levels are not known. We studied peripheral blood samples from 19 adults with NF1 and 12 healthy controls. The cfDNA was isolated from plasma with QIAamp Circulating Nucleic Acid Kit and quantified using the Qubit 2.0 Fluorometer. The cfDNA concentration of each sample was normalized relative to the plasma protein concentration. The normalized median concentration of cfDNA in plasma was 19.3 ng/ml (range 6.6-78.6) among individuals with NF1 and 15.9 ng/ml (range 4.8-47.0) among controls (p = .369). Individuals with NF1 who also had plexiform neurofibroma (pNF) showed non-significantly elevated cfDNA concentration compared to individuals with NF1 and without known pNF (median 25.4 vs. 18.8 ng/ml, p = .122). The effect of NF1 on cfDNA seems to be relatively small and NF1 is therefore unlikely to hamper the use of cfDNA-based assays.
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Affiliation(s)
- Roope A Kallionpää
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Kaisa Ahramo
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Marianna Aaltonen
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland.,Turku University of Applied Sciences, Turku, Finland
| | - Paula Pennanen
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Juha Peltonen
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sirkku Peltonen
- Department of Dermatology and Venereology, University of Turku, Turku, Finland.,Department of Dermatology, Turku University Hospital, Turku, Finland.,Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Dermatology and Venereology, Region Västra Götaland Sahlgrenska University Hospital, Gothenburg, Sweden
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5
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Ware SA, Desai N, Lopez M, Leach D, Zhang Y, Giordano L, Nouraie M, Picard M, Kaufman BA. An automated, high-throughput methodology optimized for quantitative cell-free mitochondrial and nuclear DNA isolation from plasma. J Biol Chem 2020; 295:15677-15691. [PMID: 32900851 DOI: 10.1074/jbc.ra120.015237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/03/2020] [Indexed: 02/06/2023] Open
Abstract
Progress in the study of circulating, cell-free nuclear DNA (ccf-nDNA) in cancer detection has led to the development of noninvasive clinical diagnostic tests and has accelerated the evaluation of ccf-nDNA abundance as a disease biomarker. Likewise, circulating, cell-free mitochondrial DNA (ccf-mtDNA) is under similar investigation. However, optimal ccf-mtDNA isolation parameters have not been established, and inconsistent protocols for ccf-nDNA collection, storage, and analysis have hindered its clinical utility. Until now, no studies have established a method for high-throughput isolation that considers both ccf-nDNA and ccf-mtDNA. We initially optimized human plasma digestion and extraction conditions for maximal recovery of these DNAs using a magnetic bead-based isolation method. However, when we incorporated this method onto a high-throughput platform, initial experiments found that DNA isolated from identical human plasma samples displayed plate edge effects resulting in low ccf-mtDNA reproducibility, whereas ccf-nDNA was less affected. Therefore, we developed a detailed protocol optimized for both ccf-mtDNA and ccf-nDNA recovery that uses a magnetic bead-based isolation process on an automated 96-well platform. Overall, we calculate an improved efficiency of recovery of ∼95-fold for ccf-mtDNA and 20-fold for ccf-nDNA when compared with the initial procedure. Digestion conditions, liquid-handling characteristics, and magnetic particle processor programming all contributed to increased recovery without detectable positional effects. To our knowledge, this is the first high-throughput approach optimized for ccf-mtDNA and ccf-nDNA recovery and serves as an important starting point for clinical studies.
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Affiliation(s)
- Sarah A Ware
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nikita Desai
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mabel Lopez
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel Leach
- Optimize Laboratory Consultants, LLC, Lansdale, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Luca Giordano
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Martin Picard
- Division of Behavioral Medicine, Departments of Psychiatry and Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Conteduca V, Gurioli G, Brighi N, Lolli C, Schepisi G, Casadei C, Burgio SL, Gargiulo S, Ravaglia G, Rossi L, Altavilla A, Farolfi A, Menna C, Colangione SP, Pulvirenti M, Romeo A, De Giorgi U. Plasma Androgen Receptor in Prostate Cancer. Cancers (Basel) 2019; 11:E1719. [PMID: 31689899 PMCID: PMC6896184 DOI: 10.3390/cancers11111719] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/24/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
The therapeutic landscape of prostate cancer has expanded rapidly over the past 10 years, and there is now an even greater need to understand the biological mechanisms of resistance and to develop noninvasive biomarkers to guide treatment. The androgen receptor (AR) is known to be involved in the pathogenesis and progression of prostate cancer. Recently, highly sensitive next-generation sequencing and PCR-based methods for analyzing androgen receptor gene (AR) copy numbers (CN) and mutations in plasma were established in cell-free DNA (cfDNA) of patients with castration-resistant prostate cancer (CRPC) treated with different drugs. The study of cfDNA holds great promise for improving treatment in CRPC, especially in the advanced stage of the disease. Recent findings showed the significant association of plasma AR aberrations with clinical outcome in CRPC patients treated with AR-directed therapies, whereas no association was observed in patients treated with taxanes. This suggests the potential for using plasma AR as a biomarker for selecting treatment, i.e., hormone therapy or chemotherapy, and the possibility of modulating taxane dose. In recent years, plasma AR status has also been investigated in association with novel agents, such as 177Lu-PSMA radioligand therapy and PARP inhibitors. This review will focus on AR testing in plasma that may have clinical utility for treatment selection in advanced prostate cancer.
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Affiliation(s)
- Vincenza Conteduca
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giorgia Gurioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Nicole Brighi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Cristian Lolli
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giuseppe Schepisi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Chiara Casadei
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Salvatore Luca Burgio
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Stefania Gargiulo
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giorgia Ravaglia
- Unit of Biostatistics and Clinical Trials, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Lorena Rossi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Amelia Altavilla
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Alberto Farolfi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Cecilia Menna
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Sarah Pia Colangione
- Radiotherapy Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Mario Pulvirenti
- Department of Urology, Morgagni Pierantoni Hospital, 47121 Forli, Italy.
| | - Antonino Romeo
- Radiotherapy Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Ugo De Giorgi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
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7
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Xia WY, Gao L, Dai EH, Chen D, Xie EF, Yang L, Zhang SC, Zhang BF, Xu J, Pan SY. Liquid biopsy for non-invasive assessment of liver injury in hepatitis B patients. World J Gastroenterol 2019; 25:3985-3995. [PMID: 31413532 PMCID: PMC6689808 DOI: 10.3748/wjg.v25.i29.3985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/13/2019] [Accepted: 07/05/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatitis B is a major public health problem in China. Accurate liver injury assessment is essential for clinical evidence-based treatment. Liver biopsy is considered the gold standard method to stage liver disease, but it is not widely used in resource-limited settings. Therefore, non-invasive liquid biopsy tests are needed.
AIM To assess liver injury in hepatitis B patients using quantified cell free DNA combined with other serum biomarker as a liquid biopsy-based method.
METHODS A cohort of 663 subjects including 313 hepatitis B patients and 350 healthy controls were enrolled. Ultrasound-guided liver biopsies followed by histopathological assessments were performed for the 263 chronic hepatitis B patients to determine the degree of liver injury. Cell-free DNA was quantified using a novel duplex real-time polymerase chain reaction assay.
RESULTS Compared with healthy controls, patients with hepatitis B virus (HBV) infection had significantly higher plasma DNA, serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), bilirubin, and HBV DNA levels (P < 0.01). Serum ALT, AST, bilirubin, and plasma DNA levels of patients with marked-severe inflammation were significantly higher than those with mild-moderate inflammation (P < 0.01). There was a statistically significant correlation between hepatocyte inflammation severity and serum bilirubin (R2 = 0.673, P < 0.01) or plasma DNA (R2 = 0.597, P < 0.01) levels. The areas under the curves of serum ALT, bilirubin, plasma DNA, and their combination to distinguish between patients with mild–moderate and marked-severe inflammation were 0.8059, 0.7910, 0.7921, and 0.9564, respectively.
CONCLUSION The combination of plasma DNA, serum ALT, and bilirubin could be a candidate liquid biopsy for non-invasive assessment of liver injury in hepatitis B patients.
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Affiliation(s)
- Wen-Ying Xia
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Li Gao
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Er-Hei Dai
- Department of Laboratory Medicine, the Fifth Hospital of Shijiazhuang, Shijiazhuang 050021, Hebei Province, China
| | - Dan Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Er-Fu Xie
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Li Yang
- Department of Laboratory Medicine, the Fifth Hospital of Shijiazhuang, Shijiazhuang 050021, Hebei Province, China
| | - Shi-Chang Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Bing-Feng Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Jian Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Shi-Yang Pan
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
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8
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Haller N, Ehlert T, Schmidt S, Ochmann D, Sterzing B, Grus F, Simon P. Circulating, Cell-Free DNA for Monitoring Player Load in Professional Football. Int J Sports Physiol Perform 2019; 14:718-26. [PMID: 30427238 DOI: 10.1123/ijspp.2018-0756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Purpose: Player monitoring in elite sport settings is becoming increasingly important. Questionnaire-based methods and biomarkers such as circulating, cell-free DNA (cfDNA) are suggested for load monitoring. cfDNA concentrations were shown to increase depending on total distance covered in football and were associated with overtraining in weight lifters. Thus, the objective of this study was to examine whether cfDNA is feasible as a monitoring tool in elite football players. Methods: Capillary blood samples from 22 male elite football players were collected over 4 mo of a regular season. Sampling was conducted the day before, 1 day after, or several days after regular-season games and/or training. In addition, each player filled in a visual analogue scale (VAS) questionnaire including the items "general perceived exertion," "muscular fatigue," and "mental fatigue." Performance during training and games was tracked by the Catapult system and with the OPTA system, respectively. Results: cfDNA values were significantly elevated in players the day after regular-season games (1.4-fold; P = .0004) in line with the scores of the VAS. Both parameters showed significantly higher values during midweek-game weeks. cfDNA concentrations correlated with training data, and VAS was correlated with the tracking of the season games. However, cfDNA and VAS did not correlate with each other. Conclusions: cfDNA concentrations at rest and VAS scores are influenced by previous load in professional football players. Future studies will reveal whether cfDNA might serve as a practically applicable marker for player load in football players.
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Abstract
PURPOSE The need for less invasive procedures for lung cancer probing is critically needed to better understand the disease. The purpose of the current study aims to explore the use of circulating tumor DNA (ctDNA) derived from plasma and urine specimens. METHODS Matched peripheral blood and morning urine specimens were obtained from 160 late stage NSCLC patients. The amount of ctDNA was quantified for each of the patients. Activating and sensitizing EGFR mutations commonly found in NSCLC patients were profiled. Longitudinal analysis was performed to compared DNA variations during disease progression. RESULTS Measurement of EGFR mutations in NSCLC patients using plasma and urinal DNA demonstrated strong concordance to conventional tissue biopsy profiling. Baseline matched tumor samples yielded 82.8% and 84.0% for plasma and urinal DNA respectively. For these measurements, the positive predictive value was 100% for plasma and urinal DNA. In the longitudinal study, we observed strong links to disease severity and survival analysis showed a clear trend with patients having higher DNA concentrations to have worse outcome especially for urinal DNA. HR for patients stratified using plasma and urinal DNA were 1.23 and 2.55 respectively. CONCLUSION Measurements of circulating DNA within body fluids presented potentially new tools for the disease management of NSCLC patients with EGFR mutations. We demonstrated both plasma and urinal DNA correlated well to tissue biopsies and were potentially prognostic to address patients' survival outcome.
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Affiliation(s)
- Hao Zhang
- Centre for Cardiothoracic Surgery, Xiangyang Central Hospital, Hospital Affiliated to Hubei University of Arts and Science, Xiangyang 441021, Hubei, China.,Centre for Cardiothoracic Surgery, Xiangyang Central Hospital, Hospital Affiliated to Hubei University of Arts and Science, Xiangyang 441021, Hubei, China
| | - Bin He
- Centre for Cardiothoracic Surgery, Xiangyang Central Hospital, Hospital Affiliated to Hubei University of Arts and Science, Xiangyang 441021, Hubei, China.,Centre for Cardiothoracic Surgery, Xiangyang Central Hospital, Hospital Affiliated to Hubei University of Arts and Science, Xiangyang 441021, Hubei, China
| | - Jun Cui
- Centre for Cardiothoracic Surgery, Xiangyang Central Hospital, Hospital Affiliated to Hubei University of Arts and Science, Xiangyang 441021, Hubei, China
| | - Mingzhang Zhao
- General Thoracic Surgery, Yicheng People's Hospital, Xiangyang 441400, Hubei, China
| | - Zengwang Zhang
- Centre for Cardiothoracic Surgery, Xiangyang Central Hospital, Hospital Affiliated to Hubei University of Arts and Science, Xiangyang 441021, Hubei, China
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10
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Knol AC, Vallée A, Herbreteau G, Nguyen JM, Varey E, Gaultier A, Théoleyre S, Saint-Jean M, Peuvrel L, Brocard A, Quéreux G, Khammari A, Denis MG, Dréno B. Clinical significance of BRAF mutation status in circulating tumor DNA of metastatic melanoma patients at baseline. Exp Dermatol 2018; 25:783-8. [PMID: 27194447 DOI: 10.1111/exd.13065] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2016] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA is a promising non-invasive tool for cancer monitoring. The main objective of our work was to investigate the relationship between mutant BRAF DNA in plasma and clinical response. Thirty-eight stage IV patients with a V600 mutated BRAF melanoma were included prior to any treatment. DNA was extracted from plasma and mutant DNA was detected using the amplification-refractory mutation system method. Before the beginning of any treatment, the corresponding BRAF mutation was detected in 29 of the 38 tested plasma samples (76.3% positive per cent agreement). We observed a strong correlation between the presence of circulating mutated DNA and overall survival (OS; P=.02), and with the number of metastatic sites (P=.01). The presence of circulating mutated DNA was also strongly correlated with serum LDH activity (P<.01) and S100 protein concentration (P<.01). Finally, seven patients presented discordant BRAF status in different tumor sites. In all these patients, the test performed on ctDNA was positive, suggesting that ctDNA analysis might be less sensitive to tumor heterogeneity. Altogether, these results suggest that plasmatic mutant BRAF DNA is a prognostic factor of OS, correlated with tumor burden. In addition, it represents an interesting alternative source of DNA to detect BRAF mutations before treatment.
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Affiliation(s)
- Anne C Knol
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France
| | - Audrey Vallée
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Laboratoire de Biochimie et Plateforme de Génétique des Cancers, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Guillaume Herbreteau
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Laboratoire de Biochimie et Plateforme de Génétique des Cancers, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Jean-Michel Nguyen
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,SEB-PIMESP, CHU Nantes, Nantes Cedex 01, France
| | - Emilie Varey
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | | | - Sandrine Théoleyre
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Laboratoire de Biochimie et Plateforme de Génétique des Cancers, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Mélanie Saint-Jean
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Lucie Peuvrel
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Anabelle Brocard
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Gaëlle Quéreux
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Amir Khammari
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Marc G Denis
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France.,Laboratoire de Biochimie et Plateforme de Génétique des Cancers, CHU Hôtel-Dieu, Nantes Cedex 01, France
| | - Brigitte Dréno
- CRCNA, , INSERM U892, CNRS 6299, Nantes Cedex 01, France. .,Unité de Cancéro-Dermatologie-CIC biothérapie INSERM 0503, CHU Hôtel-Dieu, Nantes Cedex 01, France.
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11
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Shi C, Zheng Y, Li Y, Sun H, Liu S. Association between clinical characteristics and the diagnostic accuracy of circulating single-molecule amplification and resequencing technology on detection epidermal growth factor receptor mutation status in plasma of lung adenocarcinoma. J Clin Lab Anal 2017; 32. [PMID: 28670719 DOI: 10.1002/jcla.22271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/28/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related mortality in the world. Circulating single-molecule amplification and resequencing technology (cSMART) can successfully detect epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer (NSCLC). However, few studies have investigated the association between clinical characteristics and the diagnostic accuracy of cSMART technique in lung adenocarcinoma. METHODS We enrolled 95 patients, which included paraffin embedded tumor tissues and matched plasma samples. Retrospectively analyzed the correlation between clinical characteristics and sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of cSMART. RESULTS Of the 95 lung adenocarcinoma cancer patients, 49 (51.5%) and 40 (42.1%) harbored EGFR mutations respectively in tissue and plasma. In younger than 60 years group, sensitivity, specificity and consistency for cSMART were 81.0%, 100%, and 90.9% (P<.001). In metastasis group, sensitivity, specificity, and consistency for cSMART were 92.9%, 77.8%, and 87.0% (P=.001). By univariate analysis, younger than 60 years (OR=5.938; 95% confidence interval: 1.835-19.210; P=.001); metastasis group (OR=4.482; 95% confidence interval: 1.432-14.024; P=.007) were significantly correlated with a higher accuracy. By multivariate analysis, younger than 60 years (P=.003) and metastasis (P=.004) were confirmed as independent factors for diagnostic accuracy of EGFR mutation in plasma through cSMART. CONCLUSION cSMART is feasible for detection EGFR mutation in plasma when tissue is unavailable. Age and metastasis might be considered as independent factors in diagnostic accuracy of cSMART in lung adenocarcinoma.
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Affiliation(s)
- Chao Shi
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Zheng
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yin Li
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haibo Sun
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shilei Liu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China
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12
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Conteduca V, Wetterskog D, Sharabiani MTA, Grande E, Fernandez-Perez MP, Jayaram A, Salvi S, Castellano D, Romanel A, Lolli C, Casadio V, Gurioli G, Amadori D, Font A, Vazquez-Estevez S, González del Alba A, Mellado B, Fernandez-Calvo O, Méndez-Vidal MJ, Climent MA, Duran I, Gallardo E, Rodriguez A, Santander C, Sáez MI, Puente J, Gasi Tandefelt D, Wingate A, Dearnaley D, Demichelis F, De Giorgi U, Gonzalez-Billalabeitia E, Attard G. Androgen receptor gene status in plasma DNA associates with worse outcome on enzalutamide or abiraterone for castration-resistant prostate cancer: a multi-institution correlative biomarker study. Ann Oncol 2017; 28:1508-1516. [PMID: 28472366 PMCID: PMC5834043 DOI: 10.1093/annonc/mdx155] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND There is an urgent need to identify biomarkers to guide personalized therapy in castration-resistant prostate cancer (CRPC). We aimed to clinically qualify androgen receptor (AR) gene status measurement in plasma DNA using multiplex droplet digital PCR (ddPCR) in pre- and post-chemotherapy CRPC. METHODS We optimized ddPCR assays for AR copy number and mutations and retrospectively analyzed plasma DNA from patients recruited to one of the three biomarker protocols with prospectively collected clinical data. We evaluated associations between plasma AR and overall survival (OS) and progression-free survival (PFS) in 73 chemotherapy-naïve and 98 post-docetaxel CRPC patients treated with enzalutamide or abiraterone (Primary cohort) and 94 chemotherapy-naïve patients treated with enzalutamide (Secondary cohort; PREMIERE trial). RESULTS In the primary cohort, AR gain was observed in 10 (14%) chemotherapy-naïve and 33 (34%) post-docetaxel patients and associated with worse OS [hazard ratio (HR), 3.98; 95% CI 1.74-9.10; P < 0.001 and HR 3.81; 95% CI 2.28-6.37; P < 0.001, respectively], PFS (HR 2.18; 95% CI 1.08-4.39; P = 0.03, and HR 1.95; 95% CI 1.23-3.11; P = 0.01, respectively) and rate of PSA decline ≥50% [odds ratio (OR), 4.7; 95% CI 1.17-19.17; P = 0.035 and OR, 5.0; 95% CI 1.70-14.91; P = 0.003, respectively]. AR mutations [2105T>A (p.L702H) and 2632A>G (p.T878A)] were observed in eight (11%) post-docetaxel but no chemotherapy-naïve abiraterone-treated patients and were also associated with worse OS (HR 3.26; 95% CI 1.47-not reached; P = 0.004). There was no interaction between AR and docetaxel status (P = 0.83 for OS, P = 0.99 for PFS). In the PREMIERE trial, 11 patients (12%) with AR gain had worse PSA-PFS (sPFS) (HR 4.33; 95% CI 1.94-9.68; P < 0.001), radiographic-PFS (rPFS) (HR 8.06; 95% CI 3.26-19.93; P < 0.001) and OS (HR 11.08; 95% CI 2.16-56.95; P = 0.004). Plasma AR was an independent predictor of outcome on multivariable analyses in both cohorts. CONCLUSION Plasma AR status assessment using ddPCR identifies CRPC with worse outcome to enzalutamide or abiraterone. Prospective evaluation of treatment decisions based on plasma AR is now required. CLINICAL TRIAL NUMBER NCT02288936 (PREMIERE trial).
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Androstenes/adverse effects
- Androstenes/therapeutic use
- Antineoplastic Agents, Hormonal/adverse effects
- Antineoplastic Agents, Hormonal/therapeutic use
- Benzamides
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/genetics
- DNA Mutational Analysis
- Disease Progression
- Disease-Free Survival
- Europe
- Humans
- Kaplan-Meier Estimate
- Male
- Middle Aged
- Multiplex Polymerase Chain Reaction
- Multivariate Analysis
- Mutation
- Nitriles
- Odds Ratio
- Patient Selection
- Phenylthiohydantoin/adverse effects
- Phenylthiohydantoin/analogs & derivatives
- Phenylthiohydantoin/therapeutic use
- Precision Medicine
- Predictive Value of Tests
- Proportional Hazards Models
- Prospective Studies
- Prostatic Neoplasms, Castration-Resistant/blood
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/mortality
- Receptors, Androgen/blood
- Receptors, Androgen/genetics
- Risk Factors
- Time Factors
- Treatment Outcome
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Affiliation(s)
- V. Conteduca
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - D. Wetterskog
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - M. T. A. Sharabiani
- Research Data Management and Statistics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - E. Grande
- Department of Medical Oncology, Hospital Ramón y Cajal, Madrid
| | - M. P. Fernandez-Perez
- Department of Hematology & Medical Oncology, Hospital Universitario Morales Meseguer, IMIB-Universidad de Murcia, Murcia
| | - A. Jayaram
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Academic Urology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - S. Salvi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - D. Castellano
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - A. Romanel
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - C. Lolli
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - V. Casadio
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - G. Gurioli
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - D. Amadori
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - A. Font
- Oncology Unit, Institut Català d'Oncologia-Hospital Germans Trias i Pujol, Badalona
| | | | | | - B. Mellado
- Department of Medical Oncology, IDIBAPS Hospital Clinic, Barcelona
| | | | - M. J. Méndez-Vidal
- Department of Medical Oncology, Hospital Universitario Reina Sofía, Córdoba
| | - M. A. Climent
- Department of Medical Oncology, Instituto Valenciano de Oncología Valencia, Valencia
| | - I. Duran
- Department of Medical Oncology, Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla
| | - E. Gallardo
- Department of Medical Oncology, H.U. Parc Taulí, Sabadell, Barcelona
| | - A. Rodriguez
- Department of Medical Oncology, Hospital de León, León
| | - C. Santander
- Department of Medical Oncology, Hospital Universitario Miguel Servet, Zaragoza
| | - M. I. Sáez
- Department of Medical Oncology, Hospital Regional y Hospital Virgen de la Victoria, Malaga
| | - J. Puente
- Department of Medical Oncology, Hospital Clínico San Carlos, Madrid, Spain
| | - D. Gasi Tandefelt
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - A. Wingate
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - D. Dearnaley
- Academic Urology Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | | | | | - F. Demichelis
- Centre for Integrative Biology, University of Trento, Trento, Italy
- Institute for Precision Medicine, Weill Cornell Medicine, New York, USA
| | - U. De Giorgi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - E. Gonzalez-Billalabeitia
- Department of Hematology & Medical Oncology, Hospital Universitario Morales Meseguer, IMIB-Universidad de Murcia, Murcia
- Department of Medical Oncology, Universidad Católica San Antonio de Murcia-UCAM, Murcia, Spain
| | - G. Attard
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Academic Urology Unit, The Royal Marsden NHS Foundation Trust, London, UK
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13
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Nakamura T, Watanabe N, Sato A, Komiya K, Umeguchi H, Hosomi T, Hirai M, Sueoka E, Kimura S, Sueoka-Aragane N. Plasma T790M and HGF as potential predictive markers for EGFR-TKI re-challenge. Oncol Lett 2017; 13:4939-4946. [PMID: 28588734 DOI: 10.3892/ol.2017.6085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/23/2017] [Indexed: 12/15/2022] Open
Abstract
Re-challenge with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI) has been suggested to potentially improve survival in certain populations of patients with advanced lung cancer, but predictive markers for the success of EGFR-TKI re-challenge have not been identified. The present study analyzed 16 re-challenges with EGFR-TKI undertaken in 12 patients with lung adenocarcinoma by investigating T790M and hepatocyte growth factor (HGF) in plasma coupled with clinical characteristics. EGFR mutations in plasma DNA were detected using the wild inhibiting PCR and quenched probe system for exon 19 deletions, and T790M and L858R were detected using the mutation-biased PCR and quenched probe system. HGF levels in the plasma were measured by enzyme-linked immunosorbent assay, and the ratio of HGF levels prior to re-challenge to those prior to the previous EGFR-TKI treatment was calculated. Two re-challenges demonstrated partial response, six remained as stable disease and eight had progressive disease (PD). A total of 4 of the 5 patients with a history of T790M positivity based on plasma DNA levels had PD. A total of 7 of the 8 patients who had ≥1.5-fold elevation of HGF prior to re-challenge with EGFR-TKI suffered PD. Elevation of the HGF ratio to ≥1.5 was significantly associated with poor response to EGFR-TKI re-challenge. Having no history of T790M and an HGF ratio <1.5 was significantly associated with a positive response to EGFR-TKI re-challenge. A combination of T790M detection and HGF quantification using plasma is a potentially useful assay system for predicting the effect of EGFR-TKI re-challenge. Future prospective studies are required to confirm the predictive validity of these markers.
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Affiliation(s)
- Tomomi Nakamura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Naomi Watanabe
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Akemi Sato
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Kazutoshi Komiya
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Hitomi Umeguchi
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | | | | | - Eisaburo Sueoka
- Department of Laboratory Medicine, Saga University Hospital, Saga 849-8501, Japan
| | - Shinya Kimura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Naoko Sueoka-Aragane
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
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14
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Carozzi FM, Bisanzi S, Carrozzi L, Falaschi F, Lopes Pegna A, Mascalchi M, Picozzi G, Peluso M, Sani C, Greco L, Ocello C, Paci E. Multimodal lung cancer screening using the ITALUNG biomarker panel and low dose computed tomography. Results of the ITALUNG biomarker study. Int J Cancer 2017; 141:94-101. [PMID: 28387927 DOI: 10.1002/ijc.30727] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/31/2017] [Indexed: 12/19/2022]
Abstract
Asymptomatic high-risk subjects, randomized in the intervention arm of the ITALUNG trial (1,406 screened for lung cancer), were enrolled for the ITALUNG biomarker study (n = 1,356), in which samples of blood and sputum were analyzed for plasma DNA quantification (cut off 5 ng/ml), loss of heterozygosity and microsatellite instability. The ITALUNG biomarker panel (IBP) was considered positive if at least one of the two biomarkers included in the panel was positive. Subjects with and without lung cancer diagnosis at the end of the screening cycle with LDCT (n = 517) were evaluated. Out of 18 baseline screen detected lung cancer cases, 17 were IBP positive (94%). Repeat screen-detected lung cancer cases were 18 and 12 of them positive at baseline IBP test (66%). Interval cancer cases (2-years) and biomarker tests after a suspect Non Calcific Nodule follow-up were investigated. The single test versus multimodal screening measures of accuracy were compared in a simulation within the screened ITALUNG intervention arm, considering screen-detected and interval cancer cases. Sensitivity was 90% at baseline screening. Specificity was 71 and 61% for LDCT and IBP as baseline single test, and improved at 89% with multimodal, combined screening. The positive predictive value was 4.3% for LDCT at baseline and 10.6% for multimodal screening. Multimodal screening could improve the screening efficiency at baseline and strategies for future implementation are discussed. If IBP was used as primary screening test, the LDCT burden might decrease of about 60%.
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Affiliation(s)
- Francesca Maria Carozzi
- Regional Cancer Prevention Laboratory, ISPO-Cancer Prevention and Research Institute, Florence, Italy
| | - Simonetta Bisanzi
- Regional Cancer Prevention Laboratory, ISPO-Cancer Prevention and Research Institute, Florence, Italy
| | - Laura Carrozzi
- Cardiopulmonary Department, University Hospital of Pisa, Pisa, Italy
| | - Fabio Falaschi
- Radiology Department, University Hospital of Pisa, Pisa, Italy
| | | | - Mario Mascalchi
- Radiodiagnostic Section, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Giulia Picozzi
- Radiodiagnostic Unit, ISPO-Cancer Prevention and Research Institute, Florence, Italy
| | - Marco Peluso
- Regional Cancer Prevention Laboratory, ISPO-Cancer Prevention and Research Institute, Florence, Italy
| | - Cristina Sani
- Regional Cancer Prevention Laboratory, ISPO-Cancer Prevention and Research Institute, Florence, Italy
| | - Luana Greco
- Biologist, formerly at ISPO-Cancer Prevention and Research Institute, Florence, Italy
| | | | - Eugenio Paci
- Retired, formerly at ISPO-Cancer Prevention and Research Institute, Florence, Italy
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15
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Rezvani N, Alibakhshi R, Vaisi-Raygani A, Bashiri H, Saidijam M. Detection of SPG20 gene promoter-methylated DNA, as a novel epigenetic biomarker, in plasma for colorectal cancer diagnosis using the MethyLight method. Oncol Lett 2017; 13:3277-3284. [PMID: 28521434 DOI: 10.3892/ol.2017.5815] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/17/2017] [Indexed: 02/06/2023] Open
Abstract
Aberrant promoter methylation of genes is a common epigenetic alteration in colorectal cancer (CRC). In the present study, spastic paraplegia 20 (SPG20) promoter-methylated DNA, as a potential diagnostic biomarker, was investigated in plasma and tumor tissue samples from patients with CRC. To the best of our knowledge, the quantification of SPG20 promoter-methylated DNA in plasma samples remains unreported. SPG20 promoter methylation was investigated in 32 paired tumor and healthy adjacent tissues, 37 plasma samples from patients with CRC, and in 37 plasma samples from a healthy control group, using the MethyLight method. The percentage of methylated reference (PMR) values was determined for each sample, and the sensitivity and specificity of this unique biomarker were evaluated. PMR values were significantly higher in plasma samples from patients with CRC compared with in those from the control group (P<0.05). Plasma specimens from patients and healthy controls exhibited median PMR values of 7.7 (95% CI, 4.15-15.28) and 0.59 (95% CI, 0.14-1.12), respectively. Notably, the median PMR values were identified as 42.39 (95% CI, 27.69-72.26) and 3.61 (95% CI, 1.07-5.29) in tumor and adjacent healthy tissues, respectively. Using receiver-operating characteristics curve analysis, the area under curve (AUC) was demonstrated to be 0.984 for plasma samples, exhibiting a sensitivity of 81.1% and a specificity of 96.9%. Furthermore, the AUC was 0.996 for tissue samples, revealing a sensitivity of 93.8% and specificity of 99.96%. Results from the present study indicate that the identification of SPG20 promoter-methylated DNA in plasma is a potential diagnostic biomarker for the detection of CRC. Furthermore, the results demonstrate a satisfactory sensitivity and specificity, indicating the importance of SPG20 methylation as a novel noninvasive biomarker.
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Affiliation(s)
- Nayebali Rezvani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran.,Department of Clinical Biochemistry, Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran
| | - Reza Alibakhshi
- Department of Clinical Biochemistry, Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran
| | - Assad Vaisi-Raygani
- Department of Clinical Biochemistry, Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran.,Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran.,Molecular Diagnostic Research Center, Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran
| | - Homayoon Bashiri
- Department of Gastroenterology, Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
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16
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Chen YS, Chen MH, Lu CH, Chen PC, Chen HL, Yang IH, Tsai NW, Lin WC. Associations among Cognitive Functions, Plasma DNA, and White Matter Integrity in Patients with Early-Onset Parkinson's Disease. Front Neurosci 2017; 11:9. [PMID: 28174514 PMCID: PMC5258716 DOI: 10.3389/fnins.2017.00009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/04/2017] [Indexed: 12/22/2022] Open
Abstract
Early-onset Parkinson's disease (EOPD) patients are symptomatic at a relatively young age, and the impacts of the disease on both the patients and their caregivers are dramatic. Few studies have reported on the cognitive impairments seen in EOPD, and the results of these studies have been diverse. Furthermore, it is still unclear what microstructural white matter (WM) changes are present in EOPD patients. As such, we conducted this study to investigate the microstructural WM changes experienced by EOPD patients and their association with cognitive function and plasma DNA levels. We enrolled 24 EOPD patients and 33 sex- and age-matched healthy volunteers who underwent complete neuro-psychological testing (NPT) to evaluate their cognitive function and diffusion tensor imaging (DTI) scanning to determine their fiber integrity. The plasma DNA measurements included measurements of nuclear and mitochondrial DNA levels. Fractional anisotropy (FA) maps were compared using voxel-based statistics to determine differences between the two groups. The differences in DTI indices and NPT scores were correlated after adjusting for age, sex, and education. Our results demonstrate that patients with EOPD have elevated nuclear DNA levels and wide spectrums of impairments in NPT, especially in the executive function and visuospatial function domains. Exploratory group-wise comparisons of the DTI indices revealed that the patients with EOPD exhibited lower DTI parameters in several brain locations. These poorer DTI parameters were associated with worse cognitive performances and elevated plasma nuclear DNA levels, especially in the anterior thalamic radiation region. Our findings suggest that the thalamus and its adjacent anterior thalamic radiation may be important in the pathogenesis of EOPD, as they appear to become involved in the disease process at an early stage.
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Affiliation(s)
- Yueh-Sheng Chen
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine Kaohsiung, Taiwan
| | - Meng-Hsiang Chen
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine Kaohsiung, Taiwan
| | - Cheng-Hsien Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of MedicineKaohsiung, Taiwan; Department of Biological Science, National Sun Yat-Sen UniversityKaohsiung, Taiwan
| | - Pei-Chin Chen
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine Kaohsiung, Taiwan
| | - Hsiu-Ling Chen
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of MedicineKaohsiung, Taiwan; Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming UniversityTaipei, Taiwan
| | - I-Hsiao Yang
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine Kaohsiung, Taiwan
| | - Nai-Wen Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine Kaohsiung, Taiwan
| | - Wei-Che Lin
- Department of Diagnostic Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine Kaohsiung, Taiwan
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Haller N, Tug S, Breitbach S, Jörgensen A, Simon P. Increases in Circulating Cell-Free DNA During Aerobic Running Depend on Intensity and Duration. Int J Sports Physiol Perform 2017; 12:455-62. [PMID: 27617389 DOI: 10.1123/ijspp.2015-0540] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PURPOSE Increases in concentrations of circulating cell-free DNA (cfDNA) have recently been demonstrated to occur in a variety of exhausting and vigorous exercise settings. Here, the authors assessed the association of cfDNA with exercise duration and intensity in a controlled test-retest setting of a regenerative up-to-moderate-level aerobic run. METHODS In a pretest, the lactate threshold (LT) was determined in 13 participants (range 10.8-13.4 km/h) by using a step-wise incremental running test. The speed of the 2 endurance runs was set to 9.6 km/h for 40 min; for the participants with an LT below the median (12.8 km/h; G1), this was a moderate aerobic run, and for those with an LT above the median, this was a regenerative run (G2). Capillary cfDNA, lactate, and rating of perceived exertion (RPE) were assessed before, every 10 min during, and after the runs. RESULTS During the last 30 min of the 2 runs, lactate did not increase, whereas cfDNA increased steadily (3.46-fold for G1 and 2.05-fold for G2). Intraclass correlation for cfDNA was high (r = .81, P < .0001) for all runners but higher for male participants (r = .92, P < .0001). The correlations of cfDNA and lactate with RPEs were r = .58 (P < .0001) and r = .32 (P < .05), respectively. CONCLUSIONS Both duration and level of intensity were significantly associated with accumulation of cfDNA. The correlation with RPE and the high test-retest reliability suggest that cfDNA might be applicable as a marker to monitor individual training load for aerobic and intermittent exercises. Future randomized, controlled, longitudinal training studies will have to reveal the full potential of cfDNA as an exercise-physiology marker.
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Lo YMD, Lam WKJ. Tracing the tissue of origin of plasma DNA-feasibility and implications. Ann N Y Acad Sci 2016; 1376:14-7. [PMID: 27525383 DOI: 10.1111/nyas.13163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/01/2016] [Indexed: 12/01/2022]
Abstract
Scientists have been exploring cell-free DNA in plasma for a wider clinical application in addition to noninvasive prenatal testing. Tracing the tissue of origin of plasma DNA is the next important step. In this perspective, we discuss different approaches recently reported for tracing the tissue of origin of plasma DNA and the implications.
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Affiliation(s)
- Yuk Ming Dennis Lo
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China. .,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Wai Kei Jacky Lam
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
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Abstract
Circulating tumor DNA (ctDNA) in the plasma or serum of cancer patients provides an opportunity for non-invasive sampling of tumor DNA. This 'liquid biopsy' allows for interrogations of DNA such as quantity, chromosomal alterations, sequence mutations and epigenetic changes, and can be used to guide and improve treatment throughout the course of the disease. This tremendous potential for real-time 'tracking' in a cancer patient has led to substantial research efforts in the ctDNA field. ctDNA can be distinguished from non-tumor DNA by the presence of tumor-specific mutations and copy number variations, and also by aberrant DNA methylation, with both DNA sequence and methylation changes corresponding to those found in the tumor. Aberrant methylation of specific promoter regions can be a very consistent feature of cancer, in contrast to mutations, which typically occur at a wide range of sites. This consistency makes ctDNA methylation amenable to the design of widely applicable clinical assays. In this review, we examine ctDNA methylation in the context of monitoring disease status, treatment response and determining the prognosis of cancer patients.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Kate L Mahon
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Goli Samimi
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
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Ghanbari R, Mosakhani N, Sarhadi VK, Armengol G, Nouraee N, Mohammadkhani A, Khorrami S, Arefian E, Paryan M, Malekzadeh R, Knuutila S. Simultaneous Underexpression of let-7a-5p and let-7f-5p microRNAs in Plasma and Stool Samples from Early Stage Colorectal Carcinoma. Biomark Cancer 2016; 7:39-48. [PMID: 26793011 PMCID: PMC4711391 DOI: 10.4137/bic.s25252] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/17/2015] [Accepted: 09/23/2015] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is the third most common malignancy and the second most common cause of cancer death worldwide. Early detection of CRC can improve patient survival rates; thus, the identification of noninvasive diagnostic markers is urgently needed. MicroRNAs (miRNAs) have extensive potential to diagnose several diseases, including cancer. In this study, we compared the expression pattern of miRNAs from plasma and stool samples of patients with early stages of CRC (I, II) with that of healthy subjects. We performed miRNA profiling using microarrays on plasma and stool samples of eight patients with CRC and four healthy subjects. Seven miRNAs were found to be underexpressed in both plasma and stool samples of patients with CRC versus healthy subjects. Then, we aimed to verify two out of these seven differentially expressed miRNAs (let-7a-5p and let-7f-5p) by quantitative reverse transcriptase polymerase chain reaction on a larger set of plasma and stool samples of 51 patients with CRC and 26 healthy subjects. We confirmed the results of microarray analysis since their expression was significantly lower in stool and plasma samples of patients with CRC. Moreover, receiver operating characteristic curve analysis demonstrated that fecal let-7f expression levels have significant sensitivity and specificity to distinguish between patients with CRC and healthy subjects. In conclusion, if the results are confirmed in larger series of patients, underexpressed let-7a-5p and let-7f-5p miRNAs in both plasma and stool samples of patients with CRC may serve potentially as noninvasive molecular biomarkers for the early detection of CRC.
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Affiliation(s)
- Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Mosakhani
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland
| | - Virinder K Sarhadi
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland
| | - Gemma Armengol
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland.; Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Nazila Nouraee
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Moddares University, Tehran, Iran
| | - Ashraf Mohammadkhani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Khorrami
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mahdi Paryan
- Research and Development Department, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland
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21
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Li Z, Jiang L, Bai H, Wang Z, Zhao J, Duan J, Yang X, An T, Wang J. Prevalence and clinical significance of BRAF V600E in Chinese patients with lung adenocarcinoma. Thorac Cancer 2015; 6:269-74. [PMID: 26273372 PMCID: PMC4448387 DOI: 10.1111/1759-7714.12177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/07/2014] [Indexed: 01/03/2023] Open
Abstract
Background The purpose of this study was to investigate the prevalence, distribution, and prognostic role of v-raf murine sarcoma viral oncogene homolog B (BRAF) V600E mutations in Chinese patients with lung adenocarcinoma (ADC), and to explore the possibility of BRAF V600E mutation detection in plasma DNA. Methods Data from 190 patients with lung ADCs treated at the Peking University Cancer Hospital from July 2011 to March 2012 were collected. The amplification refractory mutation system was used for BRAF V600E testing and denaturing high-performance liquid chromatography for epidermal growth factor receptor (EGFR) mutation detection. In BRAF V600E-mutant cases, paired plasma DNA was tested for mutation status of BRAF V600E and EGFR. The distribution and prognostic role of BRAF V600E mutations were analyzed using SPSS 13.0. Results Among 190 patients with advanced lung ADC, eight (4.2%) cases carried BRAF V600E mutations. V600E mutations presented more frequently in women than in men (6 of 96, 6.3% vs. P = 0.1). BRAF and EGFR mutations were concomitantly presented in three patients. Five of the eight patients with BRAF V600E mutations had matched plasma DNA samples and V600E mutations were found in three plasma samples. Conclusion The prevalence of BRAF V600E mutations in Chinese patients with lung ADC is 4.2%. Circulating plasma DNA may be used for BRAF V600E mutation analysis in lung adenocarcinoma.
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Affiliation(s)
- Zhenxiang Li
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Leilei Jiang
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Hua Bai
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Zhijie Wang
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Jun Zhao
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Jianchun Duan
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Xiaodan Yang
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Tongtong An
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
| | - Jie Wang
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Medical Oncology, Beijing Cancer Hospital & Institute, Peking University School of Oncology Beijing, China
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Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
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23
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Imwong M, Woodrow CJ, Hendriksen ICE, Veenemans J, Verhoef H, Faiz MA, Mohanty S, Mishra S, Mtove G, Gesase S, Seni A, Chhaganlal KD, Day NPJ, Dondorp AM, White NJ. Plasma concentration of parasite DNA as a measure of disease severity in falciparum malaria. J Infect Dis 2014; 211:1128-33. [PMID: 25344520 PMCID: PMC4354984 DOI: 10.1093/infdis/jiu590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In malaria-endemic areas, Plasmodium falciparum parasitemia is common in apparently healthy children and severe malaria is commonly misdiagnosed in patients with incidental parasitemia. We assessed whether the plasma Plasmodium falciparum DNA concentration is a useful datum for distinguishing uncomplicated from severe malaria in African children and Asian adults. P. falciparum DNA concentrations were measured by real-time polymerase chain reaction (PCR) in 224 African children (111 with uncomplicated malaria and 113 with severe malaria) and 211 Asian adults (100 with uncomplicated malaria and 111 with severe malaria) presenting with acute falciparum malaria. The diagnostic accuracy of plasma P. falciparum DNA concentrations in identifying severe malaria was 0.834 for children and 0.788 for adults, similar to that of plasma P. falciparum HRP2 levels and substantially superior to that of parasite densities (P < .0001). The diagnostic accuracy of plasma P. falciparum DNA concentrations plus plasma P. falciparum HRP2 concentrations was significantly greater than that of plasma P. falciparum HRP2 concentrations alone (0.904 for children [P = .004] and 0.847 for adults [P = .003]). Quantitative real-time PCR measurement of parasite DNA in plasma is a useful method for diagnosing severe falciparum malaria on fresh or archived plasma samples.
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Affiliation(s)
| | - Charles J Woodrow
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine, Churchill Hospital, University of Oxford
| | - Ilse C E Hendriksen
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine, Churchill Hospital, University of Oxford
| | - Jacobien Veenemans
- Cell Biology and Immunology Group, Wageningen University Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, the Netherlands
| | - Hans Verhoef
- MRC International Nutrition Group, London School of Hygiene and Tropical Medicine, United Kingdom Cell Biology and Immunology Group, Wageningen University MRC Keneba, the Gambia
| | | | | | - Saroj Mishra
- Department of Medicine, Ispat Hospital, Rourkela, India
| | - George Mtove
- Amani Centre, National Institute for Medical Research, Muheza
| | - Samwel Gesase
- Korogwe Research Laboratory, National Institute for Medical Research, Tanga, Tanzania
| | | | - Kajal D Chhaganlal
- Hospital Central da Beira Faculty of Health Sciences, Catholic University of Mozambique, Beira, Mozambique
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine, Churchill Hospital, University of Oxford
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine, Churchill Hospital, University of Oxford
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine, Churchill Hospital, University of Oxford
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24
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Sorensen BS, Wu L, Wei W, Tsai J, Weber B, Nexo E, Meldgaard P. Monitoring of epidermal growth factor receptor tyrosine kinase inhibitor-sensitizing and resistance mutations in the plasma DNA of patients with advanced non-small cell lung cancer during treatment with erlotinib. Cancer 2014; 120:3896-901. [PMID: 25103305 PMCID: PMC4303984 DOI: 10.1002/cncr.28964] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND The feasibility of monitoring epidermal growth factor receptor (EGFR) mutations in plasma DNA from patients with advanced non-small cell lung cancer (NSCLC) during treatment with erlotinib and its relation to disease progression was investigated. METHODS The amount of EGFR-mutant DNA was tested in plasma DNA from patients with advanced NSCLC with allele-specific polymerase chain reaction assays. Blood samples from 23 patients with adenocarcinoma of NSCLC that carried tyrosine kinase inhibitor-sensitizing EGFR mutations were taken immediately before treatment with erlotinib. Additional blood samples were taken at timed intervals until erlotinib treatment was withdrawn. RESULTS The amount of plasma DNA with sensitizing EGFR mutations was found to be reduced after the first cycle of erlotinib treatment in 22 of 23 patients (96%). No patients presented with the resistant T790M mutation in the pretreatment sample, but at the time of disease progression the mutation was detected in plasma from 9 patients (39%). The quantitative data from the current study demonstrated that when a T790M mutation emerged in the blood it was accompanied by an increase in the original sensitizing EGFR mutation. When T790M was detected, it was found to be present in all subsequent blood samples from that patient. Most interestingly, the results of the current study demonstrated that monitoring the EGFR mutations in the blood allows for the detection of the T790M mutation up to 344 days before disease progression is clinically evident (range, 15-344 days). CONCLUSIONS The results of the current study demonstrated that serial monitoring of EGFR mutations in plasma DNA is feasible and may allow for the early detection of resistance mutations. These results warrant further studies to explore the clinical usefulness of such analysis.
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Affiliation(s)
- Boe S Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
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Rodrigues Filho EM, Simon D, Ikuta N, Klovan C, Dannebrock FA, Oliveira de Oliveira C, Regner A. Elevated cell-free plasma DNA level as an independent predictor of mortality in patients with severe traumatic brain injury. J Neurotrauma 2014; 31:1639-46. [PMID: 24827371 DOI: 10.1089/neu.2013.3178] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Trauma is the leading cause of death in individuals less than 45 years old worldwide, and up to 50% of trauma fatalities are because of brain injury. Prediction of outcome is one of the major problems associated with severe traumatic brain injury (TBI), and research efforts have focused on the investigation of biomarkers with prognostic value after TBI. Therefore, our aim was to investigate whether cell-free DNA concentrations correlated to short-term primary outcome (survival or death) and Glasgow Coma Scale (GCS) scores after severe TBI. A total of 188 patients with severe TBI were enrolled in this prospective study; outcome variables comprised survival and neurological assessment using the GCS at intensive care unit (ICU) discharge. Control blood samples were obtained from 25 healthy volunteers. Peripheral venous blood was collected at admission to the ICU. Plasma DNA was measured using a real-time quantitative polymerase chain reaction (PCR) assay for the β-globin gene. There was correlation between higher DNA levels and both fatal outcome and lower hospital admission GCS scores. Plasma DNA concentrations at the chosen cutoff point (≥171,381 kilogenomes-equivalents/L) predicted mortality with a specificity of 90% and a sensitivity of 43%. Logistic regression analysis showed that elevated plasma DNA levels were independently associated with death (p<0.001). In conclusion, high cell-free DNA concentration was a predictor of short-term mortality after severe TBI.
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Yeang CH, Ma GC, Hsu HW, Lin YS, Chang SM, Cheng PJ, Chen CA, Ni YH, Chen M. Genome-wide normalized score: a novel algorithm to detect fetal trisomy 21 during non-invasive prenatal testing. Ultrasound Obstet Gynecol 2014; 44:25-30. [PMID: 24700679 DOI: 10.1002/uog.13377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/19/2014] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
OBJECTIVES Non-invasive prenatal testing for fetal trisomy 21 (T21) by massively parallel shotgun sequencing (MPSS) is available for clinical use but its efficacy is limited by several factors, e.g. the proportion of cell-free fetal DNA in maternal plasma and sequencing depth. Existing algorithms discard DNA reads from the chromosomes for which testing is not being performed (i.e. those other than chromosome 21) and are thus more susceptible to diluted fetal DNA and limited sequencing depth. We aimed to describe and evaluate a novel algorithm for aneuploidy detection (genome-wide normalized score (GWNS)), which normalizes read counts by the proportions of DNA fragments from chromosome 21 in normal controls. METHODS We assessed the GWNS approach by comparison with two existing algorithms, i.e. Z-score and normalized chromosome value (NCV), using theoretical approximations and computer simulations in a set of 86 cases (64 euploid and 22 T21 cases). We then validated GWNS by studying an expanded set of clinical samples (n = 208). Finally, dilution experiments were undertaken to compare performance of the three algorithms (Z-score, NCV, GWNS) when fetal DNA concentration was low. RESULTS At fixed levels of significance and power, GWNS required a smaller fetal DNA proportion and fewer total MPSS reads compared to Z-score or NCV. In dilution experiments, GWNS also outperformed the other two methods by reaching the correct diagnosis with the lowest range of fetal DNA concentrations (GWNS, 3.83-4.75%; Z-score, 4.75-5.22%; NCV, 6.47-8.58%). CONCLUSION Our results demonstrate that GWNS is comparable to Z-score and NCV methods regarding the performance of detecting fetal T21. Dilution experiments suggest that GWNS may perform better than the other methods when fetal fraction is low.
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Affiliation(s)
- C H Yeang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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Takane K, Midorikawa Y, Yagi K, Sakai A, Aburatani H, Takayama T, Kaneda A. Aberrant promoter methylation of PPP1R3C and EFHD1 in plasma of colorectal cancer patients. Cancer Med 2014; 3:1235-45. [PMID: 24861485 PMCID: PMC4302673 DOI: 10.1002/cam4.273] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/17/2014] [Accepted: 04/23/2014] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a common epigenetic alteration involved in colorectal cancer (CRC). In our previous study, we performed methylated DNA immunoprecipitation-on-chip analysis combined with gene re-expression analysis by 5-aza-2′-deoxycytidine treatment, to identify methylation genes in CRC genome widely. Among these genes, 12 genes showed aberrant hypermethylation frequently in >75% of 149 CRC samples but did not in normal samples. In this study, we aim to find out any of these methylation genes to be utilized for CRC detection using plasma DNA samples. Primers for methylation-specific PCR and pyrosequencing were designed for seven of the 12 genes. Among them, PPP1R3C and EFHD1 were rarely hypermethylated in peripheral blood cells, but frequently hypermethylated in 24 CRC tissue samples and their corresponding plasma samples. In plasma samples, PPP1R3C was methylated in 81% (97/120) of CRC patients, but only in 19% (18/96) of noncancer patients (P = 6 × 10−20, Fisher's exact test). In combined analysis with EFHD1, both genes were methylated in 53% (64/120) of CRC patients, but only in 4% (4/96) of noncancer patients (P = 2 × 10−16), giving high specificity of 96%. At least one of the two genes was methylated in 90% (108/120) of CRC patients, and 36% (35/96) of control patients, giving high sensitivity of 90%. Compared with low sensitivity of carcinoembryonic antigen (17% at stage I, 40% at stage II) and CA19-9 (0% at stage I, 13% at stage II) for early-stage CRCs, sensitivity of aberrant methylation was significantly higher: PPP1R3C methylation at 92% (11/12) for stage I and 77% (23/30) for stage II, and methylation of at least one gene at 100% (12/12) for stage I and 87% (26/30) for stage II. PPP1R3C methylation or its combined use of EFHD1 methylation was highly positive in CRC plasma samples, and they might be useful in detection of CRC, especially for early-stage CRCs.
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Affiliation(s)
- Kiyoko Takane
- Department of Digestive Surgery and Pathology, Nihon University School of Medicine, Tokyo, Japan; Department of Molecular Oncology, Graduate school of Medicine, Chiba University, Chiba, Japan
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Pan S, Gu B, Wang H, Yan Z, Wang P, Pei H, Xie W, Chen D, Liu G. Comparison of four DNA extraction methods for detecting Mycobacterium tuberculosis by real-time PCR and its clinical application in pulmonary tuberculosis. J Thorac Dis 2013; 5:251-7. [PMID: 23825755 DOI: 10.3978/j.issn.2072-1439.2013.05.08] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 05/13/2013] [Indexed: 11/14/2022]
Abstract
OBJECTIVES China is one of the countries with a high burden of Mycobacterium tuberculosis (MTB) infection. One challenge for the earlier diagnosis of tuberculosis is the DNA extraction of MTB. This study was to compare four MTB DNA extraction methods, and use the best one in the diagnosis of pulmonary tuberculosis. METHODS A total of 43 serum and 94 plasma samples were collected from 124 clinical diagnosed pulmonary tuberculosis patients. Four different MTB DNA extraction methods, including phenol-chloroform method, Qiagen kit, Omega kit and magnetic bead method, were compared to determine which method displayed the highest sensitivity. A quantitative fluorescent PCR assay was also designed for the detection of MTB DNA. RESULTS The highest DNA extraction efficiency (52.8%) and the best reproducibility (coefficient of variance =26.7%) were observed using the magnetic bead method. For 39 of the 124 (31.5%) pulmonary tuberculosis patients, MTB DNA was detected in their plasma or serum samples. Interestingly, 35.3% (12/34) of smear-negative cases were MTB DNA positive. CONCLUSIONS In conclusion, magnetic bead method is the best one for the DNA extraction of MTB. The detection of MTB DNA may provide valuable information for the diagnosis of acid-fast bacilli (AFB) negative pulmonary tuberculosis patients.
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Affiliation(s)
- Shiyang Pan
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; ; National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
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