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Kresse SH, Brandt-Winge S, Pharo H, Flatin BTB, Jeanmougin M, Vedeld HM, Lind GE. Evaluation of commercial kits for isolation and bisulfite conversion of circulating cell-free tumor DNA from blood. Clin Epigenetics 2023; 15:151. [PMID: 37710283 PMCID: PMC10503171 DOI: 10.1186/s13148-023-01563-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND DNA methylation biomarkers in circulating cell-free DNA (cfDNA) have great clinical potential for cancer management. Most methods for DNA methylation analysis require bisulfite conversion, causing DNA degradation and loss. This is particularly challenging for cfDNA, which is naturally fragmented and normally present in low amounts. The aim of the present study was to identify an optimal combination of cfDNA isolation and bisulfite conversion kits for downstream analysis of DNA methylation biomarkers in plasma. RESULTS Of the five tested bisulfite conversion kits (EpiJET Bisulfite Conversion Kit, EpiTect Plus DNA Bisulfite Kit (EpiTect), EZ DNA Methylation-Direct Kit, Imprint DNA Modification Kit (Imprint) and Premium Bisulfite Kit), the highest and lowest DNA yield and recovery were achieved using the EpiTect kit and the Imprint kit, respectively, with more than double the amount of DNA for the EpiTect kit. Of the three tested cfDNA isolation kits (Maxwell RSC ccfDNA Plasma Kit, QIAamp Circulating Nucleic Acid Kit (CNA) and QIAamp MinElute ccfDNA Mini Kit), the CNA kit yielded around twice as much cfDNA compared to the two others kits, although with more high molecular weight DNA present. When comparing various combinations of cfDNA isolation kits and bisulfite conversion kits, the CNA kit and the EpiTect kit were identified as the best-performing combination, resulting in the highest yield of bisulfite converted cfDNA from normal plasma, as measured by droplet digital PCR (ddPCR). As a proof of principle, this kit combination was used to process plasma samples from 13 colorectal cancer patients for subsequent ddPCR methylation analysis of BCAT1 and IKZF1. Methylation of BCAT1 and/or IKZF1 was identified in 6/10 (60%) stage IV patients and 1/3 (33%) stage III patients. CONCLUSIONS Based on a thorough evaluation of five bisulfite conversion kits and three cfDNA isolation kits, both individually and in combination, the CNA kit and the EpiTect kit were identified as the best-performing kit combination, with highest DNA yield and recovery across a range of DNA input amounts. The combination was successfully used for detection of clinically relevant DNA methylation biomarkers in plasma from cancer patients.
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Affiliation(s)
- Stine H Kresse
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Sara Brandt-Winge
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Heidi Pharo
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Bjørnar T B Flatin
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway.
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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2
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Richter F, Henssen C, Steiert TA, Meissner T, Mehdorn AS, Röcken C, Franke A, Egberts JH, Becker T, Sebens S, Forster M. Combining Solid and Liquid Biopsy for Therapy Monitoring in Esophageal Cancer. Int J Mol Sci 2023; 24:10673. [PMID: 37445849 DOI: 10.3390/ijms241310673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
Esophageal cancer (EC) has one of the highest mortality rates among cancers, making it imperative that therapies are optimized and dynamically adapted to individuals. In this regard, liquid biopsy is an increasingly important method for residual disease monitoring. However, conflicting detection rates (14% versus 60%) and varying cell-free circulating tumor DNA (ctDNA) levels (0.07% versus 0.5%) have been observed in previous studies. Here, we aim to resolve this discrepancy. For 19 EC patients, a complete set of cell-free DNA (cfDNA), formalin-fixed paraffin-embedded tumor tissue (TT) DNA and leukocyte DNA was sequenced (139 libraries). cfDNA was examined in biological duplicates and/or longitudinally, and TT DNA was examined in technical duplicates. In baseline cfDNA, mutations were detected in 12 out of 19 patients (63%); the median ctDNA level was 0.4%. Longitudinal ctDNA changes were consistent with clinical presentation. Considerable mutational diversity was observed in TT, with fewer mutations in cfDNA. The most recurrently mutated genes in TT were TP53, SMAD4, TSHZ3, and SETBP1, with SETBP1 being reported for the first time. ctDNA in blood can be used for therapy monitoring of EC patients. However, a combination of solid and liquid samples should be used to help guide individualized EC therapy.
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Affiliation(s)
- Florian Richter
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Clara Henssen
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | | | - Tobias Meissner
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA
| | - Anne-Sophie Mehdorn
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Jan-Hendrik Egberts
- Department of Surgery, Israelitisches Krankenhaus Hamburg, 22297 Hamburg, Germany
| | - Thomas Becker
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
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3
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Yuwono NL, Boyd MAA, Henry CE, Werner B, Ford CE, Warton K. Circulating cell-free DNA undergoes significant decline in yield after prolonged storage time in both plasma and purified form. Clin Chem Lab Med 2022; 60:1287-1298. [DOI: 10.1515/cclm-2021-1152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/16/2022] [Indexed: 11/15/2022]
Abstract
Abstract
Objectives
Circulating DNA (cirDNA) is generally purified from plasma that has been biobanked for variable lengths of time. In long-term experiments or clinical trials, the plasma can be stored frozen for up to several years. Therefore, it is crucial to determine the stability of cirDNA to ensure confidence in sample quality upon analysis. Our main objective was to determine the effect of storage for up to 2 years on cirDNA yield and fragmentation.
Methods
We stored frozen EDTA plasma and purified cirDNA from 10 healthy female donors, then quantified cirDNA yield at baseline, and at regular intervals for up to 2 years, by qPCR and Qubit. We also compared cirDNA levels in non-haemolysed and haemolysed blood samples after 16 months of storage and tested the effect of varying DNA extraction protocol parameters.
Results
Storage up to two years caused an annual cirDNA yield decline of 25.5% when stored as plasma and 23% when stored as purified DNA, with short fragments lost more rapidly than long fragments. Additionally, cirDNA yield was impacted by plasma input and cirDNA elution volumes, but not by haemolysis.
Conclusions
The design of long-term cirDNA-based studies and clinical trials should factor in the deterioration of cirDNA during storage.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Mollie Ailie Acheson Boyd
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Claire Elizabeth Henry
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Bonnita Werner
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women’s and Children’s Health, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales , Sydney , Australia
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4
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Cédile O, Veyhe SR, Hansen MH, Titlestad K, Nyvold CG. Investigation of circulating DNA integrity after blood collection. Biotechniques 2021; 71:550-555. [PMID: 34645292 DOI: 10.2144/btn-2020-0167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Method summary Concentrations of circulating DNA in blood plasma were compared using NanoDrop, Qubit, quantitative PCR and Bioanalyzer, and DNA integrity was evaluated with the Bioanalyzer according to the time of plasma preparation.
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Affiliation(s)
- Oriane Cédile
- Haematology-Pathology Research Laboratory, Research Unit for Haematology & Research Unit for Pathology, University of Southern Denmark & Odense University Hospital, Odense, Denmark.,OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | | | - Marcus Høy Hansen
- Haematology-Pathology Research Laboratory, Research Unit for Haematology & Research Unit for Pathology, University of Southern Denmark & Odense University Hospital, Odense, Denmark
| | - Kjell Titlestad
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Charlotte Guldborg Nyvold
- Haematology-Pathology Research Laboratory, Research Unit for Haematology & Research Unit for Pathology, University of Southern Denmark & Odense University Hospital, Odense, Denmark.,OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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5
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Krasic J, Abramovic I, Vrtaric A, Nikolac Gabaj N, Kralik-Oguic S, Katusic Bojanac A, Jezek D, Sincic N. Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics. Front Cell Dev Biol 2021; 9:686149. [PMID: 34552921 PMCID: PMC8451956 DOI: 10.3389/fcell.2021.686149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/13/2021] [Indexed: 01/18/2023] Open
Abstract
While tissue biopsy has for the longest time been the gold-standard in biomedicine, precision/personalized medicine is making the shift toward liquid biopsies. Cell-free DNA (cfDNA) based genetic and epigenetic biomarkers reflect the molecular status of its tissue-of-origin allowing for early and non-invasive diagnostics of different pathologies. However, selection of preanalytical procedures (including cfDNA isolation) as well as analytical methods are known to impact the downstream results. Calls for greater standardization are made continuously, yet comprehensive assessments of the impact on diagnostic parameters are lacking. This study aims to evaluate the preanalytic and analytic factors that influence cfDNA diagnostic parameters in blood and semen. Text mining analysis has been performed to assess cfDNA research trends, and identify studies on isolation methods, preanalytical and analytical impact. Seminal and blood plasma were tested as liquid biopsy sources. Traditional methods of cfDNA isolation, commercial kits (CKs), and an in-house developed protocol were tested, as well as the impact of dithiothreitol (DTT) on cfDNA isolation performance. Fluorimetry, qPCR, digital droplet PCR (ddPCR), and bioanalyzer were compared as cfDNA quantification methods. Fragment analysis was performed by qPCR and bioanalyzer while the downstream application (cfDNA methylation) was analyzed by pyrosequencing. In contrast to blood, semen as a liquid biopsy source has only recently begun to be reported as a liquid biopsy source, with almost half of all publications on it being review articles. Experimental data revealed that cfDNA isolation protocols give a wide range of cfDNA yields, both from blood and seminal plasma. The addition of DTT to CKs has improved yields in seminal plasma and had a neutral/negative impact in blood plasma. Capillary electrophoresis and fluorometry reported much higher yields than PCR methods. While cfDNA yield and integrity were highly impacted, cfDNA methylation was not affected by isolation methodology or DTT. In conclusion, NucleoSnap was recognized as the kit with the best overall performance. DTT improved CK yields in seminal plasma. The in-house developed protocol has shown near-kit isolation performance. ddPCR LINE-1 assay for absolute detection of minute amounts of cfDNA was established and allowed for quantification of samples inhibited in qPCR. cfDNA methylation was recognized as a stable biomarker unimpacted by cfDNA isolation method. Finally, semen was found to be an abundant source of cfDNA offering potential research opportunities and benefits for cfDNA based biomarkers development related to male reproductive health.
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Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Irena Abramovic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Alen Vrtaric
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nora Nikolac Gabaj
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Sasa Kralik-Oguic
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Clinical Institute of Laboratory Diagnostics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
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6
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Till JE, Black TA, Gentile C, Abdalla A, Wang Z, Sangha HK, Roth JJ, Sussman R, Yee SS, O'Hara MH, Thompson JC, Aggarwal C, Hwang WT, Elenitoba-Johnson KSJ, Carpenter EL. Optimization of Sources of Circulating Cell-Free DNA Variability for Downstream Molecular Analysis. J Mol Diagn 2021; 23:1545-1552. [PMID: 34454115 DOI: 10.1016/j.jmoldx.2021.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 06/10/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
Circulating cell-free DNA (ccfDNA) is used increasingly as a cancer biomarker for prognostication, as a correlate for tumor volume, or as input for downstream molecular analysis. Determining optimal blood processing and ccfDNA quantification are crucial for ccfDNA to serve as an accurate biomarker as it moves into the clinical realm. Whole blood was collected from 50 subjects, processed to plasma, and used immediately or frozen at -80°C. Plasma ccfDNA was extracted and concentration was assessed by real-time quantitative PCR (qPCR), fluorimetry, and droplet digital PCR (ddPCR). For the 24 plasma samples from metastatic pancreatic cancer patients, the variant allele fractions (VAF) of KRAS G12/13 pathogenic variants in circulating tumor DNA (ctDNA) were measured by ddPCR. Using a high-speed (16,000 × g) or slower-speed (4100 × g) second centrifugation step showed no difference in ccfDNA yield or ctDNA VAF. A two- versus three-spin centrifugation protocol also showed no difference in ccfDNA yield or ctDNA VAF. A higher yield was observed from fresh versus frozen plasma by qPCR and fluorimetry, whereas a higher yield was observed for frozen versus fresh plasma by ddPCR, however, no difference was observed in ctDNA VAF. Overall, our findings suggest factors to consider when implementing a ccfDNA extraction and quantification workflow in a research or clinical setting.
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Affiliation(s)
- Jacob E Till
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor A Black
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Caren Gentile
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aseel Abdalla
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhuoyang Wang
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hareena K Sangha
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacquelyn J Roth
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robyn Sussman
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark H O'Hara
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey C Thompson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charu Aggarwal
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kojo S J Elenitoba-Johnson
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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7
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Revuelta-López E, Barallat J, Cserkóová A, Gálvez-Montón C, Jaffe AS, Januzzi JL, Bayes-Genis A. Pre-analytical considerations in biomarker research: focus on cardiovascular disease. Clin Chem Lab Med 2021; 59:1747-1760. [PMID: 34225398 DOI: 10.1515/cclm-2021-0377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022]
Abstract
Clinical biomarker research is growing at a fast pace, particularly in the cardiovascular field, due to the demanding requirement to provide personalized precision medicine. The lack of a distinct molecular signature for each cardiovascular derangement results in a one-size-fits-all diagnostic and therapeutic approach, which may partially explain suboptimal outcomes in heterogeneous cardiovascular diseases (e.g., heart failure with preserved ejection fraction). A multidimensional approach using different biomarkers is quickly evolving, but it is necessary to consider pre-analytical variables, those to which a biological sample is subject before being analyzed, namely sample collection, handling, processing, and storage. Pre-analytical errors can induce systematic bias and imprecision, which may compromise research results, and are easy to avoid with an adequate study design. Academic clinicians and investigators must be aware of the basic considerations for biospecimen management and essential pre-analytical recommendations as lynchpin for biological material to provide efficient and valid data.
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Affiliation(s)
- Elena Revuelta-López
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Jaume Barallat
- Biochemistry Service, University Hospital Germans Trias i Pujol, Badalona, Spain
| | - Adriana Cserkóová
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Carolina Gálvez-Montón
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Allan S Jaffe
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - James L Januzzi
- Cardiology Division, Massachusetts General Hospital Harvard Medical School, Harvard University, Boston, MA, USA
| | - Antoni Bayes-Genis
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Heart Institute, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, 08916 Badalona, Barcelona, Spain
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8
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Colmer SF, Luethy D, Abraham M, Stefanovski D, Hurcombe SD. Utility of cell-free DNA concentrations and illness severity scores to predict survival in critically ill neonatal foals. PLoS One 2021; 16:e0242635. [PMID: 33901192 PMCID: PMC8075268 DOI: 10.1371/journal.pone.0242635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 11/18/2022] Open
Abstract
Plasma cell-free DNA (cfDNA) levels have been associated with disease and survival status in septic humans and dogs. To date, studies investigating cfDNA levels in association with critical illness in foals are lacking. We hypothesized that cfDNA would be detectable in the plasma of foals, that septic and sick-nonseptic foals would have significantly higher cfDNA levels compared to healthy foals, and that increased cfDNA levels would be associated with non-survival. Animals used include 80 foals of 10 days of age or less admitted to a tertiary referral center between January and July, 2020 were stratified into three categories: healthy (n = 34), sick non-septic (n = 11) and septic (n = 35) based on specific criteria. This was a prospective clinical study. Blood was collected from critically ill foals at admission or born in hospital for cfDNA quantification and blood culture. Previously published sepsis score (SS) and neonatal SIRS score (NSIRS) were also calculated. SS, NSIRS, blood culture status and cfDNA concentrations were evaluated to predict survival. Continuous variables between groups were compared using Kruskal-Wallis ANOVA with Dunn’s post hoc test. Comparisons between two groups were assessed using the Mann-Whitney U-test or Spearman rank for correlations. The performance of cfDNA, sepsis score and NSIRS score to predict survival was assessed by receiver operator characteristic (ROC) curve analysis including area under the curve, sensitivity and specificity using cutoffs. Plasma cfDNA was detectable in all foals. No significant differences in cfDNA concentration were detected between healthy foals and septic foals (P = 0.65) or healthy foals and sick non-septic foals (P = 0.88). There was no significant association between cfDNA and culture status, SS, NSIRS or foal survival. SS (AUC 0.85) and NSIRS (AUC 0.83) were superior to cfDNA (AUC 0.64) in predicting survival. Although cfDNA was detectable in foal plasma, it offers negligible utility to diagnose sepsis or predict survival in critical illness in neonates.
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Affiliation(s)
- Sarah Florence Colmer
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Daniela Luethy
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Michelle Abraham
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Darko Stefanovski
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Samuel David Hurcombe
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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9
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Jiang X, Li H, Liu J, Sun H, Zhang L, Li W, Yao J, Cheng Y. Feasibility Analysis of Cell-Free DNA Derived from Plasma of Lung Cancer Patients for Next-Generation Sequencing. Biopreserv Biobank 2020; 18:117-121. [PMID: 32083487 DOI: 10.1089/bio.2019.0115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose: The quality of specimens directly affects the experimental results. The stability and structural integrity of nucleic acids in samples have a decisive influence on high-throughput sequencing results. Next-generation sequencing (NGS) provides the most comprehensive criteria for evaluating the specimen quality. To test the quality of cell-free DNA (cfDNA) from lung cancer plasma samples stored in our biobank, we conducted a study to evaluate the quality in terms of the genetic level. Methods: A total of 189 peripheral blood samples were collected from patients from patients with EGFR-positive nonsmall cell lung cancer who were seen and treated in Jilin Provincial Cancer Hospital from August 2012 to March 2018. Twelve milliliters of peripheral blood samples were collected and centrifuged at 4°C, 2000 rpm for 15 minutes. Plasma samples were dispensed into cryotubes and stored at -80°C. Plasma cfDNA was extracted by a DNA extraction kit (Qiagen) and the DNA concentration was detected by a Qubit 3.0 fluorometer. Results: The total volume of cfDNA extraction at baseline was 50 μL, the median concentration according to Qubit was 0.633 ng/μL, the range was 0.331-6.09 ng/μL, and the median total DNA was 34.25 ng, ranging from 20.35 to 304.5 ng. The median value of the Qubit concentration in advanced plasma samples was 0.838 ng/μL, ranging from 0.24 to 21.9 ng/μL, and median total DNA was 41.9 ng, ranging from 12.0 to 1095.0 ng. Based on the aforementioned quality assessment factors, 4 of 189 frozen lung cancer baseline plasma samples were not included in further analyses, and for the remaining 185 cases of cfDNA >20 ng, the pass rate was 97.9%. In 143 frozen lung cancer advanced stage plasma samples, 133 cases of cfDNA >20 ng, the pass rate was 93%. Conclusion: Frozen lung cancer plasma samples stored in the biobank for 1-6 years at -80°C under certain conditions still retain a high level of cfDNA, which is suitable for NGS detection.
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Affiliation(s)
- Xueli Jiang
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Hui Li
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China.,Medical Oncology Translational Research Lab, Jilin Provincial Cancer Hospital, Changchun, China
| | - Jingjing Liu
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Heping Sun
- Clinical Trial Institution, Jilin Provincial Cancer Hospital, Changchun, China
| | - Linna Zhang
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Wenxiu Li
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Jie Yao
- Biobank, Jilin Provincial Cancer Hospital, Changchun, China
| | - Ying Cheng
- Medical Oncology Translational Research Lab, Jilin Provincial Cancer Hospital, Changchun, China.,Department of Medical Thoracic Oncology, Jilin Provincial Cancer Hospital, Changchun, China
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