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Devonshire A, Jones G, Gonzalez AF, Kofanova O, Trouet J, Pinzani P, Gelmini S, Bonin S, Foy C. Interlaboratory evaluation of quality control methods for circulating cell-free DNA extraction. N Biotechnol 2023; 78:13-21. [PMID: 37730172 DOI: 10.1016/j.nbt.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Analysis of circulating cell-free DNA (ccfDNA) isolated from liquid biopsies is rapidly being implemented into clinical practice. However, diagnostic accuracy is significantly impacted by sample quality and standardised approaches for assessing the quality of ccfDNA are not yet established. In this study we evaluated the application of nucleic acid "spike-in" control materials to aid quality control (QC) and standardisation of cfDNA isolation for use in in vitro diagnostic assays. We describe an approach for the design and characterisation of in-process QC materials, illustrating it with a spike-in material containing an exogenous Arabidopsis sequence and DNA fragments approximating to ccfDNA and genomic DNA lengths. Protocols for inclusion of the spike-in material in plasma ccfDNA extraction and quantification of its recovery by digital PCR (dPCR) were assessed for their suitability for process QC in an inter-laboratory study between five expert laboratories, using a range of blood collection devices and ccfDNA extraction methods. The results successfully demonstrated that spiking plasmid-derived material into plasma did not deleteriously interfere with endogenous ccfDNA recovery. The approach performed consistently across a range of commonly-used extraction protocols and was able to highlight differences in efficiency and variability between the methods, with the dPCR quantification assay performing with good repeatability (generally CV <5%). We conclude that initial findings demonstrate that this approach appears "fit for purpose" and spike-in recovery can be combined with other extraction QC metrics for monitoring the performance of a process over time, or in the context of external quality assessment.
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Affiliation(s)
- Alison Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK.
| | - Gerwyn Jones
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
| | - Ana Fernandez Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
| | - Olga Kofanova
- Integrated BioBank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1, rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Johanna Trouet
- Integrated BioBank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1, rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Pamela Pinzani
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Stefania Gelmini
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Serena Bonin
- DSM-Dept. Medical Sciences, University of Trieste, Trieste, Italy
| | - Carole Foy
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
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2
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Analytic and Clinical Validation of a Pan-Cancer NGS Liquid Biopsy Test for the Detection of Copy Number Amplifications, Fusions and Exon Skipping Variants. Diagnostics (Basel) 2022; 12:diagnostics12030729. [PMID: 35328282 PMCID: PMC8947661 DOI: 10.3390/diagnostics12030729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 02/01/2023] Open
Abstract
Liquid biopsies are an integral part of the diagnosis of cancer. Here, we have extended previous validation studies of a new targeted NGS panel to include the detection of copy number amplifications (CNAs), fusions, and exon skipping variants. Detection of these gene classes included specimens from clinical and healthy donors and cell lines (fusions: ROS1, EML4-ALK, NTRK1; exon skipping: MET exon 14; CNAs: HER2, CDK6, EGFR, MYC, and MET). The limit of detection (LOD) for fusion/skipping was 42 copies (QC threshold was three copies) and was verified using three additional fusion/skipping variants. LOD for CNAs was 1.40-fold-change (QC threshold = 1.15-fold change) and was verified with three additional CNAs. In repeatability and intermediate precision (within lab) studies, all fusion/skipping variants were detected in all runs and all days of testing (n = 18/18; 100%); average CV for repeatability was 20.5% (range 8.7–34.8%), and for intermediate precision it was 20.8% (range 15.7–30.5%). For CNAs, 28/29 (96.6%) copy gains were detected. For CNAs, the average CV was 1.85% (range 0% to 5.49%) for repeatability and 6.59% (range 1.65% to 9.22%) for intermediate precision. The test panel meets the criteria for being highly sensitive and specific and extends its utility for the serial detection of clinically relevant variants in cancer.
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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4
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Mellert H, Reese J, Jackson L, Maxwell V, Tschida C, Pestano GA. Targeted Next-Generation Sequencing of Liquid Biopsy Samples from Patients with NSCLC. Diagnostics (Basel) 2021; 11:155. [PMID: 33494470 PMCID: PMC7912015 DOI: 10.3390/diagnostics11020155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/02/2023] Open
Abstract
Liquid biopsy tests have become an integral part of the molecular diagnosis of patients with non-small cell lung cancer (NSCLC). We describe a new test panel that uses very low input (20 ng) of cell-free nucleic acids extracted from human plasma, which is designed to yield results in less than 72 h. In this study, we performed novel amplicon-based targeted next-generation sequencing with a semiconductor-based system, the Ion GeneStudio S5 Prime. The analytic performance of the assay was evaluated using contrived and retrospectively collected clinical specimens. The cumulative percent coefficient of variation for the new test process was very precise at 8.4% for inter-day, 4.0% for inter-operator and 3.4% for inter-instrument. We also observed significant agreement (95.7-100%) with an orthogonal, high-sensitivity droplet digital™ Polymerase Chain Reaction (ddPCR) test. This method offers a valuable supplement to assessing targeted mutations from blood while conserving specimens and maintaining sensitivity, with rapid turn-around times to actionable results.
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Affiliation(s)
- Hestia Mellert
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, USA; (J.R.); (L.J.); (V.M.); (C.T.); (G.A.P.)
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5
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Garcia-Heredia I, Bhattacharjee AS, Fornas O, Gomez ML, Martínez JM, Martinez-Garcia M. Benchmarking of single-virus genomics: a new tool for uncovering the virosphere. Environ Microbiol 2021; 23:1584-1593. [PMID: 33368907 DOI: 10.1111/1462-2920.15375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 12/11/2020] [Accepted: 12/20/2020] [Indexed: 01/03/2023]
Abstract
Metagenomics and single-cell genomics have enabled the discovery of relevant uncultured microbes. Recently, single-virus genomics (SVG), although still in an incipient stage, has opened new avenues in viral ecology by allowing the sequencing of one single virus at a time. The investigation of methodological alternatives and optimization of existing procedures for SVG is paramount to deliver high-quality genomic data. We report a sequencing dataset of viral single-amplified genomes (vSAGs) from cultured and uncultured viruses obtained by applying different conditions in each SVG step, from viral preservation and novel whole-genome amplification (WGA) to sequencing platforms and genome assembly. Sequencing data showed that cryopreservation and mild fixation were compatible with WGA, although fresh samples delivered better genome quality data. The novel TruPrime WGA, based on primase-polymerase features, and WGA-X employing a thermostable phi29 polymerase, were proven to be with sufficient sensitivity in SVG. The Oxford Nanopore (ON) sequencing platform did not provide a significant improvement of vSAG assembly compared to Illumina alone. Finally, the SPAdes assembler performed the best. Overall, our results represent a valuable genomic dataset that will help to standardized and advance new tools in viral ecology.
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Affiliation(s)
| | | | - Oscar Fornas
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.,Flow Cytometry Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Monica L Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | | | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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7
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Bai R, Li L, Chen X, Chen N, Song W, Cui J. Neoadjuvant and Adjuvant Immunotherapy: Opening New Horizons for Patients With Early-Stage Non-small Cell Lung Cancer. Front Oncol 2020; 10:575472. [PMID: 33163406 PMCID: PMC7581706 DOI: 10.3389/fonc.2020.575472] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/03/2020] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the most common malignant tumor with the highest mortality, and about 84% are non-small cell lung cancer (NSCLC). However, only a small proportion of patients with newly diagnosed lung tumors can receive curative surgery and have a high risk of postoperative recurrence. At present, there are many perioperative treatment methods being continuously explored, such as chemotherapy and targeted therapy, continuously enriching the content of neoadjuvant and adjuvant therapy in early-stage NSCLC. But disappointingly, for patients with driver gene mutation, the significant disease-free survival (DFS) benefit of targeted drugs failed to translate into overall survival (OS) benefit, and for negative patients, chemotherapy has reached a plateau in improving efficacy and survival. Immunotherapy represented by immune checkpoint inhibitors (ICIs) has been researched in more and more clinical trials in patients with early-stage operable disease, gradually enriching the existing treatments. This review focuses on the research progress of clinical trials of neoadjuvant and adjuvant therapy with ICIs in early-stage NSCLC, the exploration of response evaluation and predictive biomarkers, and the urgent problems to be solved in the future.
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Affiliation(s)
| | | | | | | | | | - Jiuwei Cui
- Cancer Center, The First Hospital of Jilin University, Changchun, China
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8
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Zhang R, Hu Y, Zhou T, Han W, Liu Y, Qian J, Chen Y, Liu X, Liu S, Yu Y, Zeng H, Zhang H, Li Y. The mutation profiles of cell-free DNA in patients with oesophageal squamous cell carcinoma who were responsive and non-responsive to neoadjuvant chemotherapy. J Thorac Dis 2020; 12:4274-4283. [PMID: 32944339 PMCID: PMC7475527 DOI: 10.21037/jtd-20-230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background The aim of this study was to evaluate the clinical value of plasma cell-free DNA (cfDNA) mutation profiles in patients with oesophageal squamous cell carcinoma (OSCC) who received neoadjuvant chemotherapy. Methods Twenty-two OSCC patients received neoadjuvant chemotherapy and were divided into two groups according to their response to the therapy. Fifteen patients were in the responsive group, and seven patients were in the non-responsive group. The blood samples were collected, and the plasma cfDNA mutation profiles were sequenced by a cancer gene-targeted next-generation sequencing (NGS) panel. Results The driver gene molecular mutation burden (MMB) was significantly higher in the non-responsive group compared with the responsive group. Furthermore, we found that the differential MMB included the DNA damage response, Wnt, PI3K, Hippo, RTK/RAS, p53, and AHR pathway. The MMB yielded an area under the receiver operation characteristic (ROC) curve of 0.89 for predicting the response to neoadjuvant chemotherapy. The cfDNA copy number variations (CNVs) yielded an area under ROC curve of 1.0 for predicting the response to neoadjuvant chemotherapy. Conclusions The driver gene MMB and CNVs in plasma cfDNA may be potential biomarkers for predicting the response to neoadjuvant chemotherapy in patients with OSCC.
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Affiliation(s)
- Ruixiang Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou, China
| | - Ying Hu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Tao Zhou
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Wenbo Han
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Yang Liu
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Juanjuan Qian
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Yanhui Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xianben Liu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou, China
| | - Shilei Liu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou, China
| | - Yongkui Yu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou, China
| | - Hui Zeng
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yin Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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9
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Hu Y, Chen Y, Guo H, Yu J, Chen Y, Liu Y, Lan L, Li J, Wang H, Zhang H. Molecular Alterations in Circulating Cell-Free DNA in Patients with Colorectal Adenoma or Carcinoma. Cancer Manag Res 2020; 12:5159-5167. [PMID: 32636678 PMCID: PMC7335290 DOI: 10.2147/cmar.s244520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this study was to evaluate the clinical value of plasma cell-free DNA (cfDNA) in the diagnosis of colorectal cancer (CRC). Patients and Methods The plasma cfDNA and tissue DNA mutation profiles were investigated in 77 patients (9 colon polyps, 18 colon adenoma, 26 colon cancer, and 24 rectal cancer) by a cancer gene-targeted NGS panel. Results During the progression from adenoma to carcinoma, mutations occur in genes such as RAS, Wnt, Hippo, Nrf2, TGFβ, PI3K, Notch, and P53, as well as in those encoding cell cycle pathway components. The somatic mutation burden and plasma cfDNA concentration were significantly higher in the colon carcinoma group than in the adenoma and colon polyp groups. The combination of plasma cfDNA concentration, CEA, and cfDNA had a significantly greater area under the curve than cfDNA or CEA alone. Right-sided colon cancer tissues showed a greater distribution of somatic mutations among more genes than left-sided colon cancer tissues. In addition, tissue tumor mutational burden (TMB) was higher in the right-sided colon cancer group than in the rectal cancer or left-sided colon cancer group (P<0.05). Conclusion These results may indicate that somatic mutations in plasma cfDNA are potential biomarkers for the diagnosis of CRC. In addition, somatic mutations may be distributed in more genes and pathways in right-sided colon cancer than in left-side colon cancer.
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Affiliation(s)
- Ying Hu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, People's Republic of China
| | - Yawei Chen
- Genecast Precision Medicine Technology Institute, Beijing 100000, People's Republic of China
| | - Hao Guo
- Genecast Precision Medicine Technology Institute, Beijing 100000, People's Republic of China
| | - Jianing Yu
- Genecast Precision Medicine Technology Institute, Beijing 100000, People's Republic of China
| | - Yanhui Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, People's Republic of China
| | - Yang Liu
- Genecast Precision Medicine Technology Institute, Beijing 100000, People's Republic of China
| | - Ling Lan
- Department of Gastroenterology, Zhengzhou University People's Hospital, Zhengzhou 450003, People's Republic of China
| | - Jian Li
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450000, People's Republic of China
| | - Huaqing Wang
- Department of Medical Oncology, Tianjin Union Medical Center, The Affiliated Hospital of Nankai University, Tianjin 300000, People's Republic of China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, People's Republic of China
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Abstract
Abstract
It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.
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Affiliation(s)
- Michael Fleischhacker
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Drontheimer Str. 39 – 40 , 13359 Berlin , Germany
| | - Bernd Schmidt
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Berlin , Germany
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11
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Calderón-Franco D, Lin Q, van Loosdrecht MCM, Abbas B, Weissbrodt DG. Anticipating Xenogenic Pollution at the Source: Impact of Sterilizations on DNA Release From Microbial Cultures. Front Bioeng Biotechnol 2020; 8:171. [PMID: 32232035 PMCID: PMC7082761 DOI: 10.3389/fbioe.2020.00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/19/2020] [Indexed: 11/23/2022] Open
Abstract
The dissemination of DNA and xenogenic elements across waterways is under scientific and public spotlight due to new gene-editing tools, such as do-it-yourself (DIY) CRISPR-Cas kits deployable at kitchen table. Over decades, prevention of spread of genetically modified organisms (GMOs), antimicrobial resistances (AMR), and pathogens from transgenic systems has focused on microbial inactivation. However, sterilization methods have not been assessed for DNA release and integrity. Here, we investigated the fate of intracellular DNA from cultures of model prokaryotic (Escherichia coli) and eukaryotic (Saccharomyces cerevisiae) cells that are traditionally used as microbial chassis for genetic modifications. DNA release was tracked during exposure of these cultures to conventional sterilization methods. Autoclaving, disinfection with glutaraldehyde, and microwaving are used to inactivate broths, healthcare equipment, and GMOs produced at kitchen table. DNA fragmentation and PCR-ability were measured on top of cell viability and morphology. Impact of these methods on DNA integrity was verified on a template of free λ DNA. Intense regular autoclaving (121°C, 20 min) resulted in the most severe DNA degradation and lowest household gene amplification capacity: 1.28 ± 0.11, 2.08 ± 0.03, and 4.96 ± 0.28 logs differences to the non-treated controls were measured from E. coli, S. cerevisiae, and λ DNA, respectively. Microwaving exerted strong DNA fragmentation after 100 s of exposure when free λ DNA was in solution (3.23 ± 0.06 logs difference) but a minor effect was observed when DNA was released from E. coli and S. cerevisiae (0.24 ± 0.14 and 1.32 ± 0.02 logs differences with the control, respectively). Glutaraldehyde prevented DNA leakage by preserving cell structures, while DNA integrity was not altered. The results show that current sterilization methods are effective on microorganism inactivation but do not safeguard an aqueous residue exempt of biologically reusable xenogenic material, being regular autoclaving the most severe DNA-affecting method. Reappraisal of sterilization methods is required along with risk assessment on the emission of DNA fragments in urban systems and nature.
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Affiliation(s)
| | | | | | | | - David G. Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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12
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Yi C, He Y, Xia H, Zhang H, Zhang P. Review and perspective on adjuvant and neoadjuvant immunotherapies in NSCLC. Onco Targets Ther 2019; 12:7329-7336. [PMID: 31564915 PMCID: PMC6735538 DOI: 10.2147/ott.s218321] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/14/2019] [Indexed: 12/26/2022] Open
Abstract
Postoperative patients have risk recurring, even for completed resected early stage non-small-cell lung cancer (NSCLC). To control the recurrence rate, neoadjuvant and adjuvant therapies have been applied widely in clinical practice; however, neoadjuvant and adjuvant immunotherapy clinical trials on NSCLC are still being explored. In this review, we summarized the research progress and outline the issues need to be solved on adjuvant and neoadjuvant immunotherapies in NSCLC.
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Affiliation(s)
- Chengxiang Yi
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University School of Medicine, Tongji University, Shanghai 200433, People's Republic of China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Haoran Xia
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Helin Zhang
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
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De Corte D, Martínez JM, Cretoiu MS, Takaki Y, Nunoura T, Sintes E, Herndl GJ, Yokokawa T. Viral Communities in the Global Deep Ocean Conveyor Belt Assessed by Targeted Viromics. Front Microbiol 2019; 10:1801. [PMID: 31496997 PMCID: PMC6712177 DOI: 10.3389/fmicb.2019.01801] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/22/2019] [Indexed: 11/20/2022] Open
Abstract
Viruses are an abundant, diverse and dynamic component of marine and terrestrial ecosystems. In the ocean, viruses play a key role in the biogeochemical cycles and controlling microbial abundance, diversity and evolution. Recent metagenomics studies assessed the structure of the viral community in the upper ocean. However, little is known about the compositional changes in viral communities along the deep ocean conveyor belt. To assess potential changes in the viral community in the global deep-water circulation system, water samples were collected in the core of the North Atlantic Deep Water (NADW) (∼2,500 m) and Pacific Antarctic Bottom Water (∼4,000 m). Microbial and viral abundance were evaluated by flow cytometry. Subsequently, flow cytometry was used to sort virus-like particles and next generation sequencing was applied to build DNA libraries from the sorted virus populations. The viral communities were highly diverse across different oceanic regions with high dissimilarity between samples. Only 18% of the viral protein clusters were shared between the NADW and the Pacific Antarctic Bottom Water. Few viral groups, mainly associated with uncultured environmental and uncultured Mediterranean viruses were ubiquitously distributed along the global deep-water circulation system. Thus, our results point to a few groups of widely distributed abundant viruses in addition to the presence of rare and diverse types of viruses at a local scale.
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Affiliation(s)
- Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | | | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Eva Sintes
- Department of Limnology and Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Gerhard J Herndl
- Department of Limnology and Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands
| | - Taichi Yokokawa
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Koessler T, Addeo A, Nouspikel T. Implementing circulating tumor DNA analysis in a clinical laboratory: A user manual. Adv Clin Chem 2019; 89:131-188. [PMID: 30797468 DOI: 10.1016/bs.acc.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Liquid biopsy, the analysis of cell-free circulating tumor DNA (ctDNA), is becoming one of the most promising tools in oncology. It has already shown its usefulness in selecting and modulating therapy via remote analysis of the tumor genome and holds important promises in cancer therapy and management, such as assessing the success of key therapeutic steps, monitoring residual disease, early detection of relapses, and establishing prognosis. Yet, ctDNA analysis is technically challenging and its implementation in the laboratory raises multiple strategic and practical issues. As for oncology clinics, integration of this novel test in well-established therapeutic protocols can also pose numerous questions. The current review is intended as a field guide for (1) diagnostic laboratories wishing to implement, validate and possibly accredit ctDNA testing and (2) clinical oncologists interested in integrating the various applications of liquid biopsies in their daily practice. We provide advice and practical recommendations based on our own experience with the technical validations of these methods and on a review of the current literature, with a focus toward gastro-intestinal, lung and breast cancers.
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Affiliation(s)
- Thibaud Koessler
- Department of Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Alfredo Addeo
- Department of Oncology, Geneva University Hospital, Geneva, Switzerland
| | - Thierry Nouspikel
- Service of Medical Genetics, Diagnostics Department, Geneva University Hospital, Geneva, Switzerland.
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Grölz D, Hauch S, Schlumpberger M, Guenther K, Voss T, Sprenger-Haussels M, Oelmüller U. Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows-Venous Whole Blood and Plasma. CURRENT PATHOBIOLOGY REPORTS 2018; 6:275-286. [PMID: 30595972 PMCID: PMC6290703 DOI: 10.1007/s40139-018-0180-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsy analyses based on circulating cell-free nucleic acids, circulating tumor cells or other diseased cells from organs, and exosomes or other microvesicles in blood offer new means for non-invasive diagnostic applications. The main goal of this review is to explain the importance of preserving whole blood specimens after blood draw for use as liquid biopsies, and to summarize preservation solutions that are currently available. RECENT FINDINGS Despite the great potential of liquid biopsies for diagnostics and disease management, besides non-invasive prenatal testing (NIPT), only a few liquid biopsy applications are fully implemented for routine in vitro diagnostic testing. One major barrier is the lack of standardized pre-analytical workflows, including the collection of consistent quality blood specimens and the generation of good-quality plasma samples therefrom. Broader use of liquid biopsies in clinical routine applications therefore requires improved pre-analytical procedures to enable high-quality specimens to obtain unbiased analyte profiles (DNA, RNA, proteins, etc.) as they are in the patient's body. SUMMARY A growing number of stabilizing reagents and dedicated blood collection tubes are available for the post-collection preservation of circulating cell-free DNA (ccfDNA) profiles in whole blood. In contrast, solutions for the preservation of circulating tumor cells (CTC) that enable both, enumeration and molecular analyses are rare. Solutions for extracellular vesicle (EV) populations, including exosomes, do not yet exist.
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Affiliation(s)
- Daniel Grölz
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Siegfried Hauch
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Kalle Guenther
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Thorsten Voss
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Uwe Oelmüller
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
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Kumar M, Choudhury Y, Ghosh SK, Mondal R. Application and optimization of minimally invasive cell-free DNA techniques in oncogenomics. Tumour Biol 2018; 40:1010428318760342. [PMID: 29484962 DOI: 10.1177/1010428318760342] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer. This potential of cell-free DNA in several other cancers has yet to be explored based on clinical relevance by optimizing the preanalytical factors. This review has highlighted the crucial parameters from blood collection to cell-free DNA analysis that has a significant impact on the accuracy and reliability of clinical data. The quantity of cell-free DNA is also a limiting factor. Therefore, a proper preanalytical factor for blood collection, its stability, centrifugation speed, and plasma storage condition are to be optimized for developing cancer-specific biomarkers useful for clinical purpose. Liquid biopsy-based origin of cell-free DNA has revolutionized the area of cancer research. Lack of preanalytical and analytical procedures may be considered for identification of novel biomarkers through next-generation sequencing of tumor-originated cell-free DNA in contradiction to tissue biopsy for cancer-specific biomarkers.
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Affiliation(s)
- Manish Kumar
- 1 Department of Biotechnology, Assam University, Silchar, India
| | | | - Sankar Kumar Ghosh
- 1 Department of Biotechnology, Assam University, Silchar, India.,2 University of Kalyani, Kalyani, India
| | - Rosy Mondal
- 3 Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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17
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Rodríguez-Lee M, Kolatkar A, McCormick M, Dago AD, Kendall J, Carlsson NA, Bethel K, Greenspan EJ, Hwang SE, Waitman KR, Nieva JJ, Hicks J, Kuhn P. Effect of Blood Collection Tube Type and Time to Processing on the Enumeration and High-Content Characterization of Circulating Tumor Cells Using the High-Definition Single-Cell Assay. Arch Pathol Lab Med 2018; 142:198-207. [PMID: 29144792 PMCID: PMC7679174 DOI: 10.5858/arpa.2016-0483-oa] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care. OBJECTIVE - To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA). DESIGN - Blood samples of patients with early- and advanced-stage breast cancer were collected into cell-free DNA (CfDNA), EDTA, acid-citrate-dextrose solution, and heparin BCTs. Time-to-assay was evaluated at 24 and 72 hours, representing the fastest possible and more routine domestic shipping intervals, respectively. RESULTS - We detected the highest CTC levels and the lowest levels of negative events in CfDNA BCT at 24 hours. At 72 hours in this BCT, all CTC subpopulations were decreased with the larger effect observed in high-definition CTCs and cytokeratin-positive cells smaller than white blood cells. Overall cell retention was also optimal in CfDNA BCT at 24 hours. Whole-genome copy number variation profiles were generated from single cells isolated from all BCT types and TTAs. Cells from CfDNA BCT at 24-hour TTA exhibited the least noise. CONCLUSIONS - Circulating tumor cells can be identified and characterized under a variety of collection, handling, and processing conditions, but the highest quality can be achieved with optimized conditions. We quantified performance differences of the HD-SCA for specific preanalytic variables that may be used as a guide to develop best practices for implementation into patient care and/or research biorepository processes.
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18
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Hyland CA, Millard GM, O'Brien H, Schoeman EM, Lopez GH, McGowan EC, Tremellen A, Puddephatt R, Gaerty K, Flower RL, Hyett JA, Gardener GJ. Non-invasive fetal RHD genotyping for RhD negative women stratified into RHD gene deletion or variant groups: comparative accuracy using two blood collection tube types. Pathology 2017; 49:757-764. [PMID: 29096879 DOI: 10.1016/j.pathol.2017.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/17/2017] [Accepted: 08/27/2017] [Indexed: 12/19/2022]
Abstract
Non-invasive fetal RHD genotyping in Australia to reduce anti-D usage will need to accommodate both prolonged sample transport times and a diverse population demographic harbouring a range of RHD blood group gene variants. We compared RHD genotyping accuracy using two blood sample collection tube types for RhD negative women stratified into deleted RHD gene haplotype and RHD gene variant cohorts. Maternal blood samples were collected into EDTA and cell-free (cf)DNA stabilising (BCT) tubes from two sites, one interstate. Automated DNA extraction and polymerase chain reaction (PCR) were used to amplify RHD exons 5 and 10 and CCR5. Automated analysis flagged maternal RHD variants, which were classified by genotyping. Time between sample collection and processing ranged from 2.9 to 187.5 hours. cfDNA levels increased with time for EDTA (range 0.03-138 ng/μL) but not BCT samples (0.01-3.24 ng/μL). For the 'deleted' cohort (n=647) all fetal RHD genotyping outcomes were concordant, excepting for one unexplained false negative EDTA sample. Matched against cord RhD serology, negative predictive values using BCT and EDTA tubes were 100% and 99.6%, respectively. Positive predictive values were 99.7% for both types. Overall 37.2% of subjects carried an RhD negative baby. The 'variant' cohort (n=15) included one novel RHD and eight hybrid or African pseudogene variants. Review for fetal RHD specific signals, based on one exon, showed three EDTA samples discordant to BCT, attributed to high maternal cfDNA levels arising from prolonged transport times. For the deleted haplotype cohort, fetal RHD genotyping accuracy was comparable for samples collected in EDTA and BCT tubes despite higher cfDNA levels in the EDTA tubes. Capacity to predict fetal RHD genotype for maternal carriers of hybrid or pseudogene RHD variants requires stringent control of cfDNA levels. We conclude that fetal RHD genotyping is feasible in the Australian environment to avoid unnecessary anti-D immunoglobulin prophylaxis.
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Affiliation(s)
- Catherine A Hyland
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia.
| | - Glenda M Millard
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia
| | - Helen O'Brien
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia
| | - Elizna M Schoeman
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia
| | - Genghis H Lopez
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia
| | - Eunike C McGowan
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia
| | - Anne Tremellen
- Mater Research Institute, University of Queensland, South Brisbane, Qld, Australia
| | - Rachel Puddephatt
- High Risk Obstetrics, RPA Women and Babies, Royal Prince Alfred Hospital, Camperdown, Sydney, NSW, Australia
| | - Kirsten Gaerty
- The Mater Centre for Maternal Fetal Medicine, Mater Mothers' Hospital, South Brisbane, Qld, Australia
| | - Robert L Flower
- Clinical Services and Research, Australian Red Cross Blood Service, Kelvin Grove, Brisbane, QLD, Australia
| | - Jonathan A Hyett
- High Risk Obstetrics, RPA Women and Babies, Royal Prince Alfred Hospital, Camperdown, Sydney, NSW, Australia; Discipline of Obstetrics, Gynaecology and Neonatology, Faculty of Medicine, Central Clinical School, Royal Prince Alfred Hospital, The University of Sydney, Sydney, NSW, Australia
| | - Glenn J Gardener
- Mater Research Institute, University of Queensland, South Brisbane, Qld, Australia; The Mater Centre for Maternal Fetal Medicine, Mater Mothers' Hospital, South Brisbane, Qld, Australia
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19
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Evaluation of Streck BCT and PAXgene Stabilised Blood Collection Tubes for Cell-Free Circulating DNA Studies in Plasma. Mol Diagn Ther 2017. [DOI: 10.1007/s40291-017-0284-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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20
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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21
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Comparative analysis of circulating tumor DNA stability In K3EDTA, Streck, and CellSave blood collection tubes. Clin Biochem 2016; 49:1354-1360. [DOI: 10.1016/j.clinbiochem.2016.03.012] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/09/2016] [Accepted: 03/07/2016] [Indexed: 12/24/2022]
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22
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Medina Diaz I, Nocon A, Mehnert DH, Fredebohm J, Diehl F, Holtrup F. Performance of Streck cfDNA Blood Collection Tubes for Liquid Biopsy Testing. PLoS One 2016; 11:e0166354. [PMID: 27832189 PMCID: PMC5104415 DOI: 10.1371/journal.pone.0166354] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023] Open
Abstract
Objectives Making liquid biopsy testing widely available requires a concept to ship whole blood at ambient temperatures while retaining the integrity of the cell-free DNA (cfDNA) population and stability of blood cells to prevent dilution of circulating tumor DNA (ctDNA) with wild-type genomic DNA. The cell- and DNA-stabilizing properties of Streck Cell-Free DNA BCT blood collection tubes (cfDNA BCTs) were evaluated to determine if they can be utilized in combination with highly sensitive mutation detection technologies. Methods Venous blood from healthy donors or patients with advanced colorectal cancer (CRC) was collected in cfDNA BCTs and standard K2EDTA tubes. Tubes were stored at different temperatures for various times before plasma preparation and DNA extraction. The isolated cfDNA was analyzed for overall DNA yield of short and long DNA fragments using qPCR as well as for mutational changes using BEAMing and Plasma Safe-Sequencing (Safe-SeqS). Results Collection of whole blood from healthy individuals in cfDNA BCTs and storage for up to 5 days at room temperature did not affect the DNA yield and mutation background levels (n = 60). Low-frequency mutant DNA spiked into normal blood samples as well as mutant circulating tumor DNA in blood samples from CRC patients collected in cfDNA BCTs were reliably detected after 3 days of storage at room temperature. However, blood samples stored at ≤ 10°C and at 40°C for an extended period of time showed elevated normal genomic DNA levels and an abnormally large cellular plasma interface as well as lower plasma volumes. Conclusion Whole blood shipped in cfDNA BCTs over several days can be used for downstream liquid biopsy testing using BEAMing and Safe-SeqS. Since the shipping temperature is a critical factor, special care has to be taken to maintain a defined room temperature range to obtain reliable mutation testing results.
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Affiliation(s)
- Inga Medina Diaz
- Research and Development, Sysmex Inostics GmbH, Hamburg, Germany
| | - Annette Nocon
- Research and Development, Sysmex Inostics GmbH, Hamburg, Germany
| | | | | | - Frank Diehl
- Research and Development, Sysmex Inostics GmbH, Hamburg, Germany
- * E-mail:
| | - Frank Holtrup
- Research and Development, Sysmex Inostics GmbH, Hamburg, Germany
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23
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Sherwood JL, Corcoran C, Brown H, Sharpe AD, Musilova M, Kohlmann A. Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC). PLoS One 2016; 11:e0150197. [PMID: 26918901 PMCID: PMC4769175 DOI: 10.1371/journal.pone.0150197] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/10/2016] [Indexed: 12/29/2022] Open
Abstract
Introduction Non-invasive mutation testing using circulating tumour DNA (ctDNA) is an attractive premise. This could enable patients without available tumour sample to access more treatment options. Materials & Methods Peripheral blood and matched tumours were analysed from 45 NSCLC patients. We investigated the impact of pre-analytical variables on DNA yield and/or KRAS mutation detection: sample collection tube type, incubation time, centrifugation steps, plasma input volume and DNA extraction kits. Results 2 hr incubation time and double plasma centrifugation (2000 x g) reduced overall DNA yield resulting in lowered levels of contaminating genomic DNA (gDNA). Reduced “contamination” and increased KRAS mutation detection was observed using cell-free DNA Blood Collection Tubes (cfDNA BCT) (Streck), after 72 hrs following blood draw compared to EDTA tubes. Plasma input volume and use of different DNA extraction kits impacted DNA yield. Conclusion This study demonstrated that successful ctDNA recovery for mutation detection in NSCLC is dependent on pre-analytical steps. Development of standardised methods for the detection of KRAS mutations from ctDNA specimens is recommended to minimise the impact of pre-analytical steps on mutation detection rates. Where rapid sample processing is not possible the use of cfDNA BCT tubes would be advantageous.
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Affiliation(s)
- James L. Sherwood
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
- * E-mail:
| | - Claire Corcoran
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Helen Brown
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Alan D. Sharpe
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Milena Musilova
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Alexander Kohlmann
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
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Qin J, Sanmann JN, Kittrell JS, Althof PA, Kaspar EE, Hunsley BA. A formalin-free method for stabilizing cells for nucleic acid amplification, hybridization and next-generation sequencing. BMC Res Notes 2015; 8:755. [PMID: 26645067 PMCID: PMC4673747 DOI: 10.1186/s13104-015-1725-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/20/2015] [Indexed: 11/15/2022] Open
Abstract
Background Formalin has been widely used by pathology laboratories. Its carcinogenicity has led researchers to explore formalin substitutes. Streck Cell Preservative (SCP) is a formalin-free preservative that can preserve cellular antigens. This study was undertaken to investigate the effects of cell preservation using SCP on nucleic acid amplification, hybridization, and next-generation sequencing (NGS) as compared to control frozen cells and cells fixed in the traditional cell and tissue fixative, 10 % neutral buffered formalin (NBF). Findings The breast cancer cell line, SKBR-3, was used as a model system. Prior to nucleic acid extraction and fluorescence in situ hybridization (FISH), cells were fixed in SCP or NBF overnight at room temperature with frozen cells in parallel. Analysis showed that similar DNA extraction yields and amplification profiles determined by PCR in SCP preserved cells and control frozen cells, whereas NBF preserved cells had decreased DNA yield and impaired PCR amplification. Molecular cytogenetic studies by FISH technique indicated that the ratios of ERBB2 (HER-2/neu) signals to the chromosome 17 centromere (CEP17) were comparable for frozen cells and SCP preserved cells. The fluorescence images of both SCP fixed and control frozen cells were also clear and comparable. On the contrary, the same analysis was unsuccessful with NBF preserved cells due to poor hybridization quality. Our data also demonstrated that SCP had negligible effect on NGS testing. Conclusion We conclude that SCP can be used as an alternative to NBF as a preservative for maintaining the integrity of nucleic acids for nucleic acid amplification, sequencing and FISH analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1725-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianbing Qin
- Research and Development Division, Streck, Inc., 109th Street, Omaha, NE, 68128, USA.
| | - Jennifer N Sanmann
- Munroe-Meyer Institute for Genetics and Rehabilitation, Cytogenetic and Human Genetics Laboratories, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Jeff S Kittrell
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
| | - Pamela A Althof
- Munroe-Meyer Institute for Genetics and Rehabilitation, Cytogenetic and Human Genetics Laboratories, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Erin E Kaspar
- Munroe-Meyer Institute for Genetics and Rehabilitation, Cytogenetic and Human Genetics Laboratories, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Bradford A Hunsley
- Research and Development Division, Streck, Inc., 109th Street, Omaha, NE, 68128, USA.
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25
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Toro PV, Erlanger B, Beaver JA, Cochran RL, VanDenBerg DA, Yakim E, Cravero K, Chu D, Zabransky DJ, Wong HY, Croessmann S, Parsons H, Hurley PJ, Lauring J, Park BH. Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA. Clin Biochem 2015; 48:993-8. [PMID: 26234639 DOI: 10.1016/j.clinbiochem.2015.07.097] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 01/27/2023]
Abstract
OBJECTIVES Circulating plasma DNA is being increasingly used for biomedical and clinical research as a substrate for genetic testing. However, cell lysis can occur hours after venipuncture when using standard tubes for blood collection, leading to an increase in contaminating cellular DNA that may hinder analysis of circulating plasma DNA. Cell stabilization agents can prevent cellular lysis for several days, reducing the need for immediate plasma preparation after venipuncture, thereby facilitating the ease of blood collection and sample preparation for clinical research. However, the majority of cell stabilizing reagents have not been formally tested for their ability to preserve circulating plasma tumor DNA. DESIGN & METHODS In this study, we compared the properties of two cell stabilizing reagents, the cell-free DNA BCT tube and the PAXgene tube, by collecting blood samples from metastatic breast cancer patients and measuring genome equivalents of plasma DNA by droplet digital PCR. We compared wild type PIK3CA genome equivalents and also assayed for two PIK3CA hotspot mutations, E545K and H1047R. RESULTS Our results demonstrate that blood stored for 7 days in BCT tubes did not show evidence of cell lysis, whereas PAXgene tubes showed an order of magnitude increase in genome equivalents, indicative of considerable cellular lysis. CONCLUSIONS We conclude that BCT tubes can prevent lysis and cellular release of genomic DNA of blood samples from cancer patients when stored at room temperature, and could therefore be of benefit for blood specimen collections in clinical trials.
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Affiliation(s)
- Patricia Valda Toro
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bracha Erlanger
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julia A Beaver
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rory L Cochran
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dustin A VanDenBerg
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Yakim
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel J Zabransky
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Yuen Wong
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Croessmann
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heather Parsons
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Paula J Hurley
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Brady Urologic Institute, Department of Urology, USA
| | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA.
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Qin J, Alt JR, Hunsley BA, Williams TL, Fernando MR. Stabilization of circulating tumor cells in blood using a collection device with a preservative reagent. Cancer Cell Int 2014; 14:23. [PMID: 24602297 PMCID: PMC3995911 DOI: 10.1186/1475-2867-14-23] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 02/28/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The enumeration and characterization of circulating tumor cells (CTCs) in the blood of cancer patients is useful for cancer prognostic and treatment monitoring purposes. The number of CTCs present in patient blood is very low; thus, robust technologies have been developed to enumerate and characterize CTCs in patient blood samples. One of the challenges to the clinical utility of CTCs is their inherent fragility, which makes these cells very unstable during transportation and storage of blood samples. In this study we investigated Cell-Free DNA BCT™ (BCT), a blood collection device, which stabilizes blood cells in a blood sample at room temperature (RT) for its ability to stabilize CTCs at RT for an extended period of time. METHODS Blood was drawn from each donor into K3EDTA tube, CellSave tube and BCT. Samples were then spiked with breast cancer cells (MCF-7), transported and stored at RT. Spiked cancer cells were counted using the Veridex CellSearch™ system on days 1 and 4. The effect of storage on the stability of proteins and nucleic acids in the spiked cells isolated from K3EDTA tube and BCT was determined using fluorescence staining and confocal laser scanning microscopy. RESULTS MCF-7 cell recovery significantly dropped when transported and stored in K3EDTA tubes. However, in blood collected into CellSave tubes and BCTs, the MCF-7 cell count was stable up to 4 days at RT. Epithelial cell adhesion molecule (EpCAM) and cytokeratin (CK) in MCF-7 cells isolated from BCTs was stable at RT for up to 4 days, whereas in MCF-7 cells isolated from K3EDTA blood showed reduced EpCAM and CK protein expression. Similarly, BCTs stabilized c-fos and cyclin D1 mRNAs as compared to K3EDTA tubes. CONCLUSION Cell-Free DNA™ BCT blood collection device preserves and stabilizes CTCs in blood samples for at least 4 days at RT. This technology may facilitate the development of new non-invasive diagnostic and prognostic methodologies for CTC enumeration as well as characterization.
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Affiliation(s)
- Jianbing Qin
- R&D Division, Streck, Inc,, 7002 S 109 Street, La Vista, NE 68128, USA.
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