151
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Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA. Sci Rep 2020; 10:6190. [PMID: 32277101 PMCID: PMC7148341 DOI: 10.1038/s41598-020-63102-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients.
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152
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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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153
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Han D, Li R, Shi J, Tan P, Zhang R, Li J. Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing. Theranostics 2020; 10:5501-5513. [PMID: 32373224 PMCID: PMC7196304 DOI: 10.7150/thno.45554] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/29/2020] [Indexed: 12/19/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) of microbial cell-free DNA (mcfDNA sequencing) is becoming an attractive diagnostic modality for infectious diseases, allowing broad-range pathogen detection, noninvasive sampling, and rapid diagnosis. At this key juncture in the translation of metagenomics into clinical practice, an integrative perspective is needed to understand the significance of emerging mcfDNA sequencing technology. In this review, we summarized the actual performance of the mcfDNA sequencing tests recently used in health care settings for the diagnosis of a variety of infectious diseases and further focused on the practice considerations (challenges and solutions) for improving the accuracy and clinical relevance of the results produced by this evolving technique. Such knowledge will be helpful for physicians, microbiologists and researchers to understand what is going on in this quickly progressing field of non-invasive pathogen diagnosis by mcfDNA sequencing and promote the routine implementation of this technique in the diagnosis of infectious disease.
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Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
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154
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Calandri M, Siravegna G, Yevich SM, Stranieri G, Gazzera C, Kopetz S, Fonio P, Gupta S, Bardelli A, Veltri A, Odisio BC. Liquid biopsy, a paradigm shift in oncology: what interventional radiologists should know. Eur Radiol 2020; 30:4496-4503. [PMID: 32193642 DOI: 10.1007/s00330-020-06700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/21/2020] [Accepted: 01/31/2020] [Indexed: 02/08/2023]
Abstract
The acquisition of adequate tumor sample is required to verify primary tumor type and specific biomarkers and to assess response to therapy. Historically, invasive surgical procedures were the standard methods to acquire tumor samples until advancements in imaging and minimally invasive equipment facilitated the paradigm shift image-guided biopsy. Image-guided biopsy has improved sampling yield and minimized risk to the patient; however, there are still limitations, such as its invasive nature and its consequent limitations to longitudinal tumor monitoring. The next paradigm shift in sampling technique will need to address these issues to provide a more reliable and less invasive technique. Recently, liquid biopsy (LB) has emerged as a non-invasive alternative to tissue sampling. This technique relies on direct sampling of blood or other bodily fluids in contact with the tumor in order to collect circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and circulating RNAs-in particular microRNA (miRNAs). Clinical applications of LB involve different steps of cancer patient management including screening, detection of disease recurrence, and evaluation of acquired resistance. With any paradigm shift, old techniques are often relegated to a secondary option. Although image-guided biopsies may appear as a passive spectator on the rapid advancement of LB, the two techniques may well be codependent. Interventional radiology may be integral to directly sample the liquid surrounding or draining from the tumor. In addition, LB may help to correctly select the patients for image-guided loco-regional treatments, to determine its treatment endpoint, and to early detect recurrence. KEY POINTS: • Liquid biopsy is a novel technology with potential high impact in the management of patients undergoing image-guided procedures. • Interventional radiology procedures may increase liquid biopsy sensitivity through direct fluid sampling. • Liquid biopsy techniques may provide a venue for improving patients' selection and enhance outcomes of interventional loco-regional therapies performed by interventional radiologists.
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Affiliation(s)
- Marco Calandri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Giulia Siravegna
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo (To), Candiolo, TO, Italy.,Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Steven M Yevich
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Giuseppe Stranieri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy
| | - Carlo Gazzera
- Radiology Institute, Città della Salute e della Scienza - Torino Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Paolo Fonio
- Radiology Institute, Città della Salute e della Scienza - Torino Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Sanjay Gupta
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Turin, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo (To), Candiolo, TO, Italy
| | - Andrea Veltri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Bruno C Odisio
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA.
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155
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Maia MC, Salgia M, Pal SK. Harnessing cell-free DNA: plasma circulating tumour DNA for liquid biopsy in genitourinary cancers. Nat Rev Urol 2020; 17:271-291. [PMID: 32203306 DOI: 10.1038/s41585-020-0297-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2020] [Indexed: 12/11/2022]
Abstract
In the era of precision oncology, liquid biopsy techniques, especially the use of plasma circulating tumour DNA (ctDNA) analysis, represent a paradigm shift in the use of genomic biomarkers with considerable implications for clinical practice. Compared with tissue-based tumour DNA analysis, plasma ctDNA is more convenient to test, more readily accessible, faster to obtain and less invasive, minimizing procedure-related risks and offering the opportunity to perform serial monitoring. Additionally, genomic profiles of ctDNA have been shown to reflect tumour heterogeneity, which has important implications for the identification of resistant clones and selection of targeted therapy well before clinical and radiographic changes occur. Moreover, plasma ctDNA testing can also be applied to cancer screening, risk stratification and quantification of minimal residual disease. These features provide an unprecedented opportunity for early treatment of patients, improving the chances of treatment success.
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Affiliation(s)
- Manuel Caitano Maia
- Department of Medical Oncology, Centro de Oncologia do Paraná, Curitiba, PR, Brazil. .,Latin American Cooperative Oncology Group, Genitourinary Group, Porto Alegre, Brazil.
| | - Meghan Salgia
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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156
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Greytak SR, Engel KB, Parpart-Li S, Murtaza M, Bronkhorst AJ, Pertile MD, Moore HM. Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance. Clin Cancer Res 2020; 26:3104-3109. [PMID: 32122922 DOI: 10.1158/1078-0432.ccr-19-3015] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/25/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.
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Affiliation(s)
| | | | | | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Mark D Pertile
- Victorian Clinical Genetics Services (VCGS), Parkville, Australia
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, NCI, Bethesda, Maryland.
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157
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Álvarez-Alegret R, Rojo Todo F, Garrido P, Bellosillo B, Rodríguez-Lescure Á, Rodríguez-Peralto JL, Vera R, de Álava E, García-Campelo R, Remon J. [Liquid biopsy in oncology: A consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology]. REVISTA ESPAÑOLA DE PATOLOGÍA : PUBLICACIÓN OFICIAL DE LA SOCIEDAD ESPAÑOLA DE ANATOMÍA PATOLÓGICA Y DE LA SOCIEDAD ESPAÑOLA DE CITOLOGÍA 2020; 53:234-245. [PMID: 33012494 DOI: 10.1016/j.patol.2019.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/27/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022]
Abstract
The proportion of cancer patients with tumours that harbour a potentially targetable genomic alteration is increasing considerably. The diagnosis of these genomic alterations can lead to tailoring of treatment, at the onset of disease or during progression, as well as providing additional, predictive information on the efficacy of immunotherapy. However, in up to 25% of cases, the initial tissue biopsy is inadequate for precision oncology and, in many cases, tumour genomic profiling at progression is not possible due to technical limitations of obtaining new tumour tissue specimens. Efficient diagnostic alternatives are therefore required for molecular stratification, such as liquid biopsy. This technique enables the evaluation of the tumour genomic profile dynamically and as well as capturing intra-patient genomic heterogeneity. To date, there are several diagnostic techniques available for use in liquid biopsy, each with different precision and performance levels. The objective of this consensus statement of the Spanish Society of Pathology (SEAP) and the Spanish Society of Medical Oncology (SEOM) is to evaluate the viability and effectiveness of the different methodological approaches of liquid biopsy in cancer patients, and the potential application of this method to current clinical practice. The experts contributing to this consensus statement agree that, according to current evidence, liquid biopsy is an acceptable alternative to tumour tissue biopsy for the study of biomarkers in various clinical settings. It is therefore important to standardise pre-analytical and analytical procedures to ensure reproducibility and to generate structured and accessible clinical reports. It is essential to appoint multidisciplinary tumour molecular committees to oversee these processes and to enable the most suitable therapeutic decisions for each patient according to the genomic profile.
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Affiliation(s)
| | - Federico Rojo Todo
- Departamento de Patología, Fundación Universitaria Jiménez Díaz, CIBERONC, Madrid, España
| | - Pilar Garrido
- Universidad de Alcalá; Departamento de Oncología Médica, IRYCIS, Hospital Universitario Ramón y Cajal, CIBERONC, Madrid, España
| | - Beatriz Bellosillo
- Departamento de Patología, Hospital del Mar, CIBERONC, Barcelona, España
| | - Álvaro Rodríguez-Lescure
- Departamento de Oncología Médica, Hospital General Universitario de Elche y Vega Baja, GEICAM, Elche, España
| | | | - Ruth Vera
- Departamento de Oncología Médica, Complejo Hospitalario de Navarra, Navarra Institute for health research (IdiSNA), Pamplona, España
| | - Enrique de Álava
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, CIBERONC, Departamento de Citología e Histología Normal y Patológica, Sevilla, España
| | - Rosario García-Campelo
- Departamento de Oncología Médica, Complexo Hospitalario Universitario A Coruña, A Coruña, España
| | - Jordi Remon
- Departamento de Oncología Médica, Centro Integral Oncológico Clara Campal Barcelona (CIOCCB), HM Delfos, Barcelona, España
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158
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Otandault A, Abraham JD, Al Amir Dache Z, Khalyfa A, Jariel-Encontre I, Forné T, Prévostel C, Chouaib S, Gozal D, Thierry AR. Hypoxia differently modulates the release of mitochondrial and nuclear DNA. Br J Cancer 2020; 122:715-725. [PMID: 31929518 PMCID: PMC7054557 DOI: 10.1038/s41416-019-0716-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/29/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND We investigated the influence of hypoxia on the concentration of mitochondrial and nuclear cell-free DNA (McfDNA and NcfDNA, respectively). METHOD By an ultra-sensitive quantitative PCR-based assay, McfDNA and NcfDNA were measured in the supernatants of different colorectal cell lines, and in the plasma of C57/Bl6 mice engrafted with TC1 tumour cells, in normoxic or hypoxic conditions. RESULTS Our data when setting cell culture conditions highlighted the higher stability of McfDNA as compared to NcfDNA and revealed that cancer cells released amounts of nuclear DNA equivalent to the mass of a chromosome over a 6-h duration of incubation. In cell model, hypoxia induced a great increase in NcfDNA and McfDNA concentrations within the first 24 h. After this period, cfDNA total concentrations remained stable in hypoxia consecutive to a decrease of nuclear DNA release, and noteworthy, to a complete inhibition of daily mitochondrial DNA release. In TC1-engrafted mice submitted to intermittent hypoxia, plasma NcfDNA levels are much higher than in mice bred in normoxia, unlike plasma McfDNA concentration that is not impacted by hypoxia. CONCLUSION This study suggests that hypoxia negatively modulates nuclear and, particularly, mitochondrial DNA releases in long-term hypoxia, and revealed that the underlying mechanisms are differently regulated.
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Affiliation(s)
- Amaelle Otandault
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Jean-Daniel Abraham
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Zahra Al Amir Dache
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Abdelnaby Khalyfa
- Department of Child Health and Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, 65201, USA
| | - Isabelle Jariel-Encontre
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Corinne Prévostel
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Salem Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de médecine-Univ. Paris-Sud, University Paris-Saclay, Villejuif, 94805, France
- TRIPM, Gulf Medical University, Ajman, UAE
| | - David Gozal
- Department of Child Health and Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, 65201, USA
| | - Alain R Thierry
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France.
- Université de Montpellier, Montpellier, 34090, France.
- Institut régional du cancer de Montpellier, Montpellier, 34298, France.
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159
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Chen A, Li J, Wang L, Huang Q, Zhu J, Wen S, Lyu J, Wu W. Comparison of paired cerebrospinal fluid and serum cell-free mitochondrial and nuclear DNA with copy number and fragment length. J Clin Lab Anal 2020; 34:e23238. [PMID: 32052892 PMCID: PMC7307366 DOI: 10.1002/jcla.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/11/2020] [Accepted: 01/21/2020] [Indexed: 12/22/2022] Open
Abstract
Background Most studies on cell‐free DNA (cfDNA) were only for single body fluids; however, the differences in cfDNA distribution between two body fluids are rarely reported. Hence, in this work, we compared the differences in cfDNA distribution between cerebrospinal fluid (CSF) and serum of patients with brain‐related diseases. Methods The fragment length of cfDNA was determined by using Agilent 2100 Bioanalyzer. The copy numbers of cell‐free mitochondrial DNA (cf‐mtDNA) and cell‐free nuclear DNA (cf‐nDNA) were determined by using real‐time quantitative PCR (qPCR) and droplet digital PCR (ddPCR) with three pairs of mitochondrial ND1 and nuclear GAPDH primers, respectively. Results There were short (~60 bp), medium (~167 bp), and long (>250 bp) cfDNA fragment length distributions totally obtained from CSF and serum using Agilent 2100 Bioanalyzer. The results of both qPCR and ddPCR confirmed the existence of these three cfDNA fragment ranges in CSF and serum. According to qPCR, the copy numbers of long cf‐mtDNA, medium, and long cf‐nDNA in CSF were significantly higher than in paired serum. In CSF, only long cf‐mtDNA's copy numbers were higher than long cf‐nDNA. But in serum, the copy numbers of medium and long cf‐mtDNA were higher than the corresponding cf‐nDNA. Conclusion The cf‐nDNA and cf‐mtDNA with different fragment lengths differentially distributed in the CSF and serum of patients with brain disorders, which might serve as a biomarker of human brain diseases.
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Affiliation(s)
- Aolong Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Li
- Department of Clinical Laboratory, Wenzhou People's Hospital, Wenzhou, China
| | - Lei Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qin Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jiajin Zhu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shumeng Wen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Hangzhou Medical College, Hangzhou, China
| | - Wenhe Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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160
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Dissecting Molecular Features of Gliomas: Genetic Loci and Validated Biomarkers. Int J Mol Sci 2020; 21:ijms21020685. [PMID: 31968687 PMCID: PMC7014190 DOI: 10.3390/ijms21020685] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, several studies focused on the genetics of gliomas. This allowed identifying several germline loci that contribute to individual risk for tumor development, as well as various somatic mutations that are key for disease classification. Unfortunately, none of the germline loci clearly confers increased risk per se. Contrariwise, somatic mutations identified within the glioma tissue define tumor genotype, thus representing valid diagnostic and prognostic markers. Thus, genetic features can be used in glioma classification and guided therapy. Such copious genomic variabilities are screened routinely in glioma diagnosis. In detail, Sanger sequencing or pyrosequencing, fluorescence in-situ hybridization, and microsatellite analyses were added to immunohistochemistry as diagnostic markers. Recently, Next Generation Sequencing was set-up as an all-in-one diagnostic tool aimed at detecting both DNA copy number variations and mutations in gliomas. This approach is widely used also to detect circulating tumor DNA within cerebrospinal fluid from patients affected by primary brain tumors. Such an approach is providing an alternative cost-effective strategy to genotype all gliomas, which allows avoiding surgical tissue collection and repeated tumor biopsies. This review summarizes available molecular features that represent solid tools for the genetic diagnosis of gliomas at present or in the next future.
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161
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Franczak C, Witz A, Geoffroy K, Demange J, Rouyer M, Husson M, Massard V, Gavoille C, Lambert A, Gilson P, Gambier N, Scala-Bertola J, Merlin JL, Harlé A. Evaluation of KRAS, NRAS and BRAF mutations detection in plasma using an automated system for patients with metastatic colorectal cancer. PLoS One 2020; 15:e0227294. [PMID: 31940389 PMCID: PMC6961936 DOI: 10.1371/journal.pone.0227294] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
Background Cell-free DNA detection is becoming a surrogate assay for tumor genotyping. Biological fluids often content a very low amount of cell-free tumor DNA and assays able to detect very low allele frequency mutant with a few quantities of DNA are required. We evaluated the ability of the fully-automated molecular diagnostics platform Idylla for the detection of KRAS, NRAS and BRAF hotspot mutations in plasma from patients with metastatic colorectal cancer (mCRC). Materials and methods First, we evaluated the limit of detection of the system using two set of laboratory made samples that mimic mCRC patient plasma, then plasma samples from patients with mCRC were assessed using Idylla system and BEAMing digital PCR technology. Results Limits of detection of 0.1%, 0.4% and 0.01% for KRAS, NRAS and BRAF respectively have been reached. With our laboratory made samples, sensitivity up to 0.008% has been reached. Among 15 patients’ samples tested for KRAS mutation, 2 discrepant results were found between Idylla and BEAMing dPCR. A 100% concordance between the two assays has been found for the detection of NRAS and BRAF mutations in plasma samples. Conclusions The Idylla system does not reach as high sensitivity as assays like ddPCR but has an equivalent sensitivity to modified NGS technics with a lower cost and a lower time to results. These data allowed to consider the Idylla system in a routine laboratory workflow for KRAS, NRAS and BRAF mutations detection in plasma.
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Affiliation(s)
- Claire Franczak
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Andréa Witz
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Karen Geoffroy
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Jessica Demange
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Marie Rouyer
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Marie Husson
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Vincent Massard
- Institut de Cancérologie de Lorraine, Département d'oncologie médicale, Vandoeuvre les Nancy, France
| | - Céline Gavoille
- Institut de Cancérologie de Lorraine, Département d'oncologie médicale, Vandoeuvre les Nancy, France
| | - Aurélien Lambert
- Institut de Cancérologie de Lorraine, Département d'oncologie médicale, Vandoeuvre les Nancy, France
| | - Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Nicolas Gambier
- CHRU Nancy, Department of Clinical Pharmacology and Toxicology, Nancy, France.,Université de Lorraine, UMR 7365 CNRS-UL, IMoPA, Vandœuvre-lès-Nancy, France
| | - Julien Scala-Bertola
- CHRU Nancy, Department of Clinical Pharmacology and Toxicology, Nancy, France.,Université de Lorraine, UMR 7365 CNRS-UL, IMoPA, Vandœuvre-lès-Nancy, France
| | - Jean-Louis Merlin
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Alexandre Harlé
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
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162
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Cell-free DNA donor fraction analysis in pediatric and adult heart transplant patients by multiplexed allele-specific quantitative PCR: Validation of a rapid and highly sensitive clinical test for stratification of rejection probability. PLoS One 2020; 15:e0227385. [PMID: 31929557 PMCID: PMC6957190 DOI: 10.1371/journal.pone.0227385] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Lifelong noninvasive rejection monitoring in heart transplant patients is a critical clinical need historically poorly met in adults and unavailable for children and infants. Cell-free DNA (cfDNA) donor-specific fraction (DF), a direct marker of selective donor organ injury, is a promising analytical target. Methodological differences in sample processing and DF determination profoundly affect quality and sensitivity of cfDNA analyses, requiring specialized optimization for low cfDNA levels typical of transplant patients. Using next-generation sequencing, we previously correlated elevated DF with acute cellular and antibody-mediated rejection (ACR and AMR) in pediatric and adult heart transplant patients. However, next-generation sequencing is limited by cost, TAT, and sensitivity, leading us to clinically validate a rapid, highly sensitive, quantitative genotyping test, myTAIHEART®, addressing these limitations. To assure pre-analytical quality and consider interrelated cfDNA measures, plasma preparation was optimized and total cfDNA (TCF) concentration, DNA fragmentation, and DF quantification were validated in parallel for integration into myTAIHEART reporting. Analytical validations employed individual and reconstructed mixtures of human blood-derived genomic DNA (gDNA), cfDNA, and gDNA sheared to apoptotic length. Precision, linearity, and limits of blank/detection/quantification were established for TCF concentration, DNA fragmentation ratio, and DF determinations. For DF, multiplexed high-fidelity amplification followed by quantitative genotyping of 94 SNP targets was applied to 1168 samples to evaluate donor options in staged simulations, demonstrating DF call equivalency with/without donor genotype. Clinical validation studies using 158 matched endomyocardial biopsy-plasma pairs from 76 pediatric and adult heart transplant recipients selected a DF cutoff (0.32%) producing 100% NPV for ≥2R ACR. This supports the assay’s conservative intended use of stratifying low versus increased probability of ≥2R ACR. myTAIHEART is clinically validated for heart transplant recipients ≥2 months old and ≥8 days post-transplant, expanding opportunity for noninvasive transplant rejection assessment to infants and children and to all recipients >1 week post-transplant.
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163
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Haupts A, Roth W, Hartmann N. [Liquid biopsy in colorectal cancer : An overview of ctDNA analysis in tumour diagnostics]. DER PATHOLOGE 2020; 40:244-251. [PMID: 31797045 DOI: 10.1007/s00292-019-00698-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In current routine diagnostics, the gold standard to determine the genomic profile of colorectal cancers (CRCs) is using biopsy or surgically resected tissues. However, such a tissue sample cannot represent the entire tumour heterogeneity, because it only shows a local and temporal snapshot. As a complement to tumour tissue genotyping, liquid biopsies enable minimally invasive detection of all potential tumour-specific mutations and their dynamic changes for molecular profiling. Furthermore, they can be repeated in certain intervals for monitoring response to treatment, occurrence of drug resistance and detection of relapse. This review focusses on analyzing circulating cell-free tumour DNA (ctDNA), which is mostly released from apoptotic or necrotic tumour cells into the bloodstream or by active secretion of circulating tumour cells (CTCs). Nevertheless, there are some challenges in analyzing ctDNA. First, ctDNA represents only a small fraction of total circulating DNA, because there is an enormous wild-type background of cell-free DNA (cfDNA) released by healthy cells. Second, ctDNA is highly fragmented and the amount of ctDNA in the blood is very low. In this review, we discuss the potential, fields of application as well as challenges and limitations of liquid biopsy approaches. In more detail, we discuss the possibility of using liquid biopsies as a future application for molecular characterization of CRCs, particularly for monitoring CRC patients during anti-EGFR therapy to detect resistance mutations (e.g. KRAS mutations) or further therapy-relevant mutations. In addition, we investigate whether blood-based molecular profiling is a reliable addition to routine diagnostic approaches of tissue-based molecular characterization.
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Affiliation(s)
- A Haupts
- Institut für Pathologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland.
| | - W Roth
- Institut für Pathologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland
| | - N Hartmann
- Institut für Pathologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland
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Abstract
ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity. ctDNA has shown growing clinical interest for cancer diagnosis, prognosis, theragnostics, therapeutic monitoring, and clonal evolution tracking. A major technical limit for ctDNA analysis from body fluids is the extremely low proportion of ctDNA compared to non-malignant cell-free DNA, underscoring the need for highly sensitive and specific detection techniques. The control of pre-analytical procedures appears essential for optimal ctDNA analysis and need to be standardized for clinical research applications. This chapter provides insights into major current technologies for ctDNA detection. Overall, PCR-based techniques are able to detect limited molecular alterations and have a high sensitivity suitable for monitoring purposes while NGS-based approaches are broad range molecular screening assays more specifically indicated for treatment selection. We briefly reviewed new technical innovations that are now available for ctDNA detection.
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Affiliation(s)
- Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000, Nancy, France.
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165
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Shi J, Zhang R, Li J, Zhang R. Size profile of cell-free DNA: A beacon guiding the practice and innovation of clinical testing. Theranostics 2020; 10:4737-4748. [PMID: 32308746 PMCID: PMC7163439 DOI: 10.7150/thno.42565] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Cell-free DNA (cfDNA) has pioneered the development of noninvasive prenatal testing and liquid biopsy, its emerging applications include organ transplantation, autoimmune diseases, and many other disorders; size profile of cfDNA is a crucial biological property and is essential for its clinical applications. Therefore, a thorough mastery of the characteristic and potential applications of cfDNA size profile is needed. Methods: Based on the recent researches, we summarized the size profile of cfDNA in pregnant women, tumor patients, transplant recipients and systemic lupus erythematosus (SLE) patients to explore the common features. We also concluded the applications of size profile in pre-analytical phases, analytical phases for novel assays, and preparation of quality control materials (QCMs). Results: The size profile of cfDNA shared common features in different populations, and was distributed as a "ladder" pattern with a dominant peak at ~166 bp. However, cfDNA entailed slightly discrepant characteristics due to specific tissues of origin. The dominant peaks of fetal and maternal cfDNA fragments in pregnant women were at 143 bp and 166 bp, respectively. The plasma cfDNA in tumor patients, transplant recipients, and SLE patients had a peak of around 166 bp. In pre-analytical phases, size profile served as a vital indicator to judge the eligibility of specimens, thus ensuring the successful implementation of assays. More importantly, the size profile had the potential to enrich short fragments, calculate fetal fraction, detect fetal abnormalities, predict tumor progress in analytical phase and to guide the preparation of QCMs. Conclusions: Our finding summarized the characteristics and potential applications of cfDNA size profile, providing clinical researchers with novel assays by the extensive application of cfDNA.
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Affiliation(s)
- Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Runling Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
- ✉ Corresponding author: Rui Zhang, Ph.D, Mailing address: National Center for Clinical Laboratories, Beijing Hospital, No.1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China. Tel: 86-10-58115053; Fax: 86-10-65212064; E-mail:
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166
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Cell-Free DNA Testing. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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167
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The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review. Eur J Pediatr 2020; 179:191-202. [PMID: 31897843 PMCID: PMC6971142 DOI: 10.1007/s00431-019-03545-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022]
Abstract
Cell-free DNA profiling using patient blood is emerging as a non-invasive complementary technique for cancer genomic characterization. Since these liquid biopsies will soon be integrated into clinical trial protocols for pediatric cancer treatment, clinicians should be informed about potential applications and advantages but also weaknesses and potential pitfalls. Small retrospective studies comparing genetic alterations detected in liquid biopsies with tumor biopsies for pediatric solid tumor types are encouraging. Molecular detection of tumor markers in cell-free DNA could be used for earlier therapy response monitoring and residual disease detection as well as enabling detection of pathognomonic and therapeutically relevant genomic alterations.Conclusion: Existing analyses of liquid biopsies from children with solid tumors increasingly suggest a potential relevance for molecular diagnostics, prognostic assessment, and therapeutic decision-making. Gaps remain in the types of tumors studied and value of detection methods applied. Here we review the current stand of liquid biopsy studies for pediatric solid tumors with a dedicated focus on cell-free DNA analysis. There is legitimate hope that integrating fully validated liquid biopsy-based innovations into the standard of care will advance patient monitoring and personalized treatment of children battling solid cancers.What is Known:• Liquid biopsies are finding their way into routine oncological screening, diagnosis, and disease monitoring in adult cancer types fast.• The most widely adopted source for liquid biopsies is blood although other easily accessible body fluids, such as saliva, pleural effusions, urine, or cerebrospinal fluid (CSF) can also serve as sources for liquid biopsiesWhat is New:• Retrospective proof-of-concept studies in small cohorts illustrate that liquid biopsies in pediatric solid tumors yield tremendous potential to be used in diagnostics, for therapy response monitoring and in residual disease detection.• Liquid biopsy diagnostics could tackle some long-standing issues in the pediatric oncology field; they can enable accurate genetic diagnostics in previously unbiopsied tumor types like renal tumors or brain stem tumors leading to better treatment strategies.
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168
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations. Crit Rev Clin Lab Sci 2019:1-17. [PMID: 31865831 DOI: 10.1080/10408363.2019.1700902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of cancer improves the efficacy of curative therapies. However, due to the difficulties involved in distinguishing between small early-stage tumors and normal biological variation, early detection of cancer is an extremely challenging task and there are currently no clinically validated biomarkers for a pan-cancer screening test. It is thus of particular significance that increasing evidence indicates the potential of circulating tumor DNA (ctDNA) molecules, which are fragmented segments of DNA shed from tumor cells into adjacent body fluids and the circulatory system, to serve as molecular markers for early cancer detection and thereby allow early intervention and improvement of therapeutic and survival outcomes. This is possible because ctDNA molecules bear cancer-specific fragmentation patterns, nucleosome depletion motifs, and genetic and epigenetic alterations, as distinct from plasma DNA originating from non-cancerous tissues/cells. Compared to traditional biomarkers, ctDNA analysis therefore presents the distinctive advantage of detecting tumor-specific alterations. However, based on a thorough survey of the literature, theoretical and empirical evidence suggests that current ctDNA analysis strategies, which are mainly based on DNA mutation detection, do not demonstrate the necessary diagnostic sensitivity and specificity that is required for broad clinical implementation in a screening context. Therefore, in this review we explain the biological, physiological, and analytical challenges toward the development of clinically meaningful ctDNA tests. In addition, we explore some approaches that can be implemented in order to increase the sensitivity and specificity of ctDNA assays.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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169
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Abdulmawjood B, Roma-Rodrigues C, Fernandes AR, Baptista PV. Liquid biopsies in myeloid malignancies. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:1044-1061. [PMID: 35582281 PMCID: PMC9019201 DOI: 10.20517/cdr.2019.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022]
Abstract
Hematologic malignancies are the most common type of cancer affecting children and young adults, and encompass diseases, such as leukemia, lymphoma, and myeloma, all of which impact blood associated tissues such as the bone marrow, lymphatic system, and blood cells. Clinical diagnostics of these malignancies relies heavily on the use of bone marrow samples, which is painful, debilitating, and not free from risks for leukemia patients. Liquid biopsies are based on minimally invasive assessment of markers in the blood (and other fluids) and have the potential to improve the efficacy of diagnostic/therapeutic strategies in leukemia patients, providing a useful tool for the real time molecular profiling of patients. The most promising noninvasive biomarkers are circulating tumor cells, circulating tumor DNA, microRNAs, and exosomes. Herein, we discuss the role of assessing these circulating biomarkers for the understanding of tumor progression and metastasis, tumor progression dynamics through treatment and for follow-up.
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Affiliation(s)
- Bilal Abdulmawjood
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
| | - Catarina Roma-Rodrigues
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
| | - Pedro V Baptista
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
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170
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Christou N, Meyer J, Popeskou S, David V, Toso C, Buchs N, Liot E, Robert J, Ris F, Mathonnet M. Circulating Tumour Cells, Circulating Tumour DNA and Circulating Tumour miRNA in Blood Assays in the Different Steps of Colorectal Cancer Management, a Review of the Evidence in 2019. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5953036. [PMID: 31930130 PMCID: PMC6942724 DOI: 10.1155/2019/5953036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/02/2019] [Accepted: 08/17/2019] [Indexed: 12/24/2022]
Abstract
Despite many advances in the diagnosis and treatment of colorectal cancer (CRC), its incidence and mortality rates continue to make an impact worldwide and in some countries rates are mounting. Over the past decade, liquid biopsies have been the object of fundamental and clinical research with regard to the different steps of CRC patient care such as screening, diagnosis, prognosis, follow-up, and therapeutic response. They are attractive because they are considered to encompass both the cellular and molecular heterogeneity of tumours. They are easily accessible and can be applied to large-scale settings despite the cost. However, liquid biopsies face drawbacks in detection regardless of whether we are testing for circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), or miRNA. This review highlights the different advantages and disadvantages of each type of blood-based biopsy and underlines which specific one may be the most useful and informative for each step of CRC patient care.
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Affiliation(s)
- Niki Christou
- Endocrine, General and Digestive Surgery Department, CHU de Limoges, Limoges Cedex 87042, France
- Laboratoire EA3842 Contrôle de l'Activation cellulaire, Progression Tumorale et Résistances thérapeutiques «CAPTuR», Faculté de médecine, 2 Rue du Docteur Marcland, 87025 Limoges, France
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Jeremy Meyer
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Sotirios Popeskou
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Valentin David
- Laboratoire EA3842 Contrôle de l'Activation cellulaire, Progression Tumorale et Résistances thérapeutiques «CAPTuR», Faculté de médecine, 2 Rue du Docteur Marcland, 87025 Limoges, France
| | - Christian Toso
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Nicolas Buchs
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Emilie Liot
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Joan Robert
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Frederic Ris
- Department of Visceral Surgery, University Hospital of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Muriel Mathonnet
- Endocrine, General and Digestive Surgery Department, CHU de Limoges, Limoges Cedex 87042, France
- Laboratoire EA3842 Contrôle de l'Activation cellulaire, Progression Tumorale et Résistances thérapeutiques «CAPTuR», Faculté de médecine, 2 Rue du Docteur Marcland, 87025 Limoges, France
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Streleckiene G, Forster M, Inciuraite R, Lukosevicius R, Skieceviciene J. Effects of Quantification Methods, Isolation Kits, Plasma Biobanking, and Hemolysis on Cell-Free DNA Analysis in Plasma. Biopreserv Biobank 2019; 17:553-561. [PMID: 31343271 DOI: 10.1089/bio.2019.0026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cell-free DNA (cfDNA) has become a promising noninvasive clinical marker widely studied in early disease detection, monitoring, and therapy selection. However, there is lack of data on a number of cfDNA-associated procedural features such as blood plasma biobanking conditions, isolation, and quantification methods that should be taken into account as they can affect downstream applications. In this study cfDNA from 125 plasma samples from healthy individuals were isolated using three different commercial kits (bead and vacuum based). Yield of cfDNA, distribution of cfDNA fragments and absolute amount of miR-223 were estimated. Moreover, the impact of different plasma biobanking conditions and hemolytic plasma were evaluated. In conclusion, results showed that quantification method (fluorescence or microcapillary electrophoresis based) has a major impact in estimating cfDNA amount. Samples isolated by QIAamp showed a higher amount of larger (around 300 bp) DNA fragments and miRNA yield, suggesting possible applications for multiomics approach. On the other hand, the highest cfDNA yield was obtained in samples isolated by the MagMAX Isolation Kit. This kit also showed lowest coefficient of variation and low miRNA yield. Plasma storage conditions and hemolysis affected performance of isolation kits differently.
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Affiliation(s)
- Greta Streleckiene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruta Inciuraite
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
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172
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Kerachian MA, Poudineh A, Thiery JP. Cell free circulating tumor nucleic acids, a revolution in personalized cancer medicine. Crit Rev Oncol Hematol 2019; 144:102827. [DOI: 10.1016/j.critrevonc.2019.102827] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
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173
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Yang SR, Mooney KL, Libiran P, Jones CD, Joshi R, Lau HD, Stehr H, Berry GJ, Zehnder JL, Long SR, Kong CS, Kunder CA. Targeted deep sequencing of cell-free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology. Cancer Cytopathol 2019; 128:43-56. [PMID: 31751001 DOI: 10.1002/cncy.22205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/15/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Liquid biopsy using cell-free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored. METHODS We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture-based next-generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty-one serous effusions from pleural (n = 15), peritoneal (n = 5), and pericardial (n = 1) cavity were analyzed. RESULTS The supernatants provided a median cfDNA concentration of 10.3 ng/µL. Notably, all effusions were sequenced successfully to a median depth >1000×, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin-fixed, paraffin-embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P = .5), depth of coverage (P = .6), or allele frequency of pathogenic mutations (P = .7). CONCLUSION cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kelly L Mooney
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Paolo Libiran
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carol D Jones
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Rohan Joshi
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Hubert D Lau
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Steven R Long
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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174
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Abstract
The technique of cell-free DNA (cfDNA) analysis, also called liquid biopsy, has been developed over the past several years to serve as a minimal residual disease tool, as has already been done with reliability and robustness in acute leukemias. This technique has important theoretical advantages, including the simplicity of acquiring blood samples, which can easily be repeated over time, its noninvasive and quantitative nature, which provides results consistent with the results obtained from tumor genomic DNA, and its speed and low cost. cfDNA analysis, as the leading tool to quantify somatic mutations, is a major technological leap in the noninvasive management of lymphomas. This technology may empower monitoring and treatment adjustment in real time and enable the quick detection of refractory lymphomas and resistance to routine therapies. Here, we summarize the results that have established the clinical relevance of cfDNA in diagnostic and prognostic stratification and the monitoring of lymphoma treatments.
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Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, 1 Rue D'Amiens, 76038 Rouen Cedex, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, 1 Rue D'Amiens, 76038 Rouen Cedex, France
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175
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Geeurickx E, Hendrix A. Targets, pitfalls and reference materials for liquid biopsy tests in cancer diagnostics. Mol Aspects Med 2019; 72:100828. [PMID: 31711714 DOI: 10.1016/j.mam.2019.10.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
Assessment of cell free DNA (cfDNA) and RNA (cfRNA), circulating tumor cells (CTC) and extracellular vesicles (EV) in blood or other bodily fluids can enable early cancer detection, tumor dynamics assessment, minimal residual disease detection and therapy monitoring. However, few liquid biopsy tests progress towards clinical application because results are often discordant and challenging to reproduce. Reproducibility can be enhanced by the development and implementation of standard operating procedures and reference materials to identify and correct for pre-analytical variables. In this review we elaborate on the technological considerations, pre-analytical variables and the use and availability of reference materials for the assessment of liquid biopsy targets in blood and highlight initiatives towards the standardization of liquid biopsy testing.
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Affiliation(s)
- Edward Geeurickx
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, 9000, Ghent, Belgium; Cancer Research Institute Ghent, 9000, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, 9000, Ghent, Belgium; Cancer Research Institute Ghent, 9000, Ghent, Belgium.
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176
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Cell-free DNA in blood as a noninvasive insight into the sarcoma genome. Mol Aspects Med 2019; 72:100827. [PMID: 31703948 DOI: 10.1016/j.mam.2019.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
Sarcomas are malignant tumors of mesenchymal origin that arise mainly from connective and supportive tissue. Sarcomas include a wide range of histological subtypes, showing a large diversity at the molecular level, from simple to highly complex karyotypes but with few recurrent somatic changes. Therapeutic decisions increasingly rely on the molecular characteristics of the individual tumor. Circulating cell-free DNA (ctDNA) is released into peripheral blood and can be used for the genomic analysis of sarcomas. However, the diversity and heterogeneity of somatic changes observed in sarcomas pose a challenge when choosing an adequate assay for the detection of ctDNA in body fluids. In this review, we provide an overview of different studies on ctDNA from blood in bone and soft tissue sarcomas, including gastrointestinal stromal tumors. We will specifically address the technological challenges that must be considered to achieve the sensitive detection of ctDNA and discuss the clinical applications of ctDNA in the management and treatment of sarcomas.
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177
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Huang J, Wang L. Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics. Cancers (Basel) 2019; 11:cancers11111741. [PMID: 31698791 PMCID: PMC6896050 DOI: 10.3390/cancers11111741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.
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178
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Madsen AT, Hojbjerg JA, Sorensen BS, Winther-Larsen A. Day-to-day and within-day biological variation of cell-free DNA. EBioMedicine 2019; 49:284-290. [PMID: 31648993 PMCID: PMC6945267 DOI: 10.1016/j.ebiom.2019.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/25/2019] [Accepted: 10/07/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Numerous studies have shown that cell-free DNA (cfDNA) levels may serve as a non-invasive biomarker of a broad spectrum of acute and chronic pathologies. However, in order to make clinical decisions based on cfDNA measurements, it is essential to understand the magnitude of biological variation so this variation is not confused with a variation that actually represent a clinically relevant change. The present study was designed to evaluate the biological variation of cfDNA in healthy subjects and lung cancer patients. METHODS Plasma samples were collected from 33 healthy subjects and ten lung cancer patients over three days, as well as during the same day. CfDNA was quantified using droplet digital PCR. Biological variation data was estimated using mixed models. FINDINGS The within-subject variation was 25% and the between-subject variation was 30%. The reference change value for the healthy subjects was 70%. There was no systematic difference in cfDNA levels from day-to-day (p = 0⋅61), but there was a significant decline during the day (p<0⋅01). The within-subject variation in cancer patients was comparable to healthy subjects, whereas the between-subject variation was much larger (139%). No systematic differences from day-to-day were observed for the cancer patients (p>0⋅3). INTERPRETATION Our findings show that cfDNA levels fluctuate significantly during the day and exhibit considerable within-subject variation. Thus, the data presented offer a substantial contribution to the interpretation of the clinical significance of cfDNA. FUNDING Læge Sofus Carl Emil Friis og hustru Olga Doris Friis' Legat, Harboefonden, and Dagmar Marshalls Fond.
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Affiliation(s)
- Anne Tranberg Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Johanne Andersen Hojbjerg
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark.
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179
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Ivanova O, Richards LB, Vijverberg SJ, Neerincx AH, Sinha A, Sterk PJ, Maitland‐van der Zee AH. What did we learn from multiple omics studies in asthma? Allergy 2019; 74:2129-2145. [PMID: 31004501 DOI: 10.1111/all.13833] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/25/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.
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Affiliation(s)
- Olga Ivanova
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Levi B. Richards
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anne H. Neerincx
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anirban Sinha
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Peter J. Sterk
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anke H. Maitland‐van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
- Department of Paediatric Pulmonology Amsterdam UMC/ Emma Children's Hospital Amsterdam the Netherlands
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180
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Abstract
Breast cancer is a highly heterogeneous and dynamic disease, exhibiting unique somatic alterations that lead to disease recurrence and resistance. Tumor biopsy and conventional imaging approaches are not able to provide sufficient information regarding the early detection of recurrence and real time monitoring through tracking sensitive or resistance mechanisms to treatment. Circulating tumor DNA (ctDNA) analysis has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma including DNA mutations and DNA methylation patterns. Numerous studies have reported on the potential of ctDNA analysis in the management of early and advanced stages of breast cancer. Advances in high-throughput technologies, especially next generation sequencing and PCR-based assays, were highly important for the successful application of ctDNA analysis. However, before being integrated into clinical practice, ctDNA analysis needs to be standardized and validated through the performance of multicenter prospective and well-designed clinical studies. This review is focused on the clinical utility of ctDNA analysis, especially at the DNA mutation and methylation level, in breast cancer patients, incorporating the latest advances in technological approaches and involving key studies in the early and metastatic setting.
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Affiliation(s)
- Eleni Tzanikou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
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181
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Selective hybridization and capture of KRAS DNA from plasma and blood using ion-tagged oligonucleotide probes coupled to magnetic ionic liquids. Anal Chim Acta 2019; 1094:1-10. [PMID: 31761034 DOI: 10.1016/j.aca.2019.10.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/22/2022]
Abstract
Detection of circulating tumor DNA (ctDNA) presents several challenges due to single-nucleotide polymorphisms and large amounts of background DNA. Previously, we reported a sequence-specific DNA extraction procedure utilizing functionalized oligonucleotides called ion-tagged oligonucleotides (ITOs) and disubstituted ion-tagged oligonucleotides (DTOs). ITOs and DTOs are capable of hybridizing to complementary DNA for subsequent capture by a magnetic ionic liquid (MIL) through hydrophobic interactions, π-π stacking, and fluorophilic interactions. However, the performance of the ITOs and DTOs in complex sample matrices has not yet been evaluated. In this study, we compare the amount of KRAS DNA extracted using ITO and DTOs from saline, 2-fold diluted plasma, 10-fold diluted plasma, and 10-fold diluted blood. We demonstrate that ITO/DTO-MIL extraction is capable of selectively preconcentrating DNA from diluted plasma and blood without additional sample preparation steps. In comparison, streptavidin-coated magnetic beads were unable to selectively extract DNA from 10-fold diluted plasma and 10-fold diluted blood without additional sample clean-up steps. Significantly more DNA could be extracted from 2-fold diluted plasma and 10-fold diluted blood matrices using the DTO probes compared to the ITO probes, likely due to stronger interactions between the probe and MIL. The ability of the DTO-MIL method to selectively preconcentrate small concentrations of DNA from complex biological matrices suggests that this method could be beneficial for ctDNA analysis.
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182
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Kastrisiou M, Zarkavelis G, Pentheroudakis G, Magklara A. Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat? Cancers (Basel) 2019; 11:E1573. [PMID: 31623125 PMCID: PMC6826585 DOI: 10.3390/cancers11101573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022] Open
Abstract
Owing to its advantages over prior relevant technologies, massive parallel or next-generation sequencing (NGS) is rapidly evolving, with growing applications in a wide range of human diseases. The burst in actionable molecular alterations in many cancer types advocates for the practicality of using NGS in the clinical setting, as it permits the parallel characterization of multiple genes in a cost- and time-effective way, starting from low-input DNA. In advanced clinical practice, the oncological management of colorectal cancer requires prior knowledge of KRAS, NRAS, and BRAF status, for the design of appropriate therapeutic strategies, with more gene mutations still surfacing as potential biomarkers. Tumor heterogeneity, as well as the need for serial gene profiling due to tumor evolution and the emergence of novel genetic alterations, have promoted the use of liquid biopsies-especially in the form of circulating tumor DNA (ctDNA)-as a promising alternative to tissue molecular analysis. This review discusses recent studies that have used plasma NGS in advanced colorectal cancer and summarizes the clinical applications, as well as the technical challenges involved in adopting this technique in a clinically beneficial oncological practice.
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Affiliation(s)
- Myrto Kastrisiou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, 45110 Ioannina, Greece.
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183
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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184
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Progress in quantitative technique of circulating cell free DNA and its role in cancer diagnosis and prognosis. Cancer Genet 2019; 239:75-84. [PMID: 31639530 DOI: 10.1016/j.cancergen.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/24/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023]
Abstract
The interest in the potential application value of circulating cell free DNA (ccfDNA) has increased rapidly in recent years, as numerous researchers have demonstrated that the change of its level in the blood is associated with many diseases. Its potential role in cancer management is of particular concern. In comparison with traditional invasive tissue biopsy, quantitative analysis of ccfDNA level for the detection of cancer is advantageous due to the non-invasiveness of blood collection. Moreover, its clinical significance in prognosis prediction and dynamic monitoring of disease progression in cancer patients is equally worthy of attention. At the same time, quantitative detection of ccfDNA is being improved to pursue higher sensitivity due to its low concentration in the blood sample. In this review, we will summarize the progress in quantitative technology of ccfDNA and describe the possible relationship between ccfDNA level and cancer diagnosis and prognosis prediction.
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185
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Goggs R. Effect of sample type on plasma concentrations of cell-free DNA and nucleosomes in dogs. Vet Rec Open 2019; 6:e000357. [PMID: 31673376 PMCID: PMC6802997 DOI: 10.1136/vetreco-2019-000357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/20/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
Cell-free DNA (cfDNA) and nucleosomes are two biomarkers of cell death and neutrophil extracellular trap formation that are increased in dogs with sepsis, immune-mediated haemolytic anaemia, cancer and following trauma and have diagnostic and prognostic values. cfDNA and nucleosomes are typically measured in plasma samples using DNA-specific fluorophores and ELISA assays, respectively, but their concentrations may be affected by pre-analytical variables such as sample type. The present study aimed to investigate the influence of sample type on the plasma cfDNA and nucleosome concentrations of a heterogeneous group of dogs presenting to an emergency room. Triplicate samples were collected into K2-ethylenediamine tetraacetic acid, 3.2% citrate and a specialised DNA stabilisation tube (Streck BCT), processed rapidly and frozen for batch analysis. Biomarker concentrations were compared between sample types by calculation of Spearman’s correlation coefficients, and with Deming regression, Bland-Altman plots and the Friedman test. Overall, biomarker concentrations were highly correlated between the three sample types. The most concordant results were obtained using citrate samples and the DNA stabilisation tube. Matched cfDNA concentrations between the different sample types were significantly different but there was no significant difference between the nucleosome concentrations in any of the sample types. The present study suggests that cfDNA and nucleosomes can be successfully measured in various sample types, but distinct sample types do not produce interchangeable results. This argues for use of a consistent sample type within studies and suggests standardisation may be useful for the field.
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Affiliation(s)
- Robert Goggs
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
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186
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Salvianti F, Gelmini S, Costanza F, Mancini I, Sonnati G, Simi L, Pazzagli M, Pinzani P. The pre-analytical phase of the liquid biopsy. N Biotechnol 2019; 55:19-29. [PMID: 31580920 DOI: 10.1016/j.nbt.2019.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/11/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
The term 'liquid biopsy', introduced in 2013 in reference to the analysis of circulating tumour cells (CTCs) in cancer patients, was extended to cell-free nucleic acids (cfNAs) circulating in blood and other body fluids. CTCs and cfNAs are now considered diagnostic and prognostic markers, used as surrogate materials for the molecular characterisation of solid tumours, in particular for research on tumour-specific or actionable somatic mutations. Molecular characterisation of cfNAs and CTCs (especially at the single cell level) is technically challenging, requiring highly sensitive and specific methods and/or multi-step processes. The analysis of the liquid biopsy relies on a plethora of methods whose standardisation cannot be accomplished without disclosing criticisms related to the pre-analytical phase. Thus, pre-analytical factors potentially influencing downstream cellular and molecular analyses must be considered in order to translate the liquid biopsy approach into clinical practice. The present review summarises the most recent reports in this field, discussing the main pre-analytical aspects related to CTCs, cfNAs and exosomes in blood samples for liquid biopsy analysis. A short discussion on non-blood liquid biopsy samples is also included.
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Affiliation(s)
- Francesca Salvianti
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Stefania Gelmini
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy.
| | - Filomena Costanza
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Irene Mancini
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Gemma Sonnati
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Lisa Simi
- Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Viale Pieraccini,6, 50139 Florence, Italy
| | - Mario Pazzagli
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Pamela Pinzani
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
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187
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Liquid biopsy in oncology: a consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology. Clin Transl Oncol 2019; 22:823-834. [PMID: 31559582 PMCID: PMC7854395 DOI: 10.1007/s12094-019-02211-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
The proportion of cancer patients with tumours that harbour a potentially targetable genomic alteration is growing considerably. The diagnosis of these genomic alterations can lead to tailored treatment at the onset of disease or on progression and to obtaining additional predictive information on immunotherapy efficacy. However, in up to 25% of cases, the initial tissue biopsy is inadequate for precision oncology and, in many cases, tumour genomic profiling at progression is not possible due to technical limitations of obtaining new tumour tissue specimens. Efficient diagnostic alternatives are therefore required for molecular stratification, which includes liquid biopsy. This technique enables the evaluation of the tumour genomic profile dynamically and captures intra-patient genomic heterogeneity as well. To date, there are several diagnostic techniques available for use in liquid biopsy, each one of them with different precision and performance levels. The objective of this consensus statement of the Spanish Society of Pathology and the Spanish Society of Medical Oncology is to evaluate the viability and effectiveness of the different methodological approaches in liquid biopsy in cancer patients and the potential application of this method to current clinical practice. The experts contributing to this consensus statement agree that, according to current evidence, liquid biopsy is an acceptable alternative to tumour tissue biopsy for the study of biomarkers in various clinical settings. It is therefore important to standardise pre-analytical and analytical procedures, to ensure reproducibility and generate structured and accessible clinical reports. It is essential to appoint multidisciplinary tumour molecular boards to oversee these processes and to enable the most suitable therapeutic decisions for each patient according to the genomic profile.
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188
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Andrikovics H, Őrfi Z, Meggyesi N, Bors A, Varga L, Kövy P, Vilimszky Z, Kolics F, Gopcsa L, Reményi P, Tordai A. Current Trends in Applications of Circulatory Microchimerism Detection in Transplantation. Int J Mol Sci 2019; 20:E4450. [PMID: 31509957 PMCID: PMC6769866 DOI: 10.3390/ijms20184450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023] Open
Abstract
Primarily due to recent advances of detection techniques, microchimerism (the proportion of minor variant population is below 1%) has recently gained increasing attention in the field of transplantation. Availability of polymorphic markers, such as deletion insertion or single nucleotide polymorphisms along with a vast array of high sensitivity detection techniques, allow the accurate detection of small quantities of donor- or recipient-related materials. This diagnostic information can improve monitoring of allograft injuries in solid organ transplantations (SOT) as well as facilitate early detection of relapse in allogeneic hematopoietic stem cell transplantation (allo-HSCT). In the present review, genetic marker and detection platform options applicable for microchimerism detection are discussed. Furthermore, current results of relevant clinical studies in the context of microchimerism and SOT or allo-HSCT respectively are also summarized.
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Affiliation(s)
- Hajnalka Andrikovics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
- Department of Pathophysiology, Semmelweis University, 1089 Budapest, Hungary
| | - Zoltán Őrfi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Nóra Meggyesi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - András Bors
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Lívia Varga
- School of PhD Studies, Semmelweis University, 1085 Budapest, Hungary
- Hungarian National Blood Transfusion Service, 1113 Budapest, Hungary
| | - Petra Kövy
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
- School of PhD Studies, Semmelweis University, 1085 Budapest, Hungary
| | - Zsófia Vilimszky
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Fanni Kolics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - László Gopcsa
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Péter Reményi
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Attila Tordai
- Department of Pathophysiology, Semmelweis University, 1089 Budapest, Hungary.
- Department of Transfusion Medicine, Semmelweis University, 1089 Budapest, Hungary.
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189
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Yu Z, Qin S, Wang H. Alter circulating cell-free DNA variables in plasma of ovarian cancer patients. J Obstet Gynaecol Res 2019; 45:2237-2242. [PMID: 31502389 DOI: 10.1111/jog.14102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 08/14/2019] [Indexed: 12/13/2022]
Abstract
AIM Liquid biopsy shows great potential in the fields of early diagnosis and prognosis in cancer. Ovarian cancer (OC) is the seventh most common cancer and the eighth most common cause of death from cancer in women. The early diagnosis of OC is vital for subsequent treatment and outcome. Here we investigated two markers: cell-free DNA concentration (cfDNA conc) and cell-free DNA integrity (cfDI) between OC patients and healthy controls. METHODS Age-matched OC patients and healthy controls were enrolled in this study. In total, there are 20 patients and 20 healthy controls. cfDNA conc and cfDI were calculated by arthrobacter luteus (ALU) gene using quantitative real-time polymerase chain reaction (PCR). RESULTS An increased cfDNA conc in OC patients compared to healthy controls was observed (mean cfDNA conc for OC patients: 1.98 ng/μL, for healthy control: 0.51 ng/μL, P = 0.02). For cfDI, the median value of OC patients is 0.49 while the median value of healthy control is 0.61 (P = 0.038). The diagnostic value of area under the curve was 0.86 for cfDNA conc and 0.72 for cfDI. When cfDNA conc and cfDI were combined, the diagnostic value was 0.90 which indicates a good diagnostic marker. CONCLUSION As few reports of cfDNA conc and cfDI differences between OC patients and healthy controls reported, our study shows increased cfDNA concentrations and decreased cfDI in OC patients compared to healthy controls. We also propose that cfDNA biomarkers can be potential diagnostic markers in ovarian cancer.
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Affiliation(s)
- Zhou Yu
- Department of Obstetrics and Gynecology, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, China
| | - Shanshan Qin
- Department of Obstetrics and Gynecology, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, China
| | - Haidong Wang
- Department of Obstetrics and Gynecology, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, China
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190
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Tarazona N, Cervantes A. Liquid biopsy: another tool towards tailored therapy in colorectal cancer. Ann Oncol 2019; 29:7-8. [PMID: 29045545 DOI: 10.1093/annonc/mdx641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- N Tarazona
- CIBERONC, Valencia, Spain.,Department of Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - A Cervantes
- CIBERONC, Valencia, Spain.,Department of Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
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191
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Calbet-Llopart N, Potrony M, Tell-Martí G, Carrera C, Barreiro A, Aguilera P, Podlipnik S, Puig S, Malvehy J, Puig-Butillé JA. Detection of cell-free circulating BRAF V 600E by droplet digital polymerase chain reaction in patients with and without melanoma under dermatological surveillance. Br J Dermatol 2019; 182:382-389. [PMID: 31102256 DOI: 10.1111/bjd.18147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND The p.V600E mutation in the BRAF protein is the most frequent mutation in cutaneous melanoma and is a recurrent alteration found in common benign naevi. Analysis of the cell-free BRAF c.1799T>A, p.V600E mutation (cfBRAFV 600E ) in plasma has emerged as a biomarker for monitoring prognosis and treatment response in patients with melanoma. OBJECTIVES To quantify cfBRAFV 600E levels in plasma from patients with melanoma and from patients without melanoma undergoing regular follow-up of their melanocytic lesions, in order to assess the clinical significance of the test. METHODS We quantified cfBRAFV 600E by droplet digital polymerase chain reaction in plasma from 146 patients without melanoma undergoing continuous dermatological screening, from 26 stage III and seven stage IV patients with BRAF-mutant melanoma, and from 32 patients with melanoma who were free of disease for 3 or more years. RESULTS Among disease-free patients and individuals without melanoma, 52% presented a high naevus count (> 50) and 49% had clinically atypical naevi. cfBRAFV 600E was detected in 71% of patients with stage IV melanoma and 15% with stage III, and in 1·4% of individuals without melanoma. No cfBRAFV 600E mutation was detected in disease-free patients with melanoma. Individuals without melanoma had lower cfBRAFV 600E levels than patients with melanoma. We established a variant allelic frequency of 0·26% or 5 copies mL-1 of cfBRAFV 600E as the optimal cutoff value for identifying patients with melanoma with > 99% specificity. CONCLUSIONS This study suggests that naevus-related factors do not influence the detection of cfBRAFV 600E in individuals without melanoma, and supports the clinical diagnostic value of plasma cfBRAFV 600E quantification in patients with melanoma. What's already known about this topic? The analysis of the BRAF c.1799T>A (p.V600E) mutation in cell-free (cf)DNA has emerged as a potential biomarker for monitoring prognosis and treatment response in patients with metastatic BRAFV600E melanoma. The BRAFV600E alteration is a common genetic alteration found in benign proliferations such as melanocytic naevi. No information exists about the impact of the number of common acquired naevi or the presence of clinically atypical naevi in cfBRAFV600E detection in an individual. What does this study add? The cfBRAFV600E mutation is detected in plasma from a reduced number of individuals without melanoma undergoing continuous dermatological follow-up. A high number of naevi or the presence of clinically atypical naevi are factors that do not influence cfBRAFV600E detection in an individual. Both total cfBRAF concentration and cfBRAFV600E frequency are effective biomarkers in patients with advanced melanoma but not in patients at early stages or with micrometastases. What is the translational message? Detection of cfBRAFV600E in an individual is not influenced by naevus-related factors. cfBRAFV600E is a robust and reliable biomarker that can be used in dermatological surveillance programmes.
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Affiliation(s)
- N Calbet-Llopart
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - M Potrony
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - G Tell-Martí
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - C Carrera
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - A Barreiro
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - P Aguilera
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - S Podlipnik
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - S Puig
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - J Malvehy
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - J A Puig-Butillé
- Molecular Biology CORE Laboratory, Biochemistry and Molecular Genetics Department; Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
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192
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Goggs R, Jeffery U, LeVine DN, Li RHL. Neutrophil-Extracellular Traps, Cell-Free DNA, and Immunothrombosis in Companion Animals: A Review. Vet Pathol 2019; 57:6-23. [PMID: 31342866 DOI: 10.1177/0300985819861721] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Immunothrombosis is a potentially beneficial physiological process that aids innate immunity and host defense against pathogen invasion. However, this process can also be damaging when it occurs to excess or in critical blood vessels. Formation of extracellular traps by leukocytes, particularly neutrophils, is central to our understanding of immunothrombosis. In addition to degranulation and phagocytosis, extracellular traps are the third mechanism by which neutrophils combat potential pathogens. These traps consist of extracellular DNA decorated with bactericidal cellular proteins, including elastase, myeloperoxidase, and cathepsins. Neutrophils can release these structures as part of a controlled cell-death process or via a process termed vital NETosis that enables the cells to extrude DNA but remain viable. There is accumulating evidence that NETosis occurs in companion animals, including dogs, horses, and cats, and that it actively contributes to pathogenesis. Numerous studies have been published detailing various methods for identification and quantification of extracellular trap formation, including cell-free DNA, measurements of histones and proteins such as high-mobility group box-1, and techniques involving microscopy and flow cytometry. Here, we outline the present understanding of these phenomena and the mechanisms of extracellular trap formation. We critically review the data regarding measurement of NETosis in companion animals, summarize the existing literature on NETosis in veterinary species, and speculate on what therapeutic options these insights might present to clinicians in the future.
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Affiliation(s)
- Robert Goggs
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Unity Jeffery
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Dana N LeVine
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Ronald H L Li
- Department of Veterinary Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
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193
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Compton CC, Robb JA, Anderson MW, Berry AB, Birdsong GG, Bloom KJ, Branton PA, Crothers JW, Cushman-Vokoun AM, Hicks DG, Khoury JD, Laser J, Marshall CB, Misialek MJ, Natale KE, Nowak JA, Olson D, Pfeifer JD, Schade A, Vance GH, Walk EE, Yohe SL. Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine. Arch Pathol Lab Med 2019; 143:1346-1363. [PMID: 31329478 DOI: 10.5858/arpa.2019-0009-sa] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Biospecimens acquired during routine medical practice are the primary sources of molecular information about patients and their diseases that underlies precision medicine and translational research. In cancer care, molecular analysis of biospecimens is especially common because it often determines treatment choices and may be used to monitor therapy in real time. However, patient specimens are collected, handled, and processed according to routine clinical procedures during which they are subjected to factors that may alter their molecular quality and composition. Such artefactual alteration may skew data from molecular analyses, render analysis data uninterpretable, or even preclude analysis altogether if the integrity of a specimen is severely compromised. As a result, patient care and safety may be affected, and medical research dependent on patient samples may be compromised. Despite these issues, there is currently no requirement to control or record preanalytical variables in clinical practice with the single exception of breast cancer tissue handled according to the guideline jointly developed by the American Society of Clinical Oncology and College of American Pathologists (CAP) and enforced through the CAP Laboratory Accreditation Program. Recognizing the importance of molecular data derived from patient specimens, the CAP Personalized Healthcare Committee established the Preanalytics for Precision Medicine Project Team to develop a basic set of evidence-based recommendations for key preanalytics for tissue and blood specimens. If used for biospecimens from patients, these preanalytical recommendations would ensure the fitness of those specimens for molecular analysis and help to assure the quality and reliability of the analysis data.
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Affiliation(s)
- Carolyn C Compton
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - James A Robb
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Matthew W Anderson
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Anna B Berry
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - George G Birdsong
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Kenneth J Bloom
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Philip A Branton
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jessica W Crothers
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Allison M Cushman-Vokoun
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - David G Hicks
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Joseph D Khoury
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jordan Laser
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Carrie B Marshall
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Michael J Misialek
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Kristen E Natale
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jan Anthony Nowak
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Damon Olson
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - John D Pfeifer
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Andrew Schade
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Gail H Vance
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Eric E Walk
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Sophia Louise Yohe
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
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Chen Z, Zhang S, Li C, Xu C, Zhao J, Miao L. Comprehensive Evaluation of the Factors Affecting Plasma Circulating Cell-Free DNA Levels and Their Application in Diagnosing Nonsmall Cell Lung Cancer. Genet Test Mol Biomarkers 2019; 23:270-276. [PMID: 30986099 DOI: 10.1089/gtmb.2018.0106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIMS Circulating cell-free DNA (ccfDNA) is a valuable biomarker, but the ccfDNA levels are influenced by variations that occur during sample processing. The feasibility of using ccfDNA as a diagnostic biomarker requires further examination. MATERIALS AND METHODS We established a real-time PCR assay with an external standard to comprehensively evaluate the factors affecting ccfDNA levels, including the extraction kit used, freeze-thaw stability, and stability of delayed extraction. Then we compared the ccfDNA levels between benign controls (64 cases, including 23 sarcoidosis patients, 19 pneumonia patients, and 22 other lung disease patients) and nonsmall cell lung cancer (NSCLC) patients (74 patients). RESULTS The different kits showed different recovery rates. Moreover, the ccfDNA present in plasma or stored in extraction buffer was stable after freeze-thawing, and the ccfDNA concentration remained consistent for 24 h at 4°C and for 12 h at room temperature. The patients with NSCLC-III/IV exhibited significantly higher ccfDNA levels than the patients with NSCLC-I/II (293 copies/μL vs. 190 copies/μL, p = 0.0339). However, no significant differences in the plasma ccfDNA levels were observed between the benign controls and NSCLC patients (241 copies/μL vs. 233 copies/μL, p > 0.05). CONCLUSIONS Variations in sample processing procedures led to variable results. The lack of differences between the NSCLC patients and benign controls indicates that further research is necessary to better characterize ccfDNA as a biomarker for diagnosing NSCLC.
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Affiliation(s)
- Zhiyao Chen
- 1 Department of Clinical Pharmacology Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Shichao Zhang
- 1 Department of Clinical Pharmacology Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China.,2 College of Pharmaceutical Sciences, Soochow University, Suzhou, P.R. China
| | - Chang Li
- 3 Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Chun Xu
- 3 Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Jun Zhao
- 3 Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Liyan Miao
- 1 Department of Clinical Pharmacology Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China.,2 College of Pharmaceutical Sciences, Soochow University, Suzhou, P.R. China
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Liquid Biopsy in Glioblastoma: Opportunities, Applications and Challenges. Cancers (Basel) 2019; 11:cancers11070950. [PMID: 31284524 PMCID: PMC6679205 DOI: 10.3390/cancers11070950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy represents a minimally invasive procedure that can provide similar information from body fluids to what is usually obtained from a tissue biopsy sample. Its implementation in the clinical setting might significantly renew the field of medical oncology, facilitating the introduction of the concepts of precision medicine and patient-tailored therapies. These advances may be useful in the diagnosis of brain tumors that currently require surgery for tissue collection, or to perform genetic tumor profiling for disease classification and guidance of therapy. In this review, we will summarize the most recent advances and putative applications of liquid biopsy in glioblastoma, the most common and malignant adult brain tumor. Moreover, we will discuss the remaining challenges and hurdles in terms of technology and biology for its clinical application.
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Abstract
The study of cell-free DNA (cfDNA) is often challenging due to genomic DNA contamination, low concentration, and high fragmentation. Therefore, it is important to optimize pre-analytical and analytical procedures in order to maximize the performance of cfDNA-based analyses.In this chapter, we report the most common methods for the correct collection, centrifugation, storage, and DNA isolation from cell-free biological sources such as plasma, urines, cerebrospinal fluid, and pleural effusion fluid.
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Affiliation(s)
- Filippo Martignano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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Abstract
Since its discovery in human blood plasma about 70 years ago, circulating cell-free DNA (cfDNA) has become an attractive subject of research as noninvasive disease biomarker. The interest in clinical applications has gained an exponential increase, making it a popular and potential target in a wide range of research areas.cfDNA can be found in different body fluids, both in healthy and not healthy subjects. The recent and rapid development of new molecular techniques is promoting the study and the identification of cfDNA, holding the key to minimally invasive diagnostics, improving disease monitoring, clinical decision, and patients' outcome.cfDNA has already given a huge impact on prenatal medicine, and it could become, in the next future, the standard of care also in other fields, from oncology to transplant medicine and cardiovascular diseases.
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Affiliation(s)
- Rossella Ranucci
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
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Ho HL, Huang CC, Ku WH, Ho CL, Lin CH, Yu SL, Chou TY. Liquid biopsy for detection of EGFR T790M mutation in nonsmall cell lung cancer: An experience of proficiency testing in Taiwan. J Chin Med Assoc 2019; 82:473-476. [PMID: 30932938 DOI: 10.1097/jcma.0000000000000100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The use of liquid biopsy to detect epidermal growth factor receptor (EGFR) T790M mutation in nonsmall cell lung cancer (NSCLC) is a promising method to screen patients eligible for third-generation EGFR inhibitors. Proficiency testing (PT) programs involving liquid biopsy are currently lacking. In this study, we conducted a PT program to assess the quality assurance of liquid biopsy tests for detecting EGFR T790M mutation in molecular pathology laboratories in Taiwan. METHODS Whole blood samples (2 mL) with various concentrations of the EGFR T790M mutation were prepared and analyzed in six participating laboratories using their clinically validated assays. RESULTS For circulating cell-free DNA (cfDNA) isolation, three of the six participating laboratories used the cobas cfDNA Sample Preparation Kit, and three used the QIAamp Circulating Nucleic Acid Kit. For testing platforms, two of the six participating laboratories used mass spectrometry, three used the cobas EGFR mutation test, and one used a laboratory-developed test. There was 100% concordance in detection of all the given concentrations of EGFR T790M mutation between the participating laboratories and different testing platforms. The testing platforms used by all participating laboratories could successfully detect EGFR T790M mutation to an expected frequency of 1%. CONCLUSION In this first PT program using liquid biopsy in Taiwan, local clinical laboratories were suitably equipped and proficient in the use of cfDNA to test for the EGFR T790M mutation. Establishing a routine PT system to ensure the reliability and accuracy of liquid biopsy in clinical practice in Taiwan would be helpful.
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Affiliation(s)
- Hsiang-Ling Ho
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Chao-Cheng Huang
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan, ROC
| | - Wen-Hui Ku
- Department of Clinical Pathology, Taipei Institute of Pathology, Taipei, Taiwan, ROC
| | - Chung-Liang Ho
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Chia-Hung Lin
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan, ROC
| | - Teh-Ying Chou
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
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199
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Page K, Shaw JA, Guttery DS. The liquid biopsy: towards standardisation in preparation for prime time. Lancet Oncol 2019; 20:758-760. [PMID: 31162088 DOI: 10.1016/s1470-2045(19)30310-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Karen Page
- The Leicester Cancer Research Centre, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Jacqueline A Shaw
- The Leicester Cancer Research Centre, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - David S Guttery
- The Leicester Cancer Research Centre, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK.
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200
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Gregg JP, Li T, Yoneda KY. Molecular testing strategies in non-small cell lung cancer: optimizing the diagnostic journey. Transl Lung Cancer Res 2019; 8:286-301. [PMID: 31367542 PMCID: PMC6626860 DOI: 10.21037/tlcr.2019.04.14] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/14/2019] [Indexed: 01/21/2023]
Abstract
Molecular testing identifies patients with advanced non-small cell lung cancer (NSCLC) who may benefit from targeted therapy or immunotherapy (i.e., immune checkpoint inhibitor treatment for patients with high tumor mutational burden (TMB), microsatellite instability-high or mismatch repair-deficient tumors). Current guidelines state that molecular testing should be conducted at the time of initial diagnosis and tumor progression on targeted therapy. In real-world clinical practice in the United States (US), molecular testing is often not conducted or happens late in the diagnostic journey, resulting in delayed or inappropriate treatment. Herein, we review the rationale for molecular testing in advanced NSCLC, along with best-practice guidelines based on published recommendations and our own clinical experience, including a case study. We propose three strategies to optimize molecular testing in newly diagnosed patients with advanced NSCLC: (I) pulmonologists, interventional radiologists, or thoracic surgeons order molecular tests as soon as advanced NSCLC with an adenocarcinoma component is suspected; (II) liquid biopsies conducted early in the diagnostic pathway; and (III) pathologist-directed reflex testing, as conducted in other areas of oncology. To help facilitate these strategies, we outline our recommendations for optimal sample collection techniques and stewardship. In summary, we believe that implementation of these individual strategies will allow clinicians to effectively leverage available treatment options for advanced NSCLC, reducing the time to optimal treatment and improving patient outcomes.
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Affiliation(s)
- Jeffrey P. Gregg
- Department of Pathology and Laboratory Medicine, University of California, Davis Medical Center, CA, USA
| | - Tianhong Li
- Division of Hematology & Oncology, Department of Internal Medicine, School of Medicine, University of California, Davis Comprehensive Cancer Center, CA, USA
| | - Ken Y. Yoneda
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis Medical Center, CA, USA
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