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Giacomini P, Valenti F, Allegretti M, Pallocca M, De Nicola F, Ciuffreda L, Fanciulli M, Scalera S, Buglioni S, Melucci E, Casini B, Carosi M, Pescarmona E, Giordani E, Sperati F, Jannitti N, Betti M, Maugeri-Saccà M, Cecere FL, Villani V, Pace A, Appetecchia M, Vici P, Savarese A, Krasniqi E, Ferraresi V, Russillo M, Fabi A, Landi L, Minuti G, Cappuzzo F, Zeuli M, Ciliberto G. The Molecular Tumor Board of the Regina Elena National Cancer Institute: from accrual to treatment in real-world. J Transl Med 2023; 21:725. [PMID: 37845764 PMCID: PMC10577953 DOI: 10.1186/s12967-023-04595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Molecular Tumor Boards (MTB) operating in real-world have generated limited consensus on good practices for accrual, actionable alteration mapping, and outcome metrics. These topics are addressed herein in 124 MTB patients, all real-world accrued at progression, and lacking approved therapy options. METHODS Actionable genomic alterations identified by tumor DNA (tDNA) and circulating tumor DNA (ctDNA) profiling were mapped by customized OncoKB criteria to reflect diagnostic/therapeutic indications as approved in Europe. Alterations were considered non-SoC when mapped at either OncoKB level 3, regardless of tDNA/ctDNA origin, or at OncoKB levels 1/2, provided they were undetectable in matched tDNA, and had not been exploited in previous therapy lines. RESULTS Altogether, actionable alterations were detected in 54/124 (43.5%) MTB patients, but only in 39 cases (31%) were these alterations (25 from tDNA, 14 from ctDNA) actionable/unexploited, e.g. they had not resulted in the assignment of pre-MTB treatments. Interestingly, actionable and actionable/unexploited alterations both decreased (37.5% and 22.7% respectively) in a subset of 88 MTB patients profiled by tDNA-only, but increased considerably (77.7% and 66.7%) in 18 distinct patients undergoing combined tDNA/ctDNA testing, approaching the potential treatment opportunities (76.9%) in 147 treatment-naïve patients undergoing routine tDNA profiling for the first time. Non-SoC therapy was MTB-recommended to all 39 patients with actionable/unexploited alterations, but only 22 (56%) accessed the applicable drug, mainly due to clinical deterioration, lengthy drug-gathering procedures, and geographical distance from recruiting clinical trials. Partial response and stable disease were recorded in 8 and 7 of 19 evaluable patients, respectively. The time to progression (TTP) ratio (MTB-recommended treatment vs last pre-MTB treatment) exceeded the conventional Von Hoff 1.3 cut-off in 9/19 cases, high absolute TTP and Von Hoff values coinciding in 3 cases. Retrospectively, 8 patients receiving post-MTB treatment(s) as per physician's choice were noted to have a much longer overall survival from MTB accrual than 11 patients who had received no further treatment (35.09 vs 6.67 months, p = 0.006). CONCLUSIONS MTB-recommended/non-SoC treatments are effective, including those assigned by ctDNA-only alterations. However, real-world MTBs may inadvertently recruit patients electively susceptible to diverse and/or multiple treatments.
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Affiliation(s)
- Patrizio Giacomini
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy.
| | - Fabio Valenti
- UOC Translational Oncology Research, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Matteo Allegretti
- UOC Translational Oncology Research, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Matteo Pallocca
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Francesca De Nicola
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Ludovica Ciuffreda
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Maurizio Fanciulli
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Stefano Scalera
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Simonetta Buglioni
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Elisa Melucci
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Beatrice Casini
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Mariantonia Carosi
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Edoardo Pescarmona
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Elena Giordani
- UOC Translational Oncology Research, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Francesca Sperati
- Clinical Trial Center, Biostatistics and Bioinformatics, San Gallicano Dermatological Institute IRCCS, 00144, Rome, Italy
| | - Nicoletta Jannitti
- Pharmacy Unit, Medical Direction, IRCCS-Regina Elena National Cancer Institute and San Gallicano Institute, 00144, Rome, Italy
| | - Martina Betti
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Marcello Maugeri-Saccà
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
- Medical Oncology 2, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | | | - Veronica Villani
- Neuro-Oncology Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Andrea Pace
- Neuro-Oncology Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Marialuisa Appetecchia
- Oncological Endocrinology Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Patrizia Vici
- Phase IV Studies, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Antonella Savarese
- Medical Oncology 1, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Eriseld Krasniqi
- Phase IV Studies, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Virginia Ferraresi
- Sarcomas and Rare Tumors Departmental Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Michelangelo Russillo
- Sarcomas and Rare Tumors Departmental Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Alessandra Fabi
- Precision Medicine Unit in Senology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Lorenza Landi
- Clinical Trial Center: Phase 1 and Precision Medicine, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Gabriele Minuti
- Clinical Trial Center: Phase 1 and Precision Medicine, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Federico Cappuzzo
- Medical Oncology 2, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Massimo Zeuli
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
- Medical Oncology 1, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
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Wang J, Wang W, Zhou W, Zhou Y, Zhou L, Wang X, Yu B, Zhang B. Preliminary study of noninvasive prenatal screening for 22q11.2 deletion/duplication syndrome using multiplex dPCR assay. Orphanet J Rare Dis 2023; 18:278. [PMID: 37684689 PMCID: PMC10486099 DOI: 10.1186/s13023-023-02903-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVE This study aimed to establish a cell-free fetal DNA (cffDNA) assay using multiplex digital PCR (dPCR) for identifying fetuses at increased risk of 22q11.2 deletion/duplication syndrome. METHODS Six detection sites and their corresponding probes were designed for the 22q11.2 recurrent region. A dPCR assay for the noninvasive screening of 22q11.2 deletion/duplication syndrome was established. A total of 130 plasma samples from pregnant women (including 15 samples with fetal 22q11.2 deletion/duplication syndrome) were blindly tested for evaluating the sensitivity and specificity of the established assay. RESULTS DNA with different sizes of 22q11.2 deletion/duplication was detected via dPCR, indicating that the designed probes and detection sites were reasonable and effective. In the retrospective clinical samples, 11 out of 15 samples of pregnant women with 22q11.2 deletion/duplication were detected during the cffDNA assay, and accurate regional localization was achieved. Among the 115 normal samples, 111 were confirmed to be normal. Receiver operating characteristic curves were used for assessing the cut-off values and AUC for these samples. The sensitivity, specificity, and positive as well as negative predictive values were 73.3%, 96.5%, 73.3%, and 96.5%, respectively. CONCLUSION The cffDNA assay based on dPCR technology for the noninvasive detection of 22q11.2 recurrent copy number variants in fetuses detected most affected cases, including smaller but relatively common nested deletions, with a low false-positive rate. It is a potential, efficient and simple method for the noninvasive screening of 22q11.2 deletion/duplication syndrome.
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Affiliation(s)
- Jing Wang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Wei Wang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Wenbo Zhou
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Yan Zhou
- Xingzhi Biotechnology Co., LTD, Suzhou, 215000, Jiangsu Province, China
| | - Linna Zhou
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Xinyue Wang
- Xingzhi Biotechnology Co., LTD, Suzhou, 215000, Jiangsu Province, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China.
| | - Bin Zhang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China.
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Schuster CJ, Murray KN, Sanders JL, Kent ML. Application of an eDNA assay for the detection of Pseudoloma neurophilia (Microsporidia) in zebrafish ( Danio rerio) facilities. Aquaculture 2023; 564:739044. [PMID: 38562455 PMCID: PMC10983818 DOI: 10.1016/j.aquaculture.2022.739044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Environmental DNA (eDNA) water assays are beginning to be implemented for many important pathogens in confined aquaculture systems. Recirculating systems are rapidly being developed for fin fish aquaculture. Zebrafish (Danio rerio) are reared in these systems, and Pseudoloma neurophilia (Microsporidia) represents a serious challenge for zebrafish research facilities. Diagnosis of the pathogen has traditionally used histology or PCR of tissues with lethal sampling. However, with the development of a nonlethal assay to detect P. neurophilia in tank water, facilities will be able to integrate the assay into routine surveillance efforts to couple with their established protocols. Here, we first describe a modified protocol to extract and quantify parasite DNA from the environment for nonlethal detection of P. neurophilia in adult zebrafish populations. Using this modified assay, we then evaluated water samples from a longitudinal experimental infection study, targeting timepoints during initial infection. The parasite was detectable in the water immediately after initial exposure until week 4 post exposure (pe), when the parasite was undetectable until 7 weeks pe. After that time, the parasite was sporadically detected in the water for the 10-month study, likely correlating with the lifecycle of the parasite. Using water samples from the Zebrafish International Resource Center, we also validated the clinical relevance of the assay in a large zebrafish facility. The integration of this assay at ZIRC will significantly compliment surveillance and control efforts for the microsporidian parasite.
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Affiliation(s)
- Corbin J. Schuster
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
- Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403, USA
| | - Katrina N. Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403, USA
| | - Justin L. Sanders
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Michael L. Kent
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
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Wang X, Xing D, Liu Z, Zhang Y, Cheng B, Sun S, Wang Q, Dong L. Establishment and evaluation of digital PCR methods for HER2 copy number variation in breast cancer. Anal Bioanal Chem 2023; 415:725-33. [PMID: 36571590 DOI: 10.1007/s00216-022-04466-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/27/2022]
Abstract
Accurate measurement of human epidermal growth factor receptor 2 (HER2) copy number variation (CNV) is very important for guiding the tumor target therapy in breast cancer. Digital PCR (dPCR) is a sensitive and an absolute quantitative method, which can be used to detect HER2 CNV. Three HER2 exon-specific digital PCR assays along with three new reference genes assays (homo sapiens ribonuclease P RNA component H1 (RPPH1), glucose-6-phosphate isomerase (GPI), and chromosome 1 open reading frame 43 (C1ORF43), on different chromosomes) were established and validated by using standard reference material, 8 different cell lines and 110 clinical Formalin-fixed and paraffin-embedded (FFPE) samples. DPCR can achieve precise quantification of HER2 CNV by calculating the ratio of HER2/reference gene. The positive and negative coincidence rates were 98% (53/54) and 95% (53/56), respectively, compared with fluorescence in situ hybridization (FISH) diagnostic result 110 of FFPE samples. The common reference gene CEP17 used for FISH diagnostic was not suitable as single reference gene for HER2 CNV measurements by dPCR. The best practice of HER2 CNV determination by dPCR is to conduct the three duplex assays of H1 (HER2 exon 4) with the proposed three new reference genes, with a positive cut-off value of H1/RPPH1 ≥ 2.0 or H1/averaged reference gene ≥ 2.0. The proposed dPCR method in our study can accurately provide absolute copy number of HER2 and reference gene on an alternative chromosome, thus avoiding false negative caused by polysomy of chromosome 17. The improved molecular typing and diagnosis of breast cancer will better guide clinical medication.
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Yang J, Guo R, Li H, Chen G, Lin Y, Wang X, Niu C, Dong L. Development of highly accurate digital PCR method and reference material for monkeypox virus detection. Anal Bioanal Chem 2023; 415:1333-7. [PMID: 36680591 DOI: 10.1007/s00216-023-04518-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/12/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023]
Abstract
Human monkeypox has attracted attention recently. Monkeypox virus (MPXV) keeps evolving as it spreading around the world rapidly, which may threaten the health of more and more people. Here, we have developed a high order reference method based on digital PCR (dPCR) for MPXV detection, of which the limits of quantification (LoQ) and detection (LoD) are 38 and 6 copies/reaction, respectively. Pseudovirus reference materials (RM) containing the conserved F3L gene has been developed, and the homogeneity assessment showed that the RM was homogeneous. The reference value with its expanded uncertainty determined by the established dPCR is (2.74 ± 0.46) × 103 copies/μL. Six different MPXV test kits were accessed by the RM. Four out of six test kits cannot reach their claimed LoDs. The poor analytical sensitivity might cause false-negative results, which lead to incorrect diagnosis and treatment. The establishment of a high order reference method of dPCR and pseudovirus RM is very useful for improving the accuracy and reliability of MPXV detection.
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Lei S, Chen S, Zhong Q. Digital PCR for accurate quantification of pathogens: Principles, applications, challenges and future prospects. Int J Biol Macromol 2021; 184:750-759. [PMID: 34171259 DOI: 10.1016/j.ijbiomac.2021.06.132] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022]
Abstract
Pathogens pose a severe threat to food safety and human health. The traditional methods for pathogen detection can't meet the growing diagnosis and control need. Digital PCR (dPCR) attracts a considerable attention for its ability to absolutely quantify pathogens with features of high selectivity, simplicity, accuracy and rapidity. The dPCR technique that achieves absolute quantification based on end-point measurement without standard curve offers a guideline for further genetic analysis and molecular diagnosis. It could contribute to the quantification of low level of nucleic acid, early detection and timely prevention of pathogenic diseases. In this review, 1442 publications about dPCR were selected and the detections of various pathogens by dPCR were reviewed comprehensively, including viruses, bacteria, parasites and fungi. A number of examples are cited to illustrate that dPCR is a new powerful tool with desired accuracy, sensitivity, and reproducibility for quantification of different types of pathogens. Moreover, the benefits, challenges and future prospects of the dPCR were also highlighted in this review.
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Affiliation(s)
- Shuwen Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Song Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Sun Y, Ding C, Chen Q, Xie J, Yu J, Shi Y, Jiang C, Zhang Z, He H, Ge Y, Li W, He J, Gao Y. Digital PCR assay for the effective detection of COVID-19 patients with SARS-CoV-2 low viral load. J Virol Methods 2021; 295:114185. [PMID: 34051244 PMCID: PMC8149472 DOI: 10.1016/j.jviromet.2021.114185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/06/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022]
Abstract
Objective Viral nucleic acid detection by real-time reverse transcription polymerase chain reaction (qPCR) is the current standard method for diagnosis of SARS-CoV-2 infection. However, due to low viral load in some COVID-19 patients, false negative results from this method have been repeatedly reported. Method In this study, we compared the sensitivity and specificity of digital PCR (dPCR) in simulated samples and clinical samples with qPCR assay through a series of vigorous tests. Results The results showed that dPCR was more sensitive than qPCR especially for samples with low viral load (≤3 copies). In addition, dPCR had similar specificity as qPCR and could effectively distinguish other human coronaviruses and influenza virus from SARS-CoV-2. More importantly, dPCR was more sensitive than qPCR in detecting the virus in the “negative” samples from recurrent COVID-19 patients. Conclusions In summary, dPCR could serve as a powerful complement to the current qPCR method for SARS-CoV-2 detection, especially for the samples with extremely low viral load, such as recurrent COVID-19 patients.
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Affiliation(s)
- Yong Sun
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Chengchao Ding
- First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Qingqing Chen
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Jiajia Xie
- First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Junling Yu
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Yonglin Shi
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Chengcheng Jiang
- First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Zhuhui Zhang
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Hongliang He
- First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yinglu Ge
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Wenting Li
- First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jun He
- Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China.
| | - Yong Gao
- First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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Lee J, Kim JH, Kang SH, Yoo HM. Improvement of digital PCR conditions for direct detection of KRAS mutations. J Clin Lab Anal 2020; 34:e23344. [PMID: 32329932 PMCID: PMC7439326 DOI: 10.1002/jcla.23344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 03/05/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In standard analytical conditions, an isolation step is essential for circulating tumor DNA (ctDNA) analysis. The necessity of this step becomes unclear with the development of highly sensitive detection methods. The aim of this study was to evaluate ctDNA mimetic nDNA detection as reference materials (RMs) using dPCR technologies either directly from serum or without serum. METHODS To determine an absolute count of both mutation and wild-type bearing DNA molecules, genomic DNA (gDNA) and nucleosomal DNA (nDNA), which are similar in size to cell-free DNA, were evaluated. We tested 3 KRAS mutations in colorectal cancer cell lines. RESULTS We describe the recent progress in RMs. The short DNA fragments, such as sDNA and nDNA, exhibited higher quantitative values of dPCR compared to gDNA. The efficiency between Atlantis dsDNase (AD) and Micrococcal Nuclease (MN) affects DNA quantification. Moreover, there was a significant difference in dPCR output when spiking gDNA or nDNA containing KRAS mutations into FBS compared to the dPCR output under non-FBS conditions. CONCLUSION The matrix effect crucially affects the accuracy of gDNA and nDNA level estimation in the direct detection of mimic of patient samples. The form of reference material we proposed should be optimized for various conditions to develop reference materials that can accurately measure copy number and verify the detection of KRAS mutations in the matrix.
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Affiliation(s)
- Jina Lee
- Center for BioanalysisKorea Research Institute of Standards and Science (KRISS)DaejeonKorea
- College of PharmacyChungnam National UniversityDaejeonKorea
| | - Ji Hyun Kim
- Center for BioanalysisKorea Research Institute of Standards and Science (KRISS)DaejeonKorea
| | - Sun Hyung Kang
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineChungnam National University School of MedicineDaejeonKorea
| | - Hee Min Yoo
- Center for BioanalysisKorea Research Institute of Standards and Science (KRISS)DaejeonKorea
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Jacchia S, Kagkli DM, Lievens A, Angers-Loustau A, Savini C, Emons H, Mazzara M. Identification of single target taxon-specific reference assays for the most commonly genetically transformed crops using digital droplet PCR. Food Control 2018; 93:191-200. [PMID: 30393444 PMCID: PMC6058085 DOI: 10.1016/j.foodcont.2018.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 11/24/2022]
Abstract
Knowledge of the number of DNA sequences targeted by the taxon-specific reference assays is essential for correct GM quantification and is key to the harmonisation of measurement results. In the present study droplet digital PCR (ddPCR) was used to determine the number of DNA target copies of taxon-specific assays validated for real-time PCR for the four main genetically modified (GM) crops. The transferability of experimental conditions from real-time PCR to ddPCR was also explored, as well as the effect of DNA digestion. The results of this study indicate that for each crop at least one taxon-specific assay can be identified as having a single DNA target. A short list of taxon-specific reference assays is proposed as best candidates for the relative quantification of GM events for soybean, maize, cotton and oilseed rape. The investigated assays could be in most cases transferred to ddPCR without further optimisation. The use of DNA digestion did not improve ddPCR characteristics such as rain and resolution at the conditions tested.
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Affiliation(s)
- Sara Jacchia
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Dafni-Maria Kagkli
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Antoon Lievens
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | | | - Christian Savini
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Hendrik Emons
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | - Marco Mazzara
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
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