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Scriver M, von Ammon U, Youngbull C, Pochon X, Stanton JAL, Gemmell NJ, Zaiko A. Drop it all: extraction-free detection of targeted marine species through optimized direct droplet digital PCR. PeerJ 2024; 12:e16969. [PMID: 38410796 PMCID: PMC10896080 DOI: 10.7717/peerj.16969] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid management responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e., detection of species-specific eDNA without the need for filtration or DNA extraction, with seawater samples. This first proof-of-concept aquarium study was conducted with three distinct marine species: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analysing aquarium marine water samples using an optimized species-specific ddPCR assay. The results demonstrated the consistent detection of S. spallanzanii and B. neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 h. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. This study represents the first step in assessing the feasibility of direct-ddPCR technology for the detection of marine species. Our results provide information that could aid in the development of new technology, such as a field development of ddPCR systems, which could allow for automated continuous monitoring of targeted marine species, enabling point-of-need detection and rapid management responses.
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Affiliation(s)
- Michelle Scriver
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ulla von Ammon
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
| | - Cody Youngbull
- Nucleic Sensing Systems, LCC, Saint Paul, Minnesota, United States
| | - Xavier Pochon
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Anastasija Zaiko
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Sequench Ltd, Nelson, New Zealand
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2
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Hart JJ, Jamison MN, Porter AM, McNair JN, Szlag DC, Rediske RR. Fecal Impairment Framework, A New Conceptual Framework for Assessing Fecal Contamination in Recreational Waters. Environ Manage 2024; 73:443-456. [PMID: 37658902 DOI: 10.1007/s00267-023-01878-x] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Fecal pollution of surface water is a pervasive problem that negatively affects waterbodies concerning both public health and ecological functions. Current assessment methods monitor fecal indicator bacteria (FIB) to identify pollution sources using culture-based quantification and microbial source tracking (MST). These types of information assist stakeholders in identifying likely sources of fecal pollution, prioritizing them for remediation, and choosing appropriate best management practices. While both culture-based quantification and MST are useful, they yield different kinds of information, potentially increasing uncertainty in prioritizing sources for management. This study presents a conceptual framework that takes separate human health risk estimates based on measured MST and E. coli concentrations as inputs and produces an estimate of the overall fecal impairment risk as its output. The proposed framework is intended to serve as a supplemental screening tool for existing monitoring programs to aid in identifying and prioritizing sites for remediation. In this study, we evaluated the framework by applying it to two primarily agricultural watersheds and several freshwater recreational beaches using existing routine monitoring data. Based on a combination of E. coli and MST results, the proposed fecal impairment framework identified four sites in the watersheds as candidates for remediation and identified temporal trends in the beach application. As these case studies demonstrate, the proposed fecal impairment framework is an easy-to-use and cost-effective supplemental screening tool that provides actionable information to managers using existing routine monitoring data, without requiring specialized expertize.
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Affiliation(s)
- John J Hart
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA.
| | - Megan N Jamison
- Department of Chemistry, Oakland University, 146 Library Dr., Rochester, MI, 48309, USA
- The Ohio State University, 281 W Lane Ave, Columbus, OH, 43210, USA
| | - Alexis M Porter
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA
| | - James N McNair
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA
| | - David C Szlag
- Department of Chemistry, Oakland University, 146 Library Dr., Rochester, MI, 48309, USA
| | - Richard R Rediske
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA
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3
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Xu B, Powell K. Quality Control of an Isogenic H/N/KRAS-Less Mouse Embryonic Fibroblast Cell Line Panel. Methods Mol Biol 2024; 2797:337-350. [PMID: 38570471 DOI: 10.1007/978-1-0716-3822-4_24] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Isogenic H/N/KRAS-less mouse embryonic fibroblast (MEF) cell lines have been developed to assist in cell-based assays of RAS inhibitors. The quality control assessment of a panel of these isogenic MEFs is described here, with a focus on ensuring the proper insertion of the desired mutant RAS transgene, a determination of gene copy number, and an investigation of potential off-target mutations which could lead to phenotypes which are undesired in downstream experiments. Using this suite of quality control tools, a MEF cell line can be readily validated, and researchers can be assured of the rationale for an observed phenotype.
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Affiliation(s)
- Bingfang Xu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Katie Powell
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Guo J, Tian W, Lin H, Hu L, Gao X, Xia J, Yu H, Chen H, Li W, Wu W. Analytical and clinical validation of multiplex droplet digital PCR assay for detecting pathogenic fungal infection in lungs. Mycology 2023; 15:110-119. [PMID: 38558836 PMCID: PMC10976995 DOI: 10.1080/21501203.2023.2296941] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/14/2023] [Indexed: 04/04/2024] Open
Abstract
Pulmonary invasive fungal infection in immunocompromised hosts is difficult to diagnose, and current tools for diagnosis or monitoring of response to antifungal treatments have inherent limitations. Droplet digital PCR (ddPCR) has emerged as a promising tool for pulmonary pathogen detection with high sensitivity. This study presents a novel ddPCR panel for rapid and sensitive identification of pulmonary fungal pathogens. First, a ddPCR method for detecting three fungal genera, including Pneumocystis, Aspergillus, and Cryptococcus, was established and evaluated. Then, the clinical validation performance of ddPCR was compared with that of qPCR using 170 specimens, and the 6 specimens with inconsistent results were further verified by metagenomics next-generation sequencing, which yielded results consistent with the ddPCR findings. Finally, the area under the ROC curve (AUC) was used to evaluate the efficiency of ddPCR. While the qPCR identified 16 (9.41%) cases of Aspergillus and 6 (3.53%) cases of Pneumocystis, ddPCR detected 20 (11.76%) Aspergillus cases and 8 (4.71%) Pneumocystis cases. The AUC for Aspergillus, Cryptococcus, and Pneumocystis was 0.974, 0.998, and 0.975, respectively. These findings demonstrated that the ddPCR assay is a highly sensitive method for identifying pathogens responsible for invasive fungal pulmonary infections, and is a promising tool for early diagnosis. .
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Affiliation(s)
- Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenjie Tian
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huiping Lin
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liang Hu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuejuan Gao
- Pilot Gene Technologies Company Limited, Hangzhou, China
| | - Jiang Xia
- Pilot Gene Technologies Company Limited, Hangzhou, China
| | - Hao Yu
- Pilot Gene Technologies Company Limited, Hangzhou, China
| | - Hui Chen
- Department of Laboratory Medicine, Jiangxi Provincial People’s Hospital Affiliated to Nanchang University, Nanchang, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Alinger-Scharinger B, Kronberger C, Hutarew G, Hitzl W, Reitsamer R, Frederike KF, Hager M, Fischer T, Sotlar K, Jaksch-Bogensperger H. HER2 copy number determination in breast cancer using the highly sensitive droplet digital PCR method. Virchows Arch 2023:10.1007/s00428-023-03706-3. [PMID: 37996704 DOI: 10.1007/s00428-023-03706-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Human epidermal growth factor receptor 2 (HER)-positive breast cancer (BC) is characterized by an aggressive clinical course. In the case of HER2 overexpression/amplification, patients benefit from HER2-targeting therapies. Standardized diagnostic HER2 assessment includes immunohistochemistry (IHC) and/or in situ hybridization (ISH). The aim of this study was to compare this "gold standard" with the Droplet Digital™ polymerase chain reaction (ddPCR), a method that allows sensitive and precise detection of copy number variations (CNV) in FFPE (formalin-fixed, paraffin-embedded) DNA samples. Partitioning of the PCR reaction into 20,000 droplets enables a precise quantitative "CN" discrimination also in heterogeneous samples. FFPE breast cancer samples (n = 170) with routinely assessed HER2 status by IHC/ISH were retrospectively analyzed using the ddPCR CNV ERBB2 assay. Comparison of HER2 status assessment by the two methods revealed concordant results in 92.9% (158/170) of the cases. Discrepant cases were verified and interpreted. For ddPCR, a cut off value of 3 HER2 copies was set to distinguish between HER2-negative and HER2-positive BC. Results obtained with the ddPCR CNV ERBB2 assay were consistent and reproducible, and serial dilutions demonstrated a high stability and sensitivity of the method. The ddPCR CNV ERBB2 assay may be a specific and convenient tool to quantify HER2 copy numbers in BC samples. In our study, this method showed high reproducibility in accuracy of HER2 assessment compared to IHC/ISH analysis.
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Affiliation(s)
- Beate Alinger-Scharinger
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria.
| | - Cornelia Kronberger
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Georg Hutarew
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Wolfgang Hitzl
- Research Management and Technology Transfer, Paracelsus Medical University Salzburg, Strubergasse 16, 5020, Salzburg, Austria
- Department of Ophthalmology and Optometry, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
- Research Program Experimental Ophthalmology and Glaucoma Research, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Roland Reitsamer
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Klaassen-Federspiel Frederike
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Martina Hager
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Thorsten Fischer
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Karl Sotlar
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Heidi Jaksch-Bogensperger
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
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Jiang L, Song M, Song F, Zhou Y, Yao H, Li G, Luo H. Characterization of loss of chromosome Y in peripheral blood cells in male Han Chinese patients with schizophrenia. BMC Psychiatry 2023; 23:469. [PMID: 37370034 DOI: 10.1186/s12888-023-04929-z] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Schizophrenia (SCZ) has a global prevalence of 1% and increases the risk of mortality, reducing life expectancy. There is growing evidence that the risk of this disorder is higher in males than in females and it tends to develop in early adulthood. The Y chromosome is thought to be involved in biological processes other than sex determination and spermatogenesis. Studies have shown that loss of chromosome Y (LOY) in peripheral blood cells is associated with a variety of diseases (including cancer) and increased all-cause mortality. An analysis of the relationship between LOY and schizophrenia is warranted. METHODS A total of 442 Chinese males (271 patients with schizophrenia vs. 171 controls) were included in this study. The copy numbers of the Y and X chromosomes were detected by positive droplets targeting the amelogenin gene (AMEL) on the Y chromosome and X chromosome (AMELY and AMELX, respectively), using droplet digital PCR (ddPCR). The LOY percentage was defined as the difference between the concentration of AMELX and the concentration of AMELY divided by the concentration of AMELX, denoted as (X - Y)/X. RESULTS In the Han Chinese population, the LOY percentage was higher in the schizophrenia group than in the control group (p < 0.05), although there was no significant difference in the presence of LOY between the two groups. A strong correlation was found between the average of the disease duration and the average of the LOY percentage (R2 = 0.506, p = 0.032). The logistic regression analysis implied that the risk of LOY increases by 0.058 and 0.057 per year according to age at onset and duration of disease, respectively (ponset = 0.013, pduration = 0.017). CONCLUSIONS In the Han Chinese population, the LOY percentage of the disease group was significantly different from that of the control group. The age of onset and duration of schizophrenia might be risk factors for LOY in peripheral blood cells. A larger sample size and expanded clinical information are needed for more in-depth and specific analyses.
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Affiliation(s)
- Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Gangqin Li
- Department of Forensic Psychiatry, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China.
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Song M, Jiang L, Wang X, Zhou W, Wang N, Hou Y, Song F. Loss of Y chromosome in leukocytes can be regarded as a male-specific age predictor for age group estimation in forensic genetics. Mol Genet Genomics 2023:10.1007/s00438-023-02039-9. [PMID: 37285076 DOI: 10.1007/s00438-023-02039-9] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Age prediction is an important field in forensic and aging research. Traditional methods used DNA methylation, telomere shortening, and mitochondrial DNA mutations to conduct age prediction models. Sex chromosomes, like the Y chromosome, have a significant role in aging as previously reported in hematopoietic disease and many non-reproductive cancers. Until now, there is no age predictor based on the percentage of loss of Y chromosome (LOY). LOY has been previously revealed to be correlated with Alzheimer's disease, short survival, and higher risk of cancer. The possible correlation of LOY between normal aging was not fully explored. In this study, we conducted age prediction by measuring LOY percentage by droplet digital PCR (ddPCR), based on 232 healthy male samples, including 171 blood samples, 49 saliva samples, 12 semen samples. The age group of samples ranges from 0 to 99 years, with two individuals in almost every single age. Pearson correlation method was performed to calculate the correlation index. The result indicated a correlation index of 0.21 (p = 0.0059) between age and LOY percentage in blood samples, with the regression formula being y = - 0.016823 + 0.001098x. The correlation between LOY percentage and age is obvious only when the individuals were divided into different age groups (R = 0.73, p = 0.016). In the studied saliva and semen samples, p-values of the correlation are 0.11 and 0.20, respectively, showing no significant association between age and LOY percentage in these two biological materials. For the first time, we investigated male-specific age predictor based on LOY. The study showed that LOY in leukocytes can be regarded as a male-specific age predictor for age group estimation in forensic genetics. This study might be indicative for forensic applications and aging research.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Wenjing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Nian Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China.
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China.
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Nino N, Ishida T, Nakatani N, Lin KS, Win KHN, Mon CY, Nishimura A, Inoue S, Tamura A, Yamamoto N, Uemura S, Saito A, Mori T, Hasegawa D, Kosaka Y, Nozu K, Nishimura N. Minimal residual disease detected by droplet digital PCR in peripheral blood stem cell grafts has a prognostic impact on high-risk neuroblastoma patients. Heliyon 2022; 8:e10978. [PMID: 36276741 PMCID: PMC9578974 DOI: 10.1016/j.heliyon.2022.e10978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/21/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
More than half of high-risk neuroblastoma (NB) patients have experienced relapse due to the activation of chemoresistant minimal residual disease (MRD) even though they are treated by high-dose chemotherapy with autologous peripheral blood stem cell (PBSC) transplantation. Although MRD in high-risk NB patients can be evaluated by quantitative PCR with several sets of neuroblastoma-associated mRNAs (NB-mRNAs), the prognostic significance of MRD in PBSC grafts (PBSC-MRD) is unclear. In the present study, we collected 20 PBSC grafts from 20 high-risk NB patients and evaluated PBSC-MRD detected by droplet digital PCR (ddPCR) with 7NB-mRNAs (CRMP1, DBH, DDC, GAP43, ISL1, PHOX2B, and TH mRNA). PBSC-MRD in 11 relapsed patients was significantly higher than that in 9 non-relapsed patients. Patients with a higher PBSC-MRD had a lower 3-year event-free survival (P = 0.0148). The present study suggests that PBSC-MRD detected by ddPCR with 7NB-mRNAs has a prognostic impact on high-risk NB patients.
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Affiliation(s)
- Nanako Nino
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Toshiaki Ishida
- Department of Hematology and Oncology, Kobe Children's Hospital, Kobe, Japan
| | - Naoko Nakatani
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kyaw San Lin
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kaung Htet Nay Win
- Department of Public Health, Kobe University Graduate School of Health Science, Kobe, Japan
| | - Cho Yee Mon
- Department of Public Health, Kobe University Graduate School of Health Science, Kobe, Japan
| | - Akihiro Nishimura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shotaro Inoue
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akihiro Tamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nobuyuki Yamamoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Suguru Uemura
- Department of Hematology and Oncology, Kobe Children's Hospital, Kobe, Japan
| | - Atsuro Saito
- Department of Hematology and Oncology, Kobe Children's Hospital, Kobe, Japan
| | - Takeshi Mori
- Department of Hematology and Oncology, Kobe Children's Hospital, Kobe, Japan
| | - Daiichiro Hasegawa
- Department of Hematology and Oncology, Kobe Children's Hospital, Kobe, Japan
| | - Yoshiyuki Kosaka
- Department of Hematology and Oncology, Kobe Children's Hospital, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Noriyuki Nishimura
- Department of Public Health, Kobe University Graduate School of Health Science, Kobe, Japan,Corresponding author.
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Johann DJ, Laun S, Shin IJ, Weigman R, Stephens O, Roberge A, Liu M, Greisman V, Steliga M, Muesse J, Peterson E, Emmert-Buck MR, Tangrea MA. Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine. Methods Mol Biol 2022; 2394:93-107. [PMID: 35094324 DOI: 10.1007/978-1-0716-1811-0_7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Improving the utilization of tumor tissue from diagnostic biopsies is an unmet medical need. This is especially relevant today in the rapidly evolving precision oncology field where tumor genotyping is often essential for the indication of many advanced and targeted therapies. National Comprehensive Cancer Network (NCCN) guidelines now mandate molecular testing for clinically actionable targets in certain malignancies. Utilizing advanced stage lung cancer as an example, an improved genotyping approach for solid tumors is possible. The strategy involves optimization of the microdissection process and analysis of a large number of identical target cells from formalin-fixed paraffin-embedded (FFPE) specimens sharing similar characteristics, in other words, single-cell subtype analysis. The shared characteristics can include immunostaining status, cell phenotype, and/or spatial location within a histological section. Synergy between microdissection and droplet digital PCR (ddPCR) enhances the molecular analysis. We demonstrate here a methodology that illustrates genotyping of a solid tumor from a small tissue biopsy sample in a time- and cost-efficient manner, using immunostain targeting as an example.
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Affiliation(s)
- Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah Laun
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Ik Jae Shin
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Robert Weigman
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Owen Stephens
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Adam Roberge
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Meeiyueh Liu
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Valerie Greisman
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
- Biology Department, Loyola University Maryland, Baltimore, MD, USA
| | - Mathew Steliga
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jason Muesse
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Erich Peterson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Michael A Tangrea
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA.
- Biology Department, Loyola University Maryland, Baltimore, MD, USA.
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10
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Lindner L, Cayrou P, Rosahl TW, Zhou HH, Birling MC, Herault Y, Pavlovic G. Droplet digital PCR or quantitative PCR for in-depth genomic and functional validation of genetically altered rodents. Methods 2021; 191:107-119. [PMID: 33838271 DOI: 10.1016/j.ymeth.2021.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Gene targeting and additive (random) transgenesis have proven to be powerful technologies with which to decipher the mammalian genome. With the advent of CRISPR/Cas9 genome editing, the ability to inactivate or modify the function of a gene has become even more accessible. However, the impact of each generated modification may be different from what was initially desired. Minimal validation of mutant alleles from genetically altered (GA) rodents remains essential to guarantee the interpretation of experimental results. The protocol described here combines design strategies for genomic and functional validation of genetically modified alleles with droplet digital PCR (ddPCR) or quantitative PCR (qPCR) for target DNA or mRNA quantification. In-depth analysis of the results obtained with GA models through the analysis of target DNA and mRNA quantification is also provided, to evaluate which pitfalls can be detected using these two methods, and we propose recommendations for the characterization of different type of mutant allele (knock-out, knock-in, conditional knock-out, FLEx, IKMC model or transgenic). Our results also highlight the possibility that mRNA expression of any mutated allele can be different from what might be expected in theory or according to common assumptions. For example, mRNA analyses on knock-out lines showed that nonsense-mediated mRNA decay is generally not achieved with a critical-exon approach. Likewise, comparison of multiple conditional lines crossed with the same CreERT2 deleter showed that the inactivation outcome was very different for each conditional model. DNA quantification by ddPCR of G0 to G2 generations of transgenic rodents generated by pronuclear injection showed an unexpected variability, demonstrating that G1 generation rodents cannot be considered as established lines.
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Affiliation(s)
- Loic Lindner
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Pauline Cayrou
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Thomas W Rosahl
- Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Heather H Zhou
- Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Yann Herault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France.
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11
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Gurrala R, Kilanowski-Doroh IM, Hutson DD, Ogola BO, Zimmerman MA, Katakam PVG, Satou R, Mostany R, Lindsey SH. Alterations in the estrogen receptor profile of cardiovascular tissues during aging. GeroScience 2021; 43:433-442. [PMID: 33558965 PMCID: PMC8050209 DOI: 10.1007/s11357-021-00331-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 06/21/2019] [Accepted: 01/31/2021] [Indexed: 12/13/2022] Open
Abstract
Estrogen exerts protective effects on the cardiovascular system via three known estrogen receptors: alpha (ERα), beta (ERß), and the G protein-coupled estrogen receptor (GPER). Our laboratory has previously showed the importance of GPER in the beneficial cardiovascular effects of estrogen. Since clinical studies indicate that the protective effects of exogenous estrogen on cardiovascular function are attenuated or reversed 10 years post-menopause, the hypothesis was that GPER expression may be reduced during aging. Vascular reactivity and GPER protein expression were assessed in female mice of varying ages. Physiological parameters, blood pressure, and estrogen receptor transcripts via droplet digital PCR (ddPCR) were assessed in the heart, kidney, and aorta of adult, middle-aged, and aged male and female C57BL/6 mice. Vasodilation to estrogen (E2) and the GPER agonist G-1 were reduced in aging female mice and were accompanied by downregulation of GPER protein. However, ERα and GPER were the predominant receptors in all tissues, whereas ERß was detectable only in the kidney. Female sex was associated with higher mRNA for both ERα and GPER in both the aorta and the heart. Aging impacted receptor transcript in a tissue-dependent manner. ERα transcript decreased in the heart with aging, while GPER expression increased in the heart. These data indicate that aging impacts estrogen receptor expression in the cardiovascular system in a tissue- and sex-specific manner. Understanding the impact of aging on estrogen receptor expression is critical for developing selective hormone therapies that protect from cardiovascular damage.
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Affiliation(s)
- Rakesh Gurrala
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | | | - Dillion D Hutson
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Benard O Ogola
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Margaret A Zimmerman
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Prasad V G Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Brain Institute, Tulane University, New Orleans, LA, 70112, USA
| | - Ryousuke Satou
- Department of Physiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, LA, 7011, USA
| | - Ricardo Mostany
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Brain Institute, Tulane University, New Orleans, LA, 70112, USA
| | - Sarah H Lindsey
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
- Department of Physiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
- Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, LA, 7011, USA.
- Tulane Brain Institute, Tulane University, New Orleans, LA, 70112, USA.
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12
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Hussung S, Akhoundova D, Hipp J, Follo M, Klar RFU, Philipp U, Scherer F, von Bubnoff N, Duyster J, Boerries M, Wittel U, Fritsch RM. Longitudinal analysis of cell-free mutated KRAS and CA 19-9 predicts survival following curative resection of pancreatic cancer. BMC Cancer 2021; 21:49. [PMID: 33430810 PMCID: PMC7802224 DOI: 10.1186/s12885-020-07736-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Background Novel biomarkers and molecular monitoring tools hold potential to improve outcome for patients following resection of pancreatic ductal adenocarcinoma (PDAC). We hypothesized that the combined longitudinal analysis of mutated cell-free plasma KRAS (cfKRASmut) and CA 19–9 during adjuvant treatment and follow-up might more accurately predict disease course than hitherto available parameters. Methods Between 07/2015 and 10/2018, we collected 134 plasma samples from 25 patients after R0/R1-resection of PDAC during adjuvant chemotherapy and post-treatment surveillance at our institution. Highly sensitive discriminatory multi-target ddPCR assays were employed to screen plasma samples for cfKRASmut. cfKRASmut and CA 19–9 dynamics were correlated with recurrence-free survival (RFS) and overall survival (OS). Patients were followed-up until 01/2020. Results Out of 25 enrolled patients, 76% had undergone R0 resection and 48% of resected PDACs were pN0. 17/25 (68%) of patients underwent adjuvant chemotherapy. Median follow-up was 22.0 months, with 19 out of 25 (76%) patients relapsing during study period. Median RFS was 10.0 months, median OS was 22.0 months. Out of clinicopathologic variables, only postoperative CA 19–9 levels and administration of adjuvant chemotherapy correlated with survival endpoints. cfKRASmut. was detected in 12/25 (48%) of patients, and detection of high levels inversely correlated with survival endpoint. Integration of cfKRASmut and CA 19–9 levels outperformed either individual marker. cfKRASmut outperformed CA 19–9 as dynamic marker since increase during adjuvant chemotherapy and follow-up was highly predictive of early relapse and poor OS. Conclusions Integrated analysis of cfKRASmut and CA 19–9 levels is a promising approach for molecular monitoring of patients following resection of PDAC. Larger prospective studies are needed to further develop this approach and dissect each marker’s specific potential. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07736-x.
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Affiliation(s)
- Saskia Hussung
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany.,Department of Medical Oncology and Hematology, Zurich University Hospital, Raemistrasse 100, 8091, Zürich, Switzerland
| | - Dilara Akhoundova
- Department of Medical Oncology and Hematology, Zurich University Hospital, Raemistrasse 100, 8091, Zürich, Switzerland
| | - Julian Hipp
- Department of Surgery, Freiburg University Medical Center, Freiburg, Germany
| | - Marie Follo
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany
| | - Rhena F U Klar
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany
| | - Ulrike Philipp
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany
| | - Florian Scherer
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany
| | - Nikolas von Bubnoff
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany
| | - Justus Duyster
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center Freiburg (CCCF), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center Freiburg (CCCF), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Wittel
- Department of Surgery, Freiburg University Medical Center, Freiburg, Germany
| | - Ralph M Fritsch
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Freiburg University Medical Center, Freiburg, Germany. .,Department of Medical Oncology and Hematology, Zurich University Hospital, Raemistrasse 100, 8091, Zürich, Switzerland. .,Comprehensive Cancer Center Freiburg (CCCF), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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13
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Cao Z, Wu W, Wei H, Gao C, Zhang L, Wu C, Hou L. Using droplet digital PCR in the detection of Mycobacterium tuberculosis DNA in FFPE samples. Int J Infect Dis 2020; 99:77-83. [PMID: 32738487 DOI: 10.1016/j.ijid.2020.07.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/19/2020] [Accepted: 07/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Droplet digital PCR (ddPCR) is a technology that has higher sensitivity than real-time PCR for the identification of trace DNA. However, the use of ddPCR for the detection of Mycobacterium tuberculosis DNA in pathological samples has not been fully studied. METHODS A total of 65 formalin-fixed and paraffin-embedded (FFPE) specimens were included in this study. Twenty samples with definite results for tuberculosis (TB) were used to establish the ddPCR system for TB detection. ddPCR was then conducted to detect TB DNA in the 45 patients who were classified as 'possible TB' (real-time PCR results in the gray area, Ziehl-Neelsen staining-negative, and hematoxylin and eosin staining showing morphology suspicious for TB). The clinical treatment and disease outcomes were followed to assess the accuracy of ddPCR in the detection of TB DNA. RESULTS Among the 45 possible TB samples, 26 were ddPCR-positive, 12 were ddPCR-negative, and seven were in the gray area. ddPCR improved the positive rate of 57.8% (26/45) for the samples that were in the gray area by real-time PCR. Moreover, several patients received anti-TB therapy, and the effective ratio of therapy for the ddPCR-positive, ddPCR-negative, and ddPCR-gray area cases was 61.9% (13/21), 50.0% (2/4), and 33.3% (1/3), respectively. CONCLUSIONS ddPCR is more sensitive for detecting mild TB via FFPE samples than real-time PCR. The ddPCR method is of additional value in the diagnosis of TB from pathological samples.
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Lindner L, Cayrou P, Jacquot S, Birling MC, Herault Y, Pavlovic G. Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies. Methods 2020; 191:95-106. [PMID: 32721466 DOI: 10.1016/j.ymeth.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 01/05/2023] Open
Abstract
Droplet digital PCR (ddPCR) is a recent method developed for the quantification of nucleic acids sequences. It is an evolution of PCR methodology incorporating two principal differences: a PCR reaction is performed in thousands of water-oil emulsion droplets and fluorescence is measured at the end of PCR amplification. It leads to the precise and reproducible quantification of DNA and RNA sequences. Here, we present quantitative methods for DNA and RNA analysis using Bio-Rad QX100 or QX200 systems, respectively. The aim of these methods is to provide useful molecular tools for validating genetically altered animal models such as those subject to CRISPR/Cas9 genome editing, as well for expression or CNV studies. A standard procedure for simultaneous DNA and RNA extraction adapted for mouse organs is also described. These methods were initially designed for mouse studies but also work for samples from other species like rat or human. In our lab, thousands of samples and hundreds of target genes from genetically altered lines were examined using these methods. This large dataset was analyzed to evaluate technical optimizations and limitations. Finally, we propose additional recommendations to be included in dMIQE (Minimum information for publication of quantitative digital PCR experiments) guidelines when using ddPCR instruments.
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Affiliation(s)
- Loic Lindner
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Pauline Cayrou
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Sylvie Jacquot
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Yann Herault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France.
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15
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Tang C, Zhu L, Zhang L, Tan C, Peng Z, Liu B, Liu W, Hu H, Bai Y, Wang B, Lin L, Liang J, Li X, Guo Y, Liu Y. Establishment and validation of a novel droplet digital PCR assay for ultrasensitive detection and dynamic monitoring of EGFR mutations in peripheral blood samples of non-small-cell lung cancer patients. Clin Chim Acta 2020; 510:88-96. [PMID: 32645388 DOI: 10.1016/j.cca.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/03/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Droplet digital PCR (ddPCR)-based blood detection of EGFR mutations plays significant roles in the individualized therapy of non-small-cell lung cancer (NSCLC) patients. However, a standard assay that is approved by health authorities is still lacking. Additionally, the proper application of this method in clinical settings also needs further investigation. METHODS The performance of a newly established ddPCR assay was first evaluated using reference samples and then validated by comparing this method with the amplification refractory mutation system (ARMS) using cell-free DNA (cfDNA) in patients' peripheral blood. Further, the correlation between dynamic quantification of EGFR mutation in the patients and their clinical outcome of tyrosine kinase inhibitors (TKIs) therapy was investigated. RESULTS A total of 77 patients were included, with 50 in the test group and 27 in the validation group. According to the results of the reference samples and the blood samples in the test group, the cut-off value for patient detection was proposed as mutation rate ≥ 0.1% (total copy number of cfDNA ≥ 1000) or at least one copy of mutation DNA was detected (total copy number of cfDNA < 1000). With this criterion, superior sensitivity of our assay to that of ARMS was observed (P = 0.002 for Ex19Del & L858R and P < 0.001 for T790M). The dynamic quantification of EGFR mutations during TKI therapy indicated that an increase in mutation abundance was correlated with resistance, while a decline was associated with response. Notably, a rebound in mutation abundance during chemotherapy may indicate a desirable chance for TKI re-treatment. CONCLUSION The novel ddPCR assay showed superior sensitivity in the detection of EGFR mutation in blood. The dynamic quantification of EGFR mutations by this assay would greatly facilitate the administration of TKI therapy, including the monitoring of resistance and response, as well as cohort screening for retreatment.
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16
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Beau-Faller M, Pencreach E, Leduc C, Blons H, Merlio JP, Bringuier PP, de Fraipont F, Escande F, Lemoine A, Ouafik L, Denis M, Hofman P, Lacave R, Melaabi S, Langlais A, Missy P, Morin F, Moro-Sibilot D, Barlesi F, Cadranel J. Independent prognostic value of ultra-sensitive quantification of tumor pre-treatment T790M subclones in EGFR mutated non-small cell lung cancer (NSCLC) treated by first/second generation TKI, depends on variant allele frequency (VAF): Results of the French cooperative thoracic intergroup (IFCT) biomarkers France project. Lung Cancer 2019; 140:19-26. [PMID: 31841714 DOI: 10.1016/j.lungcan.2019.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/09/2019] [Accepted: 10/11/2019] [Indexed: 01/12/2023]
Abstract
OBJECTIVES T790M mutations inEGFR-mutated non-small cell lung cancer (NSCLC) account for nearly 50% of acquired resistance mechanisms to EGFR-TKIs. Earlier studies suggested that tumor T790M could also be detected in TKI-naïve EGFR-mutated NSCLC. The aim of the study is to assess the prevalence and clinical significance of quantification of tumor pre-treatment T790M subclones. MATERIALS AND METHODS We analyzed 366 EGFR-mutated NSCLC patients of the real-life IFCT Biomarkers France study with available pre-treatment formalin-fixed paraffin-embedded (FFPE) tumor DNA before treatment by first/second-generation EGFR-TKI. We used ultra-sensitive Droplet Digital Polymerase Chain Reaction (ddPCR) QX200 (BIO-RAD®, Hercules, CA, USA). All samples were tested in duplicate. RESULTS ddPCR identified T790M in 19/240 specimens (8%). T790M-positive and T790M-negative populations were not different for clinical baseline characteristics. T790M Variant Allele Frequency (VAF) was > 0.01% <0.1%, > 0.1% <1%, > 1% <10%, and >10% in five (26.3%), six (31.6%), six (31.6%), and two (10.5%) patients, respectively. T790M VAF was >0.1% in 11/13 (84%) patients with rapid (<3 months) or usual progression (3-20 months) compared to 0/3 with low progression (>20 months) (p = 0.02). In a Cox model, T790M mutation positivity was correlated with overall survival (OS) and progression-free survival (PFS) for 10% > VAF >1% (hazard ratio [HR] = 2.83, 95% confidence interval [CI] 1.13-7.07, p = 0.03; HR=3.62, 95%CI 1.43-4.92, p = 0.007, respectively) and for VAF >10% (HR = 19.14, 95%CI 4.35-84.26, p < 0.001; HR = 17.89, 95%CI 2.21-144.86, p = 0.007, respectively). CONCLUSION Ultra-sensitive detection of tumor T790M mutation concerned 8% of EGFR-mutated TKI-naïve NSCLC patients and has a negative prognostic value only for T790M VAF over 1%.
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MESH Headings
- Adenocarcinoma of Lung/drug therapy
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/pathology
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Carcinoma, Large Cell/drug therapy
- Carcinoma, Large Cell/genetics
- Carcinoma, Large Cell/pathology
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Drug Resistance, Neoplasm
- ErbB Receptors/genetics
- Female
- Follow-Up Studies
- France
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Mutation
- Prognosis
- Protein Kinase Inhibitors/therapeutic use
- Retrospective Studies
- Survival Rate
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Affiliation(s)
- Michèle Beau-Faller
- Laboratory of Biochemistry and Molecular Biology, Centre Hospitalier Universitaire de Strasbourg, Hôpital de Hautepierre, Strasbourg, France; IRFAC UMR-S1113, Inserm, Université de Strasbourg, Strasbourg, France.
| | - Erwan Pencreach
- IRFAC UMR-S1113, Inserm, Université de Strasbourg, Strasbourg, France
| | - Charlotte Leduc
- Chest Department, Centre Hospitalier Universitaire de Strasbourg, Nouvel Hôpital Civil, Strasbourg, France
| | - Hélène Blons
- HEGP, Biochimie UF de Pharmacogénétique et Oncologie Moléculaire, Paris, France
| | - Jean-Philippe Merlio
- Department of Pathology and Tumor Biology, CHU and University Bordeaux, Hôpital Haut-Lévêque, Pessac, France
| | - Pierre-Paul Bringuier
- Centre de Biologie et Pathologie Est, Service d'Anatomie et de Cytologie Pathologique, Hospices Civils de Lyon et Université Claude Bernard Lyon 1, Lyon, France
| | - Florence de Fraipont
- UM de Génétique moléculaire: Maladies Héréditaires et Oncologie, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France; UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences-Université Grenoble Alpes, Grenoble, France
| | - Fabienne Escande
- Laboratoire de Biochimie et Biologie moléculaire, CHRU Lille, LILLE, France
| | - Antoinette Lemoine
- Biochimie et Oncogénétique INSERM UMR-S1193, Hôpital Paul Brousse, Hôpitaux Universitaires Paris-Sud, Villejuif, France
| | - L'Houcine Ouafik
- Aix Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, Faculté de Médecine Secteur Nord, Service de Transfert d'Oncologie Biologique, Marseille, France
| | - Marc Denis
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
| | - Paul Hofman
- Université Côte d'Azur, and FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Inserm U1081/CNRS 7284, and Hospital-Integrated Biobank (BB-0033-00025) Pasteur Hospital, Nice, France
| | - Roger Lacave
- Faculté de Médecine Sorbonne Université, and Groupe Hospitalier HUEP, Hôpital Tenon, Unité de Génomique des Tumeurs Solides, Assistance Publique-Hôpitaux de Paris, France
| | - Samia Melaabi
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, Paris, France
| | - Alexandra Langlais
- Department of Biostatistics, French Cooperative Thoracic Intergroup, Paris, France
| | - Pascale Missy
- Clinical Research Unit, French Cooperative Thoracic Intergroup, Paris, France
| | - Franck Morin
- Clinical Research Unit, French Cooperative Thoracic Intergroup, Paris, France
| | - Denis Moro-Sibilot
- Unité d'Oncologie Thoracique, Service Hospitalier Universitaire Pneumologie Physiologie Pôle Thorax et Vaisseaux, CHU Grenoble Alpes, Grenoble, France
| | - Fabrice Barlesi
- Aix Marseille University, CNRS, INSERM, CRCM, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Jacques Cadranel
- AP-HP, Hôpital Tenon, Service de Pneumogie, GRC 04 Theranoscan, Sorbonne Université, Paris, France
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Hutson DD, Gurrala R, Ogola BO, Zimmerman MA, Mostany R, Satou R, Lindsey SH. Estrogen receptor profiles across tissues from male and female Rattus norvegicus. Biol Sex Differ 2019; 10:4. [PMID: 30635056 PMCID: PMC6329134 DOI: 10.1186/s13293-019-0219-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/01/2019] [Indexed: 01/11/2023] Open
Abstract
Background Estrogen is formed by the enzyme aromatase (CYP19A1) and signals via three identified receptors ERα (ESR1), ERß (ESR2), and the G protein-coupled estrogen receptor (GPER). Understanding the relative contribution of each receptor to estrogenic signaling may elucidate the disparate effects of this sex hormone across tissues, and recent developments in PCR technology allow absolute quantification and direct comparison of multiple targets. We hypothesized that this approach would reveal tissue- and sex-specific differences in estrogen receptor mRNA. Methods ESR1, ESR2, GPER, and CYP19A1 were measured in four cardiovascular tissues (heart, aorta, kidney, and adrenal gland), three brain areas (somatosensory cortex, hippocampus, and prefrontal cortex), and reproductive tissues (ovaries, mammary gland, uterus, testes) from six male and six female adult Sprague-Dawley rats. Results GPER mRNA expression was relatively stable across all tissues in both sexes, ranging from 5.49 to 113 copies/ng RNA, a 21-fold difference. In contrast, ESR1/ESR2 were variable across tissues although similar within an organ system. ESR1 ranged from 4.46 to 614 copies/ng RNA (138-fold difference) while ESR2 ranged from 0.154 to 83.1 copies/ng RNA (540-fold). Significant sex differences were broadly absent except for renal ESR1 (female 206 vs. male 614 copies/ng RNA, P < 0.0001) and GPER (62.0 vs. 30.2 copies/ng RNA, P < 0.05) as well as gonadal GPER (5.49 vs. 47.5 copies/ng RNA, P < 0.01), ESR2 (83.1 vs. 0.299 copies/ng RNA, P < 0.01), and CYP19A1 (322 vs. 7.18 copies/ng RNA, P < 0.01). Cardiovascular tissues showed a predominance of ESR1, followed by GPER. In contrast, GPER was the predominant transcript in the brain with similarly low levels of ESR1 and ESR2. CYP19A1 was detected at very low levels except for reproductive tissues and the hippocampus. Conclusion While the data indicates a lack of sex differences in most tissues, significant differences were found in the range of receptor gene expression across tissues as well as in the receptor profile between organ systems. The data provide a guide for future studies by establishing estrogen receptor expression across multiple tissues using absolute PCR quantification. This knowledge on tissue-specific estrogen receptor profiles will aid the development of hormonal therapies that elicit beneficial effects in specific tissues.
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Affiliation(s)
- Dillion D Hutson
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Rakesh Gurrala
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Benard O Ogola
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Margaret A Zimmerman
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Ricardo Mostany
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.,Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Ryousuke Satou
- Department of Physiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.,Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Sarah H Lindsey
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, 70112, USA. .,Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, 70112, USA. .,Department of Physiology, Tulane University School of Medicine, New Orleans, LA, 70112, USA. .,Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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18
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Zhang Y, Zhang Z, Wang Z, Wang Z, Wang C, Feng C, Yuan W, Lin X, Wu S. Development of a droplet digital PCR assay for sensitive detection of porcine circovirus 3. Mol Cell Probes 2018; 43:50-57. [PMID: 30468765 DOI: 10.1016/j.mcp.2018.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/26/2023]
Abstract
Porcine circovirus 3 (PCV3), a newly emerged circovirus, is associated with porcine dermatitis and nephropathy syndrome, reproductive failure and multi-systemic inflammation disease, and is widely distributed in pig populations worldwide. Therefore, developing specific diagnostic assays will be important for controlling this emerging pathogen. In this study, we developed a novel droplet digital PCR (ddPCR) assay targeting the PCV3 cap gene to improve the sensitivity of PCV3 detection. The established assay is highly specific to PCV3, and does not cross react with other important swine pathogens. The assay's detection limit was 1.68 ± 0.29 copies of PCV3 DNA per reaction (n = 8), an approximately 10-fold greater sensitivity than that of our previously developed quantitative real-time PCR (qPCR) assay for the same virus. The ddPCR assay results were highly reproducible, with intra- and inter-assay coefficient of variation values of <9.0%. Of the 239 archived pig tissue and serum samples, 42 tested positive for PCV3 by the ddPCR assay. Among the 42 positive samples, 31 tested positive by the qPCR assay. Notably, PCV3 was detected in the serum samples collected from commercially imported healthy boars from the US, France and the UK during 2011-2017. The overall agreement between the two assays was 95.39% (228/239). Furthermore, the linear regression analysis showed that the ddPCR and the qPCR results were significantly correlated with an R2 value of 0.9945. Collectively, these results indicate that the ddPCR assay is a robust diagnostic tool for sensitive detection of PCV3, even in samples with low viral loads.
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Affiliation(s)
- Yongning Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
| | - Zhou Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Zhanying Wang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Zili Wang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Caixia Wang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Chunyan Feng
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Xiangmei Lin
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Shaoqiang Wu
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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19
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Yoshida R, Sasaki T, Umekage Y, Tanno S, Ono Y, Ogata M, Chiba S, Mizukami Y, Ohsaki Y. Highly sensitive detection of ALK resistance mutations in plasma using droplet digital PCR. BMC Cancer 2018; 18:1136. [PMID: 30453899 PMCID: PMC6245722 DOI: 10.1186/s12885-018-5031-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023] Open
Abstract
Background On-target resistance mechanisms found in one-third of patients receiving anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) are secondary ALK mutations in ALK-rearranged non-small cell lung cancer (NSCLC). There are large variations in the resistant mutations, unlike the epithelial growth factor receptor (EGFR) T790 M seen with the use of EGFR-TKIs. Liquid biopsy approaches using cell-free DNA (cfDNA) are used for screening and monitoring of mutations in NSCLC. However, feasible protocol for the simultaneous detection of multiple secondary ALK mutations using droplet digital PCR (ddPCR) has not been developed. An efficient strategy using cfDNA in cancer diagnostics, the development of more accurate and cost-effective tools to identify informative multiple secondary ALK mutations is clinically required. Methods To establish a feasible assay to monitor ALK-TKI resistance mutations, we first evaluated the feasibility of ddPCR-based screening for cfDNA mutation detection of 10 distinct secondary ALK mutations. Positive samples were then re-analyzed using mutation-specific probes to track the growth of mutation clones with a high sensitivity. Results Blood samples from seven ALK-positive patients were analyzed using the ddPCR protocol. Secondary G1202R ALK mutations were identified in 2 of 7 patients by the screening assay. Using the mutation-specific probes, monitoring the resistant clone during the clinical course of the disease was well demonstrated in each of the patients. Conclusion The protocol for ddPCR-based liquid biopsy has a feasibility for the screening of secondary ALK-TKI resistance mutations and offers a tool for a cost-effective monitoring of progression in NSCLC. Electronic supplementary material The online version of this article (10.1186/s12885-018-5031-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryohei Yoshida
- Respiratory Center, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Takaaki Sasaki
- Respiratory Center, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Yasuhiro Umekage
- Respiratory Center, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Sachie Tanno
- Respiratory Center, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Munehiko Ogata
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Shinichi Chiba
- Center for Advanced Research and Education, Asahikawa Medical University, Hokkaido, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan.,Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Hokkaido, Japan
| | - Yoshinobu Ohsaki
- Respiratory Center, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa, Hokkaido, 078-8510, Japan
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20
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Cravero K, Medford A, Pallavajjala A, Canzoniero J, Hunter N, Chu D, Cochran RL, Waters I, Christenson ES, Kyker-Snowman K, Button B, Cole AJ, Park BH. Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity. Pract Lab Med 2018; 12:e00108. [PMID: 30140723 PMCID: PMC6104457 DOI: 10.1016/j.plabm.2018.e00108] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/06/2018] [Accepted: 08/08/2018] [Indexed: 11/24/2022] Open
Abstract
Background Genomic testing is often limited by the exhaustible nature of human tissue and blood samples. Here we describe biotinylated amplicon sequencing (BAmSeq), a method that allows for the creation of PCR amplicon based next-generation sequencing (NGS) libraries while retaining the original source DNA. Design and methods Biotinylated primers for different loci were designed to create NGS libraries using human genomic DNA from cell lines, plasma, and formalin-fixed paraffin embedded (FFPE) tissues using the BAmSeq protocol. DNA from the original template used for each BAmSeq library was recovered after separation with streptavidin magnetic beads. The recovered DNA was then used for end-point, quantitative and droplet digital PCR (ddPCR) as well as NGS using a cancer gene panel. Results Recovered DNA was analyzed and compared to the original DNA after one or two rounds of BAmSeq. Recovered DNA revealed comparable genomic distributions and mutational allelic frequencies when compared to original source DNA. Sufficient quantities of recovered DNA after BAmSeq were obtained, allowing for additional downstream applications. Conclusions We demonstrate that BAmSeq allows original DNA template to be recovered with comparable quality and quantity to the source DNA. This recovered DNA is suitable for many downstream applications and may prevent sample exhaustion, especially when DNA quantity or source material is limiting. Modification of targeted panel sequencing allows for recovery of original DNA template. Protocol provides value in the setting of scarce DNA template. Recovered DNA is suitable for NGS, ddPCR and qPCR. Recovered DNA shows no loss of genomic regions.
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Affiliation(s)
- Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arielle Medford
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aparna Pallavajjala
- The Sidney Kimmel Comprehensive Cancer Center, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jenna Canzoniero
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Natasha Hunter
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rory L Cochran
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ian Waters
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kelly Kyker-Snowman
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Berry Button
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex J Cole
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.,The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
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21
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Gao M, Qiu T, Sun Y, Wang X. The abundance and diversity of antibiotic resistance genes in the atmospheric environment of composting plants. Environ Int 2018; 116:229-238. [PMID: 29698899 DOI: 10.1016/j.envint.2018.04.028] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 05/21/2023]
Abstract
Composting is considered to reduce the introduction of antimicrobial resistance genes (ARGs) into the environment through land application of manure; however, the possible pollution of ARGs in the atmospheric environment of composting plants is unknown. In this study, 29 air samples including up- and downwind, composting, packaging, and office areas from 4 composting plants were collected. Dynamic concentrations of 22 subtypes of ARGs, class 1 integron (intl1), and 2 potential human pathogenic bacteria (HPB), and bacterial communities were investigated using droplet digital PCR and 16S rRNA gene sequencing, respectively. In this study, intl1 and 22 subtypes of ARGs (except tetQ) were detected in air of composting, packaging, office, and downwind areas. The highest concentration of 15 out of 22 subtypes of ARGs was detected in the packaging areas, and intl1 also had the maximum average concentration of 104 copies/m3, with up to (1.78 ± 0.49) × 10-2 copies/16S rRNA copy. Non-metric multi-dimensional scaling of ARGs, potential HPBs, and bacterial components all indicated that the bioaerosol pollutant pattern in packaging areas was most similar to that in composting areas, followed by office, downwind, and upwind areas. The co-occurrence between ARGs and bacterial taxa assessed by Procrustes test, mantel test, and network analysis implied that aerosolized ARG fragments from composting and packaging areas contributed to the compositions of ARG aerosols in office and downwind areas. The results presented here show that atmoshperic environments of composting plants harbor abundant and diverse ARGs, which highlight the urgent need for comprehensive evaluation of potential human health and ecological risks of composts during both production as well as land application.
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Affiliation(s)
- Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanmei Sun
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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22
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Rusch JC, Hansen H, Strand DA, Markussen T, Hytterød S, Vrålstad T. Catching the fish with the worm: a case study on eDNA detection of the monogenean parasite Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Parasit Vectors 2018; 11:333. [PMID: 29866158 PMCID: PMC5987472 DOI: 10.1186/s13071-018-2916-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/25/2018] [Indexed: 01/20/2023] Open
Abstract
Background Environmental DNA (eDNA) monitoring is growing increasingly popular in aquatic systems as a valuable complementary method to conventional monitoring. However, such tools have not yet been extensively applied for metazoan fish parasite monitoring. The fish ectoparasite Gyrodactylus salaris, introduced into Norway in 1975, has caused severe damage to Atlantic salmon populations and fisheries. Successful eradication of the parasite has been carried out in several river systems in Norway, and Atlantic salmon remain infected in only seven rivers, including three in the Drammen region. In this particular infection region, a prerequisite for treatment is to establish whether G. salaris is also present on rainbow trout upstream of the salmon migration barrier. Here, we developed and tested eDNA approaches to complement conventional surveillance methods. Methods Water samples (2 × 5 l) were filtered on-site through glass fibre filters from nine locations in the Drammen watercourse, and DNA was extracted with a CTAB protocol. We developed a qPCR assay for G. salaris targeting the nuclear ribosomal ITS1 region, and we implemented published assays targeting the mitochondrial cytochrome-b and NADH-regions for Atlantic salmon and rainbow trout, respectively. All assays were transferred successfully to droplet digital PCR (ddPCR). Results All qPCR/ddPCR assays performed well both on tissue samples and on field samples, demonstrating the applicability of eDNA detection for G. salaris, rainbow trout and Atlantic salmon in natural water systems. With ddPCR we eliminated a low cross-amplification of Gyrodactylus derjavinoides observed using qPCR, thus increasing specificity and sensitivity substantially. Duplex ddPCR for G. salaris and Atlantic salmon was successfully implemented and can be used as a method in future surveillance programs. The presence of G. salaris eDNA in the infected River Lierelva was documented, while not elsewhere. Rainbow trout eDNA was only detected at localities where the positives could be attributed to eDNA release from upstream land-based rainbow trout farms. Electrofishing supported the absence of rainbow trout in all of the localities. Conclusions We provide a reliable field and laboratory protocol for eDNA detection of G. salaris, Atlantic salmon and rainbow trout, that can complement conventional surveillance programs and substantially reduce the sacrifice of live fish. We also show that ddPCR outperforms qPCR with respect to the specific detection of G. salaris.
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Affiliation(s)
- Johannes C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway.,Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316, Oslo, Norway
| | - Haakon Hansen
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway.
| | - David A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway
| | - Turhan Markussen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 8146, Dep, NO-0033, Oslo, Norway
| | - Sigurd Hytterød
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway
| | - Trude Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway
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23
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Gao R, Feyissa BA, Croft M, Hannoufa A. Gene editing by CRISPR/Cas9 in the obligatory outcrossing Medicago sativa. Planta 2018; 247:1043-1050. [PMID: 29492697 DOI: 10.1007/s00425-018-2866-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/21/2018] [Indexed: 05/18/2023]
Abstract
The CRISPR/Cas9 technique was successfully used to edit the genome of the obligatory outcrossing plant species Medicago sativa L. (alfalfa). RNA-guided genome engineering using Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)/Cas9 technology enables a variety of applications in plants. Successful application and validation of the CRISPR technique in a multiplex genome, such as that of M. sativa (alfalfa) will ultimately lead to major advances in the improvement of this crop. We used CRISPR/Cas9 technique to mutate squamosa promoter binding protein like 9 (SPL9) gene in alfalfa. Because of the complex features of the alfalfa genome, we first used droplet digital PCR (ddPCR) for high-throughput screening of large populations of CRISPR-modified plants. Based on the results of genome editing rates obtained from the ddPCR screening, plants with relatively high rates were subjected to further analysis by restriction enzyme digestion/PCR amplification analyses. PCR products encompassing the respective small guided RNA target locus were then sub-cloned and sequenced to verify genome editing. In summary, we successfully applied the CRISPR/Cas9 technique to edit the SPL9 gene in a multiplex genome, providing some insights into opportunities to apply this technology in future alfalfa breeding. The overall efficiency in the polyploid alfalfa genome was lower compared to other less-complex plant genomes. Further refinement of the CRISPR technology system will thus be required for more efficient genome editing in this plant.
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Affiliation(s)
- Ruimin Gao
- Agriculture and Agri-Food Canada, London, ON, Canada
| | - Biruk A Feyissa
- Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Mana Croft
- Agriculture and Agri-Food Canada, London, ON, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London, ON, Canada.
- Department of Biology, University of Western Ontario, London, ON, Canada.
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24
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Abstract
Cerebrospinal fluid (CSF) contains molecules directly linked with brain function because it permeates brain tissue. The analysis of protein biomarkers in CSF is currently recommended for the diagnosis of neurodegenerative disorders, but the clinical sensitivity and specificity are still being investigated. A major drawback is that most of the currently used biomarkers of neurodegenerative diseases are proteins that are found at very low concentrations in CSF and need to be measured by immunoassays that provide relative values, which sometimes are difficult to reproduce between laboratories. In contrast, the recent availability of digital PCR platforms allows the absolute quantification of nucleic acids at single-molecule resolution, but their presence in CSF has not been characterized. CSF contains cell-free mitochondrial DNA (mtDNA) and changes in the concentration of this nucleic acid are linked to neurodegeneration. Here we describe a method to measure the concentration of cell-free circulating mtDNA directly in unpurified CSF using droplet digital PCR with either hydrolysis probes or fluorescent DNA-binding dye methods. This protocol allows the detection and absolute quantification of mtDNA content in the CSF with high analytical sensitivity, specificity, and accuracy.
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25
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Zhou B, Haney MS, Zhu X, Pattni R, Abyzov A, Urban AE. Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants. Methods Mol Biol 2018; 1768:173-190. [PMID: 29717444 DOI: 10.1007/978-1-4939-7778-9_11] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Here, we describe approaches using droplet digital polymerase chain reaction (ddPCR) to validate and quantify somatic mosaic events contributed by transposable-element insertions, copy-number variants, and single-nucleotide variants. In the ddPCR assay, sample or template DNA is partitioned into tens of thousands of individual droplets such that when DNA input is low, the vast majority of droplets contains no more than one copy of template DNA. PCR takes place in each individual droplet and produces a fluorescent readout to indicate the presence or absence of the target of interest allowing for the accurate "counting" of the number of copies present in the sample. The number of partitions is large enough to assay somatic mosaic events with frequencies down to less than 1%.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Michael S Haney
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA. .,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA.
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26
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Sun Y, Joyce PA. Application of droplet digital PCR to determine copy number of endogenous genes and transgenes in sugarcane. Plant Cell Rep 2017; 36:1775-1783. [PMID: 28849385 DOI: 10.1007/s00299-017-2193-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/02/2017] [Indexed: 05/25/2023]
Abstract
Droplet digital PCR combined with the low copy ACT allele as endogenous reference gene, makes accurate and rapid estimation of gene copy number in Q208 A and Q240 A attainable. Sugarcane is an important cultivated crop with both high polyploidy and aneuploidy in its 10 Gb genome. Without a known copy number reference gene, it is difficult to accurately estimate the copy number of any gene of interest by PCR-based methods in sugarcane. Recently, a new technology, known as droplet digital PCR (ddPCR) has been developed which can measure the absolute amount of the target DNA in a given sample. In this study, we deduced the true copy number of three endogenous genes, actin depolymerizing factor (ADF), adenine phosphoribosyltransferase (APRT) and actin (ACT) in three Australian sugarcane varieties, using ddPCR by comparing the absolute amounts of the above genes with a transgene of known copy number. A single copy of the ACT allele was detected in Q208 A , two copies in Q240 A , but was absent in Q117. Copy number variation was also observed for both APRT and ADF, and ranged from 9 to 11 in the three tested varieties. Using this newly developed ddPCR method, transgene copy number was successfully determined in 19 transgenic Q208 A and Q240 A events using ACT as the reference endogenous gene. Our study demonstrates that ddPCR can be used for high-throughput genetic analysis and is a quick, accurate and reliable alternative method for gene copy number determination in sugarcane. This discovered ACT allele would be a suitable endogenous reference gene for future gene copy number variation and dosage studies of functional genes in Q208 A and Q240 A .
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Affiliation(s)
- Yue Sun
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia.
| | - Priya Aiyar Joyce
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
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Li X, Liu Y, Shi W, Xu H, Hu H, Dong Z, Zhu G, Sun Y, Liu B, Gao H, Tang C, Liu X. Droplet digital PCR improved the EGFR mutation diagnosis with pleural fluid samples in non-small-cell lung cancer patients. Clin Chim Acta 2017; 471:177-184. [PMID: 28602964 DOI: 10.1016/j.cca.2017.06.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 11/24/2022]
Abstract
BACKGROUND Droplet digital polymerase chain reaction (ddPCR) is a promising method for analyzing minor amounts of nucleic acid. However, its application has not been reported in pleural fluid, which is an ideal sample source for epidermal growth factor receptor (EGFR) mutation analysis in non-small-cell lung cancer (NSCLC) patients. METHODS The extracted DNA from supernatants of pleural fluid was selected from our sample bank and re-analyzed by our previously established ddPCR assay. The results were compared with the former outcomes detected by direct sequencing or the amplification-refractory mutation system (ARMS). RESULTS A total of 95 samples were selected, and 64 and 31 of them had been performed with direct sequencing and ARMS tests, respectively. The EGFR mutation detection rate of ddPCR was significantly elevated, compared with both direct sequencing (75.4% vs. 43.8%, P<0.0001) and ARMS (61.3% vs. 38.7%, P=0.016). Compared with ARMS, Fisher's exact test showed that EGFR-positive patients who were redefined by ddPCR had higher objective response rates (ORRs): 57.9% vs. 16.7%, P=0.032. Compared with direct sequencing results, Kaplan-Meier curves demonstrated that EGFR-positive patients who were redefined by ddPCR had longer progression-free survival (PFS): 8.0 vs. 2.0months, P=0.0001. CONCLUSION We have demonstrated the clinical value of ddPCR in pleural fluid samples. The experience obtained from the present study is practical and favorable for the proper application of this new assay.
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Affiliation(s)
- Xiaoyan Li
- Department of Lung Cancer, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China
| | - Yi Liu
- Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China.
| | - Weiwei Shi
- Department of Oncology, the General Hospital of PLA, No. 28 Fuxing Road, Beijing, China
| | - Huayan Xu
- Department of Lung Cancer, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China
| | - Haixu Hu
- Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China
| | | | | | - Yun Sun
- Translational Science, Asia & Emerging Markets Innovative Medicine, AstraZeneca R&D, Shanghai, China
| | - Bing Liu
- Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China
| | - Hongjun Gao
- Department of Lung Cancer, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China
| | - Chuanhao Tang
- Department of Lung Cancer, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China; Department of Oncology, Peking University International Hospital, Zhongguancun Life Science Park, Beijing, China.
| | - Xiaoqing Liu
- Department of Lung Cancer, Affiliated Hospital of the Academy of Military Medical Sciences, No. 8 Dongdajie, Beijing, China.
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Gerdes L, Iwobi A, Busch U, Pecoraro S. Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms. Biomol Detect Quantif 2016; 7:9-20. [PMID: 27077048 DOI: 10.1016/j.bdq.2015.12.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/14/2015] [Accepted: 12/14/2015] [Indexed: 11/24/2022]
Abstract
Experience matrix condenses ddPCR performance parameters in graphical presentation. Assay separation value based on absolute fluorescence signal distance and variation. Separation value and experience matrix simplify choice of best assay parameters. Influence of oligonucleotide concentration and annealing/extension temperature.
Digital PCR in droplets (ddPCR) is an emerging method for more and more applications in DNA (and RNA) analysis. Special requirements when establishing ddPCR for analysis of genetically modified organisms (GMO) in a laboratory include the choice between validated official qPCR methods and the optimization of these assays for a ddPCR format. Differentiation between droplets with positive reaction and negative droplets, that is setting of an appropriate threshold, can be crucial for a correct measurement. This holds true in particular when independent transgene and plant-specific reference gene copy numbers have to be combined to determine the content of GM material in a sample. Droplets which show fluorescent units ranging between those of explicit positive and negative droplets are called ‘rain’. Signals of such droplets can hinder analysis and the correct setting of a threshold. In this manuscript, a computer-based algorithm has been carefully designed to evaluate assay performance and facilitate objective criteria for assay optimization. Optimized assays in return minimize the impact of rain on ddPCR analysis. We developed an Excel based ‘experience matrix’ that reflects the assay parameters of GMO ddPCR tests performed in our laboratory. Parameters considered include singleplex/duplex ddPCR, assay volume, thermal cycler, probe manufacturer, oligonucleotide concentration, annealing/elongation temperature, and a droplet separation evaluation. We additionally propose an objective droplet separation value which is based on both absolute fluorescence signal distance of positive and negative droplet populations and the variation within these droplet populations. The proposed performance classification in the experience matrix can be used for a rating of different assays for the same GMO target, thus enabling employment of the best suited assay parameters. Main optimization parameters include annealing/extension temperature and oligonucleotide concentrations. The droplet separation value allows for easy and reproducible assay performance evaluation. The combination of separation value with the experience matrix simplifies the choice of adequate assay parameters for a given GMO event.
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Key Words
- ABI, LifeTechnologies (formerly AppliedBiosystems)
- Bio, DNA Technology/Biosearch Technologies
- Cat. No., catalogue number
- DNA, deoxyribonucleic acid
- Droplet digital PCR (ddPCR)
- EC, European Commission
- ERM, Certified European Reference Material
- EU, European Union
- EURL-GMFF, European Reference Laboratory for GM Food and Feed
- Experience matrix
- Food/feed analysis
- GM, genetically modified
- GMO, genetically modified organism
- Genetically modified organism (GMO)
- HEX,H, hexachlorfluorescein
- L, liter
- Lec, lectin gene of soy
- MIQE, minimal information for publication of quantitative digital PCR experiments
- MRPL, minimum required performance limit
- MS, Microsoft
- MWG, Eurofins-MWG
- MeanSignal, mean fluorescence signal value
- PCR, polymerase chain reaction
- Quantification
- SD, standard deviation (of fluorescence signals)
- TAMRA,T, tetramethylrhodamin
- TIB, TIB Molbiol
- Tech, technician
- VBA, visual basic for applications
- VIC,V, fluorescent dye (LifeTechnologies)
- cp/cp, (gene) copy per (gene) copy
- dPCR, digital PCR
- ddPCR, droplet digital PCR
- fluorescein, FAM,F
- gDNA, genomic DNA
- qPCR, (quantitative) real-time PCR
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Yang R, Paparini A, Monis P, Ryan U. Comparison of next-generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples. Int J Parasitol 2014; 44:1105-13. [PMID: 25229177 DOI: 10.1016/j.ijpara.2014.08.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
Abstract
Clinical microbiology laboratories rely on quantitative PCR for its speed, sensitivity, specificity and ease-of-use. However, quantitative PCR quantitation requires the use of a standard curve or normalisation to reference genes. Droplet digital PCR provides absolute quantitation without the need for calibration curves. A comparison between droplet digital PCR and quantitative PCR-based analyses was conducted for the enteric parasite Cryptosporidium, which is an important cause of gastritis in both humans and animals. Two loci were analysed (18S rRNA and actin) using a range of Cryptosporidium DNA templates, including recombinant plasmids, purified haemocytometer-counted oocysts, commercial flow cytometry-counted oocysts and faecal DNA samples from sheep, cattle and humans. Each method was evaluated for linearity, precision, limit of detection and cost. Across the same range of detection, both methods showed a high degree of linearity and positive correlation for standards (R(2)⩾0.999) and faecal samples (R(2)⩾0.9750). The precision of droplet digital PCR, as measured by mean Relative Standard Deviation (RSD;%), was consistently better compared with quantitative PCR, particularly for the 18S rRNA locus, but was poorer as DNA concentration decreased. The quantitative detection of quantitative PCR was unaffected by DNA concentration, but droplet digital PCR quantitative PCR was less affected by the presence of inhibitors, compared with quantitative PCR. For most templates analysed including Cryptosporidium-positive faecal DNA, the template copy numbers, as determined by droplet digital PCR, were consistently lower than by quantitative PCR. However, the quantitations obtained by quantitative PCR are dependent on the accuracy of the standard curve and when the quantitative PCR data were corrected for pipetting and DNA losses (as determined by droplet digital PCR), then the sensitivity of both methods was comparable. A cost analysis based on 96 samples revealed that the overall cost (consumables and labour) of droplet digital PCR was two times higher than quantitative PCR. Using droplet digital PCR to precisely quantify standard dilutions used for high-throughput and cost-effective amplifications by quantitative PCR would be one way to combine the advantages of the two technologies.
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Affiliation(s)
- Rongchang Yang
- School of Veterinary and Life Sciences, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Andrea Paparini
- School of Veterinary and Life Sciences, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Paul Monis
- Australian Water Quality Centre, South Australian Water Corporation, 250 Victoria Square, Adelaide, SA 5000, Australia
| | - Una Ryan
- School of Veterinary and Life Sciences, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia.
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