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Silva LE, Dall Agnol AM, Rodriguez MC, Xavier AAC, Silva IV, Kioquetta JA, Guimarães NS, Rodrigues RV, Pereira PFV, Almeida RF, Alfieri AA, Headley SA. Characterization of ovine gammaherpesvirus 2 in a goat by nanoplate digital PCR and other diagnostic methods. Braz J Microbiol 2024; 55:855-866. [PMID: 37999912 PMCID: PMC10920513 DOI: 10.1007/s42770-023-01170-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
The Macavirus, ovine gammaherpesvirus 2 (OvGHV2), is the cause of sheep-associated malignant catarrhal fever (SA-MCF). Although SA-MCF occurs in a wide range of mammalian hosts, there are few descriptions of this disease and/or infection in goats. This report describes the findings observed in a goat that was infected by OvGHV2 and adds to the rare description of this infection in this animal species. A 6.5-year-old, female, Anglo Nubian goat, with a neurological syndrome, that was euthanized after severe esophageal obstruction was investigated to determine the cause of the brain disease. Histopathology revealed cerebral cortical edema, hemorrhagic rhombencephalitis, severe hepatic necrosis, and atrophic enteritis. An immunohistochemical (IHC) assay identified intracytoplasmic antigens of a malignant catarrhal fever virus (MCFV) within epithelial cells of the intestine, liver, lungs, and kidneys. A semi-nested PCR assay amplified the partial fragment of the OvGHV2 tegument protein gene from the intestine, confirming that the MCFV identified by IHC was OvGHV2. A qPCR assay that targeted the OvGHV2 polymerase gene revealed an elevated quantification cycle (Cq), while nanoplate-based digital PCR (dPCR) detected low viral copy load within the OvGHV2 DNA. Furthermore, the nucleic acids of several disease pathogens associated with diseases in ruminants were not amplified. However, the exact cause of the neurological syndrome remained obscure since nucleic acids of neurological disease pathogens such as bovine viral diarrhea virus, bovine alphaherpesvirus 1 and 5, Histophilus somni, and OvGHV2 were not detected from the brain. Collectively, the results of the Cq and dPCR confirmed that this goat was infected with a low viral load of OvGHV2, which probably was insufficient to induce the typical histopathological alterations and subsequent clinical manifestations associated with SA-MCF and/or infections by OvGHV2. Therefore, elevated viral loads of OvGHV2 would have been required for the development of histological lesions and/or clinical manifestations of SA-MCF in this goat. Furthermore, the dPCR methodology can be used for the efficient detection and quantification of OvGHV2 DNA in animals with or without clinical and/or histopathological evidence of SA-MCF. Additionally, since previous cases of OvGHV2 infections in goats did not have the typical clinical manifestations of SA-MCF, one wonders if this Macavirus can induce SA-MCF in goats.
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Affiliation(s)
- Luara Evangelista Silva
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, Paraná, 86057-970, Brazil
| | - Alais Maria Dall Agnol
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Maria Constanza Rodriguez
- Marcos Enrietti Diagnostic Center, Agência de Defesa Agropecuária Do Paraná (ADAPAR), Curitiba, Paraná, Brazil
| | - Ana Aparecida Correa Xavier
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, Paraná, 86057-970, Brazil
| | | | - Júlio Adriano Kioquetta
- Large Animal Internal Medicine, Department of Veterinary Clinics, Universidade Estadual de Londrina, Paraná, Brazil
| | - Nathalia Silva Guimarães
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Rafael Vince Rodrigues
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, Paraná, 86057-970, Brazil
| | | | - Rafaelli Ferreira Almeida
- Universidade Pitágoras UNOPAR Anhanguera, Arapongas, Paraná, Brazil
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, Paraná, 86057-970, Brazil
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Selwyn Arlington Headley
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, Paraná, 86057-970, Brazil.
- Universidade Pitágoras UNOPAR Anhanguera, Arapongas, Paraná, Brazil.
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil.
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Liu Y, Van Horn AM, Pham MTN, Dinh BNN, Chen R, Raphael SDR, Paulino A, Thaker K, Somadder A, Frost DJ, Menke CC, Slimak ZC, Slonczewski JL. Fitness trade-offs of multidrug efflux pumps in Escherichia coli K-12 in acid or base, and with aromatic phytochemicals. Appl Environ Microbiol 2024; 90:e0209623. [PMID: 38289137 PMCID: PMC10880634 DOI: 10.1128/aem.02096-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 02/22/2024] Open
Abstract
Multidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness trade-offs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-cultured Escherichia coli K-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with carbonyl cyanide 3-chlorophenylhydrazone or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical's lipophilicity (logP). Methyl salicylate and salicylamide selected strongly against AcrA, without genetic induction of drug resistance regulons. MdtEF-TolC and EmrAB-TolC each had a fitness cost at pH 5.5, but salicylate or benzoate made the fitness contribution positive. Pump fitness effects were not explained by gene expression (measured by digital PCR). Between pH 5.5 and 8.0, acrA and emrA were upregulated in the log phase, whereas mdtE expression was upregulated in the transition-to-stationary phase and at pH 5.5 in the log phase. Methyl salicylate did not affect pump gene expression. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without inducing antibiotic resistance regulons.IMPORTANCEFor drugs that are administered orally, we need to understand how ingested phytochemicals modulate drug resistance in our gut microbiome. Bacteria maintain low-level resistance by proton-motive force (PMF)-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring resistance to antimicrobial agents at first exposure while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH), which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. Non-acidic aromatic molecules have the advantage that they avoid the Mar-dependent induction of regulons conferring other forms of drug resistance. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.
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Affiliation(s)
- Yangyang Liu
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | | | - Rachel Chen
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | - Kavya Thaker
- Department of Biology, Kenyon College, Gambier, Ohio, USA
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Hays A, Wissel M, Colletti K, Soon R, Azadeh M, Smith J, Doddareddy R, Chalfant M, Adamowicz W, Ramaswamy SS, Dholakiya SL, Guelman S, Gullick B, Durham J, Rennier K, Nagilla P, Muruganandham A, Diaz M, Tierney C, John K, Valentine J, Lockman T, Liu HY, Moritz B, Ouedraogo JP, Piche MS, Smet M, Murphy J, Koenig K, Zybura A, Vyhlidal C, Mercier J, Jani N, Kubista M, Birch D, Morse K, Johansson O. Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. AAPS J 2024; 26:24. [PMID: 38316745 DOI: 10.1208/s12248-023-00880-9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024] Open
Abstract
The emerging use of qPCR and dPCR in regulated bioanalysis and absence of regulatory guidance on assay validations for these platforms has resulted in discussions on lack of harmonization on assay design and appropriate acceptance criteria for these assays. Both qPCR and dPCR are extensively used to answer bioanalytical questions for novel modalities such as cell and gene therapies. Following cross-industry conversations on the lack of information and guidelines for these assays, an American Association of Pharmaceutical Scientists working group was formed to address these gaps by bringing together 37 industry experts from 24 organizations to discuss best practices to gain a better understanding in the industry and facilitate filings to health authorities. Herein, this team provides considerations on assay design, development, and validation testing for PCR assays that are used in cell and gene therapies including (1) biodistribution; (2) transgene expression; (3) viral shedding; (4) and persistence or cellular kinetics of cell therapies.
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Affiliation(s)
- Amanda Hays
- BioAgilytix Laboratories, Durham, North Carolina, USA.
| | - Mark Wissel
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | - Russell Soon
- BioMarin Pharmaceutical Inc., Novato, California, USA
| | - Mitra Azadeh
- Ultragenyx Pharmaceutical Inc., Novato, Calfornia, USA
| | | | | | | | - Wendy Adamowicz
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | | | | | | | - Bryan Gullick
- BioAgilytix Laboratories, Durham, North Carolina, USA
| | | | | | - Pruthvi Nagilla
- Asher Biotherapeutics, Inc., South San Francisco, California, USA
| | | | - Manisha Diaz
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | | | | | - Timothy Lockman
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | - Hsing-Yin Liu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | | | | | | | - Jacqueline Murphy
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Kaylyn Koenig
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Agnes Zybura
- Labcorp Drug Development, Greenfield, Indiana, USA
| | - Carrie Vyhlidal
- KCAS Bioanalytical and Biomarker Services, Shawnee, Kansas, USA
| | | | - Niketa Jani
- BioAgilytix Laboratories, Boston, Massachusetts, USA
| | - Mikael Kubista
- Institute of Biotechnology Czech Academy of Sciences, Prague, Czech Republic
| | - Donald Birch
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Karlin Morse
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
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Herdt LR, Berroteran P, Rajagopalan M, Brown BA, Schwartz JJ. NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails. Diagnostics (Basel) 2024; 14:243. [PMID: 38337759 PMCID: PMC10854965 DOI: 10.3390/diagnostics14030243] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Molecular diagnostics has drastically improved the survival rate of patients diagnosed with non-small cell lung cancer (NSCLC) over the last 10 years. Despite advancements in molecular testing, targeted therapies, and national guideline recommendations, more than half of NSCLC patients in the United States either never receive testing or patient care is not informed via molecular testing. Here, we sought to explore the relationship between DNA/RNA input, the molecular testing method, and test success rates. On a shared set of low-input reference test materials (n = 3), we ran both a hybrid capture-based, next-generation sequencing (NGS) assay and a multiplexed digital PCR (dPCR) panel. The dPCR panel was highly sensitive and specific for low-input samples in dilution studies ranging from 40 to 1 ng DNA and from 20 to 2.5 ng RNA, while NGS had up to an 86% loss in sensitivity as contrived sample inputs were serially diluted. The dPCR panel also demonstrated a high PPA (>95%) at diluted inputs as low as 15/7.5 ng DNA/RNA on 23 banked clinical samples with the same NGS hybrid capture assay at a high input. These data suggest that digital PCR is an accurate and effective way of identifying clinically relevant NSCLC mutations at low nucleotide input and quality.
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Shahrajabian MH, Sun W. The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases. Curr Pharm Des 2024; 30:169-179. [PMID: 38243947 DOI: 10.2174/0113816128276560231218090436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/22/2024]
Abstract
Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
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Doğantürk YE, Dağ-Güzel A, Kuşkucu MA. Development of a Nanoplate-Based Digital PCR Test Method for Quantitative Detection of Human Adenovirus DNA. Infect Dis Clin Microbiol 2023; 5:353-366. [PMID: 38633848 PMCID: PMC10986707 DOI: 10.36519/idcm.2023.255] [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] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/04/2023] [Indexed: 04/19/2024]
Abstract
Objective Digital polymerase chain reaction (dPCR) assay is an advanced PCR technique that allows for the simultaneous detection and absolute quantification of diverse pathogens.Commercially validated kits available for detecting all subtypes of human adenovirus (HAdV) are limited. This study aimed to demonstrate the development of an in-house nanoplate-based dPCR assay with high sensitivity, even at low copy numbers. Materials and Methods In this methodological study, the standardized HAdV DNA was prepared by amplifying the specific hexon gene region with real-time PCR and purifying the HAdV DNA using magnetic beads from HAdV-positive extractions. Dilutions were tested in triplicate during three independent runs to determine the dynamic range, the limit of detection (LoD), the limit of quantification (LoQ), precision, and reproducibility. The primer and probe sequences used in the study were selected based on a literature review to ensure the detection of all HAdV serotypes in a single run. The selected primers were verified using the US National Center for Biotechnology Information (NBCI) nBLAST tools, and the target sequence was determined using the BioEdit software. The DNA concentration of the stock solution was measured using a Qubit fluorometer. The estimated copy number of the stock solution per milliliter was calculated based on the length of the amplified base sequence and fluorometer measurement. Results The dynamic range of the test was determined to be from 770.4 to 0.9476 cp/μl, with the LoD and LoQ values both being 0.9476 cp/μl. The coefficient of determination (r 2) value of the test was 0.9986. Conclusion The results demonstrated that the dPCR method could be an ideal tool for the diagnosis and absolute quantification of human adenoviruses, especially in low copy numbers. In order to determine the reproducibility of the test and validate the method for field use, it needs to be developed and adapted in various laboratories and supported by clinical studies.
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Affiliation(s)
- Yağmur Eylül Doğantürk
- Department of Medical Microbiology, İstanbul University-Cerrahpaşa School of Medicine, İstanbul, Türkiye
- Department of Medical Microbiology, İstanbul Aydın University School of Medicine, İstanbul, Türkiye
| | - Aylin Dağ-Güzel
- Department of Medical Microbiology, İstanbul University-Cerrahpaşa School of Medicine, İstanbul, Türkiye
- Medical Laboratory Techniques, Arel University Junior Technical Collage, İstanbul, Türkiye
| | - Mert Ahmet Kuşkucu
- Department of Medical Microbiology, İstanbul University-Cerrahpaşa School of Medicine, İstanbul, Türkiye
- Department of Medical Microbiology, Koç University School of Medicine, İstanbul, Türkiye
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Goshia T, Aralar A, Wiederhold N, Jenks JD, Mehta SR, Sinha M, Karmakar A, Sharma A, Shrivastava R, Sun H, White PL, Hoenigl M, Fraley SI. Universal Digital High Resolution Melt for the detection of pulmonary mold infections. bioRxiv 2023:2023.11.09.566457. [PMID: 37986859 PMCID: PMC10659414 DOI: 10.1101/2023.11.09.566457] [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] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Invasive mold infections (IMIs) such as aspergillosis, mucormycosis, fusariosis, and lomentosporiosis are associated with high morbidity and mortality, particularly in immunocompromised patients, with mortality rates as high as 40% to 80%. Outcomes could be substantially improved with early initiation of appropriate antifungal therapy, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high resolution melting analysis (U-dHRM) may enable rapid and robust diagnosis of IMI. This technology aims to accomplish timely pathogen detection at the single genome level by conducting broad-based amplification of microbial barcoding genes in a digital polymerase chain reaction (dPCR) format, followed by high-resolution melting of the DNA amplicons in each digital reaction to generate organism-specific melt curve signatures that are identified by machine learning. Methods A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these 19 fungal melt curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage (BAL) samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. Results U-dHRM achieved an average of 97% fungal organism identification accuracy and a turn-around-time of 4hrs. Pathogenic molds (Aspergillus, Mucorales, Lomentospora and Fusarium) were detected by U-dHRM in 73% of BALF samples suspected of IMI. Mixtures of pathogenic molds were detected in 19%. U-dHRM demonstrated good sensitivity for IMI, as defined by current diagnostic criteria, when clinical findings were also considered. Conclusions U-dHRM showed promising performance as a separate or combination diagnostic approach to standard mycological tests. The speed of U-dHRM and its ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples as well as detect emerging opportunistic pathogens may provide information that could aid in treatment decisions and improve patient outcomes.
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Affiliation(s)
- Tyler Goshia
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - April Aralar
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Nathan Wiederhold
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Jeffrey D. Jenks
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham County Department of Public Health, Durham, NC, USA
| | - Sanjay R. Mehta
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- San Diego Veterans Administration Medical Center, San Diego, CA, USA
| | | | | | | | | | - Haoxiang Sun
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - P. Lewis White
- Public Health Wales Microbiology Cardiff, and Cardiff University Centre for Trials Research/Division of Infection/Immunity, University Hospital of Wales, Cardiff, United Kingdom
| | - Martin Hoenigl
- Department of Medicine, Medical University of Graz, Graz, Austria
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
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Park SA, Masunaga N, Kagara N, Ohi Y, Gondo N, Abe K, Yoshinami T, Sota Y, Miyake T, Tanei T, Shimoda M, Sagara Y, Shimazu K. Evaluation of RASSF1A methylation in the lysate of sentinel lymph nodes for detecting breast cancer metastasis: A diagnostic accuracy study. Oncol Lett 2023; 26:475. [PMID: 37809046 PMCID: PMC10551867 DOI: 10.3892/ol.2023.14063] [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: 05/10/2023] [Accepted: 08/15/2023] [Indexed: 10/10/2023] Open
Abstract
The restriction enzyme-based digital methylation-specific polymerase chain reaction (RE-dMSP) assay is useful for diagnosing sentinel lymph node (SN) metastasis in patients with breast cancer, by detecting tumor-derived methylated Ras association domain-containing protein 1 (RASSF1A). In addition, this assay has high concordance (95.0%) with one-step nucleic acid amplification (OSNA). The present study aimed to perform RE-dMSP using OSNA lysate from more patients and to re-evaluate its clinical usage. Overall, 418 SNs from 347 patients were evaluated using both OSNA and RE-dMSP. The concordance rate was 83.3% (348/418). RASSF1A methylation of the primary tumors was negative in 36 patients. When these patients were excluded, the concordance rate improved to 88.2% (330/374). Of the 79 OSNA-negative cases, 19 were RE-dMSP-positive, although all were positive for cytokeratin 19 expression in the primary tumor, suggesting that RE-dMSP can detect tumor-derived DNA with a higher sensitivity. The percent of methylated reference of the breast tumors showed a wide variety in the 16 OSNA-positive/RE-dMSP-negative cases, and such variability of methylation could have affected the results in these patients. In conclusion, although RE-dMSP can diagnose SN metastasis with high sensitivity and accuracy, and can be a supplementary tool to OSNA in breast cancer, RE-dMSP showed certain discordance with OSNA and critically depended on the absence or heterogeneity of DNA methylation in breast tumors. Further research is expected to develop an assay targeting other DNA alterations, such as mutations.
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Affiliation(s)
- Sung Ae Park
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Nanae Masunaga
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Naofumi Kagara
- Department of Breast Surgery, Osaka General Medical Center, Osaka 558-8558, Japan
| | - Yasuyo Ohi
- Department of Breast Surgery, Hakuaikai Sagara Hospital, Kagoshima 892-0833, Japan
| | - Naomi Gondo
- Department of Breast Surgery, Hakuaikai Sagara Hospital, Kagoshima 892-0833, Japan
| | - Kaori Abe
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tetsuhiro Yoshinami
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yoshiaki Sota
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yasuaki Sagara
- Department of Breast Surgery, Hakuaikai Sagara Hospital, Kagoshima 892-0833, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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Gleerup D, Chen Y, Van Snippenberg W, Valcke C, Thas O, Trypsteen W, De Spiegelaere W. Measuring DNA quality by digital PCR using probability calculations. Anal Chim Acta 2023; 1279:341822. [PMID: 37827643 DOI: 10.1016/j.aca.2023.341822] [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] [Received: 02/07/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Accurate methods to assess DNA integrity are needed for many biomolecular methods. A multiplex digital PCR (dPCR) method designed for interspaced target sequences can be used to assess sequence integrity of large DNA strands. The ratio of single positive partitions versus double positive partitions is then used to calculate the sheared DNA strands. However, this simple calculation is only valid with low DNA concentration. We here describe a method based on probability calculations which enables DNA quality analysis in a large dynamic range of DNA concentrations. RESULTS Known DNA integrity percentages were mimicked using artificial double stranded DNA in low, intermediate and high DNA concentration scenarios, respectively 600, 12500 and 30000 copies of DNA per reaction. At low concentrations both methods were similar. However, at the intermediate concentration (12500 copies per reaction) the ratio based method started producing a larger error than the proposed probability calculation method with a mean relative error of 20.7 and 16.7 for the Bruner and the proposed method respectively. At the high concentration (30000 copies per reaction) only the proposed method provided accurate measurements with a mean relative error of 60.9 and 9.3 for the ratio based and the proposed method respectively. Furthermore, while both methods have a bias, it is constant for the proposed method, while it decreases with the integrity of the DNA for the ratio based method. The probability calculation equation was extended to 4 dimensions and a proof of concept experiment was performed, the data suggested that the 4 dimensional equation is valid. SIGNIFICANCE AND NOVELTY We here validate a method of estimating DNA integrity with dPCR using multiple probe combinations, allowing fast and flexible DNA integrity analysis. Additionally, we extend the method from 2 to 4 plex for more accurate DNA integrity measurements.
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Affiliation(s)
- David Gleerup
- Laboratory of Veterinary Morphology, Ghent University, Belgium; Ghent University Digital PCR Consortium, Ghent University, Belgium.
| | - Yao Chen
- Ghent University Digital PCR Consortium, Ghent University, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium.
| | - Willem Van Snippenberg
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Belgium.
| | - Cedric Valcke
- Department of Healthcare, HOGENT University of Applied Sciences and Arts, Belgium.
| | - Olivier Thas
- Ghent University Digital PCR Consortium, Ghent University, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium; National Institute for Applied Statistics Research Australia (NIASRA), University of Wollongong, Australia; Data Science Institute, I-BioStat, Hasselt University, Belgium.
| | - Wim Trypsteen
- Ghent University Digital PCR Consortium, Ghent University, Belgium; HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Belgium.
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Ghent University, Belgium; Ghent University Digital PCR Consortium, Ghent University, Belgium.
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10
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Griffiths KR, McLaughlin JLH, Hall F, Partis L, Hansen SC, Tulloch R, Burke DG. Development of Seven New dPCR Animal Species Assays and a Reference Material to Support Quantitative Ratio Measurements of Food and Feed Products. Foods 2023; 12:3839. [PMID: 37893732 PMCID: PMC10606771 DOI: 10.3390/foods12203839] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Laboratory testing methods to confirm the identity of meat products and eliminate food fraud regularly rely on PCR amplification of extracted DNA, with most published assays detecting mitochondrial sequences, providing sensitive presence/absence results. By targeting single-copy nuclear targets instead, relative quantification measurements are achievable, providing additional information on the proportions of meat species detected. In this Methods paper, new assays for horse, donkey, duck, kangaroo, camel, water buffalo and crocodile have been developed to expand the range of species that can be quantified, and a previously published reference assay targeting the myostatin gene has been modified to include marsupials and reptiles. The accuracy of this ratio measurement approach was demonstrated using dPCR with mixtures of meat DNA down to 0.1%. However, the limit of detection (LOD) of this approach is not just determined by the assay targets, but by the samples themselves, with food or feed ingredients and processing impacting the DNA yield and integrity. In routine testing settings, the myostatin assay can provide multiple quality control roles, including monitoring the yield and purity of extracted DNA, identifying the presence of additional meats not detected by the suite of species-specific assays and potentially estimating a sample-specific LOD based on measured copy numbers of the myostatin target. In addition to the myostatin positive control assay, a synthetic DNA reference material (RM) has been designed, containing PCR targets for beef, pork, sheep, chicken, goat, kangaroo, horse, water buffalo and myostatin, to be used as a positive template control. The availability of standardised measurement methods and associated RMs significantly improves the reliability, comparability and transparency of laboratory testing, leading to greater confidence in results.
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Affiliation(s)
- Kate R. Griffiths
- Bioanalysis Section, National Measurement Institute, Lindfield, Sydney, NSW 2070, Australia
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11
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Souto S, Olveira JG, López-Vázquez C, Bandín I, Dopazo CP. Designing and Validation of a Droplet Digital PCR Procedure for Diagnosis and Accurate Quantification of Nervous Necrosis Virus in the Mediterranean Area. Pathogens 2023; 12:1155. [PMID: 37764963 PMCID: PMC10536565 DOI: 10.3390/pathogens12091155] [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: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The viral nervous necrosis virus (VNNV) is the causative agent of an important disease affecting fish species cultured worldwide. Early and accurate diagnosis is, at present, the most effective control and prevention tool, and molecular techniques have been strongly introduced and accepted by official organizations. Among those, real-time quantitative polymerase chain reaction (rt-qPCR) is nowadays displacing other molecular techniques. However, another PCR-based technology, droplet digital PCR (ddPCR), is on the increase. It has many advantages over qPCR, such as higher sensitivity and more reliability of the quantification. Therefore, we decided to design and validate a protocol for the diagnosis and quantification of SJ and RG type VNNV using reverse transcription-ddPCR (RT-ddPCR). We obtained an extremely low limit of detection, 10- to 100-fold lower than with RT-qPCR. Quantification by RT-ddPCR, with a dynamic range of 6.8-6.8 × 104 (SJ type) or 1.04 × 101-1.04 × 105 (RG type) cps/rctn, was more reliable than with RT-qPCR. The procedure was tested and validated in field samples, providing high clinical sensitivity and negative predictive values. In conclusion, we propose this method to substitute RT-qPCR protocols because it exceeds the expectations of qPCR in the diagnosis and quantification of VNNV.
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Affiliation(s)
| | | | | | | | - Carlos P. Dopazo
- Instituto de Acuicultura, Department of Microbiology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (S.S.); (J.G.O.); (C.L.-V.); (I.B.)
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12
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Kopylova KV, Kasparov EW, Marchenko IV, Smolnikova MV. [Digital PCR as a Highly Sensitive Diagnostic Tool: A Review]. Mol Biol (Mosk) 2023; 57:771-781. [PMID: 37752642 DOI: 10.31857/s0026898423050051, edn: xwwkds] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/29/2023] [Indexed: 09/28/2023]
Abstract
Digital PCR (dPCR) is a nucleic acid quantification method that is widely used in genetic analysis. One of the most significant advantages of dPCR over other methods is the possibility of absolute quantitative determination of genetic material without construction of calibration curves, which allows one to detect even single molecules of nucleic acids, and, hence, provides early diagnosis of diseases. One specific characteristic of dPCR is the detection of the analyzed biological object in each microreaction, followed by the presentation of the analysis results in a binary system, thereby giving the method its name. The key aspects of developing the dPCR method, i.e., from the first devices based on microfluidic chip technology to modern systems capable of measuring a target at a concentration of up to 1 in 100000 copies are shown in the current work. We analyzed the data on the detection of various pathogens using dPCR, as well as summarizing various study results demonstrating the innovativeness of this method. Both the possibilities of multiplex dPCR analysis and its potential in clinical practice are presented. This review also addresses the issue of the role of dPCR in the development of noninvasive methods for analysis of oncological diseases. Possible ways of developing dPCR technology were emphasized, including its use as a "point-of-care" system.
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Affiliation(s)
- K V Kopylova
- Scientific Research Institute of Medical Problems of the North, Krasnoyarsk, 660022 Russia
| | - Ed W Kasparov
- Scientific Research Institute of Medical Problems of the North, Krasnoyarsk, 660022 Russia
| | - I V Marchenko
- Scientific Research Institute of Medical Problems of the North, Krasnoyarsk, 660022 Russia
| | - M V Smolnikova
- Scientific Research Institute of Medical Problems of the North, Krasnoyarsk, 660022 Russia
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13
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Montesdeoca S, García-Gisbert N, Calvo X, Arenillas L, Román D, Fernández-Rodríguez C, Navarro R, Costan B, Vela MDC, Camacho L, Abella E, Colomo L, Salido M, Puiggros A, Florensa L, Espinet B, Bellosillo B, Ferrer del Álamo A. Leukemic Involvement Is a Common Feature in Waldenström Macroglobulinemia at Diagnosis. Cancers (Basel) 2023; 15:4152. [PMID: 37627180 PMCID: PMC10452547 DOI: 10.3390/cancers15164152] [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: 07/21/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Waldenström Macroglobulinemia (WM) is a lymphoplasmacytic lymphoma with bone marrow (BM) involvement and IgM monoclonal gammopathy. To date, no studies have focused specifically on peripheral blood (PB) involvement. In this study, 100 patients diagnosed with WM according to the World Health Organization (WHO) criteria were included based on the demonstration of MYD88mut in BM and the availability of PB multiparametric flow cytometry (MFC) analysis. Leukemic involvement by MFC was detected in 50/100 patients. A low percentage of mature small lymphocytes in PB smears was observed in only 15 cases. MYD88mut by AS-qPCR was detected in PB in 65/100 cases. In cases with leukemic expression by MFC, MYD88mut was detected in all cases, and IGH was rearranged in 44/49 cases. In 21/50 patients without PB involvement by MFC, molecular data were consistent with circulating disease (MYD88mut by AS-qPCR 3/50, IGH rearranged 6/50, both 12/50). Therefore, PB involvement by standard techniques was detected in 71/100 patients. MYD88mut was detected in PB by dPCR in 9/29 triple negative cases. Overall, 80% of the patients presented PB involvement by any technique. Our findings support the role of PB MFC in the evaluation of patients with IgM monoclonal gammopathy and provide reliable information on correlation with molecular features. The development of a feasible MFC assay may stand as an objective tool in the classification of mature B cell neoplasms presenting with IgM monoclonal gammopathy.
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Affiliation(s)
- Sara Montesdeoca
- Laboratori d’Hematologia, Servei Diagnòstic de Laboratori, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain;
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
| | - Nieves García-Gisbert
- Laboratori de Biologia Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain; (N.G.-G.); (C.F.-R.); (M.d.C.V.); (L.C.); (B.B.)
- Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
| | - Xavier Calvo
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Leonor Arenillas
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - David Román
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Concepción Fernández-Rodríguez
- Laboratori de Biologia Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain; (N.G.-G.); (C.F.-R.); (M.d.C.V.); (L.C.); (B.B.)
- Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
| | - Rosa Navarro
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Beatriz Costan
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - María del Carmen Vela
- Laboratori de Biologia Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain; (N.G.-G.); (C.F.-R.); (M.d.C.V.); (L.C.); (B.B.)
- Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
| | - Laura Camacho
- Laboratori de Biologia Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain; (N.G.-G.); (C.F.-R.); (M.d.C.V.); (L.C.); (B.B.)
- Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
| | - Eugènia Abella
- Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
- Servei d’Hematologia Clínica, Hospital del Mar, 08003 Barcelona, Spain
| | - Lluís Colomo
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Marta Salido
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Anna Puiggros
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Lourdes Florensa
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Blanca Espinet
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
| | - Beatriz Bellosillo
- Laboratori de Biologia Molecular, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain; (N.G.-G.); (C.F.-R.); (M.d.C.V.); (L.C.); (B.B.)
- Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
| | - Ana Ferrer del Álamo
- Grup de Recerca Translacional en Neoplasies Hematològiques (GRETNHE), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (X.C.); (L.A.); (D.R.); (R.N.); (B.C.); (L.C.); (M.S.); (A.P.); (L.F.); (B.E.)
- Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, 08003 Barcelona, Spain
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14
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Tumpach C, Rhodes A, Kim Y, Ong J, Liu H, Chibo D, Druce J, Williamson D, Hoh R, Deeks SG, Yukl SA, Roche M, Lewin SR, Telwatte S. Adaptation of Droplet Digital PCR-Based HIV Transcription Profiling to Digital PCR and Association of HIV Transcription and Total or Intact HIV DNA. Viruses 2023; 15:1606. [PMID: 37515292 PMCID: PMC10384802 DOI: 10.3390/v15071606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
In most people living with HIV (PLWH) on effective antiretroviral therapy (ART), cell-associated viral transcripts are readily detectable in CD4+ T cells despite the absence of viremia. Quantification of HIV RNA species provides insights into the transcriptional activity of proviruses that persist in cells and tissues throughout the body during ART ('HIV reservoir'). One such technique for HIV RNA quantitation, 'HIV transcription profiling', developed in the Yukl laboratory, measures a series of HIV RNA species using droplet digital PCR. To take advantage of advances in digital (d)PCR, we adapted the 'HIV transcription profiling' technique to Qiagen's dPCR platform (QIAcuity) and compared its performance to droplet digital (dd)PCR (Bio-Rad QX200 system). Using RNA standards, the two technologies were tested in parallel and assessed for multiple parameters including sensitivity, specificity, linearity, and intra- and inter-assay variability. The newly validated dPCR assays were then applied to samples from PLWH to determine HIV transcriptional activity relative to HIV reservoir size. We report that HIV transcriptional profiling was readily adapted to dPCR and assays performed similarly to ddPCR, with no differences in assay characteristics. We applied these assays in a cohort of 23 PLWH and found that HIV reservoir size, based on genetically intact proviral DNA, does not predict HIV transcriptional activity. In contrast, levels of total DNA correlated with levels of most HIV transcripts (initiated, proximally and distally elongated, unspliced, and completed, but not multiply spliced), suggesting that a considerable proportion of HIV transcripts likely originate from defective proviruses. These findings may have implications for measuring and assessing curative strategies and clinical trial outcomes.
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Affiliation(s)
- Carolin Tumpach
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Youry Kim
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jesslyn Ong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Haoming Liu
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Deborah Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Walter and Eliza Hall Institute, Melbourne 3052, Australia
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Steven G. Deeks
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Steven A. Yukl
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
- San Francisco Veteran Affairs Medical Center, San Francisco, CA 94121, USA
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Infectious and Inflammatory Diseases Theme, School of Health and Biomedical Sciences, RMIT University, Melbourne 3000, Australia
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne 3004, Australia
| | - Sushama Telwatte
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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15
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Flütsch S, Wiestner F, Butticaz L, Moor D, Stölting KN. Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp. BMC Genomics 2023; 24:375. [PMID: 37403035 DOI: 10.1186/s12864-023-09429-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR). RESULTS We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR. CONCLUSIONS We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.
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Affiliation(s)
- Sabrina Flütsch
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
| | - Fabian Wiestner
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Lisa Butticaz
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Dominik Moor
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Kai N Stölting
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
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16
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Hinney B, Wiedermann S, Bosco A, Rinaldi L, Hofer M, Joachim A, Krücken J, Steinborn R. Development of a three-colour digital PCR for early and quantitative detection of benzimidazole resistance-associated single nucleotide polymorphisms in Haemonchus contortus. Int J Parasitol Drugs Drug Resist 2023; 22:88-95. [PMID: 37348434 PMCID: PMC10336075 DOI: 10.1016/j.ijpddr.2023.06.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/24/2023]
Abstract
Haemonchus contortus is the most pathogenic nematode in small ruminants and anthelmintic resistance (AR) hampers its efficient control. Early detection of AR status is required to reduce selection for AR and cannot be achieved using phenotypic tests. For benzimidazoles (BZs), the detection of AR-associated alleles characterised by single nucleotide polymorphisms (SNPs) in the isotype 1 β-tubulin gene allows early AR detection in strongyles. The F200Y, F167Y, E198A and E198L polymorphisms have been described in BZ-resistant populations with a clear variation in frequencies between regions. A novel digital PCR (dPCR) enables the detection of all of the above-described polymorphisms in H. contortus. Assays were validated using synthetic DNA fragments containing these SNPs. Then, larvae obtained and pooled at farm level from 26 Austrian and 10 Italian sheep farms were analysed. For all assays a detection limit of 15 copies/μl of resistance alleles and a high level of accuracy were demonstrated, allowing to detect allele frequencies of 1% in most samples. In Austrian samples, elevated frequencies of F200Y resistance alleles were detected on all farms. Polymorphisms in codon 167 and codon 198 were identified in H. contortus from Austria for the first time. In Italian samples, the frequency of resistance alleles was still comparatively low, but F200Y resistance alleles were traceable. In conclusion we developed for the first time dPCR assays that target all SNPs of relevance associated with BZ-resistance in H. contortus. Future research on AR development could benefit from an early onset of SNP-based surveillance that would include the developed assays for all SNPs of relevance. Improved surveillance in the long term will include other important, though less pathogenic, nematode genera in the analyses.
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Affiliation(s)
- Barbara Hinney
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Sandra Wiedermann
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Antonio Bosco
- Laboratory of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Laura Rinaldi
- Laboratory of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Martin Hofer
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | - Anja Joachim
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag Str. 7, 14163, Berlin, Germany
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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17
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Bogožalec Košir A, Lužnik D, Tomič V, Milavec M. Evaluation of DNA Extraction Methods for Reliable Quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Biosensors (Basel) 2023; 13:bios13040463. [PMID: 37185538 PMCID: PMC10136035 DOI: 10.3390/bios13040463] [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] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Dane Lužnik
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
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18
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Thomassen M, Mesman RLS, Hansen TVO, Menendez M, Rossing M, Esteban‐Sánchez A, Tudini E, Törngren T, Parsons MT, Pedersen IS, Teo SH, Kruse TA, Møller P, Borg Å, Jensen UB, Christensen LL, Singer CF, Muhr D, Santamarina M, Brandao R, Andresen BS, Feng B, Canson D, Richardson ME, Karam R, Pesaran T, LaDuca H, Conner BR, Abualkheir N, Hoang L, Calléja FMGR, Andrews L, James PA, Bunyan D, Hamblett A, Radice P, Goldgar DE, Walker LC, Engel C, Claes KBM, Macháčková E, Baralle D, Viel A, Wappenschmidt B, Lazaro C, Vega A, Vreeswijk MPG, de la Hoya M, Spurdle AB. Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants: Application of a points-based ACMG/AMP approach. Hum Mutat 2022; 43:1921-1944. [PMID: 35979650 PMCID: PMC10946542 DOI: 10.1002/humu.24449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]
Abstract
Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splicing event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data, and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the points-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength.
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Affiliation(s)
- Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdence CDenmark
| | - Romy L. S. Mesman
- Department of Human GeneticsLeiden University Medical CenterLeidenthe Netherlands
| | - Thomas V. O. Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Mireia Menendez
- Hereditary Cancer ProgramCatalan Institute of Oncology, ONCOBELL‐IDIBELL‐IDTP, CIBERONCHospitalet de LlobregatSpain
| | - Maria Rossing
- Center for Genomic Medicine, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Therese Törngren
- Division of Oncology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Inge S. Pedersen
- Molecular Diagnostics, Aalborg University HospitalAalborgDenmark
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
- Department of Clinical MedicineAalborg UniversityAalborgDenmark
| | - Soo H. Teo
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
- Department of Surgery, Faculty of MedicineUniversity of MalayaKuala LumpurMalaysia
| | - Torben A. Kruse
- Department of Clinical GeneticsOdense University HospitalOdence CDenmark
| | - Pål Møller
- Department of Tumour BiologyThe Norwegian Radium Hospital, Oslo University HospitalOsloNorway
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Uffe B. Jensen
- Department of Clinical GeneticsAarhus University HospitalAarhus NDenmark
| | | | - Christian F. Singer
- Department of OB/GYN and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Daniela Muhr
- Department of OB/GYN and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Marta Santamarina
- Fundación Pública Galega de Medicina XenómicaSantiago de CompostelaSpain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGASSantiago de CompostelaSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - Rita Brandao
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Bing‐Jian Feng
- Department of DermatologyHuntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUtahUSA
| | - Daffodil Canson
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | | | | | | | | | | | | | | | | | - Lesley Andrews
- Hereditary Cancer Clinic, Nelune Comprehensive Cancer Care CentreSydneyNew South WalesAustralia
| | - Paul A. James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Dave Bunyan
- Human Development and Health, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Amanda Hamblett
- Middlesex Health Shoreline Cancer CenterWestbrookConnecticutUSA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of ResearchFondazione IRCCS Istituto Nazionale dei Tumori (INT)MilanItaly
| | - David E. Goldgar
- Department of DermatologyHuntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUtahUSA
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | | | - Eva Macháčková
- Department of Cancer Epidemiology and GeneticsMasaryk Memorial Cancer InstituteBrnoCzech Republic
| | - Diana Baralle
- Human Development and Health, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Alessandra Viel
- Division of Functional Onco‐genomics and GeneticsCentro di Riferimento Oncologico di Aviano (CRO), IRCCSAvianoItaly
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Conxi Lazaro
- Hereditary Cancer ProgramCatalan Institute of Oncology, ONCOBELL‐IDIBELL‐IDTP, CIBERONCHospitalet de LlobregatSpain
| | - Ana Vega
- Fundación Pública Galega de Medicina XenómicaSantiago de CompostelaSpain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGASSantiago de CompostelaSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - ENIGMA Consortium
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
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19
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Jiang W, Chen L, Wang J, Shao X, Jiang M, Chen Z, Wang J, Huang Y, Fei P. Open-top light-sheet imaging of CLEAR emulsion for high-throughput loss-free analysis of massive fluorescent droplets. Biomed Phys Eng Express 2022; 8. [PMID: 35767965 DOI: 10.1088/2057-1976/ac7d0f] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Digital droplet PCR (ddPCR) is classified as the third-generation PCR technology that enables absolute quantitative detection of nucleic acid molecules and has become an increasingly powerful tool for clinic diagnosis. We previously established a CLEAR-dPCR technique based on the combination of CLEAR droplets generated by micro-centrifuge-based microtubule arrays (MiCA) andinsitu3D readout by light-sheet fluorescence imaging. This CLEAR-dPCR technique attains very high readout speed and dynamic range. Meanwhile, it is free from sample loss and contamination, showing its advantages over commercial d-PCR technologies. However, a conventional orthogonal light-sheet imaging setup in CLEAR d-PCR cannot image multiple centrifuge tubes, thereby limiting its widespread application to large-scale, high-speed dd-PCR assays. Herein, we propose an in-parallel 3D dd-PCR readout technique based on an open-top light-sheet microscopy setup. This approach can continuously scan multiple centrifuge tubes which contain CLEAR emulsions with highly diverse concentrations, and thus further boost the scale and throughput of our 3D dd-PCR technique.
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Affiliation(s)
- Wen Jiang
- School of Optical and Electronic Information , Huazhong University of Science and Technology, E417, Wuhan, Hubei, 430074, CHINA
| | - Longbiao Chen
- School of Optical and Electronic Information , Huazhong University of Science and Technology, E417, Wuhan, Hubei, 430074, CHINA
| | - Jie Wang
- Huazhong University of Science and Technology, E417, School of Optical and Electronic Information, Wuhan, Hubei, 430074, CHINA
| | - Xinyang Shao
- Peking-Tsinghua Center for Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing, Beijing, 100871, CHINA
| | - Mengcheng Jiang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Biomedical Pioneering Innovation Center (BIOPIC), Beijing, Beijing, 100871, CHINA
| | - Zitian Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Biomedical Pioneering Innovation Center (BIOPIC), Beijing, Beijing, 100871, CHINA
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, School of Life Sciences, Beijing, Beijing, 100084, CHINA
| | - Yanyi Huang
- College of Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, College of Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Beijing, 100871, CHINA
| | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, E417, Wuhan, 430074, CHINA
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20
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Zaytseva M, Usman N, Salnikova E, Sanakoeva A, Valiakhmetova A, Chervova A, Papusha L, Novichkova G, Druy A. Methodological Challenges of Digital PCR Detection of the Histone H3 K27M Somatic Variant in Cerebrospinal Fluid. Pathol Oncol Res 2022; 28:1610024. [PMID: 35498161 PMCID: PMC9039021 DOI: 10.3389/pore.2022.1610024] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022]
Abstract
Cell-free DNA (cfDNA) in body fluids is invaluable for cancer diagnostics. Despite the impressive potential of liquid biopsies for the diagnostics of central nervous system (CNS) tumors, a number of challenges prevent introducing this approach into routine laboratory practice. In this study, we adopt a protocol for sensitive detection of the H3 K27M somatic variant in cerebrospinal fluid (CSF) by using digital polymerase chain reaction (dPCR). Optimization of the protocol was carried out stepwise, including preamplification of the H3 target region and adjustment of dPCR conditions. The optimized protocol allowed detection of the mutant allele starting from DNA quantities as low as 9 picograms. Analytical specificity was tested using a representative group of tumor tissue samples with known H3 K27M status, and no false-positive cases were detected. The protocol was applied to a series of CSF samples collected from patients with CNS tumors (n = 18) using two alternative dPCR platforms, QX200 Droplet Digital PCR system (Bio-Rad) and QIAcuity Digital PCR System (Qiagen). In three out of four CSF specimens collected from patients with H3 K27M-positive diffuse midline glioma, both platforms allowed detection of the mutant allele. The use of ventricular access for CSF collection appears preferential, as lumbar CSF samples may produce ambiguous results. All CSF samples collected from patients with H3 wild-type tumors were qualified as H3 K27M-negative. High agreement of the quantitative data obtained with the two platforms demonstrates universality of the approach.
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Affiliation(s)
- Margarita Zaytseva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natalia Usman
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Salnikova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Agunda Sanakoeva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Andge Valiakhmetova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Almira Chervova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Ludmila Papusha
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexander Druy
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Research Institute of Medical Cell Technologies, Yekaterinburg, Russia
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21
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Shin W, Lee CJ, Lee YM, Choi YB, Mun S, Han K. Rapid identification of SARS-CoV-2 in the point-of-care using digital PCR-based Dr. PCR™ Di20K COVID-19 Detection Kit without viral RNA extraction. Genes Genomics 2022; 44:617-628. [PMID: 35353341 PMCID: PMC8965542 DOI: 10.1007/s13258-022-01242-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/11/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Since COVID-19 was declared the pandemic by the WHO, it has continued to spread. There is a need for rapid, efficient, and accurate diagnostic kits and techniques to control its spread. OBJECTIVE The diagnostic capability of the qRT-PCR-based Real-Q 2019-nCoV Detection Kit and dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit was compared and evaluated. METHODS Diagnostic tests for COVID-19 were performed using two different COVID-19 kits and 301 individual specimens with confirmed COVID-19 positive/negative at the government-accredited medical institution. Assessment of diagnostic capability was measured through diagnostic sensitivity, specificity, Cohen's Kappa coefficient, and dilutional linearity tests. RESULTS The COVID-19 diagnostic test results using two kits and 301 individual specimens perfectly matched the pre-diagnosis results of the medical institution. In addition, the measurement results of diagnostic sensitivity and specificity were "1", indicating high diagnostic capability. Cohen's Kappa coefficient value is "1", which means that the diagnosis concordance between the two kits is "Almost Perfect". As a result of dilutional linearity tests to evaluate their detection capability, both kits were measured with very high detection reliability. CONCLUSION Here, we propose that the dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit has the advantages of the dPCR method reported in the previous study and is suitable for point-of-care testing (POCT) by overcoming the limitations of space, test time, cross-over contamination, and biosafety due to omitting RNA extraction process.
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Affiliation(s)
- Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea
| | - Cherl-Joon Lee
- Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Yong-Moon Lee
- Department of Pathology, Dankook University College of Medicine, Chenonan, 31116, Republic of Korea
| | - Young-Bong Choi
- Department of Chemistry, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea.
- Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
- DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan, 31116, Republic of Korea.
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22
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Abstract
Digital PCR (dPCR) surpasses the performance of earlier PCR formats because of highly precise, absolute quantification and other unique merits. A simple thermocycling approach and durable microcarrier are of great value for dPCR advancement and application. Herein, a near-infrared (NIR) controlled thermocycling approach by embedding magnetic graphene oxide (GO) composite into the agarose microcarriers is developed. The core-shell composite is constructed by sequentially encapsulating GO and silica outside the magnetic nanocores. Benefiting from these additives, the resultant composite agarose gains appealing features as light-driven temperature changing, switchable gel-sol phase transforming, biocompatibility, and magnetic traction. By further emulsifying into droplets via the microfluidics method, the influence of typical parameters including material loading amount, laser intensity, and droplet diameter at various ranges is investigated for assembling microcarriers with different responsiveness. Then a paradigm of the NIR program can be easily tailored for PCR thermocycling. Finally, the feasibility of the approach is verified by detecting statistically diluted Klebsiella pneumoniae DNA samples, from 0.1 to 2 copies per drop. It is anticipated that this method has promising prospects for dPCR-based and other temperature-controlled applications.
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Affiliation(s)
- Lexiang Zhang
- Joint Centre of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) & Wenzhou Institute-University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Parvin Rokshana
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) & Wenzhou Institute-University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Yunru Yu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) & Wenzhou Institute-University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Yuanjin Zhao
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) & Wenzhou Institute-University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) & Wenzhou Institute-University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
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23
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Hasanau T, Pisarev E, Kisil O, Nonoguchi N, Le Calvez-Kelm F, Zvereva M. Detection of TERT Promoter Mutations as a Prognostic Biomarker in Gliomas: Methodology, Prospects, and Advances. Biomedicines 2022; 10:728. [PMID: 35327529 PMCID: PMC8945783 DOI: 10.3390/biomedicines10030728] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
This article reviews the existing approaches to determining the TERT promoter mutational status in patients with various tumoral diseases of the central nervous system. The operational characteristics of the most common methods and their transferability in medical practice for the selection or monitoring of personalized treatments based on the TERT status and other related molecular biomarkers in patients with the most common tumors, such as glioblastoma, oligodendroglioma, and astrocytoma, are compared. The inclusion of new molecular markers in the course of CNS clinical management requires their rapid and reliable assessment. Availability of molecular evaluation of gliomas facilitates timely decisions regarding patient follow-up with the selection of the most appropriate treatment protocols. Significant progress in the inclusion of molecular biomarkers for their subsequent clinical application has been made since 2016 when the WHO CNS classification first used molecular markers to classify gliomas. In this review, we consider the methodological approaches used to determine mutations in the promoter region of the TERT gene in tumors of the central nervous system. In addition to classical molecular genetical methods, other methods for determining TERT mutations based on mass spectrometry, magnetic resonance imaging, next-generation sequencing, and nanopore sequencing are reviewed with an assessment of advantages and disadvantages. Beyond that, noninvasive diagnostic methods based on the determination of the mutational status of the TERT promoter are discussed.
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Affiliation(s)
- Tsimur Hasanau
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Eduard Pisarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Kisil
- Gause Institute of New Antibiotics, 119021 Moscow, Russia;
| | - Naosuke Nonoguchi
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, Takatsuki 569-8686, Japan;
| | - Florence Le Calvez-Kelm
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), 69372 Lyon, France;
| | - Maria Zvereva
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Abstract
The accurate assessment of Erwinia amylovora live cell populations in fire blight cankers by classic microbiology methods has major limitations. Some of them are the presence of competitive microbiota in samples that inhibit E. amylovora's growth and the release of toxic compounds by plant material during sample processing, which may hamper the pathogen's ability to form colonies on solid media. Digital PCR (dPCR) combined with the photo-reactive DNA-binding dye propidium monoazide (PMA) allows selective detection and quantification of live E. amylovora cells in woody samples while overcoming the constraints of culture-dependent methods. This work describes a reliable viability dPCR procedure to determine E. amylovora live cell concentrations in fire blight cankers from pome fruit trees. This protocol can be adapted for the analysis of other types of plant material and enables investigation of ecological, epidemiological, and management significance of cankers as a relatively underexplored part of the fire blight disease cycle.
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Affiliation(s)
- Ricardo Delgado Santander
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Hudson Valley Research Laboratory, Highland, NY, USA
| | - Katarina Gašić
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Hudson Valley Research Laboratory, Highland, NY, USA
- Institute for Plant Protection and Environment, Department of Plant Diseases, Laboratory for Phytopathology, Belgrade, Serbia
| | - Srđan Goran Aćimović
- CenterVirginia Polytechnic Institute and State University, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research and Extension Center, Winchester, VA, USA.
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25
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Morcia C, Bergami R, Scaramagli S, Delogu C, Andreani L, Carnevali P, Tumino G, Ghizzoni R, Terzi V. A Digital PCR Assay to Quantify the Percentages of Hulled vs. Hulless Wheat in Flours and Flour-Based Products. Biology (Basel) 2021; 10:biology10111138. [PMID: 34827131 PMCID: PMC8614899 DOI: 10.3390/biology10111138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Several food products, made from hulled wheats, are now offered by the market, ranging from grains and pasta to flour and bakery products. The possibility of verifying the authenticity of wheat species used at any point in the production chain is relevant, in defense of both producers and consumers. A chip digital PCR assay has been developed to detect and quantify percentages of hulless (i.e., common and durum wheat) and hulled (i.e., einkorn, emmer and spelt) wheats in grains, flours and food products. The assay has been designed on a polymorphism in the miRNA172 target site of the AP2-5 transcription factor localized on chromosome 5A and involved in wheat spike morphogenesis and grain threshability. The assay has been evaluated even in a real-time PCR system to assess its applicability and to compare the analytical costs between dPCR and real-time PCR approaches.
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Affiliation(s)
- Caterina Morcia
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy; (C.M.); (R.G.)
| | - Raffaella Bergami
- Coop Italia, Via del Lavoro, 6/8, I-40033 Casalecchio di Reno, BO, Italy; (R.B.); (S.S.)
| | - Sonia Scaramagli
- Coop Italia, Via del Lavoro, 6/8, I-40033 Casalecchio di Reno, BO, Italy; (R.B.); (S.S.)
| | - Chiara Delogu
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, LO, Italy; (C.D.); (L.A.)
| | - Lorella Andreani
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, LO, Italy; (C.D.); (L.A.)
| | | | - Giorgio Tumino
- Plant Breeding, Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Roberta Ghizzoni
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy; (C.M.); (R.G.)
| | - Valeria Terzi
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy; (C.M.); (R.G.)
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26
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Whale AS, von der Heide EK, Kohlenberg M, Brinckmann A, Baedker S, Karalay O, Fernandez-Gonzalez A, Busby EJ, Bustin SA, Hauser H, Missel A, O'Sullivan DM, Huggett JF, Pfaffl MW, Nolan T. Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics. Methods 2021; 201:5-14. [PMID: 34454016 PMCID: PMC8387146 DOI: 10.1016/j.ymeth.2021.08.006] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious, acute respiratory disease caused mainly by person-to-person transmission of the coronavirus SARS-CoV-2. Its emergence has caused a world-wide acute health crisis, intensified by the challenge of reliably identifying individuals likely to transmit the disease. Diagnosis is hampered by the many unknowns surrounding this disease, including those relating to infectious viral burden. This uncertainty is exacerbated by disagreement surrounding the clinical relevance of molecular testing using reverse transcription quantitative PCR (RT-qPCR) for the presence of viral RNA, most often based on the reporting of quantification cycles (Cq), which is also termed the cycle threshold (Ct) or crossing point (Cp). Despite it being common knowledge that Cqs are relative values varying according to a wide range of different parameters, there have been efforts to use them as though they were absolute units, with Cqs below an arbitrarily determined value, deemed to signify a positive result and those above, a negative one. Our results investigated the effects of a range of common variables on Cq values. These data include a detailed analysis of the effect of different carrier molecules on RNA extraction. The impact of sample matrix of buccal swabs and saliva on RNA extraction efficiency was demonstrated in RT-qPCR and the impact of potentially inhibiting compounds in urine along with bile salts were investigated in RT-digital PCR (RT-dPCR). The latter studies were performed such that the impact on the RT step could be separated from the PCR step. In this way, the RT was shown to be more susceptible to inhibitors than the PCR. Together, these studies demonstrate that the consequent variability of test results makes subjective Cq cut-off values unsuitable for the identification of infectious individuals. We also discuss the importance of using reliable control materials for accurate quantification and highlight the substantial role played by dPCR as a method for their development.
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Affiliation(s)
- Alexandra S Whale
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Eva K von der Heide
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Max Kohlenberg
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Anja Brinckmann
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Silke Baedker
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | - Oezlem Karalay
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | | | - Eloise J Busby
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Stephen A Bustin
- Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK.
| | - Heiko Hauser
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Andreas Missel
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | - Denise M O'Sullivan
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
| | - Tania Nolan
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany; Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK.
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27
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Borchardt MA, Boehm AB, Salit M, Spencer SK, Wigginton KR, Noble RT. The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology. Environ Sci Technol 2021; 55:10210-10223. [PMID: 34286966 DOI: 10.1021/acs.est.1c01767/suppl_file/es1c01767_si_001.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.
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Affiliation(s)
- Mark A Borchardt
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, California 94305, United States
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Susan K Spencer
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Rachel T Noble
- Insitute for the Environment, University of North Carolina, Chapel Hill, North Carolina 27517, United States
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28
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Borchardt MA, Boehm AB, Salit M, Spencer SK, Wigginton KR, Noble RT. The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology. Environ Sci Technol 2021; 55:10210-10223. [PMID: 34286966 DOI: 10.1021/acs.est.1c01767] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.
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Affiliation(s)
- Mark A Borchardt
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, California 94305, United States
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Susan K Spencer
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Rachel T Noble
- Insitute for the Environment, University of North Carolina, Chapel Hill, North Carolina 27517, United States
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29
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Brandolini M, Taddei F, Marino MM, Grumiro L, Scalcione A, Turba ME, Gentilini F, Fantini M, Zannoli S, Dirani G, Sambri V. Correlating qRT-PCR, dPCR and Viral Titration for the Identification and Quantification of SARS-CoV-2: A New Approach for Infection Management. Viruses 2021; 13:v13061022. [PMID: 34071726 PMCID: PMC8229388 DOI: 10.3390/v13061022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/05/2021] [Accepted: 05/26/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Wuhan, China, in late 2019 and is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) represents the gold standard for diagnostic assays even if it cannot precisely quantify viral RNA copies. Thus, we decided to compare qRT-PCR with digital polymerase chain reaction (dPCR), which is able to give an accurate number of RNA copies that can be found in a specimen. However, the aforementioned methods are not capable to discriminate if the detected RNA is infectious or not. For this purpose, it is necessary to perform an endpoint titration on cell cultures, which is largely used in the research field and provides a tissue culture infecting dose per mL (TCID50/mL) value. Both research and diagnostics call for a model that allows the comparison between the results obtained employing different analytical methods. The aim of this study is to define a comparison among two qRT-PCR protocols (one with preliminary RNA extraction and purification and an extraction-free qRT-PCR), a dPCR and a titration on cell cultures. The resulting correlations yield a faithful estimation of the total number of RNA copies and of the infectious viral burden from a Ct value obtained with diagnostic routine tests. All these estimations take into consideration methodological errors linked to the qRT-PCR, dPCR and titration assays.
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Affiliation(s)
- Martina Brandolini
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Francesca Taddei
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Maria Michela Marino
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Laura Grumiro
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Agata Scalcione
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | | | - Fabio Gentilini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy;
| | - Michela Fantini
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Silvia Zannoli
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Giorgio Dirani
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Hub Laboratory, 47522 Pievesestina, Italy; (M.B.); (F.T.); (M.M.M.); (L.G.); (A.S.); (M.F.); (S.Z.); (G.D.)
- Department of Experimental, Diagnostic and Specialty Medicine—DIMES, Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy
- Correspondence:
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van Snippenberg W, Gleerup D, Rutsaert S, Vandekerckhove L, De Spiegelaere W, Trypsteen W. Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA. Methods 2021:S1046-2023(21)00132-8. [PMID: 33992770 DOI: 10.1016/j.ymeth.2021.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 01/10/2023] Open
Abstract
The development of an HIV-1 cure is hampered by the existence of a persistent (latent) reservoir that contains a small proportion of replication-competent intact proviruses which refuels viral replication upon treatment discontinuation. Therefore, an accurate evaluation and quantification of these (intact) proviruses is essential to determine the efficacy of HIV-1 cure strategies which aim to eliminate this reservoir. Here, we present two triplex digital PCR assays which resulted from a combination of two existing methods, the IPDA (a 2-colour digital PCR based method) and Q4PCR assays (4 colour qPCR method), and tested the functionality on a three-colour digital PCR platform. In the present paper, we provide a step-by-step experimental protocol for these triplex digital PCR assays and validate their performance on a latently infected Jurkat cell-line model and HIV-1 patient samples. Our data demonstrates the potential and flexibility of increasing the number of subgenomic regions of HIV-1 within the IPDA to acquire sensitive detection of the HIV-1 reservoir while benefitting from the advantages of a dPCR setup.
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Fava C, Bernardi S, Gottardi EM, Lorenzatti R, Galeotti L, Ceccherini F, Cordoni F, Daraio F, Giugliano E, Jovanovski A, Petiti J, Varotto M, Barberio D, Rege-Cambrin G, Berchialla P, Sciannameo V, Malagola M, Saglio G, Russo D. Alignment of Qx100/Qx200 Droplet Digital (Bio-Rad) and QuantStudio 3D (Thermofisher) Digital PCR for Quantification of BCR-ABL1 in Ph+ Chronic Myeloid Leukemia. Diseases 2021; 9:35. [PMID: 34062996 DOI: 10.3390/diseases9020035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 01/06/2023] Open
Abstract
In recent years, the digital polymerase chain reaction has received increasing interest as it has emerged as a tool to provide more sensitive and accurate detection of minimal residual disease. In order to start the process of data alignment, we assessed the consistency of the BCR-ABL1 quantification results of the analysis of 16 RNA samples at different levels of disease. The results were obtained by two different laboratories that relied on The Qx100/Qx200 Droplet Digital PCR System (Bio-Rad) and Quant Studio 3D dPCR System (Thermofisher) platforms. We assessed the compatibility between the estimated values by linear regression, Bland-Altman bias-plot, and Mann-Whitney nonparametric test. The results confirmed the compatibility of the measures, allowing us tocompute an 'alignment factor' (AF), equal to 1.41, which was further validated by a different series of experiments. We conclude that the performed measurements by the two laboratories are comparable, and also equalized through the introduction of an alignment factor.
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Du Cheyne C, Chen Y, De Craene J, Thas O, De Spiegelaere W. Development of a 3':5' digital PCR assay to determine horse mRNA integrity. Anal Biochem 2021; 626:114217. [PMID: 33939972 DOI: 10.1016/j.ab.2021.114217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Here we developed a triplex digital PCR (dPCR) 3':5' assay for assessing RNA integrity in equine samples as rapid and simple alternative to RT-qPCR. This dPCR assay not only provides a straight forward analysis of the mRNA integrity, but also of its quantity.
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Wang Y, Gao W, Wu M, Zhang X, Liu W, Zhou Y, Jia C, Cong H, Chen X, Zhao J. EGFR mutation detection of lung circulating tumor cells using a multifunctional microfluidic chip. Talanta 2021; 225:122057. [PMID: 33592778 DOI: 10.1016/j.talanta.2020.122057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/20/2022]
Abstract
Microfluidics has become a reliable platform for circulating tumor cells (CTCs) detection because of its high integration, small size, low consumption of reagents and rapid response. Here, we developed a multifunctional microfluidic device consists of three parts, including CTCs capture area, single-layer membrane valves area, and microcavity nucleic acid detection and analysis region based on digital polymerase chain reaction (dPCR), allowing CTCs capture, lysis, and genetic characterization to be performed on a single chip. The CTCs capture chip is coupled to the nucleic acid detection chip via a control valve. CTCs were firstly trapped in the CTC capture area, and then lysed using proteinase K to release nucleic acids. Subsequently CTCs lysate was transferred into nucleic acid detection area consisting of 12800 micro-cavity chambers for nucleic acids detection. To evaluate the performance of this chip, this study detected EGFR-L858R mutation in lung cancer cell lines H1975 and A549 cells, as well as leukocytes from normal donors. The results showed that positive signals were only observed in H1975 cells, and the detected value had a high linear relationship with the expected value (R2 = 0.9897). In conclusion, this multi-functional microfluidic chip that integrates CTCs capture, lysis and nucleic acid detection can successfully detect gene mutations in CTCs, providing reference for tumor-targeted drugs and precise diagnosis and treatment.
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Tozzo P, Delicati A, Zambello R, Caenazzo L. Chimerism Monitoring Techniques after Hematopoietic Stem Cell Transplantation: An Overview of the Last 15 Years of Innovations. Diagnostics (Basel) 2021; 11:diagnostics11040621. [PMID: 33808342 PMCID: PMC8065704 DOI: 10.3390/diagnostics11040621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 01/14/2023] Open
Abstract
Chimerism analysis is a well-established method for monitoring the state of hematopoietic stem cell transplantation (HSCT) over time by analyzing peripheral blood or bone marrow samples of the recipient in several malignant and non-malignant hematologic diseases. From a clinical point of view, a continuous monitoring is fundamental for an effective early therapeutic intervention. This paper provides a comparative overview of the main molecular biology techniques which can be used to study chimerism after bone marrow transplantation, focusing on their advantages and disadvantages. According to the examined literature, short tandem repeats (STR) analysis through simple PCR coupled with capillary electrophoresis (STR-PCR) is the most powerful method which guarantees a high power of differentiation between different individuals. However, other methods such as real-time quantitative PCR (qPCR), digital PCR (dPCR), and next-generation sequencing (NGS) technology were developed to overcome the technical limits of STR-PCR. In particular, these other techniques guarantee a higher sensitivity, which allows for the detection of chimerism at an earlier stage, hence expanding the window for therapeutic intervention. After a comparative evaluation of the various techniques, it seems clear that STR-PCR still remains the gold standard option for chimerism study, even if it is likely that both dPCR and NGS could supplement or even replace the common methods of STR analysis.
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Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy; (A.D.); (L.C.)
- Correspondence: ; Tel.: +39-049-827-2235
| | - Arianna Delicati
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy; (A.D.); (L.C.)
| | - Renato Zambello
- Department of Medicine (DIMED), Hematology and Clinical Immunology Section, Padova University School of Medicine, 35121 Padova, Italy;
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy; (A.D.); (L.C.)
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Huggett JF. The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clin Chem 2021; 66:1012-1029. [PMID: 32746458 DOI: 10.1093/clinchem/hvaa125] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.
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Vitale SR, Helmijr JA, Gerritsen M, Coban H, van Dessel LF, Beije N, van der Vlugt-Daane M, Vigneri P, Sieuwerts AM, Dits N, van Royen ME, Jenster G, Sleijfer S, Lolkema M, Martens JWM, Jansen MPHM. Detection of tumor-derived extracellular vesicles in plasma from patients with solid cancer. BMC Cancer 2021; 21:315. [PMID: 33761899 PMCID: PMC7992353 DOI: 10.1186/s12885-021-08007-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 10/27/2020] [Accepted: 03/03/2021] [Indexed: 02/08/2023] Open
Abstract
Background Extracellular vesicles (EVs) are actively secreted by cells into body fluids and contain nucleic acids of the cells they originate from. The goal of this study was to detect circulating tumor-derived EVs (ctEVs) by mutant mRNA transcripts (EV-RNA) in plasma of patients with solid cancers and compare the occurrence of ctEVs with circulating tumor DNA (ctDNA) in cell-free DNA (cfDNA). Methods For this purpose, blood from 20 patients and 15 healthy blood donors (HBDs) was collected in different preservation tubes (EDTA, BCT, CellSave) and processed into plasma within 24 h from venipuncture. EVs were isolated with the ExoEasy protocol from this plasma and from conditioned medium of 6 cancer cell lines and characterized according to MISEV2018-guidelines. RNA from EVs was isolated with the ExoRNeasy protocol and evaluated for transcript expression levels of 96 genes by RT-qPCR and genotyped by digital PCR. Results Our workflow applied on cell lines revealed a high concordance between cellular mRNA and EV-RNA in expression levels as well as variant allele frequencies for PIK3CA, KRAS and BRAF. Plasma CD9-positive EV and GAPDH EV-RNA levels were significantly different between the preservation tubes. The workflow detected only ctEVs with mutant transcripts in plasma of patients with high amounts (> 20%) of circulating tumor DNA (ctDNA). Expression profiling showed that the EVs from patients resemble healthy donors more than tumor cell lines supporting that most EVs are derived from healthy tissue. Conclusions We provide a workflow for ctEV detection by spin column-based generic isolation of EVs and PCR-based measurement of gene expression and mutant transcripts in EV-RNA derived from cancer patients’ blood plasma. This workflow, however, detected tumor-specific mutations in blood less often in EV-RNA than in cfDNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08007-z.
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Affiliation(s)
- Silvia R Vitale
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Clinical and Experimental Medicine - Center for Experimental Oncology and Hematology, University of Catania, Catania, Italy
| | - Jean A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Marjolein Gerritsen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hicret Coban
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisanne F van Dessel
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Nick Beije
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Michelle van der Vlugt-Daane
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine - Center for Experimental Oncology and Hematology, University of Catania, Catania, Italy
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Martijn Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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Gliddon HD, Kaforou M, Alikian M, Habgood-Coote D, Zhou C, Oni T, Anderson ST, Brent AJ, Crampin AC, Eley B, Heyderman R, Kern F, Langford PR, Ottenhoff THM, Hibberd ML, French N, Wright VJ, Dockrell HM, Coin LJ, Wilkinson RJ, Levin M. Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification. Front Immunol 2021; 12:637164. [PMID: 33763081 PMCID: PMC7982854 DOI: 10.3389/fimmu.2021.637164] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 12/02/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)-digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2-100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3-100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.
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Affiliation(s)
- Harriet D Gliddon
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,National Public Health Speciality Training Programme, South West, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom.,Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Tolu Oni
- School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzanne T Anderson
- Brighton and Sussex Medical School, Brighton, United Kingdom.,Brighton and Malawi Liverpool Wellcome Trust Unit, Blantyre, Malawi
| | - Andrew J Brent
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Chilumba, Malawi.,London School of Hygiene & Tropical Medicine, London, United Kingdom.,Karonga Prevention Study, Chilumba, Malawi
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Robert Heyderman
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Florian Kern
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom.,Brighton and Sussex University Hospitals National Health Service (NHS) Trust, Brighton, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Tropical and Infectious Disease Unit, Royal Liverpool and Broadgreen University Hospitals National Health Service (NHS) Trust, Liverpool, United Kingdom.,Centre for Global Vaccine Research, Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Victoria J Wright
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Hazel M Dockrell
- Department of Immunology and Infection, and Tuberculosis (TB) Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Imperial College London, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michael Levin
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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Niu C, Dong L, Gao Y, Zhang Y, Wang X, Wang J. Quantitative analysis of RNA by HPLC and evaluation of RT- dPCR for coronavirus RNA quantification. Talanta 2021; 228:122227. [PMID: 33773731 PMCID: PMC7898971 DOI: 10.1016/j.talanta.2021.122227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/31/2021] [Accepted: 02/13/2021] [Indexed: 01/23/2023]
Abstract
Nucleic acid detection and quantification have been known to be important at various fields, from genetically modified organisms and gene expression to virus detection. For DNA molecules, digital PCR has been developed as an absolute quantification method which is not dependent on external calibrators. While when it comes to RNA molecules, reverse transcription (RT) step must be taken before PCR amplification to obtain cDNA. With different kinds of reverse transcriptase (RTase) and RT reaction conditions being used in laboratory assays, the efficiency of RT process differs a lot which led variety in quantification results of RNA molecules. In this study, we developed HPLC method combined with enzymatic digestion of RNA to nucleotides for quantification of RNA without RT process. This method was metrologically traceable to four nuceloside monophosphate (NMP) Certification Reference Materials of National Institute of Metrology, China (NIMC) for insurance of accuracy. The established method was used to evaluate the reverse transcription digital polymerase chain reaction (RT-dPCR) of three target genes of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) RNA, including open reading frame 1ab (ORF1ab), nucleocapsid protein (N) and envelope protein (E) gene. Three available RT kits had been evaluated and disparities were observed for the RT efficiency varied from 9% to 182%. It is thus demonstrated that HPLC combined with enzymatic digestion could be a useful method to quantify RNA molecules and evaluate RT efficiency. It is suggested that RT process should be optimized and identified in RNA quantification assays.
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Affiliation(s)
- Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Jing Wang
- Department of Metrological Services and Quality System, National Institute of Metrology, Beijing, 100013, China
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Liu H, Lei Y. A critical review: Recent advances in “digital” biomolecule detection with single copy sensitivity. Biosens Bioelectron 2021; 177:112901. [PMID: 33472132 PMCID: PMC7836387 DOI: 10.1016/j.bios.2020.112901] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
Detection of a single biomolecule, ranging from nucleic acids, proteins, viruses to bacteria, is of paramount importance in various fields including biology, environment, food and agriculture industry, public health, and medicine. With the understanding of the biological functions of these biomolecules (or bioparticles) and their impacts on public health, environmental pollution, and food safety, advanced detection techniques are unprecedentedly demanded for their early and/or sensitive detection. In this critical review, a series of elegant research about digital detection of biomolecules with potential single copy sensitivity is reviewed and summarized with the focus on the design principle and the innovation of how to accomplish the “digital” detection concept. Starting with a brief introduction on the importance of digital detection, recent advances in “digital” biomolecule detection with single copy sensitivity are grouped and discussed based on the difference of signal reporting systems, including surrogate signal development for “digital” detection, direct visualization for “digital” detection, and nucleic acid amplification enabled “digital” detection. Interdisciplinary combination and integration of different cutting-edge techniques are also discussed with details. The review is closed with the conclusion and future trends.
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40
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Duong K, Ou J, Li Z, Lv Z, Dong H, Hu T, Zhang Y, Hanna A, Gordon S, Crynen G, Head SR, Ordoukhanian P, Wang Y. Increased sensitivity using real-time dPCR for detection of SARS-CoV-2. Biotechniques 2021; 70:7-20. [PMID: 33222514 PMCID: PMC7888512 DOI: 10.2144/btn-2020-0133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
A real-time dPCR system was developed to improve the sensitivity, specificity and quantification accuracy of end point dPCR. We compared three technologies - real-time qPCR, end point dPCR and real-time dPCR - in the context of SARS-CoV-2. Some improvement in limit of detection was obtained with end point dPCR compared with real-time qPCR, and the limit of detection was further improved with the newly developed real-time dPCR technology through removal of false-positive signals. Real-time dPCR showed increased linear dynamic range compared with end point dPCR based on quantitation from amplification curves. Real-time dPCR can improve the performance of TaqMan assays beyond real-time qPCR and end point dPCR with better sensitivity and specificity, absolute quantification and a wider linear range of detection.
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Affiliation(s)
- Kyra Duong
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
| | - Jiajia Ou
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Zhaoliang Li
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Zhaoqing Lv
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Hao Dong
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Tao Hu
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Yunyun Zhang
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Ava Hanna
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
| | - Skyler Gordon
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Gogce Crynen
- Bioinformatics Core Facility, Scripps Research, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Steven R Head
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Phillip Ordoukhanian
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Yan Wang
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
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Rashid H, Hossain B, Siddiqua T, Kabir M, Noor Z, Ahmed M, Haque R. Fecal MicroRNAs as Potential Biomarkers for Screening and Diagnosis of Intestinal Diseases. Front Mol Biosci 2020; 7:181. [PMID: 32850969 PMCID: PMC7426649 DOI: 10.3389/fmolb.2020.00181] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of conserved endogenous, small non-coding RNA molecules with a length of 18–25 nucleotides that regulate gene expression by RNA interference processes, including mRNA chopping, mRNA deadenylation, and translation inhibition. miRNAs maintain the physiological functions of the intestine and are instrumental in gut pathogenesis. miRNAs play an important role in intercellular communication and are present in all body fluids, including stools with different composition and concentrations. However, under diseased conditions, miRNAs are aberrantly expressed and act as negative regulators of gene expression. The stable and differentially expressed miRNAs in stool enables miRNAs to be used as potential biomarkers for screening of various intestinal diseases. In this review, we summarize the expressed miRNA profile in stool and highlight miRNAs as biomarkers with potential clinical and diagnostic applications, and we aim to address the prospects for recent advanced techniques for screening miRNA in diagnosis and prognosis of intestinal disorders.
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Affiliation(s)
- Humaira Rashid
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Biplob Hossain
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Towfida Siddiqua
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mamun Kabir
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Zannatun Noor
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mamun Ahmed
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Rashidul Haque
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
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Aralar A, Yuan Y, Chen K, Geng Y, Ortiz Velez D, Sinha M, Lawrence SM, Fraley SI. Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting. J Clin Microbiol 2020; 58:e00325-20. [PMID: 32295887 DOI: 10.1128/JCM.00325-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/05/2020] [Indexed: 12/23/2022] Open
Abstract
Applying digital PCR (dPCR) technology to challenging clinical and industrial detection tasks has become more prevalent because of its capability for absolute quantification and rare target detection. However, practices learned from quantitative PCR (qPCR) that promote assay robustness and wide-ranging utility are not readily applied in dPCR. These include internal amplification controls to account for false-negative reactions and amplicon high-resolution melt (HRM) analysis to distinguish true positives from false positives. Incorporation of internal amplification controls in dPCR is challenging because of the limited fluorescence channels available on most machines, and the application of HRM analysis is hindered by the separation of heating and imaging functions on most dPCR systems. We use a custom digital HRM platform to assess the utility of HRM-based approaches for mitigation of false positives and false negatives in dPCR. We show that detection of an exogenous internal control using dHRM analysis reduces the inclusion of false-negative partitions, changing the calculated DNA concentration up to 52%. The integration of dHRM analysis enables classification of partitions that would otherwise be considered ambiguous "rain," which accounts for up to ∼3% and ∼10% of partitions in intercalating dye and hydrolysis probe dPCR, respectively. We focused on developing an internal control method that would be compatible with broad-based microbial detection in dPCR-dHRM. Our approach can be applied to a number of DNA detection methods including microbial profiling and may advance the utility of dPCR in clinical applications where accurate quantification is imperative.
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Sponziello M, Brunelli C, Verrienti A, Grani G, Pecce V, Abballe L, Ramundo V, Damante G, Russo D, Lombardi CP, Durante C, Rossi ED, Straccia P, Fadda G, Filetti S. Performance of a dual-component molecular assay in cytologically indeterminate thyroid nodules. Endocrine 2020; 68:458-465. [PMID: 32232767 DOI: 10.1007/s12020-020-02271-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/14/2020] [Indexed: 10/24/2022]
Abstract
PURPOSE Deciding whether patients with a cytologically indeterminate thyroid nodule should be referred for surgery or for active surveillance is an important challenge for clinicians. The aim of this study was to evaluate the performance of a novel dual-component molecular assay as an ancillary molecular method for resolving indeterminate thyroid nodule cytology. METHODS We selected 156 thyroid nodules from those that had undergone fine-needle aspiration processed by liquid-based cytology and surgical resection between June 2016 and December 2017. The sample set included 63 nodules cytologically classified as indeterminate, and 93 other nodules randomly selected from those with non-diagnostic, benign, suspicious, or malignant cytology. Nucleic acids from each nodule were subjected to next-generation sequencing analysis for mutation detection in 23 genes and to digital polymerase chain reaction (PCR) evaluation for miR-146b-5p expression levels. RESULTS Used alone, mutation analysis in the indeterminate subset (cancer prevalence: 22.5%) displayed high sensitivity (89%) and NPV (96%). In contrast, the miR-146b-5p assay offered high specificity (93%) and PPV (93%). Combined use of both analyses improved panel performance by eliminating false-negative results. CONCLUSIONS These preliminary data suggest that a dual-component molecular test can increase the diagnostic accuracy of thyroid cytology alone by reducing the number of nodules that will be classified as indeterminate and increasing those that can be reliably classified as benign. If these findings are confirmed, this test can be considered for use in clinical practice and is expected to reduce diagnostic surgery and health care costs, and to improve patient quality of life.
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Affiliation(s)
- Marialuisa Sponziello
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Chiara Brunelli
- Division of Anatomic Pathology and Histology, Catholic University of Sacred Heart, Foundation "Agostino Gemelli" University Hospital, Rome, Italy
| | - Antonella Verrienti
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy.
| | - Giorgio Grani
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Valeria Pecce
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Luana Abballe
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Valeria Ramundo
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Giuseppe Damante
- Department of Medicine, University of Udine, 33100, Udine, Italy
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100, Catanzaro, Italy
| | - Celestino Pio Lombardi
- Division of Endocrine Surgery, Catholic University of Sacred Heart, Foundation "Agostino Gemelli" University Hospital, Rome, Italy
| | - Cosimo Durante
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
| | - Esther Diana Rossi
- Division of Anatomic Pathology and Histology, Catholic University of Sacred Heart, Foundation "Agostino Gemelli" University Hospital, Rome, Italy
| | - Patrizia Straccia
- Division of Anatomic Pathology and Histology, Catholic University of Sacred Heart, Foundation "Agostino Gemelli" University Hospital, Rome, Italy
| | - Guido Fadda
- Division of Anatomic Pathology and Histology, Catholic University of Sacred Heart, Foundation "Agostino Gemelli" University Hospital, Rome, Italy
| | - Sebastiano Filetti
- Department of Translational and Precision Medicine, "Sapienza" University of Rome, 00161, Rome, Italy
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44
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Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
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Vitale SR, Groenendijk FH, van Marion R, Beaufort CM, Helmijr JC, Jan Dubbink H, N. M. Dinjens W, Ewing-Graham PC, Smolders R, van Doorn HC, Boere IA, Berns EMJJ, Helleman J, Jansen MPHM. TP53 Mutations in Serum Circulating Cell-Free Tumor DNA As Longitudinal Biomarker for High-Grade Serous Ovarian Cancer. Biomolecules 2020; 10:biom10030415. [PMID: 32156073 PMCID: PMC7175353 DOI: 10.3390/biom10030415] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/06/2020] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to determine an optimal workflow to detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients and to define whether TP53 mutations are suitable as biomarker for disease. TP53 was investigated in tissue and archived serum from 20 HGSOC patients by a next-generation sequencing (NGS) workflow alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels and customized dPCR assays were used for tissue DNA and longitudinal cfDNAs, and Oncomine NGS panel with molecular barcoding was used for baseline cfDNAs. TP53 missense mutations were observed in 17 tissue specimens and in baseline cfDNA for 4/8 patients by AmpliSeq, 6/9 patients by Oncomine, and 4/6 patients by dPCR. Mutations in cfDNA were detected in 4/6 patients with residual disease and 3/4 patients with disease progression within six months, compared to 5/11 patients with no residual disease and 6/13 patients with progression after six months. Finally, mutations were detected at progression in 5/6 patients, but not during chemotherapy. NGS with molecular barcoding and dPCR were most optimal workflows to detect TP53 mutations in baseline and longitudinal serum cfDNA, respectively. TP53 mutations were undetectable in cfDNA during treatment but re-appeared at disease progression, illustrating its promise as a biomarker for disease monitoring.
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Affiliation(s)
- Silvia R. Vitale
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, 95123 Catania, Italy
- Correspondence: ; Tel.: +39-095-3781946
| | - Floris H. Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Corine M. Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Jean C. Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Hendrikus Jan Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Patricia C. Ewing-Graham
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Ramon Smolders
- Department of Gynaecology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.S.); (H.C.v.D.)
| | - Helena C. van Doorn
- Department of Gynaecology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.S.); (H.C.v.D.)
| | - Ingrid A. Boere
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Els M. J. J. Berns
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Jozien Helleman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Maurice P. H. M. Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
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Abstract
The recombinant Vesicular Stomatitis Virus (rVSV) is an emerging platform for viral vector-based vaccines. Promising results have been reported in clinical trials for the rVSV-ZEBOV vaccine for Ebola virus disease prevention. In this study, we describe the titration tools elaborated to assess the titre of rVSV-ZEBOV productions. • A streamlined Median Tissue Culture Infectious Dose (TCID50) assay to determine the infectious titer of this vaccine was established. • A digital polymerase chain reaction (dPCR) assay to assess the total number of viral particles present in cell-free culture supernatants of rVSV productions was developed. • These assays are used to titre rVSV-ZEBOV samples and characterize the ratio of total particles to infectious units for monitoring process robustness and product quality attributes and can be used to titre samples generated in the production of further rVSV vectors.
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Affiliation(s)
- Jean-François Gélinas
- Department of Bioengineering, McGill University, 3480 University, Montréal, Québec H3A 0E9, Canada
| | - Sascha Kiesslich
- Department of Bioengineering, McGill University, 3480 University, Montréal, Québec H3A 0E9, Canada
| | - Rénald Gilbert
- Department of Bioengineering, McGill University, 3480 University, Montréal, Québec H3A 0E9, Canada
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Amine A. Kamen
- Department of Bioengineering, McGill University, 3480 University, Montréal, Québec H3A 0E9, Canada
- Corresponding author.
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Peng C, Zheng M, Ding L, Chen X, Wang X, Feng X, Wang J, Xu J. Accurate Detection and Evaluation of the Gene-Editing Frequency in Plants Using Droplet Digital PCR. Front Plant Sci 2020; 11:610790. [PMID: 33381141 PMCID: PMC7767858 DOI: 10.3389/fpls.2020.610790] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/11/2020] [Indexed: 05/05/2023]
Abstract
Gene-editing techniques are becoming powerful tools for modifying target genes in organisms. Although several methods have been reported that detect mutations at targeted loci induced by the CRISPR/Cas system in different organisms, they are semiquantitative and have difficulty in the detection of mutants in processed food samples containing low initial concentrations of DNA and may not accurately quantify editing frequency, especially at very low frequencies in a complex polyploid plant genome. In this study, we developed a duplexed dPCR-based method for the detection and evaluation of gene-editing frequencies in plants. We described the design, performance, accurate quantification, and comparison with other detection systems. The results show that the dPCR-based method is sensitive to different kinds of gene-editing mutations induced by gene-editing. Moreover, the method is applicable to polyploid plants and processed food samples containing low initial concentrations of DNA. Compared with qPCR and NGS-based methods, the dPCR method has a lower limit of detection (LOD) of the editing frequency and a better relationship with the expected editing frequency in detecting the edited region of gene-edited rice samples. Taken together, the duplexed dPCR assay is accurate and precise, and it will be a powerful tool for the detection and evaluation of gene-editing frequencies in plants in gene-editing technology.
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Affiliation(s)
- Cheng Peng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ming Zheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Lin Ding
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoyun Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaofu Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xuping Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Junmin Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junfeng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Junfeng Xu,
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Mao X, Liu C, Tong H, Chen Y, Liu K. Principles of digital PCR and its applications in current obstetrical and gynecological diseases. Am J Transl Res 2019; 11:7209-7222. [PMID: 31934273 PMCID: PMC6943456] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Digital PCR (dPCR) is a revolutionary technique to precisely quantify nucleic acids. For its high sensitivity and specificity, this technique has been widely replicated worldwide. To verify its applicability, we reviewed all the related articles in PubMed database published before May 10, 2019. Original articles and reviews on the topics were selected. Entered key words included "digital PCR/dPCR", "advantage", "combined use", "microfluidic chip", "gynecological cancer/tumor". We found that dPCR has shown great potential in clinical operations, like tumor liquid biopsy, non-invasive prenatal diagnosis, microorganism detection, and next-generation sequencing library quality-control.
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Affiliation(s)
- Xiaodong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Chao Liu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Hua Tong
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Yajun Chen
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Kangsheng Liu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
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49
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Saxena D, Sheikh S, Kao G, Binder ZA, Alonso-Basanta M, O'Rourke DM, Nasrallah MP, Dorsey JF. Rapid and ultrasensitive digital PCR ( dPCR) profiling of EGFRvIII in tumor cells and tissues. Neurooncol Adv 2019; 1:vdz030. [PMID: 31807732 PMCID: PMC6881905 DOI: 10.1093/noajnl/vdz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Amplification of the epidermal growth factor receptor (EGFR) gene is commonly found in glioblastoma (GBM). About 57% GBM overexpresses EGFR and are associated with tumor progression, poor prognosis, and shorter life expectancy. Molecular profiling of solid tumors usually takes several weeks and may be biased by intrinsic tumor heterogeneity. Methods The unique sequence created by the fusion of exon 1 and exon 8 in EGFRvIII was used to guide the design of primers and a Minor Groove Binder (MGB) probe. Extracted total RNA was reverse transcribed and pre-amplified by PCR, followed by detection of the EGFRvIII mutation by dPCR. Results The lowest limit of quantification of our EGFRvIII assay was 0.003%. The EGFRvIII variant was identified in patient-derived glioma neurosphere cell lines, xenograft mouse model, and patient-derived tumor specimens. The overall workflow can be accomplished within 24 hours. In certain samples, EGFRvIII was detected when next-generation sequencing was unable to identify the variant. This finding highlights the ability of the dPCR assay to identify EGFRvIII mutations in heterogeneous solid tumors such as GBM in a rapid fashion by profiling samples from spatially distinct areas of tumors from the same patient. Conclusions In this study, we developed a highly sensitive digital PCR (dPCR) platform and leveraged our assay to detect the variant III alteration of EGFR (EGFRvIII) and amplified EGFR in patient-derived glioma neurosphere cell lines, orthotopic xenograft GBM mouse models, and patient-derived tumor specimens in less than 24 hours from minute quantities of starting material.
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Affiliation(s)
- Deeksha Saxena
- Department of Radiation Oncology.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | | | - Gary Kao
- Department of Radiation Oncology
| | - Zev A Binder
- Department of Neurosurgery.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | | | - Donald M O'Rourke
- Department of Neurosurgery.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, Division of Neuropathology.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | - Jay F Dorsey
- Department of Radiation Oncology.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
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50
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Cresswell F, Lange C, van Crevel R. Improving the diagnosis of tuberculous meningitis: good, but not good enough. Clin Microbiol Infect 2019; 26:134-136. [PMID: 31639473 DOI: 10.1016/j.cmi.2019.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/06/2019] [Accepted: 10/09/2019] [Indexed: 11/29/2022]
Affiliation(s)
- F Cresswell
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK; Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda; Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - C Lange
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany; German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Germany; Department of Internal Medicine, Karolinska Institute, Stockholm, Sweden.
| | - R van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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