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Luo Y, Hu Q, Yu Y, Lyu W, Shen F. Experimental investigation of confinement effect in single molecule amplification via real-time digital PCR on a multivolume droplet array SlipChip. Anal Chim Acta 2024; 1304:342541. [PMID: 38637051 DOI: 10.1016/j.aca.2024.342541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Digital polymerase chain reaction (digital PCR) is an important quantitative nucleic acid analysis method in both life science research and clinical diagnostics. One important hypothesis is that by physically constraining a single nucleic acid molecule in a small volume, the relative concentration can be increased therefore further improving the analysis performance, and this is commonly defined as the confinement effect in digital PCR. However, experimental investigation of this confinement effect can be challenging since it requires a microfluidic device that can generate partitions of different volumes and an instrument that can monitor the kinetics of amplification. (96). RESULTS Here, we developed a real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip) that can generate droplet of 125 nL, 25 nL, 5 nL, and 1 nL by a simple "load-slip" operation. In the digital region, by reducing the volume, the relative concentration is increased, the amplification kinetic can be accelerated, and the time to reach the fluorescence threshold, or Cq value, can be reduced. When the copy number per well is much higher than one, the relative concentration is independent of the partition volume, thus the amplification kinetics are similar in different volume partitions. This system is not limited to studying the kinetics of digital nucleic acid amplification, it can also extend the dynamic range of the digital nucleic acid analysis by additional three orders of magnitude by combining a digital and an analog quantification algorithm. (140). SIGNIFICANCE In this study, we experimentally investigated for the first time the confinement effect in the community of digital PCR via a new real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip). And a wider dynamic range of quantification methods compared to conventional digital PCR was validated by this system. This system provides emerging opportunities for life science research and clinical diagnostics. (63).
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Affiliation(s)
- Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China.
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2
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Ganguly R, Lee CS. A Poisson-Independent Approach to Precision Nucleic Acid Quantification in Microdroplets. ACS APPLIED BIO MATERIALS 2024; 7:3441-3451. [PMID: 38658190 DOI: 10.1021/acsabm.4c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Digital PCR (dPCR) has become indispensable in nucleic acid (NA) detection across various fields, including viral diagnostics and mutant detection. However, misclassification of partitions in dPCR can significantly impact accuracy. Despite existing methods to minimize misclassification bias, accurate classification remains elusive, especially for nonamplified target partitions. To address these challenges, this study introduces an innovative microdroplet-based competitive PCR platform for nucleic acid quantification in microfluidic devices independent of Poisson statistics. In this approach, the target concentration (T) is determined from the concentration of competitor DNA (C) at the equivalence point (E.P.), where C/T is 1. Competitive PCR ensures that the ratio of target to competitor DNA remains constant during amplification, reflected in the resultant fluorescence intensity, allowing the quantification of target DNA concentration at the equivalence point. The unique amplification technique eliminates Poisson distribution, addressing misclassification challenges. Additionally, our approach reduces the need for post-PCR procedures and shortens analytical time. We envision this platform as versatile, reproducible, and easily adaptable for driving significant progress in molecular biology and diagnostics.
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Affiliation(s)
- Reya Ganguly
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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3
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Cleveland MH, He HJ, Milavec M, Bae YK, Vallone PM, Huggett JF. Digital PCR for the characterization of reference materials. Mol Aspects Med 2024; 96:101256. [PMID: 38359699 DOI: 10.1016/j.mam.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.
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Affiliation(s)
- Megan H Cleveland
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
| | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Peter M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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4
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González-de-Olano D, Navarro-Navarro P, Muñoz-González JI, Sánchez-Muñoz L, Henriques A, de-Andrés-Martín A, Peralta-Arjonilla D, Mayado A, Jara-Acevedo M, García-Montero AC, Orfao A, Álvarez-Twose I. Clinical impact of the TPSAB1 genotype in mast cell diseases: A REMA study in a cohort of 959 individuals. Allergy 2024; 79:711-723. [PMID: 37818990 DOI: 10.1111/all.15911] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND A close association between hereditary alpha-tryptasemia (HAT) and mast cell (MC) disorders has been previously reported. However, the relationship between HAT and the diagnostic subtypes and clinical features of MC disorders still remains to be established. OBJECTIVE To determine the prevalence of HAT in healthy donors (HD) vs patients with different diagnostic subtypes of MC activation syndromes (MCAS) and mastocytosis, and its relationship with the clinical behavior of the disease. METHODS A total of 959 subjects were studied including 346 healthy donors (HD), 464 mastocytosis, and 149 non-clonal MCAS patients. Molecular studies to assess the TPSAB1 genotype were performed, and data on serum baseline tryptase (sBT) and basal MC-mediator release episodes and triggers of anaphylaxis were collected. RESULTS HAT was detected in 15/346 (4%) HD versus 43/149 (29%) non-clonal MCAS and 84/464 (18%) mastocytosis cases. Among mastocytosis, HAT was more frequently found in patients with MC-restricted KITD816V (21% vs. 10% among multilineage KITD816V patients; p = .008). Overall, median sBT was higher in cases presenting with HAT (28.9 vs. 24.5 ng/mL; p = .008), while no significant differences in sBT were observed among HAT+ mastocytosis patients depending on the presence of 1 vs. ≥2 extra copies of the α-tryptase gene (44.1 vs. 35.2 ng/mL, p > .05). In turn, anaphylaxis was more frequently observed in HAT+ versus HAT- mastocytosis patients (76% vs. 65%; p = .018), while HAT+ and HAT- patients who did not refer anaphylaxis as the presenting symptom (n = 308) showed a similar prevalence of subsequent anaphylaxis (35% vs. 36%, respectively). CONCLUSION The frequency of HAT in MC disorders varies according to the diagnostic subtype of the disease. HAT does not imply a higher risk (and severity) of anaphylaxis in mastocytosis patients in whom anaphylaxis is not part of the presenting symptoms of the disease.
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Affiliation(s)
- David González-de-Olano
- Department of Allergy, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
| | - Paula Navarro-Navarro
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Department of Medicine and Citometry Service (NUCLEUS), Cancer Research Center (IBMCC, USAL-CSIC), Universidad de Salamanca, Salamanca, Spain
- Sequencing Service (NUCLEUS), Universidad de Salamanca, Salamanca, Spain
| | - Javier I Muñoz-González
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Laura Sánchez-Muñoz
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Instituto de Estudios de Mastocitosis de Castilla La Mancha (CLMast), Virgen del Valle Hospital, Toledo, Spain
| | - Ana Henriques
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Instituto de Estudios de Mastocitosis de Castilla La Mancha (CLMast), Virgen del Valle Hospital, Toledo, Spain
| | | | | | - Andrea Mayado
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Department of Medicine and Citometry Service (NUCLEUS), Cancer Research Center (IBMCC, USAL-CSIC), Universidad de Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - María Jara-Acevedo
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Sequencing Service (NUCLEUS), Universidad de Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Andrés C García-Montero
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Alberto Orfao
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Department of Medicine and Citometry Service (NUCLEUS), Cancer Research Center (IBMCC, USAL-CSIC), Universidad de Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Iván Álvarez-Twose
- Spanish Network on Mastocytosis (REMA), Toledo and Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Instituto de Estudios de Mastocitosis de Castilla La Mancha (CLMast), Virgen del Valle Hospital, Toledo, Spain
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5
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Isham IM, Najimudeen SM, Cork SC, Gupta A, Abdul-Careem MF. Comparison of quantitative PCR and digital PCR assays for quantitative detection of infectious bronchitis virus (IBV) genome. J Virol Methods 2024; 324:114859. [PMID: 38061673 DOI: 10.1016/j.jviromet.2023.114859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
The quantitative polymerase chain reaction (qPCR) technique is an extensively used molecular tool for the detection and quantification of viral genome load. However, since the qPCR assay is a relative quantification method that relies on an external calibration curve it has a lower assay precision and sensitivity. The digital PCR (dPCR) technique is a good alternative to the qPCR assay as it offers highly precise and direct quantification of viral genome load in samples. In this study, performance characteristics such as the quantification range, sensitivity, precision, and specificity of the dPCR technique was compared to qPCR technique for the detection and quantification of IBV genome loads in serial dilutions of IBV positive plasmid DNA, and IBV infected chicken tissue and swab samples. The quantification range of the qPCR assay was wider than that of the dPCR assay, however dPCR had a higher sensitivity compared to qPCR. The precision of quantification of DNA in plasmid samples in terms of repeatability and reproducibility of results was higher when using the dPCR assay compared to qPCR assay. The quantification results of IBV genome load in infected samples by the qPCR and dPCR assays displayed a high correlation. Hence, our findings suggest that dPCR could be used in avian virology research for improved precision and sensitivity in detection and quantification of viral genome loads.
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Affiliation(s)
- Ishara M Isham
- Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Shahnas M Najimudeen
- Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Susan C Cork
- Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Ashish Gupta
- Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Mohamed Faizal Abdul-Careem
- Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
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6
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Gokemeijer J, Balasubramanian N, Ogasawara K, Grudzinska-Goebel J, Upreti VV, Mody H, Kasar S, Vepachedu VR, Xu W, Gupta S, Tarcsa E, Dodge R, Herr K, Yang TY, Tourdot S, Jawa V. An IQ Consortium Perspective on Best Practices for Bioanalytical and Immunogenicity Assessment Aspects of CAR-T and TCR-T Cellular Therapies Development. Clin Pharmacol Ther 2024; 115:188-200. [PMID: 37983584 DOI: 10.1002/cpt.3111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
CAR-T therapies have shown remarkable efficacy against hematological malignancies in the clinic over the last decade and new studies indicate that progress is being made to use these novel therapies to target solid tumors as well as treat autoimmune disease. Innovation in the field, including TCR-T, allogeneic or "off the shelf" CAR-T, and autoantigen/armored CAR-Ts are likely to increase the efficacy and applications of these therapies. The unique aspects of these cell-based therapeutics; patient-derived cells, intracellular expression, in vivo expansion, and phenotypic changes provide unique bioanalytical challenges to develop pharmacokinetic and immunogenicity assessments. The International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) Translational and ADME Sciences Leadership Group (TALG) has brought together a group of industry experts to discuss and consider these challenges. In this white paper, we present the IQ consortium perspective on the best practices and considerations for bioanalytical and immunogenicity aspects toward the optimal development of CAR-T and TCR-T cell therapies.
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Affiliation(s)
- Jochem Gokemeijer
- Discovery Biotherapeutics, Bristol Myers Squibb, Cambridge, Massachusetts, USA
| | - Nanda Balasubramanian
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Ken Ogasawara
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | | | - Vijay V Upreti
- Clinical Pharmacology, Modeling & Simulation, Amgen, Inc., South San Francisco, California, USA
| | - Hardik Mody
- Clinical Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Siddha Kasar
- Oncology Precision & Translational Medicine, Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Venkata R Vepachedu
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Weifeng Xu
- Preclinical Development, Bioanalytical, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Swati Gupta
- Development Biological Sciences, Immunology, AbbVie, Irvine, California, USA
| | - Edit Tarcsa
- Abbvie Bioresearch Center, Worcester, Massachusetts, USA
| | - Robert Dodge
- Novartis Institutes for BioMedical Research, One Health Plaza, East Hanover, New Jersey, USA
| | - Kate Herr
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Tong-Yuan Yang
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Vibha Jawa
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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Mahmood K, Jampani P, Clarke JM, Wolf S, Wang X, Wahidi MM, Giovacchini CX, Dorry M, Shofer SL, Shier J, Jones G, Antonia SJ, Nixon AB. High Yield of Pleural Cell-Free DNA for Diagnosis of Oncogenic Mutations in Lung Adenocarcinoma. Chest 2023; 164:252-261. [PMID: 36693563 PMCID: PMC10331627 DOI: 10.1016/j.chest.2023.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Pleural cytology is currently used to assess targetable mutations in patients with advanced lung adenocarcinoma. However, it is fraught with low diagnostic yield. RESEARCH QUESTION Can pleural cell-free DNA (cfDNA) be used to assess targetable mutations in lung adenocarcinoma patients with malignant pleural effusions (MPE)? STUDY DESIGN AND METHODS Patients with lung adenocarcinoma MPE were recruited prospectively between January 2017 and September 2021. Oncogenic mutations were assessed by treating providers using pleural fluid cytology or lung cancer biopsies. Pleural and plasma cfDNA were used to assess the mutations using next-generation sequencing (NGS). RESULTS Fifty-four pleural fluid samples were collected from 42 patients. The diagnostic yield to detect oncogenic mutations for pleural cfDNA, pleural cytology, biopsy, and plasma cfDNA was 49/54 (90.7%), 16/33 (48.5%), 22/25 (88%), and 24/32 (75%), respectively, P < .001. The agreement of mutations in positive samples between pleural cfDNA and pleural cytology was 100%, whereas the agreement of pleural cfDNA with biopsies was 89.4%. The median concentration (interquartile range) of pleural cfDNA was higher than plasma: 28,444 (4,957-67,051) vs 2,966.5 (2,167-5,025) copies of amplifiable DNA per mL, P < .01. Median of 5 mL (interquartile range, 4.5-5) of pleural fluid supernatant was adequate for cfDNA testing. INTERPRETATION The diagnostic yield of pleural cfDNA NGS for oncogenic mutations in lung adenocarcinoma patients is comparable to tumor biopsies and higher than pleural cytology and plasma cfDNA. The pleural cfDNA can be longitudinally collected, can be readily incorporated in clinical workflow, and may decrease the need for additional biopsies.
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Affiliation(s)
- Kamran Mahmood
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC.
| | - Parvathi Jampani
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
| | - Jeffrey M Clarke
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
| | - Steven Wolf
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC
| | - Xiaofei Wang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC
| | - Momen M Wahidi
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Coral X Giovacchini
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Michael Dorry
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Scott L Shofer
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Jessica Shier
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | | | - Scott J Antonia
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
| | - Andrew B Nixon
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
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9
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Lee H, Seo J, Shin S, Lee ST, Choi JR. Development and validation of sensitive BCR::ABL1 fusion gene quantitation using next-generation sequencing. Cancer Cell Int 2023; 23:106. [PMID: 37248544 DOI: 10.1186/s12935-023-02938-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND BCR::ABL1 fusion has significant prognostic value and is screened for chronic myeloid leukemia (CML) disease monitoring as a part of routine molecular testing. To overcome the limitations of the current standard real-time quantitative polymerase chain reaction (RQ-PCR), we designed and validated a next-generation sequencing (NGS)-based assay to quantify BCR::ABL1 and ABL1 transcript copy numbers. METHODS After PCR amplification of the target sequence, deep sequencing was performed using an Illumina Nextseq 550Dx sequencer and in-house-designed bioinformatics pipeline. The Next-generation Quantitative sequencing (NQ-seq) assay was validated for its analytical performance, including precision, linearity, and limit of detection, using serially diluted control materials. A comparison with conventional RQ-PCR was performed with 145 clinical samples from 77 patients. RESULTS The limit of detection of the NQ-seq was the molecular response (MR) 5.6 [BCR::ABL1 0.00028% international scale (IS)]. The NQ-seq exhibited excellent precision and linear range from MR 2.0 to 5.0. The IS value from the NQ-seq was highly correlated with conventional RQ-PCR. CONCLUSIONS We conclude that the NQ-seq is an effective tool for monitoring BCR::ABL1 transcripts in CML patients with high sensitivity and reliability. Prospective assessment of the unselected large series is required to validate the clinical impact of this NGS-based monitoring strategy.
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Affiliation(s)
- Hyeonah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Seo
- Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
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10
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Wang D, Liu E, Liu H, Jin X, Niu C, Gao Y, Su X. A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum. Front Cell Infect Microbiol 2023; 12:1110684. [PMID: 36710974 PMCID: PMC9874294 DOI: 10.3389/fcimb.2022.1110684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R2 = 0.91; stems: R2 = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.
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Affiliation(s)
- Di Wang
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Enliang Liu
- 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyang Liu
- 3Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xi Jin
- 4Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Chunyan Niu
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| | - Xiaofeng Su
- 5Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
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11
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Wang D, Jiao X, Jia H, Cheng S, Jin X, Wang Y, Gao Y, Su X. Detection and quantification of Verticillium dahliae and V. longisporum by droplet digital PCR versus quantitative real-time PCR. Front Cell Infect Microbiol 2022; 12:995705. [PMID: 36072220 PMCID: PMC9441566 DOI: 10.3389/fcimb.2022.995705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Vascular wilt, caused by Verticillium dahliae and V. longisporum, limits the quality and yield of agricultural crops. Although quantitative real-time PCR (qPCR) has greatly improved the diagnosis of these two pathogens over traditional, time-consuming isolation methods, the relatively poor detection sensitivity and high measurement bias for traceable matrix-rich samples need to be improved. Here, we thus developed a droplet digital PCR (ddPCR) assay for accurate, sensitive detection and quantification of V. dahliae and V. longisporum. We compared the analytical and diagnostic performance in detail of ddPCR and the corresponding qPCR assay against the genomic DNA (gDNA) of the two fungi from cultures and field samples. In our study, the species specificity, quantification linearity, analytical sensitivity, and measurement viability of the two methods were analyzed. The results indicated that ddPCR using field samples enhanced diagnostic sensitivity, decreased quantification bias, and indicated less susceptibility to inhibitors compared with qPCR. Although ddPCR was as sensitive as qPCR when using gDNA from cultures of V. dahliae and V. longisporum, its detection rates using field samples were much higher than those of qPCR, potentially due to the inhibition from residual matrix in the extracts. The results showed that digital PCR is more sensitive and accurate than qPCR for quantifying trace amounts of V. dahliae and V. longisporum and can facilitate management practices to limit or prevent their prevalence.
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Affiliation(s)
- Di Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xinya Jiao
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Haijiang Jia
- Raw Material Technology Center of Guangxi Tobacco, Nanning, China
| | - Shumei Cheng
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
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12
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Henriksen TV, Reinert T, Rasmussen MH, Demuth C, Løve US, Madsen AH, Gotschalck KA, Iversen LH, Andersen CL. Comparing single-target and multi-target approaches for postoperative circulating tumor DNA detection in stage II-III colorectal cancer patients. Mol Oncol 2022; 16:3654-3665. [PMID: 35895438 PMCID: PMC9580876 DOI: 10.1002/1878-0261.13294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Circulating tumour DNA (ctDNA) detection for postoperative risk stratification in cancer patients has great clinical potential. However, low ctDNA abundances complicates detection. Multitarget (MT) detection strategies have been developed to increase sensitivity. Yet, empirical evidence supporting performance gains of MT vs. single‐target (ST) strategies in a postoperative setting is limited. We compared ctDNA detection in 379 paired plasma samples from 112 stage II–III colorectal cancer patients by ST digital PCR and MT sequencing of 16 patient‐specific variants. The strategies exhibited good concordance (90%, Cohen's Kappa 0.79), with highly correlated ctDNA quantifications (Pearson r = 0.985). A difference was observed in ctDNA detection preoperatively (ST 72/92, MT 88/92). However, no difference was observed immediately after surgery in recurrence (ST 11/22, MT 10/22) or nonrecurrence (both 2/34) patients. In serial samples, detection was similar within recurrence (ST 13/16, MT 14/16) and nonrecurrence (ST 3/49, MT 1/49) patients. Both approaches yielded similar lead times to standard‐of‐care radiology (ST 4.0 months, MT 4.1 months). Our findings do not support significant performance gains of the MT strategy over the ST strategy for postoperative ctDNA detection.
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Affiliation(s)
- Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Uffe Schou Løve
- Department of Surgery, Regional Hospital Viborg, Banevejen 7C, DK-8800, Viborg, Denmark
| | - Anders Husted Madsen
- Department of Surgery, Regional Hospital Herning, Hospitalsparken 15, DK-7400, Herning, Denmark
| | | | - Lene Hjerrild Iversen
- Department of Surgery, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 35, DK-8200, Aarhus N, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
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13
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International co-validation on absolute quantification of single nucleotide variants of KRAS by digital PCR. Anal Bioanal Chem 2022; 414:5899-5906. [DOI: 10.1007/s00216-022-04155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/01/2022]
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14
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Cropper E, Coble MD, Kavlick MF. Assessment of human nuclear and mitochondrial DNA qPCR assays for quantification accuracy utilizing NIST SRM 2372a. Forensic Sci Int Genet 2022; 59:102711. [DOI: 10.1016/j.fsigen.2022.102711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 12/01/2022]
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15
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Generation of TRIM28 Knockout K562 Cells by CRISPR/Cas9 Genome Editing and Characterization of TRIM28-Regulated Gene Expression in Cell Proliferation and Hemoglobin Beta Subunits. Int J Mol Sci 2022; 23:ijms23126839. [PMID: 35743282 PMCID: PMC9224613 DOI: 10.3390/ijms23126839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/10/2022] Open
Abstract
TRIM28 is a scaffold protein that interacts with DNA-binding proteins and recruits corepressor complexes to cause gene silencing. TRIM28 contributes to physiological functions such as cell growth and differentiation. In the chronic myeloid leukemia cell line K562, we edited TRIM28 using CRISPR/Cas9 technology, and the complete and partial knockout (KO) cell clones were obtained and confirmed using quantitative droplet digital PCR (ddPCR) technology. The amplicon sequencing demonstrated no off-target effects in our gene editing experiments. The TRIM28 KO cells grew slowly and appeared red, seeming to have a tendency towards erythroid differentiation. To understand how TRIM28 controls K562 cell proliferation and differentiation, transcriptome profiling analysis was performed in wild-type and KO cells to identify TRIM28-regulated genes. Some of the RNAs that encode the proteins regulating the cell cycle were increased (such as p21) or decreased (such as cyclin D2) in TRIM28 KO cell clones; a tumor marker, the MAGE (melanoma antigen) family, which is involved in cell proliferation was reduced. Moreover, we found that knockout of TRIM28 can induce miR-874 expression to downregulate MAGEC2 mRNA via post-transcriptional regulation. The embryonic epsilon-globin gene was significantly increased in TRIM28 KO cell clones through the downregulation of transcription repressor SOX6. Taken together, we provide evidence to demonstrate the regulatory network of TRIM28-mediated cell growth and erythroid differentiation in K562 leukemia cells.
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16
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Schwinghammer C, Koopmann J, Chitadze G, Karawajew L, Brüggemann M, Eckert C. Droplet Digital PCR: A New View on Minimal Residual Disease Quantification in Acute Lymphoblastic Leukemia. J Mol Diagn 2022; 24:856-866. [PMID: 35691569 DOI: 10.1016/j.jmoldx.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/05/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022] Open
Abstract
Real-time quantitative PCR (qPCR) using immunoglobulin/T-cell receptor gene rearrangements has been used as the gold standard for minimal residual disease (MRD) monitoring in acute lymphoblastic leukemia (ALL) for >20 years. Recently, new PCR-based technologies have emerged, such as droplet digital PCR (ddPCR), which could offer several methodologic advances for MRD monitoring. In the current work, qPCR and ddPCR were compared in an unbiased blinded prospective study (n = 88 measurements) and in a retrospective study with selected critical low positive samples (n = 65 measurements). The former included flow cytometry (Flow; n = 31 measurements) as a third MRD detection method. Published guidelines (qPCR) and the latest, revised evaluation criteria (ie, ddPCR, Flow) have been applied for data analysis. The prospective study shows that ddPCR outperforms qPCR with a significantly better quantitative limit of detection and sensitivity. The number of critical MRD estimates below quantitative limit was reduced by sixfold and by threefold in the retrospective and prospective cohorts, respectively. Furthermore, the concordance of quantitative values between ddPCR and Flow was higher than between ddPCR and qPCR, probably because ddPCR and Flow are absolute quantification methods independent of the diagnostic sample, unlike qPCR. In summary, our data highlight the advantages of ddPCR as a more precise and sensitive technology that could be used to refine response monitoring in ALL.
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Affiliation(s)
- Claudia Schwinghammer
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Koopmann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Guranda Chitadze
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Leonid Karawajew
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Brüggemann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cornelia Eckert
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.
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17
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Weisgerber D, Hatori M, Li X, Abate AR. Polyhedral Particles with Controlled Concavity by Indentation Templating. Anal Chem 2022; 94:7475-7482. [PMID: 35578791 PMCID: PMC9161221 DOI: 10.1021/acs.analchem.1c04884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/31/2022] [Indexed: 11/30/2022]
Abstract
Current methods for fabricating microparticles offer limited control over size and shape. Here, we demonstrate a droplet microfluidic method to form polyhedral microparticles with controlled concavity. By manipulating Laplace pressure, buoyancy, and particle rheology, we generate microparticles with diverse shapes and curvatures. Additionally, we demonstrate the particles provide increased capture efficiency when used for particle-templated emulsification. Our approach enables microparticles with enhanced chemical and biological functionality.
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Affiliation(s)
- Daniel
W. Weisgerber
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
| | - Makiko Hatori
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
| | - Xiangpeng Li
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
| | - Adam R. Abate
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
- Chan
Zuckerberg Biohub 499
Illinois Street, San Francisco, California 94158, United States
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18
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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19
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Corbisier P, Buttinger G, Savini C, Sacco MG, Gatto F, Emons H. Expression of GM content in mass fraction from digital PCR data. Food Control 2022; 133:108626. [PMID: 35241875 PMCID: PMC8756621 DOI: 10.1016/j.foodcont.2021.108626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 11/17/2022]
Abstract
Nowadays the quantification of the content of genetically modified (GM) constituents in food or feed products is performed by using either quantitative real-time PCR (qPCR) or digital PCR (dPCR). The latter is increasingly used. Therefore, experimental protocols for the quantification of 52 GM events authorised in the EU have been converted into a digital format and minimum performance characteristics for dPCR methods are detailed. Because of the need to harmonise the transformation of PCR results between two different measurement scales, 50 conversion factors for Certified Reference Materials (CFCRM) have been experimentally determined by three and sometimes four independent expert laboratories. The uncertainty of each CFCRM has been estimated to express dPCR results in mass fraction with a consistent uncertainty contribution. In 38 out of 58 cases, the validated qPCR methods (for 52 event-specific and 6 taxon-specific measurements) could easily be transferred into dPCR methods by using the same oligo sequences, final oligo concentration or annealing temperatures for the dPCR procedure. Laboratories have nevertheless used different strategies to improve the resolution or to reduce the so-called rain in their dPCR outcome. Those modifications were needed for PCR procedures that could not be converted without changes into a digital format. Therefore, exclusion/quality criteria such as the maximum rate of partitions with intermediate fluorescence “rain”, the minimum resolution and repeatability are suggested for dPCR methods. The CFCRM determined in this study were generally in agreement with the declared zygosity of the GM parental donor for hemizygous maize events. In a limited number of GM events the CFCRM values were significantly different when measured with different maize-specific (ZmAdh1 or hmgA) genes. Digital PCR protocols for the quantification of 52 GM events Minimum performance criteria for digital PCR results Conversion factors to express GM content determined by digital PCR in mass fraction Harmonised measurement system for official GMO controls in the EU
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Affiliation(s)
- Philippe Corbisier
- European Commission, Joint Research Centre JRC, Retieseweg 111, 2440, Geel, Belgium
| | - Gerhard Buttinger
- European Commission, Joint Research Centre JRC, Retieseweg 111, 2440, Geel, Belgium
| | - Cristian Savini
- European Commission, Joint Research Centre JRC, Via Enrico Fermi 2749, 21027, Ispra, VA, Italy
| | - Maria Grazia Sacco
- European Commission, Joint Research Centre JRC, Via Enrico Fermi 2749, 21027, Ispra, VA, Italy
| | - Francesco Gatto
- European Commission, Joint Research Centre JRC, Via Enrico Fermi 2749, 21027, Ispra, VA, Italy
| | - Hendrik Emons
- European Commission, Joint Research Centre JRC, Retieseweg 111, 2440, Geel, Belgium
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20
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Shim WC, Woo S, Park JW. Nanoscale Force-Mapping-Based Quantification of Low-Abundance Methylated DNA. NANO LETTERS 2022; 22:1324-1330. [PMID: 35080393 DOI: 10.1021/acs.nanolett.1c04637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
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Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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21
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Lee SS, Kim S, Yoo HM, Lee DH, Bae YK. Development of SARS-CoV-2 packaged RNA reference material for nucleic acid testing. Anal Bioanal Chem 2022; 414:1773-1785. [PMID: 34958396 PMCID: PMC8711077 DOI: 10.1007/s00216-021-03846-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
Nucleic acid tests to detect the SARS-CoV-2 virus have been performed worldwide since the beginning of the COVID-19 pandemic. For the quality assessment of testing laboratories and the performance evaluation of molecular diagnosis products, reference materials (RMs) are required. In this work, we report the production of a lentiviral SARS-CoV-2 RM containing approximately 12 kilobases of its genome including common diagnostics targets such as RdRp, N, E, and S genes. The RM was measured with multiple assays using two different digital PCR platforms. To measure the homogeneity and stability of the lentiviral SARS-CoV-2 RM, reverse transcription droplet digital PCR (RT-ddPCR) was used with in-house duplex assays. The copy number concentration of each target gene in the extracted RNA solution was then converted to that of the RM solution. Their copy number values are measured to be from 1.5 × 105 to 2.0 × 105 copies/mL. The RM has a between-bottle homogeneity of 4.80-8.23% and is stable at 4 °C for 1 week and at -70 °C for 6 months. The lentiviral SARS-CoV-2 RM closely mimics real samples that undergo identical pre-analytical processes for SARS-CoV-2 molecular testing. By offering accurate reference values for the absolute copy number of viral target genes, the developed RM can be used to improve the reliability of SARS-CoV-2 molecular testing.
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Affiliation(s)
- Sang-Soo Lee
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Seil Kim
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon, 34113, Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Hee Min Yoo
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Da-Hye Lee
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea.
| | - Young-Kyung Bae
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea.
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
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22
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Milavec M, Cleveland MH, Bae YK, Wielgosz RI, Vonsky M, Huggett JF. Metrological framework to support accurate, reliable, and reproducible nucleic acid measurements. Anal Bioanal Chem 2021; 414:791-806. [PMID: 34738220 PMCID: PMC8568362 DOI: 10.1007/s00216-021-03712-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
Nucleic acid analysis is used in many areas of life sciences such as medicine, food safety, and environmental monitoring. Accurate, reliable measurements of nucleic acids are crucial for maximum impact, yet users are often unaware of the global metrological infrastructure that exists to support these measurements. In this work, we describe international efforts to improve nucleic acid analysis, with a focus on the Nucleic Acid Analysis Working Group (NAWG) of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM). The NAWG is an international group dedicated to improving the global comparability of nucleic acid measurements; its primary focus is to support the development and maintenance of measurement capabilities and the dissemination of measurement services from its members: the National Metrology Institutes (NMIs) and Designated Institutes (DIs). These NMIs and DIs provide DNA and RNA measurement services developed in response to the needs of their stakeholders. The NAWG members have conducted cutting edge work over the last 20 years, demonstrating the ability to support the reliability, comparability, and traceability of nucleic acid measurement results in a variety of sectors.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Megan H Cleveland
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Robert I Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Maxim Vonsky
- D.I. Mendeleev Institute for Metrology, Moskovsky pr., 19, Saint-Petersburg, 190005, Russian Federation
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK.,School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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23
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Williams PM, Forbes T, P. Lund S, Cole KD, He HJ, Karlovich C, Paweletz CP, Stetson D, Yee LM, Connors DE, Keating SM, Destenaves B, Cleveland MH, Lau CJ, Barrett JC, Kelloff GJ, McCormack RT. Validation of ctDNA Quality Control Materials Through a Precompetitive Collaboration of the Foundation for the National Institutes of Health. JCO Precis Oncol 2021; 5:PO.20.00528. [PMID: 34250423 PMCID: PMC8232894 DOI: 10.1200/po.20.00528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/05/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
We report the results from a Foundation for the National Institutes of Health Biomarkers Consortium project to address the absence of well-validated quality control materials (QCMs) for circulating tumor DNA (ctDNA) testing. This absence is considered a cause of variance and inconsistencies in translating ctDNA results into clinical actions. METHODS In this phase I study, QCMs with 14 clinically relevant mutations representing single nucleotide variants, insertions or deletions (indels), translocations, and copy number variants were sourced from three commercial manufacturers with variant allele frequencies (VAFs) of 5%, 2.5%, 1%, 0.1%, and 0%. Four laboratories tested samples in quadruplicate using two allele-specific droplet digital polymerase chain reaction and three (amplicon and hybrid capture) next-generation sequencing (NGS) panels. RESULTS The two droplet digital polymerase chain reaction assays reported VAF values very close to the manufacturers' claimed concentrations for all QCMs. NGS assays reported most single nucleotide variants and indels, but not translocations, close to the expected VAF values. Notably, two NGS assays reported lower VAF than expected for all translocations in all QCM mixtures, possibly related to technical challenges detecting these variants. The ability to call ERBB2 copy number amplifications varied across assays. All three QCMs provided valuable insight into assay precision. Each assay across all variant types demonstrated dropouts at 0.1%, suggesting that the QCM can serve for testing of an assay's limit of detection with confidence claims for specific variants. CONCLUSION These results support the utility of the QCM in testing ctDNA assay analytical performance. However, unique designs and manufacturing methods for the QCM, and variations in a laboratory's testing configuration, may require testing of multiple QCMs to find the best reagents for accurate result interpretation.
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Affiliation(s)
- P. Mickey Williams
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD
| | - Thomas Forbes
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD
| | - Steven P. Lund
- National Institute of Standards and Technology, Gaithersburg, MD
| | - Kenneth D. Cole
- National Institute of Standards and Technology, Gaithersburg, MD
| | - Hua-Jun He
- National Institute of Standards and Technology, Gaithersburg, MD
| | - Chris Karlovich
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD
| | - Cloud P. Paweletz
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel Stetson
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Laura M. Yee
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Dana E. Connors
- Foundation for the National Institutes of Health, Bethesda, MD
| | | | | | | | - Christie J. Lau
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - J. Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
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24
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Levy CN, Hughes SM, Roychoudhury P, Reeves DB, Amstuz C, Zhu H, Huang ML, Wei Y, Bull ME, Cassidy NA, McClure J, Frenkel LM, Stone M, Bakkour S, Wonderlich ER, Busch MP, Deeks SG, Schiffer JT, Coombs RW, Lehman DA, Jerome KR, Hladik F. A highly multiplexed droplet digital PCR assay to measure the intact HIV-1 proviral reservoir. Cell Rep Med 2021; 2:100243. [PMID: 33948574 PMCID: PMC8080125 DOI: 10.1016/j.xcrm.2021.100243] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 01/16/2023]
Abstract
Quantifying the replication-competent HIV reservoir is essential for evaluating curative strategies. Viral outgrowth assays (VOAs) underestimate the reservoir because they fail to induce all replication-competent proviruses. Single- or double-region HIV DNA assays overestimate it because they fail to exclude many defective proviruses. We designed two triplex droplet digital PCR assays, each with 2 unique targets and 1 in common, and normalize the results to PCR-based T cell counts. Both HIV assays are specific, sensitive, and reproducible. Together, they estimate the number of proviruses containing all five primer-probe regions. Our 5-target results are on average 12.1-fold higher than and correlate with paired quantitative VOA (Spearman's ρ = 0.48) but estimate a markedly smaller reservoir than previous DNA assays. In patients on antiretroviral therapy, decay rates in blood CD4+ T cells are faster for intact than for defective proviruses, and intact provirus frequencies are similar in mucosal and circulating T cells.
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Affiliation(s)
- Claire N. Levy
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Sean M. Hughes
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chelsea Amstuz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Yulun Wei
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Marta E. Bull
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Noah A.J. Cassidy
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jan McClure
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lisa M. Frenkel
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mars Stone
- Vitalent Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of San Francisco, San Francisco, CA, USA
- School of Medicine, University of San Francisco, San Francisco, CA, USA
| | - Sonia Bakkour
- Vitalent Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of San Francisco, San Francisco, CA, USA
- School of Medicine, University of San Francisco, San Francisco, CA, USA
| | - Elizabeth R. Wonderlich
- Department of Infectious Disease Research, Southern Research, 431 Aviation Way, Frederick, MD, USA
| | - Michael P. Busch
- Vitalent Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of San Francisco, San Francisco, CA, USA
| | - Steven G. Deeks
- School of Medicine, University of San Francisco, San Francisco, CA, USA
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dara A. Lehman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Florian Hladik
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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25
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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: 214] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [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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26
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He X, Ding J, Xu Z, Li N, Yang J, Chen H, Lu D. Development of a new genetic reference material system based on Saccharomyces cerevisiae cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:473-482. [PMID: 33614823 PMCID: PMC7868937 DOI: 10.1016/j.omtm.2021.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
As an important quality control link of molecular diagnosis, genetic reference materials (RMs) are widely used in various gene detection platforms such as mutation detection, gene quantification, and second generation sequencing. However, contamination, construction, and storage of existing genetic RMs still remain challenges. Here, we established a new genetic RM system based on Saccharomyces cerevisiae. We chose the non-small cell lung cancer (NSCLC) mutation hotspots in Kirsten rat sarcoma viral oncogene (KRAS) and epidermal growth factor receptor (EGFR), using clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas9) system-mediated gene editing technology, combined with the high homologous recombination efficiency of Saccharomyces cerevisiae. A single copy of the target gene was inserted into the yeast genome, and the inserted target gene was stably inherited with the passage of yeast cells. The copy number calculation for the target gene can replays by cell counting. The RM system was evaluated by sequence, copy number, stability, and homogeneity. In summary, the recombinant yeast cell line has ease of construction and screening, stable genetic characteristics, accurate copy number calculation, and convenient culture and preservation. Our findings may provide new ideas and directions for the research and industrialization of genetic RMs.
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Affiliation(s)
- Xin He
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jiaqi Ding
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Zhenhua Xu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Na Li
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingmin Yang
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
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27
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Sugimoto H, Chen S, Minembe JP, Chouitar J, He X, Wang H, Fang X, Qian MG. Insights on Droplet Digital PCR-Based Cellular Kinetics and Biodistribution Assay Support for CAR-T Cell Therapy. AAPS JOURNAL 2021; 23:36. [PMID: 33655393 PMCID: PMC7925486 DOI: 10.1208/s12248-021-00560-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 01/03/2023]
Abstract
Characterizing in vivo cellular kinetics and biodistribution of chimeric antigen receptor T (CAR-T) cells is critical for toxicity assessment, nonclinical and clinical efficacy studies. To date, the standardized assay to characterize CAR-T cell distribution, expansion, contraction, and persistence profiles is not readily available. To overcome this limitation and increase comparability among studies, we have established a universal protocol for analysis. We established a duplexing ddPCR protocol for the CAR-T transgene and reference gene to normalize the genomic DNA input prepared from mouse blood and tissues. The high-throughput gDNA extraction method enabled highly reproducible gDNA extraction while eliminating labor-intensive steps. The investigational CAR-T cells were intravenously injected into immunodeficient mice bearing human colorectal cancer xenografts. The blood and tissue samples were collected to measure the cellular kinetics by ddPCR and flow cytometry. The standard curves were linear throughout the calibration range with acceptable intra- and inter-day precision and accuracy. The gDNA recovery study performed by spiking in the exo-gene plasmid DNA or CAR-T cells revealed that the recovery ranged from 60 to 100% in blood and tissue homogenates. The use of both units of copy/μg gDNA and copy/μL blood met the current regulatory requirement and allowed for a systematic understanding of CAR-T cell expansion and a direct comparison with the flow cytometry data. A standardized ddPCR assay, including automated gDNA extraction procedures, has been established for evaluating cellular kinetics and biodistribution in CAR-T cell therapies.
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Affiliation(s)
- Hiroshi Sugimoto
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 125 Binney Street, Cambridge, Massachusetts, 02142, USA.
| | - Susan Chen
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Jean-Pierre Minembe
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Johara Chouitar
- Department of Immuno Oncology DDU, Takeda Pharmaceuticals International Co, 40 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Xingyue He
- Department of Immuno Oncology DDU, Takeda Pharmaceuticals International Co, 40 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Haiqing Wang
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Xiaodong Fang
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA.
| | - Mark G Qian
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
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28
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Choi Y, Song Y, Kim YT, Lee SJ, Lee KG, Im SG. Multifunctional Printable Micropattern Array for Digital Nucleic Acid Assay for Microbial Pathogen Detection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:3098-3108. [PMID: 33423455 DOI: 10.1021/acsami.0c16862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The digital nucleic acid assay is a precise, sensitive, and reproducible method for determining the presence of individual target molecules separated in designated partitions; thus, this technique can be used for the nucleic acid detection. Here, we propose a multifunctional micropattern array capable of isolating individual target molecules into partitions and simultaneous on-site cell lysis to achieve a direct DNA extraction and digitized quantification thereof. The multifunctional micropattern array is fabricated by the deposition of a copolymer film, poly(2-dimethylaminomethyl styrene-co-hydroxyethyl methacrylate) (pDH), directly on a microfluidic chip surface via the photoinitiated chemical vapor deposition process, followed by hydrophobic microcontact printing (μCP) to define each partition for the nucleic acid isolation. The pDH layer is a positively charged surface, which is desirable for the bacterial lysis and DNA capture, while showing exceptional water stability for more than 24 h. The hydrophobic μCP-treated pDH surface is stable under aqueous conditions at a high temperature (70 °C) for 1 h and enables the rapid and reliable formation of thousands of sessile microdroplets for the compartmentalization of an aqueous sample solution without involving bulky and costly microfluidic devices. By assembling the multifunctional micropattern array into the microfluidic chip, the isothermal amplification in each partition can detect DNA templates over a concentration range of 0.01-2 ng/μL. The untreated bacterial cells can also be directly compartmentalized via the microdroplet formation, followed by the on-site cell lysis and DNA capture on the compartmentalized pDH surface. For Escherichia coli O157:H7, Salmonella enteritidis, and Staphylococcus aureus cells, cell numbers ranging from 1.4 × 104 to 1.4 × 107 can be distinguished by using the multifunctional micropattern array, regardless of the cell type. The multifunctional micropattern array developed in this study provides a novel multifunctional compartmentalization method for rapid, simple, and accurate digital nucleic acid assays.
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Affiliation(s)
- Yunho Choi
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Younseong Song
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology, Korea Polytechnic University, 237 Sangidaehak-ro, Siheung-si, Gyeonggi-do 15073, Republic of Korea
| | - Seok Jae Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung G Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sung Gap Im
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST Institute for NanoCentury, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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29
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Zhou H, Liu D, Ma L, Ma T, Xu T, Ren L, Li L, Xu S. A SARS-CoV-2 Reference Standard Quantified by Multiple Digital PCR Platforms for Quality Assessment of Molecular Tests. Anal Chem 2021; 93:715-721. [PMID: 33289545 PMCID: PMC7737535 DOI: 10.1021/acs.analchem.0c03996] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. A reference standard with a well-characterized concentration or titer is of the utmost importance for the study of limit of detection (LoD), which is a crucial feature for a diagnostic assay. Although several reference standards of plasmids or synthetic RNA have already been announced, a reference standard for inactivated virus particles with an accurate concentration is still needed to evaluate the complete procedure. Here, we performed a collaborative study to estimate the NAT-detectable units as a viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6 × 105 ± 6.5 × 104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.
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Affiliation(s)
- Haiwei Zhou
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Donglai Liu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Liang Ma
- Department of Biomedical Devices, Bioland
Laboratory (Guangzhou Regenerative Medicine and Health Guangdong
Laboratory), Guangzhou 510320, China
| | - Tingting Ma
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Tingying Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Lili Ren
- Institute of Pathogen Biology, Chinese
Academy of Medical Sciences & Peking Union Medical College, Beijing
100730, China
| | - Liang Li
- Biotechnology Research Institute, Chinese
Academy of Agricultural Sciences, Beijing 100081,
China
| | - Sihong Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
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30
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Bartlett LJ, Boots M, Brosi BJ, de Roode JC, Delaplane KS, Hernandez CA, Wilfert L. Persistent effects of management history on honeybee colony virus abundances. J Invertebr Pathol 2020; 179:107520. [PMID: 33359478 DOI: 10.1016/j.jip.2020.107520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/09/2020] [Accepted: 12/12/2020] [Indexed: 10/22/2022]
Abstract
Infectious diseases are a major threat to both managed and wild pollinators. One key question is how the movement or transplantation of honeybee colonies under different management regimes affects honeybee disease epidemiology. We opportunistically examined any persistent effect of colony management history following relocation by characterising the virus abundances of honeybee colonies from three management histories, representing different management histories: feral, low-intensity management, and high-intensity "industrial" management. The colonies had been maintained for one year under the same approximate 'common garden' condition. Colonies in this observational study differed in their virus abundances according to management history, with the feral population history showing qualitatively different viral abundance patterns compared to colonies from the two managed population management histories; for example, higher abundance of sacbrood virus but lower abundances of various paralysis viruses. Colonies from the high-intensity management history exhibited higher viral abundances for all viruses than colonies from the low-intensity management history. Our results provide evidence that management history has persistent impacts on honeybee disease epidemiology, suggesting that apicultural intensification could be majorly impacting on pollinator health, justifying much more substantial investigation.
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Affiliation(s)
- Lewis J Bartlett
- Centre for Ecology and Conservation, University of Exeter, TR10 9FE, UK; Department of Biology, Emory University, Atlanta, GA 30322, USA; Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
| | - Michael Boots
- Centre for Ecology and Conservation, University of Exeter, TR10 9FE, UK; Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Berry J Brosi
- Department of Environmental Sciences, Emory University, Atlanta, GA 30322, USA
| | | | - Keith S Delaplane
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lena Wilfert
- Centre for Ecology and Conservation, University of Exeter, TR10 9FE, UK; Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm D-89069, Germany
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31
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Tellinghuisen J. dPCR vs. qPCR: The role of Poisson statistics at low concentrations. Anal Biochem 2020; 611:113946. [DOI: 10.1016/j.ab.2020.113946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
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32
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Park S, Lee H, Shin S, Lee ST, Lee KA, Choi JR. Analytical validation of the droplet digital PCR assay for diagnosis of spinal muscular atrophy. Clin Chim Acta 2020; 510:787-789. [PMID: 32956702 DOI: 10.1016/j.cca.2020.09.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a progressive motor neuron disease caused by homozygote loss of exon 7 on the survival motor neuron 1 (SMN1) gene. The severity of the SMA phenotype is influenced by copies of SMN2, a gene that is highly homologous with SMN1. METHODS We validated analytical performance of droplet digital polymerase chain reaction (ddPCR) for detection of copy number variation of SMN1 and SMN2 genes for diagnosis of SMA using clinical samples. For accuracy performance evaluation, ddPCR results were compared with those of multiplex ligation-dependent probe amplification (MLPA) as a reference standard. Copy numbers of SMN1/SMN2 exon 7 from 200 clinical samples were concordant between ddPCR and MLPA. RESULTS For all samples, the copy number of SMN1/SMN2 exon 7 was concordant between MLPA and ddPCR. The ddPCR also showed acceptable degrees of repeatability and total imprecision. CONCLUSION Therefore, ddPCR is expected to be useful for SMA diagnosis and to predict phenotypic severity of SMA patients by determining the copy number of SMN2 in clinical laboratories.
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Affiliation(s)
- Sunggyun Park
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Hyeonah Lee
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Li J, Zhang L, Li L, Li X, Zhang X, Zhai S, Gao H, Li Y, Wu G, Wu Y. Development of Genomic DNA Certified Reference Materials for Genetically Modified Rice Kefeng 6. ACS OMEGA 2020; 5:21602-21609. [PMID: 32905288 PMCID: PMC7469412 DOI: 10.1021/acsomega.0c02274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
The application of certified reference materials (CRMs) to genetically modified organism (GMO) detection is essential for guaranteeing the accuracy, comparability, and traceability of quantitative results over time and among laboratories. Clean leaves from GM rice Kefeng 6 were used as raw materials to develop a batch of genomic DNA (gDNA) CRMs. The optimized KF6/PLD duplex digital PCR was used for collaborative characterization of Kefeng 6 gDNA CRMs by eight qualified laboratories; this batch of gDNA CRMs was certified for two property values, namely, copy number ratio and copy number concentration, which were 1.03 ± 0.04 and (1.60 ± 0.11) × 105 copies/μL, respectively. The gDNA CRMs displayed good between-vial homogeneity when the minimum sample intake of 2 μL was taken into account. Stability studies indicated that the gDNA CRMs should be transported below 25 °C, and cold chain transport was recommended. Shelf life was assessed to be at least 12 months, and when using gDNA CRMs, freeze-thaw should not exceed 10 cycles. Compared to the available gDNA CRMs in the market, this batch of gDNA CRMs has accurate property values with combined uncertainties, providing user-friendly calibrators for GM rice Kefeng 6 inspection and monitoring. The development and characterization of Kefeng 6 gDNA CRMs contribute to the establishment of a copy number-based reference system for GMO detection.
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Affiliation(s)
- Jun Li
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Li Zhang
- School
of Life Science, South-Central University
for Nationalities, Wuhan 430074, China
| | - Liang Li
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Xiaying Li
- Development
Center of Science and Technology, Ministry
of Agriculture and Rural Affairs P. R. China, Beijing 100025, China
| | - Xiujie Zhang
- Development
Center of Science and Technology, Ministry
of Agriculture and Rural Affairs P. R. China, Beijing 100025, China
| | - Shanshan Zhai
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Hongfei Gao
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Yunjing Li
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Gang Wu
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Yuhua Wu
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
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Li J, Li L, Zhang L, Zhang X, Li X, Zhai S, Gao H, Li Y, Wu G, Wu Y. Development of a certified genomic DNA reference material for detection and quantification of genetically modified rice KMD. Anal Bioanal Chem 2020; 412:7007-7016. [PMID: 32740822 DOI: 10.1007/s00216-020-02834-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/09/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Qualitative and quantitative detection of genetically modified products is inseparable from the application of reference materials (RMs). In this study, a batch of genomic DNA (gDNA) certified reference materials (CRMs) was developed using genetically modified rice Kemingdao (KMD) homozygotes as the raw material. The gDNA CRMs in this batch showed good homogeneity; the minimum sample intake was determined to be 2 μL. The stability study showed that transportation by cold chain is preferable, no significant degradation trend was observed during a 12-month period when storing the gDNA CRMs at 4 °C and - 20 °C, and the number of freeze-thaw cycles cannot exceed 10. The property values of the copy number ratio of transgene and endogenous gene and the copy number concentration for gDNA CRMs were determined by a collaborative characterization of eight laboratories using the duplex KMD/PLD droplet digital PCR (ddPCR) assays. The uncertainty components of characterization, potential between-unit heterogeneity, and potential degradation during long-term storage were combined to estimate the expanded uncertainty of the certified value with a coverage factor k of 2.0. The certified value of copy number ratio for KMD gDNA CRM is 0.99 ± 0.05, and that of copy number concentration is (1.76 ± 0.10) × 105 copies/μL. Compared to the gDNA CRMs in availability, this batch of KMD gDNA CRMs is assigned accurate property values and can be directly used for qualitative and quantitative detection of GMOs as well as evaluation of the parameters of analytical methods with no need of further DNA concentration measurement. Graphical abstract.
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Affiliation(s)
- Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Zhang
- School of Life Science, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Xiujie Zhang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs P. R. China, Beijing, 100025, China.
| | - Xiaying Li
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs P. R. China, Beijing, 100025, China
| | - Shanshan Zhai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Hongfei Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yunjing Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
| | - Yuhua Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
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Villamil C, Calderon MN, Arias MM, Leguizamon JE. Validation of Droplet Digital Polymerase Chain Reaction for Salmonella spp. Quantification. Front Microbiol 2020; 11:1512. [PMID: 32733415 PMCID: PMC7358645 DOI: 10.3389/fmicb.2020.01512] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023] Open
Abstract
Salmonellosis is a foodborne disease caused by Salmonella spp. Although cell culture is the gold standard for its identification, validated molecular methods are becoming an alternative, because of their rapidity, selectivity, and specificity. A simplex and duplex droplet digital polymerase chain reaction (ddPCR)-based method for the identification and quantification of Salmonella using ttr, invA, hilA, spaQ, and siiA gene sequences was validated. The method has high specificity, working interval between 8 and 8,000 cp/μL in ddPCR reaction, a limit of detection of 0.5 copies/μL, and precision ranging between 5 and 10% measured as a repeatability standard deviation. The relative standard measurement uncertainty was between 2 and 12%. This tool will improve food safety in national consumption products and will increase the competitiveness in agricultural product trade.
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Affiliation(s)
- Carolina Villamil
- Departamento de Química, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Maria Mercedes Arias
- Grupo de Metrología en Bioanálisis, Instituto Nacional de Metrología, Bogota, Colombia
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Abasıyanık MF, Wolfe K, Van Phan H, Lin J, Laxman B, White SR, Verhoef PA, Mutlu GM, Patel B, Tay S. Ultrasensitive digital quantification of cytokines and bacteria predicts septic shock outcomes. Nat Commun 2020; 11:2607. [PMID: 32451375 PMCID: PMC7248118 DOI: 10.1038/s41467-020-16124-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/13/2020] [Indexed: 12/29/2022] Open
Abstract
Quantification of pathogen and host biomarkers is essential for the diagnosis, monitoring, and treatment of infectious diseases. Here, we demonstrate sensitive and rapid quantification of bacterial load and cytokines from human biological samples to generate actionable hypotheses. Our digital assay measures IL-6 and TNF-α proteins, gram-negative (GN) and gram-positive (GP) bacterial DNA, and the antibiotic-resistance gene blaTEM with femtomolar sensitivity. We use our method to characterize bronchoalveolar lavage fluid from patients with asthma, and find elevated GN bacteria and IL-6 levels compared to healthy subjects. We then analyze plasma from patients with septic shock and find that increasing levels of IL-6 and blaTEM are associated with mortality, while decreasing IL-6 levels are associated with recovery. Surprisingly, lower GN bacteria levels are associated with higher probability of death. Applying decision-tree analysis to our measurements, we are able to predict mortality and rate of recovery from septic shock with over 90% accuracy. Ultrasensitive methods for detection of biomarkers for infectious disease are needed for diagnosing, monitoring and targeting treatment. Here the authors develop a digital assay for inflammatory markers, bacterial DNA and antibotic-resistance genes and apply it to characterise asthma patients and predict mortality from septic shock.
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Affiliation(s)
- M Fatih Abasıyanık
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Krysta Wolfe
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jing Lin
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Bharathi Laxman
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Steven R White
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Philip A Verhoef
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA.,Center for Integrated Health Research, Kaiser Permanente Hawaii, Honolulu, HI, 96819, USA
| | - Gökhan M Mutlu
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA
| | - Bhakti Patel
- Department of Medicine, Section of Pulmonary/Critical Care, The University of Chicago, Chicago, IL, 60637, USA.
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA. .,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
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Oliveira B, Veigas B, Fernandes AR, Águas H, Martins R, Fortunato E, Baptista PV. Fast Prototyping Microfluidics: Integrating Droplet Digital Lamp for Absolute Quantification of Cancer Biomarkers. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1624. [PMID: 32183359 PMCID: PMC7146133 DOI: 10.3390/s20061624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022]
Abstract
Microfluidic (MF) advancements have been leveraged toward the development of state-of-the-art platforms for molecular diagnostics, where isothermal amplification schemes allow for further simplification of DNA detection and quantification protocols. The MF integration with loop-mediated isothermal amplification (LAMP) is today the focus of a new generation of chip-based devices for molecular detection, aiming at fast and automated nucleic acid analysis. Here, we combined MF with droplet digital LAMP (ddLAMP) on an all-in-one device that allows for droplet generation, target amplification, and absolute quantification. This multilayer 3D chip was developed in less than 30 minutes by using a low-cost and extremely adaptable production process that exploits direct laser writing technology in "Shrinky-dinks" polystyrene sheets. ddLAMP and target quantification were performed directly on-chip, showing a high correlation between target concentration and positive droplet score. We validated this integrated chip via the amplification of targets ranging from five to 500,000 copies/reaction. Furthermore, on-chip amplification was performed in a 10 µL volume, attaining a limit of detection of five copies/µL under 60 min. This technology was applied to quantify a cancer biomarker, c-MYC, but it can be further extended to any other disease biomarker.
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Affiliation(s)
- Beatriz Oliveira
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Hugo Águas
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Rodrigo Martins
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Elvira Fortunato
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes. J Clin Microbiol 2020; 58:JCM.01684-19. [PMID: 31896667 DOI: 10.1128/jcm.01684-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/13/2019] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx 1 and stx 2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the "top 7" Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E. coli strains, regular PCR cannot confirm whether the virulence genes are carried by adulterant or nonadulterant E. coli serogroups. Thus, traditional gold-standard STEC detection requires bacterial isolation and characterization, which are not compatible with high-throughput settings and often take a week to obtain a definitive result. In this study, we demonstrated that the partition-based multichannel digital PCR (dPCR) system can be used to detect and associate the E. coli serogroup-specific gene with major virulence genes and developed a single-cell-based dPCR approach for rapid (within 1 day) and accurate detection and confirmation of major STEC serogroups in high-throughput settings. Major virulence genes carried by each of the top 7 STEC serogroups were detected by dPCR with appropriately diluted intact bacterial cells from pure cultures, culture-spiked cattle feces, and culture-spiked ground beef. Furthermore, from 100 randomly collected, naturally shed cattle fecal samples, 3 O103 strains carrying eae and 2 O45 strains carrying stx 1 were identified by this dPCR assay and verified by the traditional isolation method. This novel and rapid dPCR assay is a culture-independent, high-throughput, accurate, and sensitive method for STEC detection and confirmation.
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Yu S, Wang XS, Cao KC, Bao XJ, Yu J. Identification of CDK6 and RHOU in Serum Exosome as Biomarkers for the Invasiveness of Non-functioning Pituitary Adenoma. ACTA ACUST UNITED AC 2020; 34:168-176. [PMID: 31601299 DOI: 10.24920/003585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective To explore circulating biomarkers for screening the invasiveness of non-functioning pituitary adenomas (NF-PAs). Methods The exosomal RNAs were extracted from serum of patients with invasive NF-PA (INF-PA) or noninvasive NF-PA (NNF-PA). Droplet digital PCR was adapted to detect the mRNA expression of candidate genes related to tumor progression or invasion, such as cyclin dependent kinase 6 (CDK6), ras homolog family member U (RHOU), and spire type actin nucleation factor 2 (SPIRE2). Student's t-test was used to analyze the statistical difference in the mRNA expression of candidate genes between the two groups. Receiver operating characteristic (ROC) curve was used to establish a model for predicting the invasiveness of NF-PAs. The accuracy, sensitivity, specificity and precision of the model were then obtained to evaluate the diagnostic performance. Results CDK6 (0.2600±0.0912 vs. 0.1789±0.0628, t=3.431, P=0.0013) and RHOU mRNA expressions (0.2696±0.1118 vs. 0.1788±0.0857, t=2.946, P=0.0052) were upregulated in INF-PAs patients' serum exosomes as compared to NNF-PAs. For CDK6, the area under the ROC curve (AUC) was 0.772 (95% CI: 0.600-0.943, P=0.005), the accuracy, sensitivity, specificity and precision were 77.27%, 83.33%, 75.00% and 55.56% to predict the invasiveness of NF-PAs. For RHOU, the AUC was 0.757 (95% CI: 0.599-0.915, P=0.007), the accuracy, sensitivity, specificity and precision were 72.73%, 83.33%, 68.75% and 50.00%. In addition, the mRNA levels of CDK6 and RHOU in serum exosomes were significantly positively correlated (r=0.935, P<0.001). After combination of the cut-off scores of the two genes, the accuracy, sensitivity, specificity and precision were 81.82%, 83.33%, 81.25% and 62.50%. Conclusions CDK6 and RHOU mRNA in serum exosomes can be used as markers for predicting invasiveness of NF-PAs. Combination of the two genes performs better in distinguishing INF-PAs from NNF-PAs. These results indicate CDK6 and RHOU play important roles in the invasiveness of NF-PAs, and the established diagnostic method is valuable for directing the clinical screening and postoperative treatment.
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Affiliation(s)
- Shan Yu
- State Key Laboratory of Medical Molecular Biology & Key Laboratory of RNA and Hematopoietic Regulation & Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Xiao-Shuang Wang
- State Key Laboratory of Medical Molecular Biology & Key Laboratory of RNA and Hematopoietic Regulation & Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Kai-Can Cao
- Department of Thoracic Surgery, Nanfang Hospital, Guangzhou 510515, China
| | - Xin-Jie Bao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology & Key Laboratory of RNA and Hematopoietic Regulation & Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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Jahne MA, Brinkman NE, Keely SP, Zimmerman BD, Wheaton EA, Garland JL. Droplet digital PCR quantification of norovirus and adenovirus in decentralized wastewater and graywater collections: Implications for onsite reuse. WATER RESEARCH 2020; 169:115213. [PMID: 31671297 PMCID: PMC7017454 DOI: 10.1016/j.watres.2019.115213] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 05/04/2023]
Abstract
Risk-based treatment of onsite wastewaters for decentralized reuse requires information on the occurrence and density of pathogens in source waters, which differ from municipal wastewater due to scaling and dilution effects in addition to variable source contributions. In this first quantitative report of viral enteric pathogens in onsite-collected graywater and wastewater, untreated graywater (n = 50 samples) and combined wastewater (i.e., including blackwater; n = 28) from three decentralized collection systems were analyzed for two norovirus genogroups (GI/GII) and human adenoviruses using droplet digital polymerase chain reaction (ddPCR). Compared to traditional quantitative PCR (qPCR), which had insufficient sensitivity to quantify viruses in graywater, ddPCR allowed quantification of norovirus GII and adenovirus in 4% and 14% of graywater samples, respectively (none quantifiable for norovirus GI). Norovirus GII was routinely quantifiable in combined wastewater by either PCR method (96% of samples), with well-correlated results between the analyses (R2 = 0.96) indicating a density range of 5.2-7.9 log10 genome copies/L. These concentrations are greater than typically reported in centralized municipal wastewater, yet agree well with an epidemiology-based model previously used to develop pathogen log-reduction targets (LRTs) for decentralized non-potable water systems. Results emphasize the unique quality of onsite wastewaters, supporting the previous LRTs and further quantitative microbial risk assessment (QMRA) of decentralized water reuse.
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Affiliation(s)
- Michael A Jahne
- Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA.
| | - Nichole E Brinkman
- Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Scott P Keely
- Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Brian D Zimmerman
- Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Emily A Wheaton
- Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Jay L Garland
- Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
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Giraldo PA, Shinozuka H, Spangenberg GC, Cogan NO, Smith KF. Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food? FRONTIERS IN PLANT SCIENCE 2019; 10:1592. [PMID: 31921242 PMCID: PMC6918800 DOI: 10.3389/fpls.2019.01592] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.
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Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Noel O.I. Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, Hamilton, VIC, Australia
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Development of certified reference material NMIJ CRM 6205-a for the validation of DNA quantification methods: accurate mass concentrations of 600-bp DNA solutions having artificial sequences. Anal Bioanal Chem 2019; 411:6091-6100. [PMID: 31289897 DOI: 10.1007/s00216-019-01992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
Abstract
Two 600-bp DNA solutions (DNA600-G and DNA600-T) were developed as certified reference material, NMIJ CRM 6205-a, for the validation of DNA quantification methods. Both DNA600-G and DNA600-T are ideal as "spike-in control" because these materials have artificial nucleic acid sequences. The certified values were determined as the mass concentration of total DNA (whole DNA materials in sample solution regardless of sequence) at 25 °C by formic acid hydrolysis/liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) and inductively coupled plasma-mass spectrometry (ICP-MS) based on the amount of phosphorus. DNAs were synthesized, and plasmids including the synthesized DNAs were cloned into Escherichia coli DH5α. The amplified plasmids were digested with a restriction enzyme and highly purified. Then, the purified DNAs were diluted with water to approximately 1 ng/μL. By using the CRM-validated methods in fields where DNA quantification is required, the reliability of DNA quantification could be improved. Graphical abstract.
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A New Strategy for the Detection of Chicken Infectious Anemia Virus Contamination in Attenuated Live Vaccine by Droplet Digital PCR. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2750472. [PMID: 31223613 PMCID: PMC6541982 DOI: 10.1155/2019/2750472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/07/2019] [Indexed: 12/19/2022]
Abstract
Chicken infectious anemia virus (CIAV) causes the atrophy of bone marrow hematopoietic and lymphoid tissues in chicks, leading to huge economic losses all over the world. The using of attenuated vaccine contaminated with CIAV increased the mortality and the pathogenicity of other diseases in many farms. However, it is difficult to detect the CIAV contamination by general detection technology due to the extremely low dose of CIAV in vaccines. In this study, we established a new method called droplet digital Polymerase Chain Reaction (ddPCR) to detect CIAV contamination of vaccines more sensitively and accurately. The lowest detection limitation of this method is 2.4 copies of CIAV plasmid or CIAV contamination at 0.1 EID50/1000 feathers in vaccines without any positive signals of other viruses. Besides, the sensitivity of ddPCR is 100 times greater than that of conventional PCR and 10 times greater than that of real-time PCR. The ddPCR technique is more sensitive and more intuitive. Therefore, it could be valuable for the detection of CIAV contamination in vaccines.
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Effects of Physico-Chemical Parameters on Actinomycetes Communities during Composting of Agricultural Waste. SUSTAINABILITY 2019. [DOI: 10.3390/su11082229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The objective of this study was to investigate the influence of physico-chemical parameters on Actinomycetes communities and to prioritize those parameters that contributed to Actinomycetes community composition during the composting of agricultural waste. Denaturing gradient gel electrophoresis of polymerase chain reaction (PCR-DGGE) and redundancy analysis (RDA) were used to determine the relationships between those parameters and Actinomycetes community composition. Quantitative PCR (qPCR) and regression analysis were used to monitor the 16S rDNA copy numbers of Actinomycetes and to analyse the correlations between physico-chemical parameters and Actinomyces 16S rDNA gene abundance, respectively. The RDA results showed that moisture content, water soluble carbon (WSC) and pH (p < 0.05) made the main contributions to the temporal variations of Actinomycetes community composition. The output of the regression analysis indicated that moisture content (R2 = 0.407, p < 0.01) showed a negative linear relationship with the Actinomyces 16S rDNA gene abundance.
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Emslie KR, H McLaughlin JL, Griffiths K, Forbes-Smith M, Pinheiro LB, Burke DG. Droplet Volume Variability and Impact on Digital PCR Copy Number Concentration Measurements. Anal Chem 2019; 91:4124-4131. [PMID: 30775910 DOI: 10.1021/acs.analchem.8b05828] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Digital polymerase chain reaction (dPCR) is increasingly being adopted by reference material producers and metrology institutes for value assignment, and for homogeneity and stability studies of nucleic acid reference materials. A reference method procedure should fulfill several requirements, and the uncertainty and biases should be completely understood. A bias in target concentration when inaccurate droplet volume is used in the droplet dPCR measurement equation has previously been documented. In this study, we characterize both intrawell and interwell droplet volume variability using optical microscopy and determine the impact of these two sources of variability on target concentration estimates. A small optical distortion across the image was measured which, without correction, biased droplet volume measurements. Longitudinal monitoring of interwell droplet volume over 39 weeks using several lots of Mastermix demonstrated a mean droplet volume of 0.786 nL and intermediate precision of 1.7%. The frequency distribution of intrawell droplet volumes varied. Some wells displayed a skewed distribution which resulted in a small bias in estimated target concentration for a simulated dPCR with target concentrations of between 62 and 8000 copies μL-1. The size and direction of this bias was influenced by the distribution pattern of the droplet volumes within the well. The proportion of Mastermix in dPCR mix affected droplet volume. A pipetting error of 10% during mixing of the premix and Mastermix resulted in a 2.6% change in droplet volume and, consequently, a bias in concentration measurements highlighting the advantages of gravimetric preparation of dPCR mixes for high accuracy measurements.
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Affiliation(s)
- Kerry R Emslie
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | | | - Kate Griffiths
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | | | - Leonardo B Pinheiro
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | - Daniel G Burke
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
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Wu Y, Li J, Li X, Zhai S, Gao H, Li Y, Zhang X, Wu G. Development and strategy of reference materials for the DNA-based detection of genetically modified organisms. Anal Bioanal Chem 2019; 411:1729-1744. [DOI: 10.1007/s00216-019-01576-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
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Giraldo PA, Cogan NOI, Spangenberg GC, Smith KF, Shinozuka H. Development and Application of Droplet Digital PCR Tools for the Detection of Transgenes in Pastures and Pasture-Based Products. FRONTIERS IN PLANT SCIENCE 2019; 9:1923. [PMID: 30671074 PMCID: PMC6331530 DOI: 10.3389/fpls.2018.01923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Implementation of molecular biotechnology, such as transgenic technologies, in forage species can improve agricultural profitability through achievement of higher productivity, better use of resources such as soil nutrients, water, or light, and reduced environmental impact. Development of detection and quantification techniques for genetically modified plants are necessary to comply with traceability and labeling requirements prior to regulatory approval for release. Real-time PCR has been the standard method used for detection and quantification of genetically modified events, and droplet digital PCR is a recent alternative technology that offers a higher accuracy. Evaluation of both technologies was performed using a transgenic high-energy forage grass as a case study. Two methods for detection and quantification of the transgenic cassette, containing modified fructan biosynthesis genes, and a selectable marker gene, hygromycin B phosphotransferase used for transformation, were developed. Real-time PCR was assessed using two detection techniques, SYBR Green I and fluorescent probe-based methods. A range of different agricultural commodities were tested including fresh leaves, tillers, seeds, pollen, silage and hay, simulating a broad range of processed agricultural commodities that are relevant in the commercial use of genetically modified pastures. The real-time and droplet digital PCR methods were able to detect both exogenous constructs in all agricultural products. However, a higher sensitivity and repeatability in transgene detection was observed with the droplet digital PCR technology. Taking these results more broadly, it can be concluded that the droplet digital PCR technology provides the necessary resolution for quantitative analysis and detection, allowing absolute quantification of the target sequence at the required limits of detection across all jurisdictions globally. The information presented here provides guidance and resources for pasture-based biotechnology applications that are required to comply with traceability requirements.
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Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria, Hamilton, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
- Agriculture Victoria, Hamilton, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
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Abstract
Digital PCR-based methods, such as droplet digital PCR, are one of the best tools for determination of absolute nucleic-acid copy numbers. These techniques avoid the need for reference materials with known target concentrations. Compared to real-time PCR, they provide higher accuracy of quantification at low target concentrations, and have higher resilience to inhibitors. In this Chapter, we describe the droplet digital PCR workflow for the detection and quantification of flavescence dorée phytoplasma.
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Affiliation(s)
- Nataša Mehle
- National Institute of Biology, Ljubljana, Slovenia.
| | - Tanja Dreo
- National Institute of Biology, Ljubljana, Slovenia
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Aliabadi A, Rounaghi GH. A novel electrochemical sensor for determination of morphine in a sub-microliter of human urine sample. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2018.10.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Zhu K, Chi J, Zhang D, Ma B, Dong X, Yang J, Zhao C, Liu H. Bio-inspired photonic crystals for naked eye quantification of nucleic acids. Analyst 2019; 144:5413-5419. [DOI: 10.1039/c9an01042d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantitative detection of nucleic acids by the naked eye was achieved based on structural color.
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Affiliation(s)
- Ke Zhu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Junjie Chi
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Dagan Zhang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Biao Ma
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Xing Dong
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Jun Yang
- Nanjing Institute for Food and Drug Control
- Nanjing
- PR China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
| | - Hong Liu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing 210096
- China
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