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Liang C, Yang H, Yang X, Long Z, Zhou Y, Wang J, Fan L, Zeng M, Wang Y, Zheng H, Wang Z, Ye P, Lin J, Shi W, Huang H, Yan H, Qian J, Li L, Liu L. Applying improved ddPCR to reliable quantification of MPXV in clinical settings. Microbiol Spectr 2024:e0001824. [PMID: 38757960 DOI: 10.1128/spectrum.00018-24] [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: 01/03/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Monkeypox virus (MPXV) poses a global health threat. Droplet digital PCR (ddPCR) holds potential as an accurate diagnostic tool for clinical microbiology. However, there is limited literature on the applicability of ddPCR in clinical settings. In this study, the clinical features of patients with MPXV during the initial outbreak in China in June 2023 were reviewed, and an optimized ddPCR method with dilution and/or inhibitor removal was developed to enhance MPXV detection efficiency. Eighty-two MPXV samples were tested from nine different clinical specimen types, including feces, urine, pharyngeal swabs, anal swabs, saliva, herpes fluid, crust, and semen, and the viral load of each specimen was quantified. A comparative analysis was performed with qPCR to assess sensitivity and specificity and to investigate the characteristics of MPXV infection by analyzing viral loads in different clinical specimens. Consequently, common pharyngeal and gastrointestinal symptoms were observed in patients with MPXV. The optimized ddPCR method demonstrated relatively high sensitivity for MPXV quantification in the clinical materials, with a limit of detection of 0.1 copies/μL. This was particularly evident in low-concentration samples like whole blood, semen, and urine. The optimized ddPCR demonstrated greater detection accuracy compared with normal ddPCR and qPCR, with an area under the curve (AUC) of 0.939. Except for crust samples, viral loads in the specimens gradually decreased as the disease progressed. Virus levels in feces and anal swabs kept a high detection rate at each stage of post-symptom onset, and feces and anal swabs samples may be suitable for clinical diagnosis and continuous monitoring of MPXV. IMPORTANCE The ddPCR technique proved to be a sensitive and valuable tool for accurately quantifying MPXV viral loads in various clinical specimen types. The findings provided valuable insights into the necessary pre-treatment protocols for MPXV diagnosis in ddPCR detection and the potentially suitable sample types for collection. Therefore, such results can aid in comprehending the potential characteristics of MPXV infection and the usage of ddPCR in clinical settings.
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Affiliation(s)
- Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Huiqin Yang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Zhenyu Long
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Jian Wang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Mou Zeng
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Haipeng Zheng
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
- The Third People's Hospital of Bijie City, Bijie, Guizhou, China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Linghua Li
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Linna Liu
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
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Sánchez-Carvajal JM, Vera-Salmoral E, Huerta B, Galán-Relaño Á, Ruedas-Torres I, Larenas-Muñoz F, Luque I, Carrasco L, Gómez-Laguna J. Droplet digital PCR as alternative to microbiological culture for Mycobacterium tuberculosis complex detection in bovine lymph node tissue samples. Front Cell Infect Microbiol 2024; 14:1349999. [PMID: 38469351 PMCID: PMC10925636 DOI: 10.3389/fcimb.2024.1349999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Bovine tuberculosis (bTB) caused by Mycobacterium tuberculosis complex (MTC) remains a significant concern for public health. Direct real-time PCR and droplet digital PCR (ddPCR) are proposed as alternative tools to enhance diagnostic precision and efficiency. This study aims to assess the diagnostic performance of a ddPCR assay targeting IS6110 for the detection of MTC DNA in both microbiological culture and fresh lymph node (LN) tissue samples obtained from cattle, in comparison with the established reference standard, the microbiological culture followed by real-time PCR. Methods The fresh LNs (N=100) were collected each from a different cattle carcass at the slaughterhouse. The limit of detection of ddPCR-IS6110 was set to 101 copies per 20 μl reaction. Results DdPCR-IS6110 detected 44 out of 49 reference-standard positive samples and yielded negative results in 47 out of 51 reference-standard negative samples, resulting in adjusted sensitivity (Se) and specificity (Sp) of 90.76% [95% confidence interval (CI): 82.58 - 98.96%)], and 100% (95% CI: 100%) respectively. The estimated adjusted false negative rate (FNR) was 9.23% (95% CI: 1.04 - 17.42%) and the false positive rate (FPR) was 0% (95% CI: 0%). When directly applied from fresh bovine LN tissues, ddPCR-IS6110 identified 47 out of 49 reference-standard positive samples as ddPCR-IS6110-positive and 42 out of 51 reference-standard negative samples as ddPCR-IS6110-negative, resulting in adjusted Se and Sp values of 94.80% [95% (CI): 88.52 - 100%] and 100% (95% CI: 100%), respectively. The adjusted FNR was 5.20% (95% CI: 0 - 11.50%) and the FPR was 0% (95% CI: 0%). Noteworthy, ddPCR-IS6110 disclosed as positive 9 samples negative to reference-standard. Discussion DdPCR-IS6110 proved to be a rapid, highly sensitive, and specific diagnostic tool as an alternative to reference-standard method.
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Affiliation(s)
- José María Sánchez-Carvajal
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Eduardo Vera-Salmoral
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Belén Huerta
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Ángela Galán-Relaño
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Inés Ruedas-Torres
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
- UK Health Security Agency (UKHSA), Salisbury, United Kingdom
| | - Fernanda Larenas-Muñoz
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Inmaculada Luque
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Librado Carrasco
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
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Haqshenas G, Garland SM, Balgovind P, Cornall A, Danielewski J, Molano M, Machalek DA, Murray G. Development of a touchdown droplet digital PCR assay for the detection and quantitation of human papillomavirus 16 and 18 from self-collected anal samples. Microbiol Spectr 2023; 11:e0183623. [PMID: 37962350 PMCID: PMC10714734 DOI: 10.1128/spectrum.01836-23] [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: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE The quantity of the human papillomavirus (HPV) is associated with disease outcome. We designed an accurate and precise digital PCR assay for quantitating HPV in anal samples, a sample type that is typically problematic due to the presence of PCR inhibitors.
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Affiliation(s)
- Gholamreza Haqshenas
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Suzanne M. Garland
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Prisha Balgovind
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Alyssa Cornall
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Jennifer Danielewski
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Monica Molano
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
| | - Dorothy A. Machalek
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Gerald Murray
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
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Rashid SA, Nazakat R, Muhamad Robat R, Ismail R, Suppiah J, Rajendran K, Raj Louis Masalamany ASS, Muhamad Hendri NA, Mohamad N, Khairul Hasni NA, Suib FA, Nik Hassan NMN, Pahrol MA, Shaharudin R. Droplet digital PCR application for the detection of SARS-CoV-2 in air sample. Front Public Health 2023; 11:1208348. [PMID: 37965510 PMCID: PMC10641526 DOI: 10.3389/fpubh.2023.1208348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) may transmit through airborne route particularly when the aerosol particles remain in enclosed spaces with inadequate ventilation. There has been no standard recommended method of determining the virus in air due to limitations in pre-analytical and technical aspects. Furthermore, the presence of low virus loads in air samples could result in false negatives. Our study aims to explore the feasibility of detecting SARS-CoV-2 ribonucleic acid (RNA) in air samples using droplet digital polymerase chain reaction (ddPCR). Active and passive air sampling was conducted between December 2021 and February 2022 with the presence of COVID-19 confirmed cases in two hospitals and a quarantine center in Klang Valley, Malaysia. SARS-CoV-2 RNA in air was detected and quantified using ddPCR and real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The comparability of two different digital PCR platforms (QX200 and QIAcuity) to RT-PCR were also investigated. Additionally negative staining transmission electron microscopy was performed to visualize virus ultrastructure. Detection rates of SARS-CoV-2 in air samples using ddPCR were higher compared to RT-PCR, which were 15.2% (22/145) and 3.4% (5/145), respectively. The sensitivity and specificity of ddPCR was 100 and 87%, respectively. After excluding 17 negative samples (50%) by both QX200 and QIAcuity, 15% samples (5/34) were found to be positive both ddPCR and dPCR. There were 23.5% (8/34) samples that were detected positive by ddPCR but negative by dPCR. In contrast, there were 11.7% (4/34) samples that were detected positive by dPCR but negative by ddPCR. The SARS-CoV-2 detection method by ddPCR is precise and has a high sensitivity for viral RNA detection. It could provide advances in determining low viral titter in air samples to reduce false negative reports, which could complement detection by RT-PCR.
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Affiliation(s)
- Siti Aishah Rashid
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Raheel Nazakat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Rosnawati Muhamad Robat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Rohaida Ismail
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Jeyanthi Suppiah
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Kamesh Rajendran
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - A. S. Santhana Raj Louis Masalamany
- Special Resource Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nur Afrina Muhamad Hendri
- Special Resource Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nadia Mohamad
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nurul Amalina Khairul Hasni
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Fatin Amirah Suib
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nik Muhamad Nizam Nik Hassan
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Muhammad Alfatih Pahrol
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Rafiza Shaharudin
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
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Zhang N, Li C, Dou X, Du Y, Tian F. Test Article for automation purposes. Crit Rev Anal Chem 2023; 53:1969-1989. [PMID: 37881955 DOI: 10.1080/10408347.2022.2042999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.
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Affiliation(s)
- Ning Zhang
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Chao Li
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Xuechen Dou
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Yaohua Du
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Feng Tian
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
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Lv N, Zhao Y, Song Y, Ji M, Zhou Y. Development of a sensitive droplet digital PCR according to the HPV infection specificity in Chinese population. BMC Cancer 2023; 23:1022. [PMID: 37872500 PMCID: PMC10594741 DOI: 10.1186/s12885-023-11529-3] [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: 06/29/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023] Open
Abstract
HPV16 and 18 are positively correlated with cervical carcinogenesis. However, HPV prevalence tends to vary according to region, nationality, and environment. The most prevalent high-risk (HR) HPV genotypes are HPV16, 52, 58, 56, 18, 33, and 45), while the low-risk (LR) genotypes are HPV6 and 11 in the Chinese population. Importantly, undetectable low-copy HPV DNA could be an important indicator of integration into the human genome and may be a precursor to cancer progression. The HPV viral load changes dramatically, either increasing or decreasing rapidly during carcinogenesis, and traditional quantitative real-time PCR (qPCR) cannot accurately capture this subtle change. Therefore, in this study, a reliable droplet digital PCR (ddPCR) method was developed to simultaneously detect and quantify HPV genotypes. The ddPCR quantitative results showed high accuracy, sensitivity, and specificity compared to qPCR results employing the same clinical specimens and supplemented the ddPCR assay for HPV52/56/58/6 genotypes according to the infection specificity of the Chinese population. In summary, this procedure is valuable for quantifying HPV DNA, especially under conditions of low template copy number in cervical intraepithelial neoplasia (CIN) and/or cervical cancer. Additionally, this method can dynamically observe the prognosis and outcome of HPV infection and thus be used as an effective means for real-time monitoring of tumor load.
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Affiliation(s)
- Nan Lv
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, 250013, People's Republic of China
| | - Yue Zhao
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, 250013, People's Republic of China
| | - Yiying Song
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, 250013, People's Republic of China
| | - Mingyu Ji
- Medical Research & Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, No.105, Jiefang Road, Lixia Area, Jinan, 250013, People's Republic of China
| | - Yunying Zhou
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, 250013, People's Republic of China.
- Medical Research & Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, No.105, Jiefang Road, Lixia Area, Jinan, 250013, People's Republic of China.
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Huang Y, Sun L, Liu W, Yang L, Song Z, Ning X, Li W, Tan M, Yu Y, Li Z. Multiplex single-cell droplet PCR with machine learning for detection of high-risk human papillomaviruses. Anal Chim Acta 2023; 1252:341050. [PMID: 36935138 DOI: 10.1016/j.aca.2023.341050] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/12/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
High-risk human papillomavirus (HPV) testing can significantly decline the incidence and mortality of cervical cancer. Microfluidic technology provides an effective method for accurate detection of high-risk HPV by utilizing multiplex single-cell droplet polymerase chain reaction (PCR). However, current strategies are limited by low-integration microfluidic chip, complex reagent system, expensive detection equipment and time-consuming droplet identification. Here, we developed a novel multiplex droplet PCR method that directly detected high-risk HPV sequences in single cells. A multiplex microfluidic chip integrating four flow-focusing structures was designed for one-step and parallel droplet preparation. Using single-cell droplet PCR, multi-target sequences were detected simultaneously based on a monochromatic fluorescence signal. We applied machine learning to automatically identify the large populations of single-cell droplets with 97% accuracy. HPV16, 18 and 45 sequences were sensitively detected without cross-contamination in mixed CaSki and Hela cells. The approach enables rapid and reliable detection of multi-target sequences in single cells, making it powerful for investigating cellular heterogeneity related to cancer diagnosis and treatment.
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Affiliation(s)
- Yizheng Huang
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linjun Sun
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Semiconductor Neural Network Intelligent Sensing and Computing Technology, Beijing, 100083, China
| | - Wenwen Liu
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Ling Yang
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Zhigang Song
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Xin Ning
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Semiconductor Neural Network Intelligent Sensing and Computing Technology, Beijing, 100083, China
| | - Weijun Li
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Semiconductor Neural Network Intelligent Sensing and Computing Technology, Beijing, 100083, China
| | - Manqing Tan
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yude Yu
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China
| | - Zhao Li
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
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Tian Y, Fei J, Luo J, Chen L, Ye J, Du W, Yu C. Development of a reverse-transcription droplet digital PCR method for quantitative detection of Cucumber green mottle mosaic virus. Heliyon 2022; 9:e12643. [PMID: 36865460 PMCID: PMC9970901 DOI: 10.1016/j.heliyon.2022.e12643] [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: 06/14/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is a re-emerging threat to the production of greenhouse cucumber and other Cucurbitaceae crops worldwide. This seed-borne virus can easily spread from a contaminated seed to seedlings and adjacent plants by mechanical contact between the foliage of diseased and healthy plants, causing extensive yield losses. An accurate method for detecting and quantifying this virus is urgently needed to ensure the safety of the global seed trade. Here, we report the development of a reverse-transcription droplet digital polymerase chain reaction (RT-ddPCR)-based method for specific and high-sensitive detection of CGMMV. By testing three primer-probe sets and optimizing reaction conditions, we showed that the newly developed RT-ddPCR method is highly specific and sensitive, with a detection limit of 1 fg/μL (0.39 copy/μL). The sensitivity of the RT-ddPCR method was compared with that of real-time fluorescence quantitative RT-PCR (RT-qPCR) using a series of plasmid dilutions and total RNAs extracted from infected cucumber seeds, and the detection limit of RT-ddPCR was 10 times higher than RT-qPCR with plasmid dilutions and 100 times higher than RT-qPCR for detecting CGMMV from infected cucumber seeds. The RT-ddPCR method was further assessed for detecting CGMMV from a total of 323 samples of Cucurbitaceae seeds, seedlings, and fruits as compared with the RT-qPCR method. We found that the infection rate of CGMMV on symptomatic fruits was as high as 100%, whereas infection rates were lower for seeds and lowest for seedlings. Notably, the results of two methods in detecting CGMMV from different cucurbit tissues showed the high consistency with Kappa value from 0.84 to 1.0, demonstrating that the newly developed RT-ddPCR method is highly reliable and practically useful for large-scale CGMMV detection and quantification.
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Affiliation(s)
- Yimin Tian
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs District, Shanghai 200135, China
| | - Jing Fei
- Technical Center for Industrial Product and Raw Material Inspection and Testing, Shanghai Customs District, Shanghai 200135, China
| | - Jinyan Luo
- Shanghai Agricultural Technology Extension Center, Shanghai 201103, China
| | - Lei Chen
- Shanghai Agricultural Technology Extension Center, Shanghai 201103, China
| | - Jun Ye
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs District, Shanghai 200135, China
| | - Wei Du
- Agricultural Technology Extension Station of Ningxia, Yinchuan 750001, China
| | - Cui Yu
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs District, Shanghai 200135, China,Corresponding author.
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9
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Ren Z, Chen R, Muhae-Ud-Din G, Fang M, Li T, Yang Y, Chen W, Gao L. Development of real-time PCR and droplet digital PCR based marker for the detection of Tilletia caries inciting common bunt of wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1031611. [PMID: 36507438 PMCID: PMC9732894 DOI: 10.3389/fpls.2022.1031611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
This is the first study reporting droplet digital PCR and quantitative real time PCR for detection of Tilletia caries (syn. T. tritici), which causes common bunt of wheat and leads to yield losses of 80% in many wheat growing areas worldwide. To establish an accurate, rapid and quantifiable detection method, we tested 100 inter simple sequence repeats (ISSR) primers and obtained a species-specific fragment (515 bp) generated by ISSR 827. Then, a specific 266 bp band for the sequence characterized amplified region (SCAR) marker was produced from T. caries. The detection limit reached 50 pg/μL. Based on the SCAR marker, we further developed a higher sensitivity of quantitative real time-polymerase chain reaction (qRT-PCR) with a detection limit of 2.4 fg/μL, and droplet digital PCR (ddPCR) with a detection limit of 0.24 fg/μL. Both methods greatly improved the detection sensitivity of T. caries, which will be contribute a lot for quickly and accurately detection of T. caries, which causes wheat common bunt.
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Affiliation(s)
- Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rongzhen Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Protection, Shenyang Agricultural University, Liaoning, China
| | - Ghulam Muhae-Ud-Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingke Fang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Tianya Li
- Department of Plant Protection, Shenyang Agricultural University, Liaoning, China
| | - Yazheng Yang
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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10
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CRISPR-Cas-mediated diagnostics. Trends Biotechnol 2022; 40:1326-1345. [PMID: 35595574 DOI: 10.1016/j.tibtech.2022.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023]
Abstract
An ideal molecular diagnostic method should be sensitive, specific, low cost, rapid, portable, and easy to operate. Traditional nucleic acid detection methods based mainly on PCR technology have not only high sensitivity and specificity, but also some limitations, such as the need for expensive equipment and skilled technicians, being both time and labor intensive, and difficult to implement in some regions. However, with the continuous development of CRISPR-Cas technology and its application in molecular diagnosis, new approaches have been used for the construction of molecular diagnostic systems. In this review, we discuss recent advances in CRISPR-based molecular diagnostic technologies and highlight the revolution they bring to the field of molecular diagnostics.
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11
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Macios A, Nowakowski A. False Negative Results in Cervical Cancer Screening-Risks, Reasons and Implications for Clinical Practice and Public Health. Diagnostics (Basel) 2022; 12:1508. [PMID: 35741319 PMCID: PMC9222017 DOI: 10.3390/diagnostics12061508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
False negative (FN) results in cervical cancer (CC) screening pose serious risks to women. We present a comprehensive literature review on the risks and reasons of obtaining the FN results of primary CC screening tests and triage methods and discuss their clinical and public health impact and implications. Misinterpretation or true lack of abnormalities on a slide are the reasons of FN results in cytology and p16/Ki-67 dual-staining. For high-risk human papillomavirus (HPV) molecular tests, those include: truly non-HPV-associated tumors, lesions driven by low-risk HPV types, and clearance of HPV genetic material before sampling. Imprecise disease threshold definition lead to FN results in visual inspection with acetic acid. Lesions with a discrete colposcopic appearance are a source of FN in colposcopic procedures. For FAM19A4 and hsa-miR124-2 genes methylation, those may originate from borderline methylation levels. Histological misinterpretation, sampling, and laboratory errors also play a role in all types of CC screening, as well as reproducibility issue, especially in methods based on human-eye evaluation. Primary HPV-based screening combined with high quality-assured immunocytochemical and molecular triage methods seem to be an optimal approach. Colposcopy with histological evaluation remains the gold standard for diagnosis but requires quality protocols and assurance measures.
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Affiliation(s)
- Anna Macios
- Doctoral School of Translational Medicine, Centre of Postgraduate Medical Education, Marymoncka Street 99/103, 01-813 Warsaw, Poland
- Department of Cancer Prevention, The Maria Sklodowska-Curie National Research Institute of Oncology, Roentgen Street 5, 02-781 Warsaw, Poland
| | - Andrzej Nowakowski
- Department of Cancer Prevention, The Maria Sklodowska-Curie National Research Institute of Oncology, Roentgen Street 5, 02-781 Warsaw, Poland
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12
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Williams J, Kostiuk M, Biron VL. Molecular Detection Methods in HPV-Related Cancers. Front Oncol 2022; 12:864820. [PMID: 35574396 PMCID: PMC9092940 DOI: 10.3389/fonc.2022.864820] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Human papillomavirus (HPV) is responsible for most cervical cancers and some head and neck cancers, including oropharyngeal squamous cell carcinoma and sinonasal carcinoma. Cervical cancer is commonly diagnosed by liquid-based cytology, followed by HPV testing using commercially available DNA polymerase chain reaction (PCR), p16 immunohistochemistry (IHC), or DNA/RNA in situ hybridization. HPV in head and neck cancers is commonly diagnosed by p16 IHC or by RT-qPCR of HPV-16 E6 and E7 oncoproteins. Droplet digital PCR has been reported as an ultrasensitive and highly precise method of nucleic acid quantification for biomarker analysis and has been used to detect oncogenic HPV in oropharyngeal and cervical cancers.
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Affiliation(s)
- Jordana Williams
- Division of Otolaryngology-Head and Neck Surgery Research Laboratory of Alberta, Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Morris Kostiuk
- Division of Otolaryngology-Head and Neck Surgery Research Laboratory of Alberta, Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Vincent L Biron
- Division of Otolaryngology-Head and Neck Surgery Research Laboratory of Alberta, Department of Surgery, University of Alberta, Edmonton, AB, Canada
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Galati L, Combes JD, Le Calvez-Kelm F, McKay-Chopin S, Forey N, Ratel M, McKay J, Waterboer T, Schroeder L, Clifford G, Tommasino M, Gheit T. Detection of Circulating HPV16 DNA as a Biomarker for Cervical Cancer by a Bead-Based HPV Genotyping Assay. Microbiol Spectr 2022; 10:e0148021. [PMID: 35225653 PMCID: PMC9045285 DOI: 10.1128/spectrum.01480-21] [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: 10/07/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Human papillomavirus (HPV) circulating tumor DNA (HPV ctDNA) was proposed as a biomarker for the detection and disease monitoring of HPV-related cancers. One hundred eighty plasma samples obtained from women diagnosed with HPV16-positive cervical cancer (CC) (n = 100), HPV16-positive premalignant lesions (cervical intraepithelial neoplasia grade 3 [CIN3]) (n = 20), and HPV DNA-negative controls (n = 60) were randomly selected from the archives for evaluating the performance of a bead-based HPV genotyping assay (E7 type-specific multiplex genotyping assay [E7-MPG]) in detecting HPV16 ctDNA. The performance of the E7-MPG was compared with those of DNA detection by droplet digital PCR (ddPCR) and detection of HPV16 E6 antibodies evaluated in an independent study. Internal controls to assess DNA quality were included in the molecular assays, i.e., beta-globin and ESR1, respectively. The sensitivity and specificity of E7-MPG and/or E6 antibodies to detect HPV16-positive CCs were evaluated. HPV16 ctDNA was detected using the E7-MPG in 42.3% of all plasma samples and in 74.7% of plasma samples from HPV16-positive CC cases. The validation of E7-MPG data by ddPCR showed that the sensitivity of the E7-MPG test for HPV16-positive CC detection was higher than that of ddPCR (74.7% versus 63.1%; P < 0.001). When both HPV16 ctDNA and E6 antibodies were considered, the sensitivity for HPV16-positive CC detection increased from 74.7% to 86.1%, while the specificity was unchanged at 97.8%. The performance of E7-MPG for the detection of HPV16 ctDNA appears to be at least as sensitive as that of ddPCR, offering an additional tool for ctDNA detection of HPV16-positive CC. The use of an additional blood marker of HPV infection, such as E6 antibodies, further improved the detection of CC. IMPORTANCE The validity of HPV ctDNA as a marker of HPV-driven cancers has been previously reported. Herein we validated an alternative to ddPCR for HPV16 ctDNA detection, using a bead-based HPV genotyping assay that offers the potential advantage of reducing the cost of clinical management due to the multiplex capability of the test, thus facilitating its use in clinical settings. In addition, we analyzed HPV ctDNA in the context of E6 antibodies as an additional HPV marker. The HPV16 ctDNA biomarker appeared to be highly specific and, to a lesser extent, sensitive for the detection of CC, mainly indicated for those at an advanced tumor stage. In this proof-of-principle study, E6 antibodies were mainly detected in early tumor stages of CC, while HPV ctDNA was mainly positive at advanced tumor stages.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer, Lyon, France
| | | | | | | | - Nathalie Forey
- International Agency for Research on Cancer, Lyon, France
| | - Mathis Ratel
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lea Schroeder
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gary Clifford
- International Agency for Research on Cancer, Lyon, France
| | | | - Tarik Gheit
- International Agency for Research on Cancer, Lyon, France
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14
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Gupta SM, Warke H, Chaudhari H, Mavani P, Katke RD, Kerkar SC, Mania-Pramanik J. Human Papillomavirus E6/E7 oncogene transcripts as biomarkers for the early detection of cervical cancer. J Med Virol 2022; 94:3368-3375. [PMID: 35257379 DOI: 10.1002/jmv.27700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/03/2022] [Indexed: 11/10/2022]
Abstract
Cancer of the cervix uteri is the fourth most common cancer worldwide with a high mortality rate. Due to the limitations of existing methods, alternative methods for triage are needed for early detection of cervical cancer precursors before progression to high grade disease.The aim of this study was to evaluate HPV E6/E7 oncogene expression as markers for early identification of cervical cancer risk in women with minor cytological abnormalities and in those with negative cytology. The detection of HPV was done using PCR and confirmed by southern hybridization. The high risk (HR) and low risk (LR) HPV types were identified by HPV typing. HPV DNA positive patients were further tested for markers of oncogene expression by real time PCR. Out of the women screened, 54/512 (10.54%) women tested positive for HPV infection. HR HPV DNA was found in 32/485 (6.60%) in women with normal cytology (Pap negative) and 22/27 (81.5%) ASCUS/LSIL cases. High-risk HPV E6/E7 oncogene transcripts were detected in 36/512 (7.03%) of these patients. The positivity rate of E6/E7 mRNA was 2.48% (12/485) in the normal cervical cytology group and 88.9% (24/27) in abnormal cervical cytology group. The HPV E6/E7mRNA test sensitivity was found to be 88.89% and specificity was 97.53%. In comparison the sensitivity of HPV DNA test was found to be 81.48% and specificity was 93.40%. In conclusion, E6 and E7 transcripts could provide a sensitive, early predictor of cervical cancer risk in women with normal cytology and minor cytological alterations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sadhana M Gupta
- Department of Infectious Diseases Biology, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Himangi Warke
- Department of Obstetrics and Gynecology, Seth G.S Medical College & King Edward Memorial Hospital, Mumbai, India
| | - Hemangi Chaudhari
- Department of Obstetrics and Gynecology, Seth G.S Medical College & King Edward Memorial Hospital, Mumbai, India
| | - Padmaja Mavani
- Department of Obstetrics and Gynecology, Seth G.S Medical College & King Edward Memorial Hospital, Mumbai, India
| | - Rajshree D Katke
- Department of Obstetrics and Gynecology, Cama and Albless Hospital, Mumbai, India
| | - Shilpa C Kerkar
- Department of Infectious Diseases Biology, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Jayanti Mania-Pramanik
- Department of Infectious Diseases Biology, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, India
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15
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Zhang N, Li C, Dou X, Du Y, Tian F. Overview and Future Perspectives of Microfluidic Digital Recombinase Polymerase Amplification (dRPA). Crit Rev Anal Chem 2022; 52:1969-1989. [PMID: 35201910 DOI: 10.1080/10408347.2022.2042669] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.
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Affiliation(s)
- Ning Zhang
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Chao Li
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Xuechen Dou
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Yaohua Du
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Feng Tian
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
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16
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De Falco F, Cutarelli A, D'Alessio N, Cerino P, Catoi C, Roperto S. Molecular Epidemiology of Ovine Papillomavirus Infections Among Sheep in Southern Italy. Front Vet Sci 2021; 8:790392. [PMID: 34881323 PMCID: PMC8645557 DOI: 10.3389/fvets.2021.790392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Ovine papillomaviruses (OaPVs) were detected and quantified, for the first time, using droplet digital polymerase chain reaction (ddPCR) and real-time quantitative PCR (qPCR) via blood samples of 165 clinically healthy sheep. OaPV DNA was detected in 126 blood samples (~76.4%). DdPCR detected OaPV DNA in 124 samples; in only two additional samples positive for real-time qPCR, ddPCR failed to detect the presence of any OaPVs. In 70 of the positive samples (~55.6%), a single OaPV infection was observed, 12 of which were caused by OaPV1 (~17.1%) and 14 by OaPV2 (20%). OaPV3 was responsible for 19 single infections (~27.1%), and OaPV4 for 25 single infections (~35.7%). Multiple OaPV coinfections were observed in 56 (~44.4%) positive samples. OaPV coinfections caused by two genotypes were observed in 31 positive samples (~55.4%), with dual OaPV3/OaPV4 infection being the most prevalent as seen in 11 blood samples. In addition, five OaPV1/OaPV4, four OaPV1/OaPV2, four OaPV2/OaPV3, four OaPV1/OaPV3, and three OaPV2/OaPV4 dual coinfections were also detected. OaPV coinfections by triple and quadruple genotypes were detected in 24 (~42.8%) and only one (~1.8%) of coinfected blood samples, respectively. Multiple infections caused by OaPV1/OaPV3/OaPV4 genotypes were the most prevalent, as observed in 12 (50%) blood samples harboring triple OaPV infections. This study showed that ddPCR is the most sensitive and accurate assay for OaPV detection and quantification thus outperforming real-time qPCR in terms of sensitivity and specificity. Therefore, ddPCR may represent the molecular diagnostic tool of choice, ultimately providing useful insights into OaPV molecular epidemiology and field surveillance.
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Affiliation(s)
- Francesca De Falco
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Anna Cutarelli
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Nicola D'Alessio
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Cornel Catoi
- Department of Pathology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Sante Roperto
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy
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17
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Huang Y, Pan H, Xu X, Lv P, Wang X, Zhao Z. Droplet digital PCR (ddPCR) for the detection and quantification of Ureaplasma spp. BMC Infect Dis 2021; 21:804. [PMID: 34380416 PMCID: PMC8359095 DOI: 10.1186/s12879-021-06355-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ureaplasma spp. are associated with various infectious diseases in females, but there is still limited evidence regarding whether they are related to nonspecific cervicitis. The aim of this study was to develop and evaluate a digital droplet PCR (ddPCR) assay for the detection and quantification of Ureaplasma spp. in cervical swabs. METHODS A total of 267 non-specific cervicitis (NSC) patients and 195 asymptomatic females were included in this study. We produced standard curves for Ureaplasma spp. to evaluate the analytical performance of the ddPCR assay. Then, we detected and quantified the bacterial load of Ureaplasma spp. in cervical swabs. RESULTS The prevalences of U. parvum were 37.8% (101/267) and 29.7% (58/195), U. urealyticum were 9.0% (24/267) and 8.7% (17/195) in the NSC group and control group, respectively. In addition, the median copy number of U. parvum was 2.5 × 104 copies/ml (n = 101) in the NSC group and 9.2 × 103 copies/ml (n = 58) in the control group. The U. parvum load in the NSC group was significantly higher than that in the asymptomatic individuals (P < 0.001). whereas the median load of U. urealyticum was 8.4 × 103 copies/ml (n = 24) and 1.4 × 103 (n = 17) copies/ml in the two groups, respectively, , the difference was not statistically significant (P = 0.450). CONCLUSIONS Our study is the first to develop a droplet digital PCR (ddPCR) method for the detection and quantification of Ureaplasma spp. in clinical samples, and the method has excellent analytical performance and a wide range of clinical application prospects.
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Affiliation(s)
- Yanfang Huang
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai, China
| | - Huifen Pan
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai, China
| | - Xiaoqin Xu
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai, China
| | - Panpan Lv
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai, China
| | - Xinxin Wang
- Department of Molecular Medicine, Biomed-Union Co. Ltd. Shanghai, Shanghai, China
| | - Zhen Zhao
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai, China.
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18
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Seyyedi N, Farjadian F, Farhadi A, Rafiei Dehbidi G, Ranjbaran R, Zare F, Ali Okhovat M, Nikouyan N, Behzad-Behbahani A. High yield gold nanoparticle-based DNA isolation method for human papillomaviruses genotypes from cervical cancer tissue samples. IET Nanobiotechnol 2021; 14:555-562. [PMID: 33010130 DOI: 10.1049/iet-nbt.2020.0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gold nanoparticles (AuNPs) are commonly used in biosensors of various kinds. However, its application to extract DNA from cancer tissues has not been extensively studied. The purification of DNA from cancer tissues is an important step in diagnostic and therapeutic development. Almost, all cervical cancer cases are associated with high-risk human papillomavirus (HR-HPV) infection. Accurate viral diagnosis has so far relied on the extraction of adequate amounts of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. Till now, no specific and sensitive DNA purification method has been introduced for the extraction of HR-HPV from FFPE tissue. Since the commercially available purification kits are not sensitive and specific enough for HR-HPV DNA targets, in this study, a DNA purification method was designed based on AuNPs to purify sufficient amounts of HR-HPV DNA from cervical cancer tissue samples. AuNPs were coated with a series of oligonucleotide probes to hybridize to specific DNA sequences of HR-HPV genotypes. Results showed that 733 out of 800 copies of type-specific HPV DNA were recovered with complete specificity, compared to 36 copies with a standard commercial kit (Qiagen FFPE). The high yield of DNA (91.6%) is the main advantage of the AuNPs-probe purification method.
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Affiliation(s)
- Noorossadat Seyyedi
- Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Farjadian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Farhadi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Rafiei Dehbidi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Ranjbaran
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farahnaz Zare
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Okhovat
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negin Nikouyan
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
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Santos FLSG, Invenção MCV, Araújo ED, Barros GS, Batista MVA. Comparative analysis of different PCR-based strategies for HPV detection and genotyping from cervical samples. J Med Virol 2021; 93:6347-6354. [PMID: 34061365 DOI: 10.1002/jmv.27118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Human papillomavirus (HPV) is the main cause of cervical cancer. Polymerase chain reaction (PCR)-based techniques are associated with accurate results with respect to HPV detection and genotyping, being able to identify viral DNA at low levels. However, differences in primer design influence their sensibility and specificity, depending on the HPV type assessed. OBJECTIVE The aim of the study was to comparatively evaluate the effectiveness of three different PCR-based strategies for HPV detection and genotyping from cervical samples. STUDY DESIGN The procedures were based on different primer design strategies, using MY09/MY11, EntroA, and type specific multiplex PCR primers. RESULTS Out of 411 samples of cervical scrapings, 45 (10.9%), 50 (12.2%), and 117 (28.5%) were positive for MY09/MY11, EntroA, and multiplex PCR, respectively. For MY09/MY11 positive samples, 36 were negative for EntroA and 23 for multiplex PCR. For EntroA positive samples, 40 were negative for MY09/MY11 and 26 for multiplex PCR. For multiplex PCR positive samples, 96 were negative for MY09/MY11 and 94 for EntroA. MY09/MY11 identified 12 different HPV types, EntroA detected eight types and multiplex PCR detected 11 HPV types. EntroA primers were able to detect HPV in more samples than MY09/MY11, while multiplex PCR, despite the limited targeted HPV types, presented higher sensibility than the other methods. CONCLUSIONS The three methods presented different advantages and disadvantages, and the present study reinforces the need to use more than one molecular strategy for HPV detection and genotyping, and the development of novel methods which could overcome the limitations of the existing tests.
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Affiliation(s)
- Fernanda L S G Santos
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | - Maria C V Invenção
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | - Edilaine D Araújo
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | - Gerlane S Barros
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | - Marcus V A Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
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20
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SARS-CoV-2 RNA Quantification Using Droplet Digital RT-PCR. J Mol Diagn 2021; 23:907-919. [PMID: 34062285 PMCID: PMC8164350 DOI: 10.1016/j.jmoldx.2021.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
Quantitative viral load assays have transformed our understanding of viral diseases. They hold similar potential to advance COVID-19 control and prevention, but SARS-CoV-2 viral load tests are not yet widely available. SARS-CoV-2 molecular diagnostic tests, which typically employ real-time RT-PCR, yield semiquantitative results only. Droplet digital RT-PCR (RT-ddPCR) offers an attractive platform for SARS-CoV-2 RNA quantification. Eight primer/probe sets originally developed for real-time RT-PCR–based SARS-CoV-2 diagnostic tests were evaluated for use in RT-ddPCR; three were identified as the most efficient, precise, and sensitive for RT-ddPCR–based SARS-CoV-2 RNA quantification. For example, the analytical efficiency for the E-Sarbeco primer/probe set was approximately 83%, whereas assay precision, measured as the coefficient of variation, was approximately 2% at 1000 input copies/reaction. Lower limits of quantification and detection for this primer/probe set were 18.6 and 4.4 input SARS-CoV-2 RNA copies/reaction, respectively. SARS-CoV-2 RNA viral loads in a convenience panel of 48 COVID-19–positive diagnostic specimens spanned a 6.2log10 range, confirming substantial viral load variation in vivo. RT-ddPCR–derived SARS-CoV-2 E gene copy numbers were further calibrated against cycle threshold values from a commercial real-time RT-PCR diagnostic platform. This log-linear relationship can be used to mathematically derive SARS-CoV-2 RNA copy numbers from cycle threshold values, allowing the wealth of available diagnostic test data to be harnessed to address foundational questions in SARS-CoV-2 biology.
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21
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Murono S. Virus-Associated Biomarkers in Oropharyngeal and Nasopharyngeal Cancers and Recurrent Respiratory Papillomatosis. Microorganisms 2021; 9:microorganisms9061150. [PMID: 34072019 PMCID: PMC8228279 DOI: 10.3390/microorganisms9061150] [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: 04/02/2021] [Revised: 04/28/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
Nasopharyngeal cancer (NPC) is known to be associated with Epstein–Barr virus (EBV). Pre-treatment and post-treatment detection of plasma cell-free EBV DNA has been shown to be useful as a diagnostic as well as a prognostic factor in NPC. On the other hand, the incidence of human papillomavirus (HPV)-associated oropharyngeal cancer (OPC) is increasing. In contrast to cervical cancer, which is classically known to be an HPV-associated malignancy, HPV testing is not clinically applied for OPC, except for p16 immunostaining as a surrogate marker of HPV infection. One of the major characteristics of HPV-associated OPC is its association with a good prognosis compared with non-HPV-associated OPC. However, some patients still have a poor prognosis. Another characteristic of HPV-associated OPC is the distinct risk factor of high sexual activity. Establishing a biomarker for the prediction of the prognosis before and/or after initial treatment, as well as for diagnosis in populations at high risk, is of marked interest. With this background, HPV DNA detection in plasma and oral rinses has become an area of focus. In this review, the current significance of HPV DNA detection in plasma and oral rinse samples, as well as serum HPV antibody levels, is evaluated.
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Affiliation(s)
- Shigeyuki Murono
- Department of Otolaryngology, Fukushima Medical University, Fukushima 960-1295, Japan
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22
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Malin K, Louise BM, Gisela H, Mats KG, Gabriella LL. Optimization of droplet digital PCR assays for the type-specific detection and quantification of five HPV genotypes, including additional data on viral loads of nine different HPV genotypes in cervical carcinomas. J Virol Methods 2021; 294:114193. [PMID: 34022300 DOI: 10.1016/j.jviromet.2021.114193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022]
Abstract
The droplet digital PCR (ddPCR) system enables high-sensitivity detection of nucleic acids and direct absolute quantification of the targets. The aim of this research was to evaluate this system for viral load (VL) analysis of the human papillomavirus (HPV) genotypes HPV31, 35, 39, 51 and 56 measured in number of viral particles per cell. The sample types used for the optimization of the ddPCR assay were formalin-fixed paraffin-embedded (FFPE) tissues and cervical liquid cytology samples. The presently optimized ddPCR assays, together with assays optimized previously for HPV16, 18, 33 and 45, with the same ddPCR method, were used for the VL analysis of cervical tumor samples. Results published previously on the present study cohort showed that women with a cervical tumor containing multiple high-risk HPV genotypes had a worse prognosis compared to women with single-genotype-infected tumors. The VL was therefore analyzed in this study for the same cohort, as a possible explanatory factor to the prognostic differences. The results of the optimization part of the study, with analysis of VL using ddPCR in DNA from varying sample types (FFPE and liquid cytology samples), showed that each of the five assays demonstrated good inter- and intra-assay means with a coefficient of variation (CV) under 8% and 6% respectably. The cohort results showed no difference in VL between tumors with multiple and single HPV infections, and therefore did most likely not constitute a contributing factor for prognostic differences observed previously. However, tumors from women aged 60 years or older or containing certain HPV genotypes and genotype genera were associated with a higher VL.
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Affiliation(s)
- Kaliff Malin
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, SE-701 82, Sweden
| | - Bohr Mordhorst Louise
- Department of Oncology, Faculty of Medicine and Health, Örebro University, Örebro, SE-701 82, Sweden
| | - Helenius Gisela
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, SE-701 82, Sweden
| | - Karlsson G Mats
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, SE-701 82, Sweden
| | - Lillsunde-Larsson Gabriella
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, SE-701 82, Sweden; School of Health Sciences, Örebro University, Örebro, SE-70182, Sweden.
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23
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Xu J, Kirtek T, Xu Y, Zheng H, Yao H, Ostman E, Oliver D, Malter JS, Gagan JR, SoRelle JA. Digital Droplet PCR for SARS-CoV-2 Resolves Borderline Cases. Am J Clin Pathol 2021; 155:815-822. [PMID: 33822853 PMCID: PMC8083587 DOI: 10.1093/ajcp/aqab041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES The Bio-Rad SARS-CoV-2 ddPCR Kit (Bio-Rad Laboratories) was the first droplet digital polymerase chain reaction (ddPCR) assay to receive Food and Drug Administration (FDA) Emergency Use Authorization approval, but it has not been evaluated clinically. We describe the performance of ddPCR-in particular, its ability to confirm weak-positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results. METHODS We clinically validated the Bio-Rad Triplex Probe ddPCR Assay. The limit of detection was determined by using serial dilutions of SARS-CoV-2 RNA in an artificial viral envelope. The ddPCR assay was performed according to the manufacturer's specifications on specimens confirmed to be positive (n = 48) or negative (n = 30) by an FDA-validated reverse transcription-polymerase chain reaction assay on the m2000 RealTime system (Abbott). Ten borderline positive cases were also evaluated. RESULTS The limit of detection was 50 copies/mL (19 of 20 positive). Forty-seven specimens spanning a range of quantification cycles (2.9-25.9 cycle numbers) were positive by this assay (47 of 48; 97.9% positive precent agreement), and 30 negative samples were confirmed as negative (30 of 30; 100% negative percent agreement). Nine of 10 borderline cases were positive when tested in triplicate. CONCLUSIONS The ddPCR of SARS-CoV-2 is an accurate method, with superior sensitivity for viral RNA detection. It could provide definitive evaluation of borderline positive cases or suspected false-negative cases.
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Affiliation(s)
- Jing Xu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Timothy Kirtek
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Xu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hui Zheng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huiyu Yao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Dwight Oliver
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey R Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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24
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Xu G, Si H, Jing F, Sun P, Wu D. A Self-Priming Microfluidic Chip with Cushion Chambers for Easy Digital PCR. BIOSENSORS-BASEL 2021; 11:bios11050158. [PMID: 34069758 PMCID: PMC8155915 DOI: 10.3390/bios11050158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/17/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
A polydimethylsiloxane (PDMS)-based self-priming microfluidic chip with cushion chambers is presented in this study for robust and easy-operation digital polymerase chain reaction (dPCR). The chip has only one inlet and can partition samples autonomously through negative pressure, provided by a de-gassed PDMS layer with a multi-level vertical branching microchannel design. Meanwhile, cushion chambers make the chip capable of very robust use for sample partitioning. Finally, the proposed microfluidic chip showed excellent performance in the absolute quantification of a target gene by performing quantitative detection of a 10-fold serial dilution DNA template. Owing to its characteristics of easy operation, low cost, and high robustness, the proposed dPCR chip is expected to further promote the extensive application of digital PCR, especially in resource-limited settings.
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Affiliation(s)
- Gangwei Xu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
| | - Huaqing Si
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
| | - Fengxiang Jing
- Shanghai Turtle Technology Company Limited, Shanghai 200439, China;
| | - Peng Sun
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
| | - Dongping Wu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
- Correspondence:
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25
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Circulating HPV DNA in the Management of Oropharyngeal and Cervical Cancers: Current Knowledge and Future Perspectives. J Clin Med 2021; 10:jcm10071525. [PMID: 33917435 PMCID: PMC8038737 DOI: 10.3390/jcm10071525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Human papillomaviruses (HPVs) are associated with invasive malignancies, including almost 100% of cervical cancers (CECs), and 35–70% of oropharyngeal cancers (OPCs). HPV infection leads to clinical implications in related tumors by determining better prognosis and predicting treatment response, especially in OPC. Currently, specific and minimally invasive tests allow for detecting HPV-related cancer at an early phase, informing more appropriately therapeutical decisions, and allowing for timely disease monitoring. A blood-based biomarker detectable in liquid biopsy represents an ideal candidate, and the use of circulating HPV DNA (ct-DNA) itself could offer the highest specificity for such a scope. Circulating HPV DNA is detectable in the greatest part of patients affected by HPV-related cancers, and studies have demonstrated its potential usefulness for CEC and OPC clinical management. Unfortunately, when using conventional polymerase chain reaction (PCR), the detection rate of serum HPV DNA is low. Innovative techniques such as droplet-based digital PCR and next generation sequencing are becoming increasingly available for the purpose of boosting HPV ct-DNA detection rate. We herein review and critically discuss the most recent and representative literature, concerning the role of HPV ctDNA in OPC and CEC in the light of new technologies that could improve the potential of this biomarker in fulfilling many of the unmet needs in the clinical management of OPC and CEC patients.
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26
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Chen L, Dong P, Yu Z. Detection of human papillomavirus infection in laryngeal and hypopharyngeal carcinoma using droplet digital PCR and its correlation with prognosis. Postgrad Med 2021; 133:619-625. [PMID: 33754942 DOI: 10.1080/00325481.2021.1904669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To use droplet digital polymerase chain reaction (ddPCR) to detect human papillomavirus (HPV) infection in squamous cell carcinoma of the larynx and hypopharynx (SCCLHP) and to analyze its association with the prognosis of patients with HPV. METHODS We used ddPCR for HPV detection in 114 patients with SCCLHP; clinical data were collected, and the patients were followed-up for prognosis analysis. Univariate and multivariate Cox regression analyses were used to complete the analysis of risk factors. This clinical study was registered (clinical trial registration no. ChiCTR2000033032). RESULT Of the total cases, 15.79% (18/114) were HPV-positive and 8 (8/18, 44.4%) patients had tumors with HPV-16. There was a significant correlation between HPV-16 and the T classification and Tumor-Node-Metastasis (TNM) (P = 0.025 and 0.036, respectively). The 3-year overall survival rates in the HPV-positive and HPV-negative patients were 39.8% and 48.6% (P = 0.776), respectively. In the univariate analysis, HPV infection was not associated with the relative risk of progression (hazard ratio [HR] = 1.109, P = 0.778). Patients with laryngeal carcinoma (HR = 1.805, P = 0.037), no alcohol consumption (HR = 0.430, P = 0.009), well-differentiated tumors (HR = 2.570, p = 0.006), TNM I-II (HR = 2.482, P = 0.003), and no lymph node metastasis (HR = 2.615, P = 0.001) had better prognoses. In the multivariate analysis, tumor location (HR = 3.044, P = 0.001), alcohol consumption (HR = 0.474, P = 0.022), tumor differentiation (HR = 2.131, P = 0.030), and lymph node metastasis (HR = 4.179, P < 0.001) were independent predictors of better overall survival in SCCLHP. CONCLUSION ddPCR is an advanced technology that can accurately diagnose HPV infection with high specificity and sensitivity. The HPV infection rate in SCCLHP was low, and there was no significant difference in the prognosis of SCCLHP.
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Affiliation(s)
- Lixiao Chen
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pin Dong
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ziwei Yu
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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27
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Santacroce L, Di Cosola M, Bottalico L, Topi S, Charitos IA, Ballini A, Inchingolo F, Cazzolla AP, Dipalma G. Focus on HPV Infection and the Molecular Mechanisms of Oral Carcinogenesis. Viruses 2021; 13:v13040559. [PMID: 33810374 PMCID: PMC8067023 DOI: 10.3390/v13040559] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
This study is focused on the epidemiological characteristics and biomolecular mechanisms that lead to the development of precancerous and cancerous conditions of oral lesions related to Human Papilloma Virus (HPV) infections. Current evidence from the literature demonstrates the role of HPV in potentially malignant oral disorders. Therefore, the underlying biomolecular processes can give arise, or contribute to, benign lesions as well as to oral carcinogenesis.
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Affiliation(s)
- Luigi Santacroce
- Interdisciplinary Department of Medicine, Microbiology and Virology Unit, School of Medicine, University of Bari “A. Moro”, 70124 Bari, Italy;
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (CEDICLO), University of Bari “A. Moro”, 70121 Bari, Italy; (L.B.); (S.T.)
- Department of Clinical Disciplines, School of Technical Medical Sciences, “A. Xhuvani” University of Elbasan, 3001 Elbasan, Albania
| | - Michele Di Cosola
- Department of Clinical and Experimental Medicine, Università degli Studi di Foggia, 71122 Foggia, Italy; (M.D.C.); (A.P.C.)
| | - Lucrezia Bottalico
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (CEDICLO), University of Bari “A. Moro”, 70121 Bari, Italy; (L.B.); (S.T.)
| | - Skender Topi
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (CEDICLO), University of Bari “A. Moro”, 70121 Bari, Italy; (L.B.); (S.T.)
- Department of Clinical Disciplines, School of Technical Medical Sciences, “A. Xhuvani” University of Elbasan, 3001 Elbasan, Albania
| | - Ioannis Alexandros Charitos
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (CEDICLO), University of Bari “A. Moro”, 70121 Bari, Italy; (L.B.); (S.T.)
- Correspondence: (I.A.C.); (A.B.)
| | - Andrea Ballini
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Campus Universitario “G. Quagliarello”, University of Bari “A. Moro”, 70125 Bari, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico L. De Crecchio 7, 80138 Naples, Italy
- Correspondence: (I.A.C.); (A.B.)
| | - Francesco Inchingolo
- Interdisciplinary Department of Medicine, University of Bari “A. Moro”, 70124 Bari, Italy; (F.I.); (G.D.)
| | - Angela Pia Cazzolla
- Department of Clinical and Experimental Medicine, Università degli Studi di Foggia, 71122 Foggia, Italy; (M.D.C.); (A.P.C.)
| | - Gianna Dipalma
- Interdisciplinary Department of Medicine, University of Bari “A. Moro”, 70124 Bari, Italy; (F.I.); (G.D.)
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Mundo L, Del Porro L, Granai M, Siciliano MC, Mancini V, Santi R, Marcar L, Vrzalikova K, Vergoni F, Di Stefano G, Schiavoni G, Segreto G, Onyango N, Nyagol JA, Amato T, Bellan C, Anagnostopoulos I, Falini B, Leoncini L, Tiacci E, Lazzi S. Frequent traces of EBV infection in Hodgkin and non-Hodgkin lymphomas classified as EBV-negative by routine methods: expanding the landscape of EBV-related lymphomas. Mod Pathol 2020; 33:2407-2421. [PMID: 32483241 PMCID: PMC7685982 DOI: 10.1038/s41379-020-0575-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
The Epstein-Barr virus (EBV) is linked to various B-cell lymphomas, including Burkitt lymphoma (BL), classical Hodgkin lymphoma (cHL) and diffuse large B-cell lymphoma (DLBCL) at frequencies ranging, by routine techniques, from 5 to 10% of cases in DLBCL to >95% in endemic BL. Using higher-sensitivity methods, we recently detected EBV traces in a few EBV-negative BL cases, possibly suggesting a "hit-and-run" mechanism. Here, we used routine and higher-sensitivity methods (qPCR and ddPCR for conserved EBV genomic regions and miRNAs on microdissected tumor cells; EBNA1 mRNA In situ detection by RNAscope) to assess EBV infection in a larger lymphoma cohort [19 BL, 34 DLBCL, 44 cHL, 50 follicular lymphomas (FL), 10 T-lymphoblastic lymphomas (T-LL), 20 hairy cell leukemias (HCL), 10 mantle cell lymphomas (MCL)], as well as in several lymphoma cell lines (9 cHL and 6 BL). qPCR, ddPCR, and RNAscope consistently documented the presence of multiple EBV nucleic acids in rare tumor cells of several cases EBV-negative by conventional methods that all belonged to lymphoma entities clearly related to EBV (BL, 6/9 cases; cHL, 16/32 cases; DLBCL, 11/30 cases), in contrast to fewer cases (3/47 cases) of FL (where the role of EBV is more elusive) and no cases (0/40) of control lymphomas unrelated to EBV (HCL, T-LL, MCL). Similarly, we revealed traces of EBV infection in 4/5 BL and 6/7 HL cell lines otherwise conventionally classified as EBV negative. Interestingly, additional EBV-positive cases (1 DLBCL, 2 cHL) relapsed as EBV-negative by routine methods while showing EBNA1 expression in rare tumor cells by RNAscope. The relapse specimens were clonally identical to their onset biopsies, indicating that the lymphoma clone can largely loose the EBV genome over time but traces of EBV infection are still detectable by high-sensitivity methods. We suggest EBV may contribute to lymphoma pathogenesis more widely than currently acknowledged.
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Affiliation(s)
- Lucia Mundo
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Leonardo Del Porro
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Massimo Granai
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Maria Chiara Siciliano
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Virginia Mancini
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Raffaella Santi
- Section of Pathology, University of Florence, Florence, Italy
| | - Lynnette Marcar
- BioMaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- Ireland, Health Research Institute (HRI), University of Limerick, Limerick, Ireland
| | - Katerina Vrzalikova
- Institute of immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | | | - Gianluca Schiavoni
- Section of Haematology and Clinical Immunology, Department of Medicine, University and Hospital of Perugia, Perugia, Italy
| | - Giovanna Segreto
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Noel Onyango
- Department of Clinical Medicine and Therapeutics, Unit of Medical Oncology, University of Nairobi, Nairobi, Kenya
| | - Joshua Akelo Nyagol
- Department of Clinical Medicine and Therapeutics, Unit of Medical Oncology, University of Nairobi, Nairobi, Kenya
| | - Teresa Amato
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Cristiana Bellan
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | | | - Brunangelo Falini
- Section of Haematology and Clinical Immunology, Department of Medicine, University and Hospital of Perugia, Perugia, Italy
| | - Lorenzo Leoncini
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Enrico Tiacci
- Section of Haematology and Clinical Immunology, Department of Medicine, University and Hospital of Perugia, Perugia, Italy.
| | - Stefano Lazzi
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy.
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Rotondo JC, Oton-Gonzalez L, Mazziotta C, Lanzillotti C, Iaquinta MR, Tognon M, Martini F. Simultaneous Detection and Viral DNA Load Quantification of Different Human Papillomavirus Types in Clinical Specimens by the High Analytical Droplet Digital PCR Method. Front Microbiol 2020; 11:591452. [PMID: 33329471 PMCID: PMC7710522 DOI: 10.3389/fmicb.2020.591452] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Human papillomaviruses (HPVs) are small DNA tumor viruses that mainly infect mucosal epithelia of anogenital and upper respiratory tracts. There has been progressive demand for more analytical assays for HPV DNA quantification. A novel droplet digital PCR (ddPCR) method was developed to simultaneously detect and quantify HPV DNA from different HPV types. DdPCR was initially tested for assay sensitivity, accuracy, specificity as well as intra- and inter-run assay variation employing four recombinant plasmids containing HPV16, HPV18, HPV11, and HPV45 DNAs. The assay was extended to investigate/quantify HPV DNA in Cervical Intraepithelial Neoplasia (CIN, n = 45) specimens and human cell lines (n = 4). DdPCR and qPCR data from clinical samples were compared. The assay showed high accuracy, sensitivity and specificity, with low intra-/inter- run variations, in detecting/quantifying HPV16/18/11/45 DNAs. HPV DNA was detected in 51.1% (23/45) CIN DNA samples by ddPCR, whereas 40% (18/45) CIN tested HPV-positive by qPCR. Five CIN, tested positive by ddPCR, were found to be negative by qPCR. In CIN specimens, the mean HPV DNA loads determined by ddPCR were 3.81 copy/cell (range 0.002–51.02 copy/cell), whereas 8.04 copy/cell (range 0.003–78.73 copy/cell) by qPCR. DdPCR and qPCR concordantly detected HPV DNA in SiHa, CaSki and Hela cells, whereas HaCaT tested HPV-negative. The correlation between HPV DNA loads simultaneously detected by ddPCR/qPCR in CINs/cell lines was good (R2 = 0.9706, p < 0.0001). Our data indicate that ddPCR is a valuable technique in quantifying HPV DNA load in CIN specimens and human cell lines, thereby improving clinical applications, such as patient management after primary diagnosis of HPV-related lesions with HPV-type specific assays.
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Affiliation(s)
- John Charles Rotondo
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Lucia Oton-Gonzalez
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Mazziotta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Carmen Lanzillotti
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Rosa Iaquinta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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30
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Voegel TM, Larrabee MM, Nelson LM. Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil. Can J Microbiol 2020; 67:174-187. [PMID: 32910858 DOI: 10.1139/cjm-2020-0033] [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] [Indexed: 11/22/2022]
Abstract
Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.
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Affiliation(s)
- Tanja M Voegel
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Melissa M Larrabee
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Louise M Nelson
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
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31
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Santeramo I, Bagnati M, Harvey EJ, Hassan E, Surmacz-Cordle B, Marshall D, Di Cerbo V. Vector Copy Distribution at a Single-Cell Level Enhances Analytical Characterization of Gene-Modified Cell Therapies. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:944-956. [PMID: 32420408 PMCID: PMC7217927 DOI: 10.1016/j.omtm.2020.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 12/28/2022]
Abstract
The ability to deliver transgenes into the human genome using viral vectors is a major enabler of the gene-modified cell therapy field. However, the control of viral transduction is difficult and can lead to product heterogeneity, impacting efficacy and safety, as well as increasing the risk of batch failure during manufacturing. To address this, we generated a novel analytical method to measure vector copy distribution at the single-cell level in a gene-modified, lentiviral-based immunotherapy model. As the limited amount of genomic DNA in a single cell hinders reliable quantification, we implemented a preamplification strategy on selected lentiviral and human gene targets in isolated live single cells, followed by quantification of amplified material by droplet digital PCR. Using a bespoke probability framework based on Bayesian statistics, we show that we can estimate vector copy number (VCN) integers with maximum likelihood scores. Notably, single-cell data are consistent with population analysis and also provide an overall measurement of transduction efficiency by discriminating transduced (VCN ≥ 1) from nontransduced (VCN = 0) cells. The ability to characterize cell-to-cell variability provides a powerful high-resolution approach for product characterization, which could ultimately allow improved control over product quality and safety.
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Affiliation(s)
- Ilaria Santeramo
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Marta Bagnati
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Emily Jane Harvey
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Enas Hassan
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Beata Surmacz-Cordle
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Damian Marshall
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Vincenzo Di Cerbo
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
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32
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Zhu X, Su S, Fu M, Peng Z, Wang D, Rui X, Wang F, Liu X, Liu B, Zhu L, Yang W, Gao N, Huang G, Jing G, Guo Y. A density-watershed algorithm (DWA) method for robust, accurate and automatic classification of dual-fluorescence and four-cluster droplet digital PCR data. Analyst 2019; 144:4757-4771. [PMID: 31290860 DOI: 10.1039/c9an00637k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Droplet digital PCR (ddPCR) is a single-molecule amplification technology with broad applications in precision medicine and clinical diagnosis. Dual-fluorescence and four-cluster ddPCR (two/four-ddPCR) assay is an effective way to quantify copy numbers. Currently, two/four-ddPCR data are usually classified with manual thresholds. For clinical applications, automatic and accurate methods are required to avoid subjectivity in diagnosis. Although there are some automatic classification algorithms, their accuracy and robustness still need to be improved to meet the needs of clinical diagnosis. Therefore, a new method is in high demand to automatically classify two/four-ddPCR data in an accurate and robust way. Here, a novel density-watershed algorithm (DWA) method was developed for the accurate, automatic and unsupervised classification of two/four-ddPCR data. First, data gridding was applied to a scatter plot of the fluorescence signal intensity to calculate data densities. Based on the data densities, the watershed algorithm was used to divide the gridded scatter plot into isolated regions automatically. Next, an optimal cluster pattern was determined based on these isolated regions, and excess regions were merged. Finally, the two/four-ddPCR data were classified based on the merged regions, and DNA template copy numbers were calculated accordingly. Using the DWA method for the quantification of both wild types and mutants of epidermal growth factor receptor (EGFR) L858R and T790M, the classification results were highly consistent with expectations, and significantly better than commonly-used automatic algorithms for now. The computed template copy numbers scaled proportionally to the relative concentration of input templates (r2 > 0.998) in four orders of magnitude with a good reproducibility, and achieved a limit of detection over 40 times lower than the commonly-used automatic algorithms. Furthermore, the DWA method was validated on 254 clinical DNA samples derived from frozen tissues, formalin-fixed paraffin-embedded tissues and peripheral blood. In most cases, the DWA method derived accurate and valid classification results. This highly effective DWA method may be widely used for automatically classifying two/four-ddPCR data, and it will greatly promote the application of ddPCR in clinical diagnosis.
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Affiliation(s)
- Xiurui Zhu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China.
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33
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Droplet digital PCR applications in the tuberculosis world. Tuberculosis (Edinb) 2019; 117:85-92. [DOI: 10.1016/j.tube.2019.07.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/24/2019] [Accepted: 07/02/2019] [Indexed: 11/23/2022]
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34
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Liu Y, Meng H, Shi L, Li L. Sensitive detection of porcine circovirus 3 by droplet digital PCR. J Vet Diagn Invest 2019; 31:604-607. [PMID: 31046639 DOI: 10.1177/1040638719847686] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Porcine circovirus 3 (PCV-3) is a newly emerging virus that poses a potential threat to the swine industry. We developed a sensitive assay utilizing droplet digital PCR (ddPCR) to detect PCV-3. Specificity of the assay was confirmed by the failure of amplification of DNA of other relevant viruses. The detection limit for ddPCR was 1 copy/μL, 10 times greater sensitivity than TaqMan real-time PCR (rtPCR). Both methods showed a high degree of linearity, although TaqMan rtPCR showed less sensitivity than ddPCR for clinical detection. Our findings indicate that ddPCR might offer faster and improved analytical sensitivity for PCV-3 detection.
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Affiliation(s)
- Yuqi Liu
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
| | - Hecheng Meng
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
| | - Lei Shi
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
| | - Lili Li
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
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35
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Pinheiro-de-Oliveira TF, Fonseca-Júnior AA, Camargos MF, Laguardia-Nascimento M, Giannattasio-Ferraz S, Cottorello ACP, de Oliveira AM, Góes-Neto A, Barbosa-Stancioli EF. Reverse transcriptase droplet digital PCR to identify the emerging vesicular virus Senecavirus A in biological samples. Transbound Emerg Dis 2019; 66:1360-1369. [PMID: 30864242 DOI: 10.1111/tbed.13168] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/13/2022]
Abstract
Senecavirus A (SVA) belonging to the family Picornaviridae, genus Senecavirus was incidentally isolated in 2002 from the PER.C6 (transformed foetal retinoblast) cell line. However, currently, this virus is associated with vesicular disease in swine and it has been reported in countries such as the United States of America, Canada, China, Thailand and Colombia. In Brazil, the SVA was firstly reported in 2015 in outbreaks of vesicular disease in swine, clinically indistinguishable of Foot-and-mouth disease, a contagious viral disease that generates substantial economic losses. In the present work, it was standardized a diagnostic tool for SVA based on RNA reverse transcriptase droplet digital PCR (RT-ddPCR) using one-step and two-step approaches. Analytical sensitivity and specificity were done in parallel with real-time PCR, RT-qPCR (one-step and two-step) for comparison of sensitivity and specificity of both methods. In the standardization of RT-ddPCR, the double-quenched probe and the temperature gradient were crucial to reduce background and improve amplitude between positive and negative droplets. The limit of detection and analytical specificity of techniques of one-step techniques showed superior performance than two-step methods described here. Additionally, the results showed 94.2% concordance (p < 0.001) for RT-ddPCR and RT-qPCR using the one-step assay approach and biological samples from Brazilian outbreaks of Senecavirus A. However, ddRT-PCR had a better performance than RT-PCR when swine serum pools were tested. According to the results, the one-step RT-ddPCR and RT-qPCR is highlighted to be used as an auxiliary diagnostic tool for Senecavirus A and for viral RNA absolute quantification in biological samples (RT-ddPCR), being a useful tool for vesicular diseases control programs.
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Affiliation(s)
| | - A A Fonseca-Júnior
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - M F Camargos
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - M Laguardia-Nascimento
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | | | - A C P Cottorello
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - A M de Oliveira
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - A Góes-Neto
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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36
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Lillsunde Larsson G, Kaliff M, Sorbe B, Helenius G, Karlsson MG. HPV16 viral characteristics in primary, recurrent and metastatic vulvar carcinoma. PAPILLOMAVIRUS RESEARCH 2018; 6:63-69. [PMID: 30391517 PMCID: PMC6249404 DOI: 10.1016/j.pvr.2018.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/06/2018] [Accepted: 10/28/2018] [Indexed: 01/06/2023]
Abstract
Vulvar carcinoma is the fourth most common gynecological malignancy. Two separate carcinogenic pathways are suggested, where one is associated with the human papillomavirus (HPV) and HPV16 the most common genotype. The aim of this study was to evaluate HPV-markers in a set of primary tumors, metastases and recurrent lesions of vulvar squamous cell carcinomas (VSCC). Ten HPV16-positive VSCC with metastatic regional lymph nodes, distant lymphoid/hematogenous metastases or local recurrent lesions were investigated for HPV genotype, HPV16 variant, HPV16 viral load, HPV16 integration and HPV16 E2BS3 and 4 methylation. In all 10 analyzed case series, the same HPV genotype (HPV16), HPV16 variant and level of viral load were detected in all lesions within a patient case. Primary tumors with a high E2/E6 ratio were found to have fewer vulvar recurrences and/or metastases after diagnosis and treatment. Also, a significantly lower viral load was evident in regional lymph nodes compared to primary tumors. The data presented strengthens the evidence for a clonal HPV-induced pathway for vulvar carcinoma.
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Affiliation(s)
- Gabriella Lillsunde Larsson
- School of Health Sciences, Örebro University, SE-701 82 Örebro, Sweden; Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden.
| | - Malin Kaliff
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Bengt Sorbe
- Department of Oncology, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Gisela Helenius
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Mats G Karlsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
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37
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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38
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Hanna G, Supplee J, Kuang Y, Mahmood U, Lau C, Haddad R, Jänne P, Paweletz C. Plasma HPV cell-free DNA monitoring in advanced HPV-associated oropharyngeal cancer. Ann Oncol 2018; 29:1980-1986. [DOI: 10.1093/annonc/mdy251] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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39
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Wojtera M, Paradis J, Husein M, Nichols AC, Barrett JW, Salvadori MI, Strychowsky JE. The prevalence of human papillomavirus in pediatric tonsils: a systematic review of the literature. J Otolaryngol Head Neck Surg 2018; 47:8. [PMID: 29378664 PMCID: PMC5789580 DOI: 10.1186/s40463-018-0255-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/17/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND HPV-related head and neck cancer rates have been increasing in recent years, with the tonsils being the most commonly affected site. However, the current rate of HPV infection in the pediatric population remains poorly defined. The objective of this study was to systematically review and evaluate the prevalence and distribution of HPV in the tonsils of pediatric patients undergoing routine tonsillectomy. METHODS AND RESULTS The literature was searched using PubMed, EMBASE, Scopus, CINAHL, Cochrane Library, and ProQuest Dissertations & Theses Global databases (inception to December 2017) by two independent review authors. Inclusion criteria included articles which evaluated the prevalence of HPV in a pediatric cohort without known warts or recurrent respiratory papillomatosis, those which used tonsil biopsy specimens for analysis, and those with six or more subjects and clear outcomes reported. Eleven studies met the inclusion criteria. Using the Oxford Clinical Evidence-based Medicine (OCEBM) guidelines, two reviewers appraised the level of evidence of each study, extracted data, and resolved discrepancies by consensus. The systematic review identified 11 articles (n = 2520). Seven studies detected HPV in the subject population, with prevalence values ranging from 0 to 21%. The level of evidence for all included studies was OCEBM Level 3. CONCLUSIONS HPV may be present in pediatric tonsillectomy specimens; however, the largest included study demonstrated a prevalence of 0%. Future testing should be performed using methods with high sensitivities and specificities, such as reverse transcript real-time PCR or digital droplet PCR.
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Affiliation(s)
- Monika Wojtera
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada
| | - Josee Paradis
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery, Victoria Hospital B3-400, 800 Commissioners Rd E, London, N6A 5W9, ON, Canada
| | - Murad Husein
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery, Victoria Hospital B3-400, 800 Commissioners Rd E, London, N6A 5W9, ON, Canada
| | - Anthony C Nichols
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery, Victoria Hospital B3-400, 800 Commissioners Rd E, London, N6A 5W9, ON, Canada
| | - John W Barrett
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery, Victoria Hospital B3-400, 800 Commissioners Rd E, London, N6A 5W9, ON, Canada
| | - Marina I Salvadori
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada.,Department of Paediatrics, Children's Hospital at London Health Sciences Centre, 800 Commissioners Rd E, London, ON, N6A 5W9, Canada
| | - Julie E Strychowsky
- Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, N6A 5C1, ON, Canada. .,Department of Otolaryngology-Head and Neck Surgery, Victoria Hospital B3-400, 800 Commissioners Rd E, London, N6A 5W9, ON, Canada.
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