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Kasu M, Ristow PG, Burrows AM, Kuplik Z, Gibbons MJ, D'Amato ME. Novel buffer for long-term preservation of DNA in biological material at room temperature 1. Biotechniques 2024:1-14. [PMID: 38949197 DOI: 10.1080/07366205.2024.2360813] [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: 12/19/2023] [Accepted: 05/24/2024] [Indexed: 07/02/2024] Open
Abstract
The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish Pelagia noctiluca comb jelly Beroe sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.
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Affiliation(s)
- Mohaimin Kasu
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Peter G Ristow
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Adria Michelle Burrows
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Zafrir Kuplik
- Department of Biodiversity & Conservation Biology, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Mark J Gibbons
- Department of Biodiversity & Conservation Biology, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Maria E D'Amato
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
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2
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Mortazavi H, Yousefi-Koma AA, Yousefi-Koma H. Extensive comparison of salivary collection, transportation, preparation, and storage methods: a systematic review. BMC Oral Health 2024; 24:168. [PMID: 38308289 PMCID: PMC10837873 DOI: 10.1186/s12903-024-03902-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Human saliva as a bodily fluid-similar to blood-is utilized for diagnostic purposes. Unlike blood sampling, collecting saliva is non-invasive, inexpensive, and readily accessible. There are no previously published systematic reviews regarding different collection, transportation, preparation, and storage methods for human saliva. DESIGN This study has been prepared and organized according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) 2020 guidelines. This systematic review has been registered at PROSPERO (Registration ID: CRD42023415384). The study question according to the PICO format was as followed: Comparison of the performance (C) of different saliva sampling, handling, transportation, and storage techniques and methods (I) assessed for analyzing stimulated or unstimulated human saliva (P and O). An electronic search was executed in Scopus, Google Scholar, and PubMed. RESULTS Twenty-three descriptive human clinical studies published between 1995 and 2022 were included. Eight categories of salivary features and biomarkers were investigated (i.e., salivary flow rate, total saliva quantity, total protein, cortisol, testosterone, DNA quality and quantity, pH and buffering pH). Twenty-two saliva sampling methods/devices were utilized. Passive drooling, Salivette®, and spitting were the most utilized methods. Sampling times with optimum capabilities for cortisol, iodine, and oral cancer metabolites are suggested to be 7:30 AM to 9:00 AM, 10:30 AM to 11:00 AM, and 14:00 PM to 20:00 PM, respectively. There were 6 storage methods. Centrifuging samples and storing them at -70 °C to -80 °C was the most utilized storage method. For DNA quantity and quality, analyzing samples immediately after collection without centrifuging or storage, outperformed centrifuging samples and storing them at -70 °C to -80 °C. Non-coated Salivette® was the most successful method/device for analyzing salivary flow rate. CONCLUSION It is highly suggested that scientists take aid from the reported categorized outcomes, and design their study questions based on the current voids for each method/device.
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Affiliation(s)
- Hamed Mortazavi
- School of Dentistry, Shahid Beheshti University of Medical Sciences, Daneshjoo Blvd, Evin, Shahid Chamran Highway, Tehran, 1983963113, Iran
| | - Amir-Ali Yousefi-Koma
- School of Dentistry, Shahid Beheshti University of Medical Sciences, Daneshjoo Blvd, Evin, Shahid Chamran Highway, Tehran, 1983963113, Iran.
- Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Janovičová Ľ, Holániová D, Vlková B, Celec P. Pre-Analytical Factors Affecting Extracellular DNA in Saliva. Diagnostics (Basel) 2024; 14:249. [PMID: 38337765 PMCID: PMC10855236 DOI: 10.3390/diagnostics14030249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA (ecDNA) in plasma, could be a promising biomarker for oral or systemic diseases. In contrast to genetics, the quantity of salivary ecDNA is of importance and can be affected by the pre-analytical processing of samples, but the details are not known. The aim of our study was to analyze the effects of centrifugation and freezing of saliva on the concentration of ecDNA in saliva. Fifteen healthy volunteers, free of any known systemic or oral diseases, were asked to collect unstimulated saliva samples. Aliquots were centrifuged at 1600× g and frozen or directly processed. The fresh or thawed cell-free saliva samples underwent subsequent centrifugation at 16,000× g. The supernatants were used for DNA isolation and quantification using fluorometry and real-time PCR. While freezing had minimal effects on the salivary ecDNA concentration, another centrifugation step decreased ecDNA considerably in both fresh and frozen samples (by 97.8% and 98.4%, respectively). This was mirrored in the quantitative PCR targeting a nuclear (decrease by 93.5%) and mitochondrial (decrease by 97.7%) ecDNA sequence. In conclusion, in this first study focusing on the technical aspects of salivary ecDNA quantitation, we show that, regardless of its subcellular origin, the concentration of ecDNA in saliva is mainly affected by additional centrifugation and not by the freezing of centrifuged cell-free saliva samples. This suggests that most salivary ecDNA likely is associated with cell debris and apoptotic bodies. Which fraction is affected by a particular disease should be the focus of further targeted studies.
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Affiliation(s)
- Ľubica Janovičová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Dominika Holániová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
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4
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Ishikawa N, Nakamura Y, Miura Y, Kuroda H, Kitamura K, Hashimoto M. Influence of the amount of saliva deposition and time elapsed after deposition on bite mark analysis. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00742-y. [PMID: 37926778 DOI: 10.1007/s12024-023-00742-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
Bite mark analysis is among the most interesting research fields in forensic odontology; however, it is limited by its dependence on the employed method as well as assessor subjectivity, particularly when using morphological analysis or DNA profiling. These limitations are due to differences in DNA collected from saliva adhering to a living or inanimate body, as well as differences in exocrine fluid secretion and deposition amount among individuals. This study aimed to analyze the effectiveness of DNA profiling when there are differences in the amount of saliva adhering to a living body and when time has elapsed since deposition. Most allele peaks could be identified in 1 µl of saliva, even 9 h after saliva deposition and examination. Consistent results were obtained following saliva deposition in an individual who had engaged in up to 9 h of free activity. The results of this study demonstrate the validity and reliability of DNA profiling for bite mark analysis and are extremely important as they can demonstrate the usefulness of the little information left by a suspect on a victim's body.
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Affiliation(s)
- Noboru Ishikawa
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, 2-9-18 Kanda-Misakicho, Chiyoda-Ku, Tokyo, 101-0061, Japan
| | - Yasutaka Nakamura
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, 2-9-18 Kanda-Misakicho, Chiyoda-Ku, Tokyo, 101-0061, Japan.
| | - Yuna Miura
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, 2-9-18 Kanda-Misakicho, Chiyoda-Ku, Tokyo, 101-0061, Japan
| | - Hidetaka Kuroda
- Department of Critical Care Medicine and Dentistry, Division of Anesthesiology, Kanagawa Dental University, 1-23 Ogawacho Yokosuka-Shi, Kanagawa, 238-8580, Japan
| | - Kei Kitamura
- Department of Histology and Developmental Biology, Tokyo Dental College, 2-9-18 Kanda-Misakicho, Chiyoda-Ku, Tokyo, 101-0061, Japan
| | - Masatsugu Hashimoto
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, 2-9-18 Kanda-Misakicho, Chiyoda-Ku, Tokyo, 101-0061, Japan
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5
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Brooks PJ, Malkin EZ, De Michino S, Bratman SV. Isolation of salivary cell-free DNA for cancer detection. PLoS One 2023; 18:e0285214. [PMID: 37130100 PMCID: PMC10153704 DOI: 10.1371/journal.pone.0285214] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023] Open
Abstract
Saliva is an emerging source of disease biomarkers, particularly for cancers of the head and neck. Although analysis of cell-free DNA (cfDNA) in saliva holds promise as a liquid biopsy for cancer detection, currently there are no standardized methodologies for the collection and isolation of saliva for the purposes of studying DNA. Here, we evaluated various saliva collection receptacles and DNA purification techniques, comparing DNA quantity, fragment size, source, and stability. Then, using our optimized techniques, we tested the ability to detect human papillomavirus (HPV) DNA- a bona fide cancer biomarker in a subset of head and neck cancers- from patient saliva samples. For saliva collection, we found that the Oragene OG-600 receptacle yielded the highest concentration of total salivary DNA as well as short fragments <300 bp corresponding to mononucleosomal cell-free DNA. Moreover, these short fragments were stabilized beyond 48 hours after collection in contrast to other saliva collection receptacles. For DNA purification from saliva, the QIAamp Circulating Nucleic Acid kit yielded the highest concentration of mononucleosome-sized DNA fragments. Freeze-thaw of saliva samples did not affect DNA yield or fragment size distribution. Salivary DNA isolated from the OG-600 receptacle was found to be composed of both single and double-stranded DNA, including mitochondrial and microbial sources. While levels of nuclear DNA were consistent over time, levels of mitochondrial and microbial DNA were more variable and increased 48 hours after collection. Finally, we found that HPV DNA was stable in OG-600 receptacles, was reliably detected within the saliva of patients with HPV-positive head and neck cancer, and was abundant among mononucleosome-sized cell-free DNA fragments. Our studies have defined optimal techniques for isolating DNA from saliva that will contribute to future applications in liquid biopsy-based cancer detection.
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Affiliation(s)
- Patricia J Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ethan Z Malkin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Steven De Michino
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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6
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Mordenti M, Capicchioni V, Corsini S, Locatelli M, Abelli E, Banchelli F, Boarini M, Sangiorgi L. Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study. J Clin Lab Anal 2022; 36:e24531. [PMID: 35666551 PMCID: PMC9279999 DOI: 10.1002/jcla.24531] [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: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Background The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. Methods Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. Results Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. Conclusion Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.
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Affiliation(s)
- Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Valentina Capicchioni
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Ministry of Education, San Marino, Repubic of San Marino
| | - Serena Corsini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Locatelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federico Banchelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manila Boarini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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7
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Costa GL, Alvarenga DAM, Aguiar ACC, Louzada J, Pereira DB, de Oliveira TF, Fonseca Júnior AA, Carvalho LH, Ferreira Alves de Brito C, Nóbrega de Sousa T. Improving the Molecular Diagnosis of Malaria: Droplet Digital PCR-Based Method Using Saliva as a DNA Source. Front Microbiol 2022; 13:882530. [PMID: 35633683 PMCID: PMC9136408 DOI: 10.3389/fmicb.2022.882530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/20/2022] [Indexed: 12/20/2022] Open
Abstract
Malaria is an acute febrile disease caused by a protozoan of the genus Plasmodium. Light microscopy (LM) is the gold standard for the diagnosis of malaria. Despite this method being rapid and inexpensive, it has a low limit of detection, which hampers the identification of low parasitemia infections. By using multicopy targets and highly sensitive molecular techniques, it is possible to change this scenario. In this study, we evaluated the performance of droplet digital PCR (ddPCR) to detect Plasmodium DNA obtained from saliva samples (whole saliva and buccal swab) of 157 individuals exposed to malaria transmission from the Brazilian Amazon region. We used the highly sensitive ddPCR method with non-ribosomal multicopy targets for Plasmodium vivax (Pvr47) and Plasmodium falciparum (Pfr364). There was good concordance between the quantitative real-time PCR (qPCR) results from the saliva and blood, except for mixed-species infections. The sensitivity of qPCR was 93% for blood, 77% for saliva, and 47% for swabs. Parasite DNA was not detected in saliva samples in low-density infections compared with the detection in blood samples. ddPCR showed increased sensitivity for detecting Plasmodium in the blood and swabs (99% in blood, 73% in saliva, and 59% in swabs). Notably, ddPCR detected more mixed infections in the blood (15%), saliva (9%), and swabs (18%) than qPCR. Our data showed that the differences between ddPCR and qPCR were the result of a higher number of P. falciparum infections detected by ddPCR. Overall, there was a moderate correlation between parasite densities estimated by the different methods in the blood. Our findings highlight the possibility of using non-invasive sample collection methods for malaria diagnosis by targeting multicopy sequences combined with highly sensitive molecular methods.
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Affiliation(s)
- Gabriel Luíz Costa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Denise Anete Madureira Alvarenga
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | | | - Jaime Louzada
- Health Sciences Center, Federal University of Roraima, Boa Vista, Brazil
| | | | | | | | - Luzia Helena Carvalho
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Cristiana Ferreira Alves de Brito
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Taís Nóbrega de Sousa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
- *Correspondence: Taís Nóbrega de Sousa
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8
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Abstract
The use of saliva as a diagnostic biofluid has been increasing in recent years, thanks to the identification and validation of new biomarkers and improvements in test accuracy, sensitivity, and precision that enable the development of new noninvasive and cost-effective devices. However, the lack of standardized methods for sample collection, treatment, and storage contribute to the overall variability and lack of reproducibility across analytical evaluations. Furthermore, the instability of salivary biomarkers after sample collection hinders their translation into commercially available technologies for noninvasive monitoring of saliva in home settings. The present review aims to highlight the status of research on the challenges of collecting and using diagnostic salivary samples, emphasizing the methodologies used to preserve relevant proteins, hormones, genomic, and transcriptomic biomarkers during sample handling and analysis.
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Affiliation(s)
- Luciana d'Amone
- Silklab, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Giusy Matzeu
- Silklab, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Fiorenzo G Omenetto
- Silklab, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Electrical and Computer Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Physics, Tufts University, Medford, Massachusetts 02155, United States.,Laboratory for Living Devices, Tufts University, Medford, Massachusetts 02155, United States
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9
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Bolani B, Oliveira GM, Dionísio TJ, Faria FAC, Fernandes MHR, Santos CF, Calvo AM. Pharmacogenetic and Pharmacokinetic Assays from Saliva Samples Can Guarantee Personalized Drug Prescription. Braz Dent J 2021; 32:3-8. [PMID: 33913999 DOI: 10.1590/0103-6440202104059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/15/2021] [Indexed: 11/22/2022] Open
Abstract
Saliva is widely used for clinical and laboratory analysis. This study proposed to use DNA extracted from saliva for genotyping and pharmacokinetics of piroxicam. A fast and efficient genotyping method was used to determine relevant allelic variants of CYP2C9 (*2 and *3), since genetic factors can influence in non-steroidal anti-inflammatory drugs (NSAIDs) metabolization. DNA Extract All Reagents Kit® was used for DNA extraction and genotyping was performed using TaqMan® GTXpress™ Master Mix, SNP genotyping assays and a Viia7 Real-Time PCR system. Volunteers performed sequential collections of saliva samples before and after taking a single dose of piroxicam (0.25 to 72 h) which were used for pharmacokinetics assays. Piroxicam concentrations were analyzed using LC-MS/MS. Sixty-six percent of volunteers were ancestral homozygous (CYP2C9*1/*1), and 34% showed one or both polymorphisms. Of these 34%, 22 individuals showed CYP2C9*2 polymorphism, 8 CYP2C9*3, and 4 CYP2C9*2/*3. Piroxicam pharmacokinetics were performed in 5 subjects. Areas under the curve (AUC0-t(h*ng/mL)) for CYP2C9*1/*1, *1/*2 and *1/*3 were, respectively, 194.33±70.93, 166 and 303. Maximum concentrations (Cmax(ng/mL)) for these genotypes were respectively 6.46±2.56, 4.3 and 10.2. Saliva sampling was a very effective matrix for both pharmacogenetic and pharmacokinetic tests, ensuring the speed of the procedure and the well-being and agreement of the participants. Once having the knowledge about the slow and fast metabolizers, it is possible to make an adequate prescription in order to avoid the adverse effects of the medication and to guarantee greater analgesic comfort to the patients respectively.
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Affiliation(s)
- Bruna Bolani
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Gabriela Moraes Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Thiago José Dionísio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | | | | | - Carlos Ferreira Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Adriana Maria Calvo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
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10
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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11
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Ponce-Rojas JC, Costello MS, Proctor DA, Kosik KS, Wilson MZ, Arias C, Acosta-Alvear D. A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein To Facilitate the Detection of SARS-CoV-2. J Clin Microbiol 2021; 59:e02403-20. [PMID: 33293367 PMCID: PMC8092744 DOI: 10.1128/jcm.02403-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022] Open
Abstract
Management of the coronavirus disease 2019 (COVID-19) pandemic requires widespread testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among them RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here, we propose an alternative method we call PEARL (precipitation-enhanced analyte retrieval) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers performance comparable to that of commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.
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Affiliation(s)
- Jose Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Michael S Costello
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Duncan A Proctor
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Kenneth S Kosik
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, Santa Barbara, California, USA
| | - Maxwell Z Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, Santa Barbara, California, USA
- Center for BioEngineering, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, Santa Barbara, California, USA
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, Santa Barbara, California, USA
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Goldoni R, Farronato M, Connelly ST, Tartaglia GM, Yeo WH. Recent advances in graphene-based nanobiosensors for salivary biomarker detection. Biosens Bioelectron 2021; 171:112723. [PMID: 33096432 PMCID: PMC7666013 DOI: 10.1016/j.bios.2020.112723] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/11/2022]
Abstract
As biosensing research is rapidly advancing due to significant developments in materials, chemistry, and electronics, researchers strive to build cutting-edge biomedical devices capable of detecting health-monitoring biomarkers with high sensitivity and specificity. Biosensors using nanomaterials are highly promising because of the wide detection range, fast response time, system miniaturization, and enhanced sensitivity. In the recent development of biosensors and electronics, graphene has rapidly gained popularity due to its superior electrical, biochemical, and mechanical properties. For biomarker detection, human saliva offers easy access with a large variety of analytes, making it a promising candidate for its use in point-of-care (POC) devices. Here, we report a comprehensive review that summarizes the most recent graphene-based nanobiosensors and oral bioelectronics for salivary biomarker detection. We discuss the details of structural designs of graphene electronics, use cases of salivary biomarkers, the performance of existing sensors, and applications in health monitoring. This review also describes current challenges in materials and systems and future directions of the graphene bioelectronics for clinical POC applications. Collectively, the main contribution of this paper is to deliver an extensive review of the graphene-enabled biosensors and oral electronics and their successful applications in human salivary biomarker detection.
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Affiliation(s)
- Riccardo Goldoni
- George W. Woodruff School of Mechanical Engineering, Institute for Electronics and Nanotechnology, Atlanta, GA, 30332, USA; School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Marco Farronato
- Department of Medicine, Surgery, and Dentistry, Università Degli Studi di Milano, Milan, Italy; Maxillofacial and Dental Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico di Milano, Italy
| | - Stephen Thaddeus Connelly
- Department of Oral & Maxillofacial Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Gianluca Martino Tartaglia
- Department of Medicine, Surgery, and Dentistry, Università Degli Studi di Milano, Milan, Italy; Maxillofacial and Dental Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico di Milano, Italy
| | - Woon-Hong Yeo
- George W. Woodruff School of Mechanical Engineering, Institute for Electronics and Nanotechnology, Atlanta, GA, 30332, USA; Wallace H. Coulter Department of Biomedical Engineering, Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, GA, 30332, USA; Center for Human-Centric Interfaces and Engineering, Neural Engineering Center, Institute for Materials, Institute for Robotics and Intelligent Machines, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Samson CA, Whitford W, Snell RG, Jacobsen JC, Lehnert K. Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing. Sci Rep 2020; 10:19255. [PMID: 33159102 PMCID: PMC7648094 DOI: 10.1038/s41598-020-76022-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022] Open
Abstract
Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequence comparisons of atypically aligning reads from eight human saliva-derived samples to RefSeq genomes revealed the majority to be of bacterial origin (63.46%). To partition the non-human reads during the alignment step, a decoy of the most prevalent bacterial genome sequences was designed and utilised. This reduced the number of atypically aligning reads when trialled on the eight saliva-derived samples by 44% and most importantly prevented the associated anomalous genotype calls. Saliva derived DNA is often contaminated by DNA from other species. This can lead to non-human reads aligning to the human reference genome using current alignment best-practices, impacting variant identification. This problem can be diminished by using a bacterial decoy in the alignment process.
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Affiliation(s)
- C A Samson
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - W Whitford
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - R G Snell
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - J C Jacobsen
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand.
| | - K Lehnert
- School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
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Han P, Ivanovski S. Saliva-Friend and Foe in the COVID-19 Outbreak. Diagnostics (Basel) 2020; 10:E290. [PMID: 32397487 PMCID: PMC7277967 DOI: 10.3390/diagnostics10050290] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) outbreak, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global ongoing pandemic. Timely, accurate and non-invasive SARS-CoV-2 detection in both symptomatic and asymptomatic patients, as well as determination of their immune status, will facilitate effective large-scale pandemic control measures to prevent the spread of COVID-19. Saliva is a biofluid whose anatomical source and location is of particularly strategic relevance to COVID-19 transmission and monitoring. This review focuses on the role of saliva as both a foe (a common mode of viral transmission via salivary droplets and potentially aerosols) and a friend (as a non-invasive diagnostic tool for viral detection and immune status surveillance) in combating COVID-19.
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Affiliation(s)
| | - Sašo Ivanovski
- School of Dentistry, The University of Queensland, Herston, QLD 4006, Australia;
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Perry SE, Huckabee M, Tompkins G, Milne T. The association between oral bacteria, the cough reflex and pneumonia in patients with acute stroke and suspected dysphagia. J Oral Rehabil 2019; 47:386-394. [DOI: 10.1111/joor.12903] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/01/2019] [Accepted: 10/29/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah E. Perry
- The University of Canterbury Rose Centre for Stroke Recovery & Research at St George’s Medical Centre Christchurch New Zealand
- University of Canterbury Christchurch New Zealand
| | - Maggie‐Lee Huckabee
- The University of Canterbury Rose Centre for Stroke Recovery & Research at St George’s Medical Centre Christchurch New Zealand
- University of Canterbury Christchurch New Zealand
- Sir John Walsh Research Institute University of Otago Dunedin New Zealand
| | - Geoffrey Tompkins
- Sir John Walsh Research Institute University of Otago Dunedin New Zealand
| | - Trudy Milne
- Sir John Walsh Research Institute University of Otago Dunedin New Zealand
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Ibrahim O, Sutherland HG, Haupt LM, Griffiths LR. Saliva as a comparable-quality source of DNA for Whole Exome Sequencing on Ion platforms. Genomics 2019; 112:1437-1443. [PMID: 31445087 DOI: 10.1016/j.ygeno.2019.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 08/05/2019] [Accepted: 08/19/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND Whole Exome Sequencing (WES) utilises overlapping fragments prone to sequencing artefacts. Saliva, a non-invasive source of DNA, has been successfully used in WES studies on various platforms. This study explored the validity and quality of DNA sourced from saliva compared to whole blood on an Ion Platform. METHODS DNA was extracted from both sample types from four individuals. WES, performed on the Ion Proton platform was assessed for quality metrics (Depth, Genotyping Quality, etc.) and variant identification for the same source sample-pairs. RESULTS No significant differences in quality metrics were identified between data obtained from whole blood and saliva samples, with several saliva samples demonstrating higher coverage depth. Variants within the same sample, from the two genomic DNA sources, had an average concordance similar to other studies and platforms with different chemistry. CONCLUSION Saliva-extracted DNA provides comparable sequencing quality to whole blood for WES on Ion Torrent Platforms.
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Affiliation(s)
- Omar Ibrahim
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia.
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