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Kim EH, Joo JY, Lee YJ, Koh JK, Choi JH, Shin Y, Cho J, Park E, Kang J, Lee K, Bhak J, Kim BC, Lee JY. Grading system for periodontitis by analyzing levels of periodontal pathogens in saliva. PLoS One 2018; 13:e0200900. [PMID: 30475813 PMCID: PMC6257921 DOI: 10.1371/journal.pone.0200900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/20/2018] [Indexed: 12/19/2022] Open
Abstract
Periodontitis is an infectious disease that is associated with microorganisms that colonize the tooth surface. Clinically, periodontal condition stability reflects dynamic equilibrium between bacterial challenge and host response. Therefore, periodontal pathogen assessment can assist in the early detection of periodontitis. Here we developed a grading system called the periodontal pathogen index (PPI) by analyzing the copy numbers of multiple pathogens both in healthy and chronic periodontitis patients. We collected 170 mouthwash samples (64 periodontally healthy controls and 106 chronic periodontitis patients) and analyzed the salivary 16S rRNA levels of nine pathogens using multiplex, quantitative real-time polymerase chain reaction. Except for Aggregatibacter actinomycetemcomitans, copy numbers of all pathogens were significantly higher in chronic periodontitis patients. We classified the samples based on optimal cut-off values with maximum sensitivity and specificity from receiver operating characteristic curve analyses (AUC = 0.91, 95% CI: 0.87-0.96) into four categories of PPI: Healthy (1-40), Moderate (41-60), At Risk (61-80), and Severe (81-100). PPI scores were significantly higher in all chronic periodontitis patients than in the controls (odds ratio: 31.7, 95% CI: 13.41-61.61) and were associated with age, scaling as well as clinical characteristics including clinical attachment level and plaque index. Our PPI grading system can be clinically useful for the early assessment of pathogenic bacterial burden and follow-up monitoring after periodontitis treatment.
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Affiliation(s)
| | - Ji-Young Joo
- Dental Research Institute, Pusan National University Dental Hospital, Yangsan, Republic of Korea
- Department of Periodontology and Institute of Translational Dental Science, Pusan National University, School of Dentistry, Yangsan, Republic of Korea
| | | | - Jae-Kwon Koh
- Dental Research Institute, Pusan National University Dental Hospital, Yangsan, Republic of Korea
| | - Jung-Hyeok Choi
- Dental Research Institute, Pusan National University Dental Hospital, Yangsan, Republic of Korea
| | | | - Juok Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Eunha Park
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | | | | | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Geromics Inc., Ulsan, Republic of Korea
- The Aging Institute, Genome Research Foundation, Osong, Republic of Korea
| | - Byung Chul Kim
- Clinomics Inc., Ulsan, Republic of Korea
- * E-mail: (BCK); (JYL)
| | - Ju-Youn Lee
- Dental Research Institute, Pusan National University Dental Hospital, Yangsan, Republic of Korea
- Department of Periodontology and Institute of Translational Dental Science, Pusan National University, School of Dentistry, Yangsan, Republic of Korea
- * E-mail: (BCK); (JYL)
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Mendoza ÁC, Volante BB, Hernández MEO, Mendoza CCC, Pliego AF, Baptista Gonzalez HA, Juárez HE. Design of a protocol for obtaining genomic DNA from saliva using mouthwash: Samples taken from patients with periodontal disease. J Oral Biol Craniofac Res 2016; 6:129-34. [PMID: 27195211 DOI: 10.1016/j.jobcr.2016.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/20/2016] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND Obtaining high quality genomic DNA safely and economically is vital for diverse studies of large populations aimed at evaluating the role of genetic factors in susceptibility to disease. AIM This study was to test a protocol for the extraction of high quality genomic DNA from saliva samples obtained with mouthwash and taken from patients with periodontal disease. METHODS Saliva samples were taken from 60 patients and then stored at room temperature. DNA extraction was carried out at distinct post-sampling times (10, 20 and 30 days). Evaluation of genomic DNA was performed with spectrophotometry, electrophoresis, and PCR genotyping and sequencing. RESULTS The greatest concentration of DNA obtained was 352 μg at 10 days post-sampling, followed by 121.025 μg and 19.59 μg at 20 and 30 days, respectively. When determining the purity of DNA with the spectrophotometric ratio of 260/230, the relations of 1.20, 1.40 and 0.781 were obtained for 10, 20 and 30 days, respectively. In all samples, it was possible to amplify the product of 485 bp and the sequence of the amplicons showed 95% similarity to the reference sequence. CONCLUSION The present protocol represents an easy, safe and economical technique for obtaining high quality genomic DNA.
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Affiliation(s)
- Ángel Chávez Mendoza
- Posgrado en Investigación en Medicina, Laboratorio de Señalización Celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México, D.F., Mexico; Centro Interdisciplinario de Ciencias de la Salud, Unidad Santo Tomás, Instituto Politécnico Nacional, Av. de Los Maestros S/N, Col. Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340 Ciudad de México, D.F., Mexico; Hospital General "Dr. Fernando Quiroz Gutiérrez", ISSSTE, General Felipe Ángeles y Canario S/N, Col. Bellavista, Delegación Álvaro Obregón, C.P. 01140 Ciudad de México, D.F., Mexico
| | - Beatriz Buentello Volante
- Departamento de Genética, Unidad de Investigación, Instituto de Oftalmología "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Delegación Cuauhtémoc, C.P. 06800 Ciudad de México, D.F., Mexico
| | - María Esther Ocharán Hernández
- Sección de Estudios de Posgrado e Investigación, Laboratorio de Señalización Celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340 Ciudad de México, D.F., Mexico
| | - Claudia Camelia Calzada Mendoza
- Sección de Estudios de Posgrado e Investigación, Laboratorio de Señalización Celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340 Ciudad de México, D.F., Mexico
| | - Arturo Flores Pliego
- Departamento de Inmunobioquimica, Instituto Nacional de Perinatología, Montes Urales 800 Col. Virreyes, Delegación Miguel Hidalgo, C.P. 11000 Ciudad de México, D.F., Mexico
| | - Héctor A Baptista Gonzalez
- Coordinación de Hematología Perinatal, Instituto Nacional de Perinatología, Montes Urales 800 Col. Virreyes, Delegación Miguel Hidalgo, C.P. 11000 Ciudad de México, D.F., Mexico
| | - Higinio Estrada Juárez
- Coordinación de Hematología Perinatal, Instituto Nacional de Perinatología, Montes Urales 800 Col. Virreyes, Delegación Miguel Hidalgo, C.P. 11000 Ciudad de México, D.F., Mexico
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Kaur G, Kumar N, Nandakumar R, Rapthap CC, Sharma G, Neolia S, Kumra H, Mahalwar P, Garg A, Kumar S, Kaur J, Hakim M, Kumar L, Mehra NK. Utility of saliva and hair follicles in donor selection for hematopoietic stem cell transplantation and chimerism monitoring. CHIMERISM 2013; 3:9-17. [PMID: 22690267 PMCID: PMC3370928 DOI: 10.4161/chim.19395] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Selection of an HLA identical donor is a critical pre-requisite for successful hematopoietic stem cell transplantation (HSCT). Most transplant centers utilize blood as the most common source of DNA for HLA testing. However, obtaining blood through phlebotomy is often challenging in patients with conditions like severe leucopenia or hemophilia, pediatric and elderly patients. We have used a simple in-house protocol and shown that HLA genotypes obtained on DNA extracted from saliva or hair are concordant with blood and hence can be used for selection of donors for HSCT or organ transplantation. Similarly, for post-HSCT chimerism monitoring, non-availability of pre-transplant DNA samples poses a major limitation of reference STR fingerprints. This study shows that DNA obtained post-HSCT from hair follicles can be used to generate pre-transplant patient specific fingerprints while the STR profiles obtained in saliva samples cannot as these display a mixed state of chimerism.
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Affiliation(s)
- Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, India Institute of Medical Sciences; New Delhi, India.
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Zhang Y, Ji C. An application of salivary DNA in twin research of Chinese children. Twin Res Hum Genet 2009; 11:546-51. [PMID: 18828738 DOI: 10.1375/twin.11.5.546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Since saliva collection is noninvasive, painless and inexpensive, it may become an alternative to obtain genomic DNA, which is critical to evaluate zygosity and the role of genetic factors in twin research. This study provided a rough description of salivary DNA in Chinese twin children, and presented the DNA yield and quality extracted from saliva in a large-scale children sample, which supplied an example for saliva sample using in genetic epidemiology. Three milliliters of saliva was collected from 356 twin children aged 6 to 15, and DNA was extracted by a commercial DNA isolation kit. The DNA yield and purity was determined by spectrophotometry at 260 nm and 280 nm. The zygosity determination of the same-sex twins and the assay of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism indicated the quality of salivary DNA. The amount of extracted DNA from three milliliters of saliva was about 34.91 microg (2.20 approximately 122.04 microg), average OD(260/280) values was 1.84. Saliva DNA is a reliable sample for the determination of twins' zygosity. We conclude that saliva may be a feasible and reliable source of DNA for genetic epidemiology studies, especially for twin research.
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Affiliation(s)
- Yue Zhang
- Institute of Child and Adolescent Health, Peking University, Beijing, China
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Rogers NL, Cole SA, Lan HC, Crossa A, Demerath EW. New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies. Am J Hum Biol 2007; 19:319-26. [PMID: 17421001 PMCID: PMC2797479 DOI: 10.1002/ajhb.20586] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Epidemiological studies may require noninvasive methods for off-site DNA collection. We compared the DNA yield and quality obtained using a whole-saliva collection device (Oragene DNA collection kit) to those from three established noninvasive methods (cytobrush, foam swab, and oral rinse). Each method was tested on 17 adult volunteers from our center, using a random crossover collection design and analyzed using repeated-measures statistics. DNA yield and quality were assessed via gel electrophoresis, spectophotometry, and polymerase chain reaction (PCR) amplification rate. The whole-saliva method provided a significantly greater DNA yield (mean +/- SD = 154.9 +/- 103.05 microg, median = 181.88) than the other methods (oral rinse = 54.74 +/- 41.72 microg, 36.56; swab = 11.44 +/- 7.39 microg, 10.72; cytobrush = 12.66 +/- 6.19, 13.22 microg) (all pairwise P < 0.05). Oral-rinse and whole-saliva samples provided the best DNA quality, whereas cytobrush and swab samples provided poorer quality DNA, as shown by lower OD(260)/OD(280) and OD(260)/OD(230) ratios. We conclude that both a 10-ml oral-rinse sample and 2-ml whole-saliva sample provide sufficient DNA quantity and better quality DNA for genetic epidemiological studies than do the commonly used buccal swab and brush techniques.
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Affiliation(s)
- Nikki L Rogers
- Lifespan Health Research Center, Department of Community Health, Wright State University School of Medicine, Dayton, Ohio 45420, USA.
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Xie X, Zhang X, Gao H, Zhang H, Chen D, Cheng J, Fei W. DNA purification and gene typing: Based on multifunctional nanobeads. ACTA ACUST UNITED AC 2004. [DOI: 10.1007/bf03184004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Laine ML, Farré MA, Crusius JB, van Winkelhoff AJ, Peña AS. The mouthwash: a non-invasive sampling method to study cytokine gene polymorphisms. J Periodontol 2000; 71:1315-8. [PMID: 10972647 DOI: 10.1902/jop.2000.71.8.1315] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND We describe a simple, non-invasive mouthwash sampling method for rapid DNA isolation to detect cytokine gene polymorphisms. In the present paper, interleukin- 1beta(IL-1B) and interleukin-1 receptor antagonist (IL-1RN) gene polymorphisms were studied. METHODS Two mouthwash samples and blood samples were collected from 11 healthy individuals. The second mouthwash sample was stored for 7 days at room temperature. Polymerase chain reaction amplification was used to identify a bi-allelic polymorphism at position +3953 in the IL-1B gene and a variable number of tandem repeats (VNTR) polymorphism in the IL-1RN gene. RESULTS Our results show that the typing of these cytokine gene polymorphisms using DNA isolated from mouthwash samples did not differ from those obtained by a phenol/chloroform isolation method from EDTA anti-coagulated blood. Moreover, reliable results from mouthwash samples were obtained after storage for at least 7 days at room temperature. CONCLUSIONS Mouthwash can be the method of choice to study gene polymorphisms in periodontitis and other chronic inflammatory diseases.
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Affiliation(s)
- M L Laine
- Academic Centre for Dentistry Amsterdam, Department of Oral Biology, The Netherlands.
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