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Condon EM, Scheibner HR, Kuzel M, Howard M, Cisse M, O'Connell M, Conley Y, Jeon S, Sadler LS, Redeker NS. The CARING study: Examining biological, behavioral, and genetic mechanisms in the intergenerational transmission of toxic stress. Res Nurs Health 2024. [PMID: 38804202 DOI: 10.1002/nur.22400] [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: 10/24/2023] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
When children experience extreme or persistent stressors (e.g., maltreatment, housing insecurity, intimate partner violence), prolonged elevation of the stress-response system can lead to disrupted development of multiple physiological systems. This response, known as toxic stress, is associated with poor physical and mental health across the life course. Emerging evidence suggests that the effects of toxic stress may be transmitted through generations, but the biological and behavioral mechanisms that link caregivers' childhood history with the health of the children they care for remain poorly understood. The purpose of this report is to describe the research protocol for The CARING (Childhood Adversity and Resilience In the Next Generation) Study, a cross-sectional study of caregivers with children aged 3-5 years designed to (1) examine the intergenerational transmission of toxic stress and protective factors; (2) explore three hypothesized pathways of transmission: parenting, daily routines, stressors, and supports; and (3) explore the extent to which genotypic variation in candidate genes related to caregiving and stress contribute to caregivers' and children's susceptibility to the effects of early childhood experiences (i.e., gene × environment interactions). We expect that findings from this study will provide critical data needed to identify targets for precision health interventions, reduce health disparities related to toxic stress, and prevent cycles of adversity among families at risk.
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Affiliation(s)
- Eileen M Condon
- University of Connecticut School of Nursing, Storrs, Connecticut, USA
| | | | - Meredith Kuzel
- University of Connecticut School of Nursing, Storrs, Connecticut, USA
| | - Mackenzie Howard
- University of Connecticut School of Nursing, Storrs, Connecticut, USA
| | - Mouhamadou Cisse
- Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Meghan O'Connell
- University of Connecticut School of Nursing, Storrs, Connecticut, USA
| | - Yvette Conley
- University of Pittsburg School of Nursing, Pittsburg, Pennsylvania, USA
| | | | | | - Nancy S Redeker
- University of Connecticut School of Nursing, Storrs, Connecticut, USA
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2
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Hole A, Tyagi G, Deshmukh A, Deshpande R, Gota V, Chaturvedi P, Krishna CM. Salivary Raman Spectroscopy: Standardization of Sampling Protocols and Stratification of Healthy and Oral Cancer Subjects. APPLIED SPECTROSCOPY 2021; 75:581-588. [PMID: 33107759 DOI: 10.1177/0003702820973260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Minimally invasive cancer detection using bio-fluids has been actively pursued due to practical limitations, though there are better suited noninvasive and online in vivo methods. Saliva is one such clinically informative bio-fluid that offers the advantages of easy and multiple sample collection. Despite its potential in cancer diagnostics, saliva analysis is challenging due to its heterogeneous composition. Recently, there has been an upsurge in saliva exploration using optical techniques. Forms of saliva such as precipitate and supernatant have been monitored, but this sampling method needs to be standardized due to the obvious loss of analytes in processing. In that context, present work details the comparison of four different saliva sampling methodologies, i.e., air-dried, lyophilized, pellet, and supernatant using Raman spectroscopy collected from 10 healthy samples. Composition-driven spectral features of all forms were compared and classified using principal component analysis and linear discriminant analysis. Analysis was carried out on all four groups in the first step. In the second step, groups of pellet and supernatant , and air-dried and lyophilized were analyzed. Findings suggest that pellet and supernatant exhibit discrete spectroscopic features and demonstrate high classification efficiency, which is indicative of their distinctive biochemical composition. On the other hand, air-dried and lyophilized forms showed overlapping spectral features and low classification, suggesting these forms retain majority spectroscopic features of whole saliva and are less prone to sampling losses. Thus, this study indicates air-dried and lyophilized forms may be more appropriate for saliva sampling using Raman spectroscopy providing the comprehensive information required for cancer diagnosis. Furthermore, the method was also tested for the classification of oral cancer and healthy subjects (n = 27) which yielded 90% stratification. The findings of the study indicate the utility of minimally invasive salivary Raman-based diagnostics in oral cancers.
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Affiliation(s)
- Arti Hole
- Chilakapati Laboratory, 29435Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Gunjan Tyagi
- Chilakapati Laboratory, 29435Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Atul Deshmukh
- Centre for Interdisciplinary Research, D.Y. Patil University, Navi Mumbai, India
| | - Raviraj Deshpande
- Clinical Pharmacology Laboratory, 29435Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Vikram Gota
- Clinical Pharmacology Laboratory, 29435Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Nagar Mumbai, India
| | - Pankaj Chaturvedi
- Homi Bhabha National Institute, Training School Complex, Nagar Mumbai, India
- Department of Surgical Oncology, Tata Memorial Hospital, Mumbai, India
| | - C Murali Krishna
- Chilakapati Laboratory, 29435Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Nagar Mumbai, India
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3
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Hughes SR, Chapleau RR. Comparing DNA quantity and quality using saliva collection following food and beverage consumption. BMC Res Notes 2019; 12:165. [PMID: 30904022 PMCID: PMC6431066 DOI: 10.1186/s13104-019-4211-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/18/2019] [Indexed: 11/10/2022] Open
Abstract
Objective With the democratization of genetic testing, researchers, clinicians, and educators must consider the varying degree of field conditions when collecting samples for genetic analyses. For genotyping or sequencing studies, study designers have multiple options from which to choose, including cheek swabs and saliva sampling. One significant benefit of saliva collection is that it can be done remotely, in the privacy of one’s home. This same benefit adds a risk of compliance. Therefore, our goal with this study was to see if the quality and quantity of the saliva collection by a saliva DNA collection kit would be affected by not following the manufacturer’s directions, i.e., drinking or eating right before collection. Results We asked five participants to collect saliva samples according to the manufacturer’s guidance and also after consuming five food items or beverages. We evaluated DNA quantity and quality post-purification using spectroscopy, electrophoresis, and polymerase chain reaction genotyping. Consistent with our hypothesis, we did not see a difference in quantity or quality of the isolated DNA. From our results, we conclude that the manufacturer’s instructions serve as an ideal guideline, but the collection devices are robust enough to permit flexibility in sampling at home or in the field. Electronic supplementary material The online version of this article (10.1186/s13104-019-4211-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Summer R Hughes
- 1st American Systems and Services, Falls Church, VA, USA.,Applied Technology & Genomics Division, Aeromedical Research Department, U.S. Air Force School of Aerospace Medicine, 711th Human Performance Wing, Air Force Research Laboratory, 2510 Fifth St, Dayton, Wright-Patterson AFB, OH, 45433, USA
| | - Richard R Chapleau
- Applied Technology & Genomics Division, Aeromedical Research Department, U.S. Air Force School of Aerospace Medicine, 711th Human Performance Wing, Air Force Research Laboratory, 2510 Fifth St, Dayton, Wright-Patterson AFB, OH, 45433, USA.
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4
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Ang JS, Aloise MN, Dawes D, Dempster MG, Fraser R, Paterson A, Stanley P, Suarez-Gonzalez A, Dawes M, Katzov-Eckert H. Evaluation of buccal swabs for pharmacogenetics. BMC Res Notes 2018; 11:382. [PMID: 29898767 PMCID: PMC6000964 DOI: 10.1186/s13104-018-3476-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/04/2018] [Indexed: 01/25/2023] Open
Abstract
Objective A simple, non-invasive sample collection method is key for the integration of pharmacogenetics into clinical practice. The aim of this study was to gain samples for pharmacogenetic testing and evaluate the variation between dry-flocked and sponge-tipped buccal swabs in yield and quality of DNA isolated. Results Thirty-one participants collected samples using dry-flocked swabs and sponge-tipped swabs. Samples were assessed for DNA yield, quality and genotyping performance on a qPCR OpenArray platform of 28 pharmacogenetic SNPs and a CYP2D6 TaqMan copy number variant. DNA from sponge-tipped swabs had a significantly greater yield compared to DNA collected with dry-flocked swabs (p = 4.4 × 10−7). Moreover, highest genotyping call rates across all assays and highest CNV confidence scores were observed in DNA samples collected from sponge-tipped swabs (97% vs. 54% dry-flocked swabs; 0.99 vs. 0.88 dry-flocked swabs, respectively). Sample collection using sponge-tipped swabs provides a DNA source of sufficient quantity and quality for pharmacogenetic variant detection using qPCR. Electronic supplementary material The online version of this article (10.1186/s13104-018-3476-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Sidney Ang
- GenXys Health Care Systems Inc., Vancouver, BC, Canada
| | | | - Diana Dawes
- GenXys Health Care Systems Inc., Vancouver, BC, Canada.,Department of Physical Therapy, University of British Columbia, Vancouver, BC, Canada
| | - Maryn G Dempster
- GenXys Health Care Systems Inc., Vancouver, BC, Canada.,Shoppers Drug Mart Corporation, Vancouver, BC, Canada
| | - Robert Fraser
- Molecular You Inc., Vancouver, BC, Canada.,Personalized Medicine Initiative, University of British Columbia, Vancouver, BC, Canada
| | - Andrea Paterson
- GenXys Health Care Systems Inc., Vancouver, BC, Canada.,Clinicare Pharmacists Inc, Vancouver, BC, Canada
| | - Paul Stanley
- GenXys Health Care Systems Inc., Vancouver, BC, Canada
| | | | - Martin Dawes
- GenXys Health Care Systems Inc., Vancouver, BC, Canada.,Department of Family Practice, University of British Columbia, Vancouver, BC, Canada
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5
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Strati P, Benton CB, Manshouri T, Zhang Y, Bove JE, Sanchez-Petitto G, Verstovsek S. JAK2 V617F detection and allele burden measurement in saliva vs. peripheral blood in patients with myelofibrosis. Leuk Res 2017; 63:53-55. [PMID: 29101828 DOI: 10.1016/j.leukres.2017.10.016] [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: 07/03/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 11/18/2022]
Abstract
We previously demonstrated that peripheral blood (PB) is a reliable source for testing JAK2V617F mutation in patients with myelofibrosis (MF); saliva has also been tested to detect such mutation, however its diagnostic accuracy as compared to PB has not been validated. In this study, we prospectively tested 167 patients with MF for JAK2V617F mutation, using both saliva and PB collected at the same time from each patient. The concordance between the 2 sources was 96%, with a sensitivity of 100% and a specificity of 90%. The only factor associated with false positivity on saliva was ongoing transfusion dependency. JAK2V617F testing using saliva is a simple, non-invasive, and potentially a more reliable method than PB for measuring JAK2 status and assessing V617F allelic burden in patients with transfusion dependency.
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Affiliation(s)
- Paolo Strati
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Christopher B Benton
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Taghi Manshouri
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ying Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Joseph E Bove
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Gabriela Sanchez-Petitto
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Srdan Verstovsek
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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6
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Langie SAS, Moisse M, Declerck K, Koppen G, Godderis L, Vanden Berghe W, Drury S, De Boever P. Salivary DNA Methylation Profiling: Aspects to Consider for Biomarker Identification. Basic Clin Pharmacol Toxicol 2017; 121 Suppl 3:93-101. [PMID: 27901320 PMCID: PMC5644718 DOI: 10.1111/bcpt.12721] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/13/2022]
Abstract
Is it not more comfortable to spit saliva in a tube than to be pricked with a needle to draw blood to analyse your health and disease risk? Many patients, study participants and (parents of) young children undoubtedly prefer non-invasive and convenient procedures. Such procedures increase compliance rates especially for longitudinal prospective studies. Saliva is an attractive biofluid providing good quality DNA to study epigenetic mechanisms underlying disease across development. In this MiniReview, we will describe the different applications of saliva in the field of epigenetics, focusing on genomewide methylation analysis. Advantages of the use of saliva and its comparability with blood will be discussed, as will the challenges in data processing and interpretation. Knowledge gaps will be identified and suggestions given on how to improve the analysis, making saliva 'the' biofluid of choice for future biomarker initiatives in many different epidemiological and public health studies.
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Affiliation(s)
- Sabine A. S. Langie
- Environmental Risk and Health UnitFlemish Institute for Technological Research (VITO)MolBelgium
- Faculty of SciencesHasselt UniversityDiepenbeekBelgium
| | | | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic SignalingDepartment of Biomedical SciencesUniversity of AntwerpWilrijkBelgium
| | - Gudrun Koppen
- Environmental Risk and Health UnitFlemish Institute for Technological Research (VITO)MolBelgium
| | - Lode Godderis
- Centre Environment & HealthDepartment of Public Health and Primary CareKU LeuvenLeuvenBelgium
- IDEWEExternal Service for Prevention and Protection at WorkHeverleeBelgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic SignalingDepartment of Biomedical SciencesUniversity of AntwerpWilrijkBelgium
| | - Stacy Drury
- The Brain InstituteTulane UniversityNew OrleansLAUSA
- Department of Psychiatry and Behavioral ScienceTulane University School of MedicineNew OrleansLAUSA
| | - Patrick De Boever
- Environmental Risk and Health UnitFlemish Institute for Technological Research (VITO)MolBelgium
- Faculty of SciencesHasselt UniversityDiepenbeekBelgium
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7
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Garbieri TF, Brozoski DT, Dionísio TJ, Santos CF, Neves LTD. Human DNA extraction from whole saliva that was fresh or stored for 3, 6 or 12 months using five different protocols. J Appl Oral Sci 2017; 25:147-158. [PMID: 28403355 PMCID: PMC5393535 DOI: 10.1590/1678-77572016-0046] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 09/06/2016] [Indexed: 11/22/2022] Open
Abstract
Objective and Material and Methods This study aimed to compare the quantity and quality of human DNA extracted from saliva that was fresh or frozen for three, six and twelve months using five different DNA extraction protocols: protocol 1 - Oragene™ commercial kit, protocol 2 - QIAamp DNA mini kit, protocol 3 - DNA extraction using ammonium acetate, protocol 4 - Instagene™ Matrix and protocol 5 - Instagene™ Matrix diluted 1:1 using proteinase K and 1% SDS. Briefly, DNA was analyzed using spectrophotometry, electrophoresis and PCR. Results Results indicated that time spent in storage typically decreased the DNA quantity with the exception of protocol 1. The purity of DNA was generally not affected by storage times for the commercial based protocols, while the purity of the DNA samples extracted by the noncommercial protocols typically decreased when the saliva was stored longer. Only protocol 1 consistently extracted unfragmented DNA samples. In general, DNA samples extracted through protocols 1, 2, 3 and 4, regardless of storage time, were amplified by human specific primers whereas protocol 5 produced almost no samples that were able to be amplified by human specific primers. Depending on the protocol used, it was possible to extract DNA in high quantities and of good quality using whole saliva, and furthermore, for the purposes of DNA extraction, saliva can be reliably stored for relatively long time periods. Conclusions In summary, a complicated picture emerges when taking into account the extracted DNA's quantity, purity and quality; depending on a given researchers needs, one protocol's particular strengths and costs might be the deciding factor for its employment.
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Affiliation(s)
- Thais Francini Garbieri
- Universidade de São Paulo, Hospital de Reabilitação de Anomalias Craniofaciais, Bauru, SP, Brasil.,Universidade de São Paulo, Faculdade de Odontologia de Bauru, Bauru, SP, Brasil
| | | | | | | | - Lucimara Teixeira das Neves
- Universidade de São Paulo, Hospital de Reabilitação de Anomalias Craniofaciais, Bauru, SP, Brasil.,Universidade de São Paulo, Faculdade de Odontologia de Bauru, Bauru, SP, Brasil
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8
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Oelsner KT, Guo Y, To SBC, Non AL, Barkin SL. Maternal BMI as a predictor of methylation of obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity. BMC Genomics 2017; 18:57. [PMID: 28068899 PMCID: PMC5223358 DOI: 10.1186/s12864-016-3473-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 12/26/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The study of epigenetic processes and mechanisms present a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool-age children at-risk for obesity despite the relevance of this developmental stage to trajectories of weight gain. We hypothesized that salivary DNA methylation patterns of key obesogenic genes in Hispanic children would 1) correlate with maternal BMI and 2) allow for identification of pathways associated with children at-risk for obesity. RESULTS Genome-wide DNA methylation was conducted on 92 saliva samples collected from Hispanic preschool children using the Infinium Illumina HumanMethylation 450 K BeadChip (Illumina, San Diego, CA, USA), which interrogates >484,000 CpG sites associated with ~24,000 genes. The analysis was limited to 936 genes that have been associated with obesity in a prior GWAS Study. Child DNA methylation at 17 CpG sites was found to be significantly associated with maternal BMI, with increased methylation at 12 CpG sites and decreased methylation at 5 CpG sites. Pathway analysis revealed methylation at these sites related to homocysteine and methionine degradation as well as cysteine biosynthesis and circadian rhythm. Furthermore, eight of the 17 CpG sites reside in genes (FSTL1, SORCS2, NRF1, DLC1, PPARGC1B, CHN2, NXPH1) that have prior known associations with obesity, diabetes, and the insulin pathway. CONCLUSIONS Our study confirms that saliva is a practical human tissue to obtain in community settings and in pediatric populations. These salivary findings indicate potential epigenetic differences in Hispanic preschool children at risk for pediatric obesity. Identifying early biomarkers and understanding pathways that are epigenetically regulated during this critical stage of child development may present an opportunity for prevention or early intervention for addressing childhood obesity. TRIAL REGISTRATION The clinical trial protocol is available at ClinicalTrials.gov ( NCT01316653 ). Registered 3 March 2011.
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Affiliation(s)
- Kathryn Tully Oelsner
- College of Medicine, Medical University of South Carolina, 96 Jonathan Lucas St, Suite 601, MSC 617, Charleston, SC 29425 USA
| | - Yan Guo
- Center for Quantitative Research, School of Medicine, Vanderbilt University, 2220 Pierce Ave, 571 Preston Research Building, Nashville, TN USA
| | - Sophie Bao-Chieu To
- Department of Biological Sciences, Vanderbilt University, 1210 BSB, 465 21st Ave S, Nashville, TN USA
| | - Amy L. Non
- Department of Anthropology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Shari L. Barkin
- Department of Pediatrics, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
- Pediatric Obesity Research, Diabetes Research and Training Center, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
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9
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Ramezani GH, Moghadam MM, Saghiri MA, Garcia-Godoy F, Asatourian A, Aminsobhani M, Scarbecz M, Sheibani N. Effect of dental restorative materials on total antioxidant capacity and calcium concentration of unstimulated saliva. J Clin Exp Dent 2017; 9:e71-e77. [PMID: 28149467 PMCID: PMC5268120 DOI: 10.4317/jced.53272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 06/01/2016] [Indexed: 01/01/2023] Open
Abstract
Background To evaluate the effect of dental amalgam and composite restorations on total antioxidant capacity (TAC) and calcium (Ca) ion concentration of unstimulated saliva. Material and Methods Forty-eight children aged 6-10 years selected and divided into three groups of sixteen (8 males, 8 females). In group A and B, samples consisted of two class II dental composite or amalgam restorations, while in group C samples were caries-free (control group). Unstimulated saliva from all samples was collected and TAC was measured by spectrophotometry using an adaptation of 2, 2’-azino-di-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) assay. The Ca ion level was estimated by an auto- analyzer. Data were analyzed with one- and two-way ANOVA test, at a p<.05 level of significance. Results Composite samples showed significantly higher TAC and lower Ca ion levels compared to amalgam and caries-free samples (p<.05). The TAC values showed only significant difference between groups (p<.05), while the Ca ion results showed significant differences within and between groups (p<.05). Conclusions Dental composite restorations increased TAC and decreased Ca ion levels more than amalgam restorations in saliva. Gender is an effective factor in changes induced in oral cavity as females showed more emphatic reaction to dental filling materials than males. Statement of Clinical Relevance Patients who have dental restorations, especially dental composites, should pay more attention to their dental hygiene, because dental restorations can increase oxidative stress and decrease Ca ion level in saliva, which might jeopardize remineralization process of tooth structures after demineralization. Key words:Amalgam, caries, composite, saliva, total antioxidant capacity.
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Affiliation(s)
- Gholam H Ramezani
- BDS, MS, DDS, Associate professor, Department of Pediatric Dentistry, Dental Branch, Islamic Azad University, Tehran, Iran
| | - Mona-Momeni Moghadam
- DDS Visiting researcher, Angiogenesis and Regenerative Group, Dr. H. Afsar Lajevardi Research Cluster, Shiraz, Iran
| | - Mohammad-Ali Saghiri
- BSc, MSc, PhD, Wisconsin institute for Medical Research and Department of Ophthalmology & Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Franklin Garcia-Godoy
- DDS, MSc, PhD, Bioscience Research Center, Health Science Center, College of Dentistry, University of Tennessee, Memphis, TN, USA
| | - Armen Asatourian
- DDS, Clinical instructor, Angiogenesis and Regenerative Sector, Dr. H. Afsar Lajevardi Research Cluster, Shiraz, Iran
| | - Mohsen Aminsobhani
- DDS, MSc, Associate professor, Endodontic Department, School of Dentistry, Tehran University of Medical Sciences and AJA University of Medical Sciences, Tehran, Iran
| | - Mark Scarbecz
- DDS, PhD, Professor, Bioscience Research Center, Health Science Center, College of Dentistry, University of Tennessee, Memphis, TN, USA
| | - Nader Sheibani
- BSc, MSc, PhD, Professor, Departments of Ophthalmology & Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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10
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Performance Characterization and Validation of Saliva as an Alternative Specimen Source for Detecting Hereditary Breast Cancer Mutations by Next Generation Sequencing. Int J Genomics 2016; 2016:2059041. [PMID: 27818992 PMCID: PMC5081504 DOI: 10.1155/2016/2059041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/22/2016] [Accepted: 09/26/2016] [Indexed: 12/12/2022] Open
Abstract
Identification of pathogenic germline mutations by next generation sequencing is a widely accepted tool for predicting the risk of hereditary cancer development. Blood is the most common source of DNA for such tests. However, blood as a sample type has many drawbacks, including the invasive collection method, poor sample stability, and a relatively high cost of collection. Therefore, in the current study we have assessed the suitability of saliva as an alternative source of genomic DNA for the identification of germline mutations in the BRCA1/2 genes by next generation sequencing (NGS). Our results show that all of the samples yielded DNA concentrations sufficient for library preparation. The concentrations of the final libraries, which were generated by PCR using target specific primers, fall into the expected range with no notable difference between libraries generated from DNA derived from saliva or blood. Quality parameters indicate that sequencing performance is comparable across sample source. An average of (98 ± 0.02)% variant calling concordance was obtained between the two specimen sources. Our data recommends saliva as a potential alternative for detecting germline mutation by next generation sequencing.
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11
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Determination of DNA profiling of siwak and toothbrush samples used in Kingdom of Saudi Arabia. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2016. [DOI: 10.1016/j.ejmhg.2016.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R. DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis. Biopreserv Biobank 2016; 14:264-70. [PMID: 27158753 PMCID: PMC4991598 DOI: 10.1089/bio.2015.0064] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-quality human DNA samples and associated information of individuals are necessary for biomedical research. Biobanks act as a support infrastructure for the scientific community by providing a large number of high-quality biological samples for specific downstream applications. For this purpose, biobank methods for sample preparation must ensure the usefulness and long-term functionality of the products obtained. Quality indicators are the tool to measure these parameters, the purity and integrity determination being those specifically used for DNA. This study analyzes the quality indicators in DNA samples derived from 118 frozen human tissues in optimal cutting temperature (OCT) reactive, 68 formalin-fixed paraffin-embedded (FFPE) tissues, 119 frozen blood samples, and 26 saliva samples. The results obtained for DNA quality are discussed in association with the usefulness for downstream applications and availability of the DNA source in the target study. In brief, if any material is valid, blood is the most approachable option of prospective collection of samples providing high-quality DNA. However, if diseased tissue is a requisite or samples are available, the recommended source of DNA would be frozen tissue. These conclusions will determine the best source of DNA, according to the planned downstream application. Furthermore our results support the conclusion that a complete procedure of DNA quantification and qualification is necessary to guarantee the appropriate management of the samples, avoiding low confidence results, high costs, and a waste of samples.
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Affiliation(s)
- Gema Lucena-Aguilar
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - Ana María Sánchez-López
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | | | - José Antonio Carrillo-Ávila
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - José Antonio López-Guerrero
- 3 Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología , Valencia, Spain .,4 Biobank, Fundación Instituto Valenciano de Oncología , Valencia, Spain
| | - Rocío Aguilar-Quesada
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
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Yi L, Wu T, Luo W, Zhou W, Wu J. A non-invasive, rapid method to genotype late-onset Alzheimer's disease-related apolipoprotein E gene polymorphisms. Neural Regen Res 2014; 9:69-75. [PMID: 25206745 PMCID: PMC4146311 DOI: 10.4103/1673-5374.125332] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2013] [Indexed: 12/21/2022] Open
Abstract
The apolipoprotein E gene ε4 allele is considered a negative factor for neural regeneration in late-onset Alzheimer's disease cases. The aim of this study was to establish a non-invasive, rapid method to genotype apolipoprotein E gene polymorphisms. Genomic DNA from mouth swab specimens was extracted using magnetic nanoparticles, and genotyping was performed by real-time PCR using TaqMan-BHQ probes. Genotyping accuracy was validated by DNA sequencing. Our results demonstrate 100% correlation to DNA sequencing, indicating reliability of our protocol. Thus, the method we have developed for apolipoprotein E genotyping is accurate and reliable, and also suitable for genotyping large samples, which may help determine the role of the apolipoprotein E ε4 allele in neural regeneration in late-onset Alzheimer's disease cases.
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Affiliation(s)
- Li Yi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Ting Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Wenyuan Luo
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Wen Zhou
- Department of Radiology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
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Haberstick BC, Smolen A, Stetler GL, Tabor JW, Roy T, Rick Casey H, Pardo A, Roy F, Ryals LA, Hewitt C, Whitsel EA, Halpern CT, Killeya-Jones LA, Lessem JM, Hewitt JK, Harris KM. Simple sequence repeats in the national longitudinal study of adolescent health: an ethnically diverse resource for genetic analysis of health and behavior. Behav Genet 2014; 44:487-97. [PMID: 24890516 DOI: 10.1007/s10519-014-9662-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 05/08/2014] [Indexed: 12/16/2022]
Abstract
Simple sequence repeats (SSRs) are one of the earliest available forms of genetic variation available for analysis and have been utilized in studies of neurological, behavioral, and health phenotypes. Although findings from these studies have been suggestive, their interpretation has been complicated by a variety of factors including, among others, limited power due to small sample sizes. The current report details the availability, diversity, and allele and genotype frequencies of six commonly examined SSRs in the ethnically diverse, population-based National Longitudinal Study of Adolescent Health. A total of 106,743 genotypes were generated across 15,140 participants that included four microsatellites and two di-nucleotide repeats in three dopamine genes (DAT1, DRD4, DRD5), the serotonin transporter, and monoamine oxidase A. Allele and genotype frequencies showed a complex pattern and differed significantly between populations. For both di-nucleotide repeats we observed a greater allelic diversity than previously reported. The availability of these six SSRs in a large, ethnically diverse sample with extensive environmental measures assessed longitudinally offers a unique resource for researchers interested in health and behavior.
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Affiliation(s)
- Brett C Haberstick
- Institute for Behavioral Genetics, University of Colorado Boulder, Campus Box 447, Boulder, CO, 80309-0447, USA,
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15
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Yi L, Huang Y, Wu T, Wu J. A magnetic nanoparticles-based method for DNA extraction from the saliva of stroke patients. Neural Regen Res 2013; 8:3036-46. [PMID: 25206624 PMCID: PMC4146207 DOI: 10.3969/j.issn.1673-5374.2013.32.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene is a risk factor for stroke, suggesting that widespread detection could help to prevent stroke. DNA from 70 stroke patients and 70 healthy controls was extracted from saliva using a magnetic nanoparticles-based method and from blood using conventional methods. Real-time PCR results revealed that the C677T polymorphism was genotyped by PCR using DNA extracted from both saliva and blood samples. The genotype results were confirmed by gene sequencing, and results for saliva and blood samples were consistent. The mutation TT genotype frequency was significantly higher in the stroke group than in controls. Homocysteine levels were significantly higher than controls in both TT genotype groups. Therefore, this noninvasive magnetic nanoparticles-based method using saliva samples could be used to screen for the MTHFR C677T polymorphism in target populations.
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Affiliation(s)
- Li Yi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ying Huang
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ting Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
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16
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Po'e EK, Heerman WJ, Mistry RS, Barkin SL. Growing Right Onto Wellness (GROW): a family-centered, community-based obesity prevention randomized controlled trial for preschool child-parent pairs. Contemp Clin Trials 2013; 36:436-49. [PMID: 24012890 DOI: 10.1016/j.cct.2013.08.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/27/2013] [Accepted: 08/30/2013] [Indexed: 12/21/2022]
Abstract
Growing Right Onto Wellness (GROW) is a randomized controlled trial that tests the efficacy of a family-centered, community-based, behavioral intervention to prevent childhood obesity among preschool-aged children. Focusing on parent-child pairs, GROW utilizes a multi-level framework, which accounts for macro (i.e., built-environment) and micro (i.e., genetics) level systems that contribute to the childhood obesity epidemic. Six hundred parent-child pairs will be randomized to a 3-year healthy lifestyle intervention or a 3-year school readiness program. Eligible children are enrolled between ages 3 and 5, are from minority communities, and are not obese. The principal site for the GROW intervention is local community recreation centers and libraries. The primary outcome is childhood body mass index (BMI) trajectory at the end of the three-year study period. In addition to other anthropometric measurements, mediators and moderators of growth are considered, including genetics, accelerometry, and diet recall. GROW is a staged intensity intervention, consisting of intensive, maintenance, and sustainability phases. Throughout the study, parents build skills in nutrition, physical activity, and parenting, concurrently forming new social networks. Participants are taught goal-setting, self-monitoring, and problem solving techniques to facilitate sustainable behavior change. The GROW curriculum uses low health literacy communication and social media to communicate key health messages. The control arm is administered to both control and intervention participants. By conducting this trial in public community centers, and by implementing a family-centered approach to sustainable healthy childhood growth, we aim to develop an exportable community-based intervention to address the expanding public health crisis of pediatric obesity.
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Affiliation(s)
- Eli K Po'e
- Department of Pediatrics, Vanderbilt University Medical Center, 2146 Belcourt Ave, Nashville, TN 37212, USA
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17
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Abstract
There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart.
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Affiliation(s)
- Ji-Ye Ai
- University of California, Los Angeles, CA, USA.
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18
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Effects of the UK Biobank collection protocol on potential biomarkers in saliva. Int J Epidemiol 2012; 41:1786-97. [DOI: 10.1093/ije/dys166] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Anthonappa RP, King NM, Rabie ABM. Evaluation of the long-term storage stability of saliva as a source of human DNA. Clin Oral Investig 2012; 17:1719-25. [PMID: 23103961 DOI: 10.1007/s00784-012-0871-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/18/2012] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The objectives of this paper are to determine the storage stability of saliva at 37 °C over an 18-month period, and its influence on the DNA yield, purity, PCR protocols and genotyping efficacy. MATERIALS AND METHODS Of the 60 participants, blood samples were obtained from 10 and saliva from 50. Samples were subjected to different storage conditions: DNA extracted immediately; DNA extracted following storage at 37 °C for 1, 6, 12 and 18 months. Subsequently, DNA yield, OD(260/280) and OD(260/230) ratios were measured. The isolated DNA was used to amplify exons 0-7 of the RUNX2 gene and subsequently sequenced. Furthermore, 25 SNPs were genotyped. RESULTS The mean DNA yield, OD(260/280) and OD(260/230) ratios obtained from blood were 67.4 ng/μl, 1.8 ± 0.05 and 1.8 ± 0.4 respectively. DNA yield obtained from saliva was significantly higher than blood (p < 0.0001), ranging from 97.4 to 125.8 ng/μl while the OD(260/280) ratio ranged from 1.8 ± 0.13 to 1.9 ± 0.1. The success rates for the 25 SNPs ranged from 98 to 100 % for blood and 96-99 % for saliva samples with the genotype frequencies in Hardy-Weinberg equilibrium (>0.01). CONCLUSIONS Saliva can be stored at 37 °C for 18 months without compromising its quality and ability to endure genetic analyses. CLINICAL RELEVANCE Saliva is a viable source of human DNA to facilitate the feasibility of large-scale genetic studies.
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Affiliation(s)
- Robert P Anthonappa
- Paediatric Dentistry, School of Dentistry, The University of Western Australia, Perth, Australia.
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20
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21
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Nunes AP, Oliveira IO, Santos BR, Millech C, Silva LP, González DA, Hallal PC, Menezes AMB, Araújo CL, Barros FC. Quality of DNA extracted from saliva samples collected with the Oragene™ DNA self-collection kit. BMC Med Res Methodol 2012; 12:65. [PMID: 22559914 PMCID: PMC3422993 DOI: 10.1186/1471-2288-12-65] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 05/04/2012] [Indexed: 11/30/2022] Open
Abstract
Background Large epidemiological studies in DNA biobanks have increasingly used less invasive methods for obtaining DNA samples, such as saliva collection. Although lower amounts of DNA are obtained as compared with blood collection, this method has been widely used because of its more simple logistics and increased response rate. The present study aimed to verify whether a storage time of 8 months decreases the quality of DNA from collected samples. Methods Saliva samples were collected with an OrageneTM DNA Self-Collection Kit from 4,110 subjects aged 14–15 years. The samples were processed in two aliquots with an 8-month interval between them. Quantitative and qualitative evaluations were carried out in 20% of the samples by spectrophotometry and genotyping. Descriptive analyses and paired t-tests were performed. Results The mean volume of saliva collected was 2.2 mL per subject, yielding on average 184.8 μg DNA per kit. Most samples showed a Ratio of OD differences (RAT) between 1.6 and 1.8 in the qualitative evaluation. The evaluation of DNA quality by TaqMan®, High Resolution Melting (HRM), and restriction fragment length polymorphism-PCR (RFLP-PCR) showed a rate of success of up to 98% of the samples. The sample store time did not reduce either the quantity or quality of DNA extracted with the Oragene kit. Conclusion The study results showed that a storage period of 8 months at room temperature did not reduce the quality of the DNA obtained. In addition, the use of the Oragene kit during fieldwork in large population-based studies allows for DNA of high quantity and high quality.
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Affiliation(s)
- Ana P Nunes
- Morphology Department, Institute of Biology, Universidade Federal de Pelotas, Pelotas, Brazil.
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22
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Pow EHN, Law MYT, Tsang PCS, Perera RAPM, Kwong DLW. Salivary Epstein-Barr virus DNA level in patients with nasopharyngeal carcinoma following radiotherapy. Oral Oncol 2011; 47:879-82. [PMID: 21767975 DOI: 10.1016/j.oraloncology.2011.06.507] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 06/15/2011] [Accepted: 06/26/2011] [Indexed: 12/12/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a solid tumor closely associated with Epstein-Barr virus (EBV) infection. The purpose of this investigation was to detect and quantify the EBV DNA level in salivary samples of NPC patients following treatment using real-time PCR. A total of 175 consecutive newly diagnosed NPC patients' whole saliva samples were collected before treatment, and the EBV DNA level was measured by real-time PCR, with the primers and probe targeting the BamHI-W region of the EBV genome. The post-treatment salivary EBV DNA level was also assessed in 46 patients. The change of EBV DNA level before and after treatment and relationship of EBV DNA level to demographic data and tumor staging were tested by Wilcoxon signed-rank test and Mann-Whitney U test, respectively with the level of significance set at 0.05. The EBV detection rate of pre-treatment saliva samples was 80%. The EBV DNA level of post-treatment saliva samples was significantly higher than the pre-treatment ones (P<0.01). There is a trend that patients with advanced-stage showed a higher EBV DNA level than patients with early-stage. The detection of EBV DNA in saliva using real-time PCR might be a feasible and non-invasive method for early diagnosis of NPC.
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Affiliation(s)
- Edmond H N Pow
- Oral Rehabilitation, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.
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23
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Koni AC, Scott RA, Wang G, Bailey MES, Peplies J, Bammann K, Pitsiladis YP. DNA yield and quality of saliva samples and suitability for large-scale epidemiological studies in children. Int J Obes (Lond) 2011; 35 Suppl 1:S113-8. [PMID: 21483410 DOI: 10.1038/ijo.2011.43] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To evaluate two saliva collection methods for DNA yield and quality as applied to a large, integrated, multicentre, European project involving the collection of biological material from children. DESIGN Cross-sectional multicentre comparative study in young children. METHODS Saliva samples were collected from 14,019 children aged 2-9 years from eight European countries participating in the IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) study. This involved either the collection of 2 ml of saliva from children who were able to spit, or using a sponge to collect whole saliva and buccal mucosal cells from the inside of the mouth of younger children unable to spit. Samples were assembled centrally in each participating centre and subsequently despatched for DNA extraction and biobanking to the University of Glasgow. A subgroup of 4678 samples (∼33% of sampled individuals) were chosen for DNA extraction before genotyping. RESULTS The whole-saliva collection method resulted in a higher DNA yield than the sponge collection method (mean±s.d.; saliva: 20.95±2.35 μg, sponge: 9.13±2.25 μg; P<0.001). DNA quality as measured by A (260)/A (280) was similar for the two collection methods. A minimum genotype calling success rate of 95% showed that both methods provide good-quality DNA for genotyping using TaqMan allelic discrimination assays. CONCLUSIONS Our results showed higher DNA yield from the whole-saliva collection method compared with the assisted sponge collection. However, both collection methods provided DNA of sufficient quantity and quality for large-scale genetic epidemiological studies.
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Affiliation(s)
- A C Koni
- College of Medicine, Veterinary and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Scotland, UK
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24
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Isaza-Guzmán DM, Arias-Osorio C, Martínez-Pabón MC, Tobón-Arroyave SI. Salivary levels of matrix metalloproteinase (MMP)-9 and tissue inhibitor of matrix metalloproteinase (TIMP)-1: A pilot study about the relationship with periodontal status and MMP-9−1562C/T gene promoter polymorphism. Arch Oral Biol 2011; 56:401-11. [DOI: 10.1016/j.archoralbio.2010.10.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/01/2010] [Accepted: 10/27/2010] [Indexed: 11/25/2022]
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25
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Lau KC, Lam CW, Law CY, Lai ST, Tsang TY, Siu CWK, To WK, Leung KF, Mak CM, Poon WT, Chan PKS, Chan YW. Non-invasive screening of HLA-DPA1 and HLA-DPB1 alleles for persistent hepatitis B virus infection: susceptibility for vertical transmission and toward a personalized approach for vaccination and treatment. Clin Chim Acta 2011; 412:952-7. [PMID: 21310144 DOI: 10.1016/j.cca.2011.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 01/24/2011] [Accepted: 01/24/2011] [Indexed: 12/17/2022]
Abstract
BACKGROUND Polymorphisms in the major histocompatibility complex (MHC) and non-MHC genes were recently reported to be associated with persistent hepatitis B virus (HBV) infection and host response to hepatitis B vaccine in Asian populations. We aimed to confirm the associations in Chinese population and develop a non-invasive screening method for the risk loci. METHODS We genotyped 2 risk alleles on the MHC loci, HLA-DPA1 (rs3077) and HLA-DPB1 (rs9277535), and 1 risk allele near a non-MHC gene, FOXP1 (rs6789153) using high-resolution melting curve analysis. With minimal processing steps and time, salivary DNA was extracted with a modified protocol of a blood kit. We compared the genotyping fidelity between peripheral blood DNA and salivary DNA. RESULTS Both rs3077 and rs9277535, but not rs6789153, are significantly associated with CHB in Chinese population (p-value<0.001). High genotype concordance between different sources of genomic DNA was obtained. CONCLUSIONS Genotyping salivary DNA using our modified methods provides a non-invasive fast screening for host susceptibility loci. The transmission mechanism of hepatitis B can now be modified by adding genetic susceptibility to the traditional vertical transmission model of hepatitis B.
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Affiliation(s)
- Kin-Chong Lau
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
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Ladouceur M, Leslie WD, Dastani Z, Goltzman D, Richards JB. An efficient paradigm for genetic epidemiology cohort creation. PLoS One 2010; 5:e14045. [PMID: 21124974 PMCID: PMC2987800 DOI: 10.1371/journal.pone.0014045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/14/2010] [Indexed: 11/27/2022] Open
Abstract
Development of novel methodologies to efficiently create large genetic epidemiology cohorts is needed. Here we describe a rapid, precise and cost-efficient method for collection of DNA from cases previously experiencing an osteoporotic fracture by identifying cases using and administrative health-care databases. Over the course of 14 months we collected DNA from 1,130 women experiencing an osteoporotic fracture, at a cost of $54 per sample. This cohort is among the larger DNA osteoporotic fracture collections in the world. The novel method described addresses a major unmet health care research need and is widely applicable to any disease that can be identified accurately through administrative data.
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Affiliation(s)
- Martin Ladouceur
- Department of Human Genetics, McGill University and Jewish General Hospital, Montreal, Canada
| | - William D. Leslie
- Departments of Medicine and Radiology, University of Manitoba, Winnipeg, Canada
| | - Zari Dastani
- Departments of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - David Goltzman
- Department of Medicine, McGill University and McGill University Health Centre, Montreal, Canada
| | - J. Brent Richards
- Department of Human Genetics, McGill University and Jewish General Hospital, Montreal, Canada
- Departments of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
- Department of Medicine, McGill University and McGill University Health Centre, Montreal, Canada
- Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- * E-mail:
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Nishita DM, Jack LM, McElroy M, McClure JB, Richards J, Swan GE, Bergen AW. Clinical trial participant characteristics and saliva and DNA metrics. BMC Med Res Methodol 2009; 9:71. [PMID: 19874586 PMCID: PMC2776600 DOI: 10.1186/1471-2288-9-71] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 10/29/2009] [Indexed: 11/18/2022] Open
Abstract
Background Clinical trial and epidemiological studies need high quality biospecimens from a representative sample of participants to investigate genetic influences on treatment response and disease. Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of saliva biospecimen samples collected through the mail, trial participant demographic and behavioral characteristics, and their association with saliva and DNA quantity and quality. Methods Saliva biospecimens were collected using the Oragene® DNA Self-Collection Kits from participants in a National Cancer Institute funded smoking cessation trial. Saliva biospecimens from 565 individuals were visually inspected for clarity prior to and after DNA extraction. DNA samples were then quantified by UV absorbance, PicoGreen®, and qPCR. Genotyping was performed on 11 SNPs using TaqMan® SNP assays and two VNTR assays. Univariate, correlation, and analysis of variance analyses were conducted to observe the relationship between saliva sample and participant characteristics. Results The biospecimen kit return rate was 58.5% among those invited to participate (n = 967) and 47.1% among all possible COMPASS participants (n = 1202). Significant gender differences were observed with males providing larger saliva volume (4.7 vs. 4.5 ml, p = 0.019), samples that were more likely to be judged as cloudy (39.5% vs. 24.9%, p < 0.001), and samples with greater DNA yield as measured by UV (190.0 vs. 138.5, p = 0.002), but reduced % human DNA content (73.2 vs. 77.6 p = 0.005) than females. Other participant characteristics (age, self-identified ethnicity, baseline cigarettes per day) were associated with saliva clarity. Saliva volume and saliva and DNA clarity were positively correlated with total DNA yield by all three quantification measurements (all r > 0.21, P < 0.001), but negatively correlated with % human DNA content (saliva volume r = -0.148 and all P < 0.010). Genotyping completion rate was not influenced by saliva or DNA clarity. Conclusion Findings from this study show that demographic and behavioral characteristics of smoking cessation trial participants have significant associations with saliva and DNA metrics, but not with the performance of TaqMan® SNP or VNTR genotyping assays. Trial registration COMPASS; registered as NCT00301145 at clinicaltrials.gov.
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Affiliation(s)
- Denise M Nishita
- Center for Health Sciences, SRI International, Menlo Park, CA, 94025, USA.
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28
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Mitsouras K, Faulhaber EA. Saliva as an alternative source of high yield canine genomic DNA for genotyping studies. BMC Res Notes 2009; 2:219. [PMID: 19874604 PMCID: PMC2781016 DOI: 10.1186/1756-0500-2-219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 10/29/2009] [Indexed: 11/10/2022] Open
Abstract
Background The domestic dog presents an attractive model system for the study of the genetic basis of disease. The development of resources such as the canine genome sequence and SNP genotyping platforms has allowed for the implementation of canine genetic studies. Successful implementation of such studies depends not only on the quality of individual DNA samples, but also on the number of samples obtained. The latter can be maximized using a non-invasive DNA collection method that can increase study participation. We compared the DNA yield and quality obtained from blood and buccal swabs to those obtained using a non-invasive saliva collection kit (Oragene ®•ANIMAL kit). We also assessed the success rate of PCR amplification and genotyping accuracy of DNA isolated using these collection methods. Findings Comparison of DNA yields from matched saliva, blood and buccal swab samples showed that yields from saliva were significantly higher than those from blood (p = 0.0198) or buccal swabs (p = 0.0008). Electrophoretic analysis revealed that blood and saliva produced higher quality DNA than buccal swabs. In addition, a 1.1-kb PCR fragment was successfully amplified using the paired DNA samples and genotyping by PCR-RFLP yielded identical results. Conclusion We demonstrate that DNA yields from canine saliva are higher than those from blood or buccal swabs. The quality of DNA extracted from saliva is sufficient for successful amplification of a 1.1-kb fragment and for accurate SNP genotyping by PCR-RFLP. We conclude that saliva presents a non-invasive alternative source of high quantities of canine genomic DNA suitable for genotyping studies.
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Affiliation(s)
- Katherine Mitsouras
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA.
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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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30
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Andreoli SB, Ribeiro WS, Quintana MI, Guindalini C, Breen G, Blay SL, Coutinho ESF, Harpham T, Jorge MR, Lara DR, Moriyama TS, Quarantini LC, Gadelha A, Vilete LMP, Yeh MSL, Prince M, Figueira I, Bressan RA, Mello MF, Dewey ME, Ferri CP, Mari JDJ. Violence and post-traumatic stress disorder in Sao Paulo and Rio de Janeiro, Brazil: the protocol for an epidemiological and genetic survey. BMC Psychiatry 2009; 9:34. [PMID: 19500422 PMCID: PMC2700799 DOI: 10.1186/1471-244x-9-34] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 06/07/2009] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND violence is a public health major concern, and it is associated with post-traumatic stress disorder and other psychiatric outcomes. Brazil is one of the most violent countries in the world, and has an extreme social inequality. Research on the association between violence and mental health may support public health policy and thus reduce the burden of disease attributable to violence. The main objectives of this project were: to study the association between violence and mental disorders in the Brazilian population; to estimate the prevalence rates of exposure to violence, post-traumatic stress disorder, common metal disorder, and alcohol hazardous use and dependence: and to identify contextual and individual factors, including genetic factors, associated with the outcomes. METHODS/DESIGN one phase cross-sectional survey carried out in Sao Paulo and Rio de Janeiro, Brazil. A multistage probability to size sampling scheme was performed in order to select the participants (3000 and 1500 respectively). The cities were stratified according to homicide rates, and in Sao Paulo the three most violent strata were oversampled. The measurements included exposure to traumatic events, psychiatric diagnoses (CIDI 2.1), contextual (homicide rates and social indicators), and individual factors, such as demographics, social capital, resilience, help seeking behaviours. The interviews were carried between June/2007 February/2008, by a team of lay interviewers. The statistical analyses will be weight-adjusted in order to take account of the design effects. Standardization will be used in order to compare the results between the two centres. Whole genome association analysis will be performed on the 1 million SNP (single nucleotide polymorphism) arrays, and additional association analysis will be performed on additional phenotypes. The Ethical Committee of the Federal University of Sao Paulo approved the study, and participants who matched diagnostic criteria have been offered a referral to outpatient clinics at the Federal University of Sao Paulo and Federal University of Rio de Janeiro.
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Affiliation(s)
| | | | - Maria Ines Quintana
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Camila Guindalini
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gerome Breen
- MRC Social, Institute of Psychiatry, King's College, London, UK
| | - Sergio Luis Blay
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Trudy Harpham
- London South Bank University, London, UK,London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Tais S Moriyama
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Lucas C Quarantini
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ary Gadelha
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Mary SL Yeh
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Martin Prince
- Centre for Public Mental Health, Health Services and Population Research Department, Institute of Psychiatry, King's College, University of London, London, UK
| | - Ivan Figueira
- Institute of Psychiatry, Universidade Federal do Rio de Janeiro (IPUB – UFRJ), Rio de Janeiro, Brazil
| | - Rodrigo A Bressan
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marcelo F Mello
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Michael E Dewey
- Centre for Public Mental Health, Health Services and Population Research Department, Institute of Psychiatry, King's College, University of London, London, UK
| | - Cleusa P Ferri
- Centre for Public Mental Health, Health Services and Population Research Department, Institute of Psychiatry, King's College, University of London, London, UK
| | - Jair de Jesus Mari
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil,Centre for Public Mental Health, Health Services and Population Research Department, Institute of Psychiatry, King's College, University of London, London, UK
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Lien KY, Liu CJ, Kuo PL, Lee GB. Microfluidic System for Detection of α-Thalassemia-1 Deletion Using Saliva Samples. Anal Chem 2009; 81:4502-9. [DOI: 10.1021/ac900453d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Chien-Ju Liu
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Pao-Lin Kuo
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Gwo-Bin Lee
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
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de Vargas Wolfgramm E, de Carvalho FM, da Costa Aguiar VR, De Nadai Sartori MP, Hirschfeld-Campolongo GC, Tsutsumida WM, Louro ID. Simplified buccal DNA extraction with FTA® Elute Cards. Forensic Sci Int Genet 2009; 3:125-7. [DOI: 10.1016/j.fsigen.2008.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/27/2008] [Accepted: 11/24/2008] [Indexed: 10/21/2022]
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Abstract
OBJECTIVE To estimate willingness of women to donate specimens for DNA analysis by needlestick compared with collection of saliva. METHODS This study was a cross-sectional survey given to women attending clinic appointments asked about their knowledge and attitudes toward genetics research and genotyping. RESULTS The majority of the 279 women surveyed would give DNA specimens by needlestick (68.3%) but more would be willing to donate saliva (75.7%), P=.003. An ethnic difference was seen in the replies about needlesticks but not regarding saliva donation. Multivariable analysis demonstrated that women who were likely to donate specimens rated themselves more knowledgeable about genes and DNA (odds ratio 2.43, 95% confidence interval 1.12-5.28) and had graduated from college or higher (odds ratio 6.74, 95% confidence interval 1.98-22.86). CONCLUSION More women are willing to donate DNA specimens by saliva than by needlestick. Knowledge and higher education predict a willingness to donate. LEVEL OF EVIDENCE III.
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Affandi JS, Price P, Imran D, Yunihastuti E, Djauzi S, Cherry CL. Can we predict neuropathy risk before stavudine prescription in a resource-limited setting? AIDS Res Hum Retroviruses 2008; 24:1281-4. [PMID: 18834321 DOI: 10.1089/aid.2008.0045] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A toxic sensory neuropathy associated with exposure to inexpensive nucleoside analogue reverse transcriptase inhibitors (NRTIs) [particularly stavudine (d4T)] causes dilemmas in the management of patients with HIV, especially in resource-poor settings. Here patients (n = 96) attending Pokdisus AIDS Clinic at the Cipto Mangunkusumo Hospital, Jakarta who had been treated with d4T were screened for symptomatic neuropathy. Clinical, demographic, and genetic factors were considered as possible neuropathy risk factors. DNA from saliva was used to examine alleles of TNFA-308, BAT1 (intron 10), TNFA-1031, IL1A+4845, and IL12B (3' UTR). The prevalence of neuropathy (symptoms and signs) was 34%. On multivariate analysis, neuropathy following d4T exposure was associated with increasing age, increasing height, and TNFA-1031*2 (model p = 0.0009). Isoniazid exposure (present in 56% of patients) was not associated with neuropathy in this cohort, where all patients had received pyridoxine coadministration. These data suggest that a simple algorithm based on patient age, height, and TNF genotype could be used to predict the individual's risk of symptomatic neuropathy prior to prescription of d4T.
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Affiliation(s)
- Jacquita S. Affandi
- School of Surgery and Pathology, University of Western Australia, Perth, Australia
| | - Patricia Price
- School of Surgery and Pathology, University of Western Australia, Perth, Australia
- Clinical Immunology and Immunogenetics, Royal Perth Hospital, Perth, Australia
| | - Darma Imran
- Pokdisus (Working Group on AIDS) Faculty of Medicine, University of Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Evy Yunihastuti
- Pokdisus (Working Group on AIDS) Faculty of Medicine, University of Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Samsuridjal Djauzi
- Pokdisus (Working Group on AIDS) Faculty of Medicine, University of Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Catherine L. Cherry
- Burnet Institute, Melbourne, Australia
- Infectious Diseases Unit, Alfred Hospital, Melbourne, Australia
- Department of Medicine, Monash University, Melbourne, Australia
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Chiappin S, Antonelli G, Gatti R, De Palo EF. Saliva specimen: a new laboratory tool for diagnostic and basic investigation. Clin Chim Acta 2007; 383:30-40. [PMID: 17512510 DOI: 10.1016/j.cca.2007.04.011] [Citation(s) in RCA: 431] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 03/30/2007] [Accepted: 04/07/2007] [Indexed: 01/31/2023]
Abstract
The assay of saliva is an increasing area of research with implications for basic and clinical purposes. Although this biological fluid is easy to manipulate and collect, careful attention must be directed to limit variation in specimen integrity. Recently, the use of saliva has provided a substantial addition to the diagnostic armamentarium as an investigative tool for disease processes and disorders. In addition to its oral indications, the analysis of saliva provides important information about the functioning of various organs within the body. In this respect, endocrine research certainly occupies a central role. The present review considers the laboratory aspects of salivary assays with respect to the different analytes including ions, drugs and various non-protein/protein compounds such as hormones and immunoglobulins. This review also examines the consequences of preanalytical variation with respect to collection strategy and subsequent storage conditions. It is likely that the use of saliva in assays will continue to expand thus providing a new instrument of investigation for physiologic as well as pathophysiologic states.
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Affiliation(s)
- Silvia Chiappin
- Section of Clinical Biochemistry, Department of Medical Diagnostic Sciences and Spec. Ther., University of Padua, c/o ex Istituto di Semeiotica Medica, Via Ospedale 105-35128, Padova, Italy
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Soo-Quee Koh D, Choon-Huat Koh G. The use of salivary biomarkers in occupational and environmental medicine. Occup Environ Med 2007; 64:202-10. [PMID: 17339296 PMCID: PMC2092532 DOI: 10.1136/oem.2006.026567] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- David Soo-Quee Koh
- Department of Community, Occupational and Family Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Block MD3, 16 Medical Drive, Singapore 117597, Singapore.
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Quinque D, Kittler R, Kayser M, Stoneking M, Nasidze I. Evaluation of saliva as a source of human DNA for population and association studies. Anal Biochem 2006; 353:272-7. [PMID: 16620753 DOI: 10.1016/j.ab.2006.03.021] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 03/09/2006] [Accepted: 03/10/2006] [Indexed: 10/24/2022]
Abstract
A simple noninvasive procedure for saliva sample collection and DNA extraction was developed. On average, the amount of human DNA (as measured by a TaqMan-based assay) was about 11.4 microg/mL saliva, which is more than can be obtained from other noninvasive samples such as cheek swabs. However, the presence of large amounts of nonhuman DNA (up to 90% of the total extracted DNA) in saliva samples does necessitate DNA quantitation methods that are specific for human DNA. We were able to reliably and accurately type different genetic markers (mDNA sequences, Y-chromosomal single-nucleotide polymorphisms, and autosomal microsatellite loci) from saliva samples stored for up to 30 days at 37 degrees C, making this method well-suited for field conditions and convenient transportation of samples back to the laboratory. Thus, saliva can be considered a reliable source of DNA for a wide variety of genetic studies.
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Affiliation(s)
- Dominique Quinque
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
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