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Janovičová Ľ, Holániová D, Vlková B, Celec P. Pre-Analytical Factors Affecting Extracellular DNA in Saliva. Diagnostics (Basel) 2024; 14:249. [PMID: 38337765 PMCID: PMC10855236 DOI: 10.3390/diagnostics14030249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA (ecDNA) in plasma, could be a promising biomarker for oral or systemic diseases. In contrast to genetics, the quantity of salivary ecDNA is of importance and can be affected by the pre-analytical processing of samples, but the details are not known. The aim of our study was to analyze the effects of centrifugation and freezing of saliva on the concentration of ecDNA in saliva. Fifteen healthy volunteers, free of any known systemic or oral diseases, were asked to collect unstimulated saliva samples. Aliquots were centrifuged at 1600× g and frozen or directly processed. The fresh or thawed cell-free saliva samples underwent subsequent centrifugation at 16,000× g. The supernatants were used for DNA isolation and quantification using fluorometry and real-time PCR. While freezing had minimal effects on the salivary ecDNA concentration, another centrifugation step decreased ecDNA considerably in both fresh and frozen samples (by 97.8% and 98.4%, respectively). This was mirrored in the quantitative PCR targeting a nuclear (decrease by 93.5%) and mitochondrial (decrease by 97.7%) ecDNA sequence. In conclusion, in this first study focusing on the technical aspects of salivary ecDNA quantitation, we show that, regardless of its subcellular origin, the concentration of ecDNA in saliva is mainly affected by additional centrifugation and not by the freezing of centrifuged cell-free saliva samples. This suggests that most salivary ecDNA likely is associated with cell debris and apoptotic bodies. Which fraction is affected by a particular disease should be the focus of further targeted studies.
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Affiliation(s)
- Ľubica Janovičová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Dominika Holániová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
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2
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Naseri S, Brewster RCL, Blumenthal PD. Novel use of menstrual blood for monitoring glycaemic control in patients with diabetes: a proof-of-concept study. BMJ SEXUAL & REPRODUCTIVE HEALTH 2022; 48:123-127. [PMID: 34759003 DOI: 10.1136/bmjsrh-2021-201211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Glycated haemoglobin (HbA1c) is the diagnostic and prognostic standard for clinical management of diabetes mellitus (DM). Unfortunately, patient adherence to guidelines for routine testing can be poor and there are significant gender-based disparities in DM management and outcomes. Recent evidence suggests that menstrual blood may be comparable to systemic blood for monitoring of common biomarkers. The objective of the present study was to assess the concordance of HbA1c levels between menstrual and systemic blood in healthy women and women with diabetes of reproductive age. METHODS In this prospective, observational cohort study, we enrolled healthy and diabetic (type 1 and type 2 DM) reproductive-age women (aged ≥18 and ≤45 years). Menstrual blood and venous systemic blood specimens were simultaneously obtained at time of menstruation, and analysed for HbA1c levels. Participants self-collected menstrual blood using a QPad, a novel, modified menstrual pad with an embedded dried blood spot strip. RESULTS Among 172 participants, 57.6% were healthy and 42.4% had a diagnosis of either type 1 or type 2 DM. There were no significant differences in mean HbA1c values in menstrual and systemic blood across the overall cohort or within the diabetic subgroup. Furthermore, HbA1c levels between blood sources were robustly correlated and demonstrated a significant linear relationship. CONCLUSIONS There is a strong concordance in HbA1c levels between menstrual and systemic blood. Empowered by self-collection technologies, these findings suggest that menstrual blood may serve as a reliable, non-invasive and potentially cost-effective alternative to serum for HbA1c monitoring among reproductive-age women with DM.
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Affiliation(s)
- Sara Naseri
- Obstetrics and Gynecology, Stanford University, Stanford, California, USA
| | | | - Paul D Blumenthal
- Obstetrics and Gynecology, Stanford University, Stanford, California, USA
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3
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Duś-Ilnicka I, Krala E, Cholewińska P, Radwan-Oczko M. The Use of Saliva as a Biosample in the Light of COVID-19. Diagnostics (Basel) 2021; 11:1769. [PMID: 34679467 PMCID: PMC8534561 DOI: 10.3390/diagnostics11101769] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Saliva is easy to collect and a biofluid that is readily available without the need for special equipment for its collection. The collection process, which is non-invasive and inexpensive, leads to obtaining a biomaterial that can serve as a source of information for molecular diagnostics of diseases in general medicine, genetics and dentistry. Unfortunately, many of the salivary methodologies are lacking important parameters to provide for not only the safety of the operator, but also the quality and reproducibility of the research. Since the COVID-19 pandemic, salivary diagnostics demonstrate a great potential for research of SARS-CoV 2. In this review, good practice for unstimulated saliva collection and patient preparation was provided, based on the latest literature and available guidelines. Schemes for saliva collection procedures were presented following an extended literature search. Descriptions of salivary probes/cups, techniques of saliva collection, and the use of specific buffering solutions for the stability of collected samples for SARS-CoV-2 detection were also evaluated.
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Affiliation(s)
- Irena Duś-Ilnicka
- Oral Pathology Department, Faculty of Dentistry, Wroclaw Medical University, ul. Krakowska 26, 50-425 Wroclaw, Poland; (E.K.); (M.R.-O.)
| | - Elżbieta Krala
- Oral Pathology Department, Faculty of Dentistry, Wroclaw Medical University, ul. Krakowska 26, 50-425 Wroclaw, Poland; (E.K.); (M.R.-O.)
| | - Paulina Cholewińska
- Institute of Animal Breeding, Faculty of Biology and Animal Breeding, Wroclaw University of Enviromental and Life Sciences, ul. Chełmońskiego 38C, 51-630 Wroclaw, Poland;
| | - Małgorzata Radwan-Oczko
- Oral Pathology Department, Faculty of Dentistry, Wroclaw Medical University, ul. Krakowska 26, 50-425 Wroclaw, Poland; (E.K.); (M.R.-O.)
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4
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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5
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Cepon-Robins TJ. Measuring attack on self: The need for field-friendly methods development and research on autoimmunity in human biology. Am J Hum Biol 2020; 33. [PMID: 33289250 DOI: 10.1002/ajhb.23544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Autoimmune and inflammatory disorder (AIID) prevalence appears to be increasing in all but the world's poorest regions and countries. Autoimmune diseases occur when there is a breakdown in processes that regulate inflammation and self-recognition by immune cells. Very few field-based studies have been conducted among Indigenous populations and underserved communities with limited access to medical care. This is due, in part, to the fact that autoimmune diseases are difficult to diagnose, even in clinical settings. In remote field settings these difficulties are compounded by the absence of infrastructure necessary for sample storage and analysis, and the lack of hospital/clinic access for more invasive diagnostic procedures. Because of these limitations, little is known about the prevalence of autoimmunity outside wealthy regions and clinical settings. AIMS The present paper discusses why AIID are of critical importance in human biology research and why more work needs to be devoted to validating, testing, and utilizing methods for detecting autoantibodies and other biomarkers related to autoimmunity in field-friendly, minimally invasively-collected samples. This paper reviews some of the methods used to diagnose AIIDs in clinical settings, and highlights methods that have been used in studies within human biology and related fields, emphasizing the invasiveness of specific methods and their feasibility in remote field settings. DISCUSSION AND CONCLUSIONS Risk for AIID is affected by several reproductive, dietary, environmental, and genetic factors. Human biologists have unique perspectives that they can bring to autoimmunity research, and more population-based studies on autoimmunity are needed within these and related fields.
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Affiliation(s)
- Tara J Cepon-Robins
- Department of Anthropology, University of Colorado Colorado Springs, Colorado Springs, Colorado, USA
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6
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Kohn JN, Kosciolek T, Marotz C, Aleti G, Guay-Ross RN, Hong SH, Hansen S, Swafford A, Knight R, Hong S. Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults. Brain Behav Immun 2020; 87:591-602. [PMID: 32061904 DOI: 10.1016/j.bbi.2020.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/04/2020] [Accepted: 02/09/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Tomasz Kosciolek
- Department of Pediatrics, United States; Current affiliation: Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | | | | | | | | | | | - Rob Knight
- Department of Pediatrics, United States; Center for Microbiome Innovation, United States; Department of Computer Science and Engineering, United States; Department of Bioengineering, United States
| | - Suzi Hong
- Department of Psychiatry, United States; Center for Microbiome Innovation, United States; Department of Family Medicine and Public Health, University of California, San Diego, United States.
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7
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Child Salivary SIgA and Its Relationship to Enteric Infections and EED Biomarkers in Maputo, Mozambique. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17093035. [PMID: 32349313 PMCID: PMC7246514 DOI: 10.3390/ijerph17093035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/03/2023]
Abstract
Characterizing child immunological responses to enteric infections with antibody detection in serum can be challenging in resource-constrained field settings, because sample collection requires trained individuals and its invasive procedure may lead to low response rates, especially among children. Saliva may present a promising non-invasive alternative. The objectives of this research were to compare salivary antibody levels in children to enteric infections and biomarkers of environmental enteric dysfunction (EED). We collected saliva samples from children aged one to six years enrolled in a sanitation trial in Maputo, Mozambique, and characterized salivary secretory immunoglobulin A (SIgA) concentrations with enzyme-linked immunosorbent assays. We used multilevel linear models to analyze cross-sectional associations between salivary SIgA and the number of concurrent enteric pathogen infections, as well as EED biomarkers in matched stool samples. Median salivary SIgA concentrations in this study population were 54 μg/mL (inter-quartile range (IQR): 34, 85 μg/mL), and SIgA levels were similar between children of different ages. SIgA was lower in children experiencing a higher number of concurrent infections -0.04 log μg/mL (95% confidence interval (CI): -0.08 to -0.005 log μg/mL), but was not associated with any of the included EED biomarkers. Contrary to evidence from high-income countries that suggests salivary SIgA increases rapidly with age in young children, the high prevalence of enteric infections may have led to a suppression of immunological development in this study sample and could in part explain the similar SIgA levels between children of different ages.
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Manmontri C, Nirunsittirat A, Piwat S, Wattanarat O, Pahumunto N, Makeudom A, Sastraruji T, Krisanaprakornkit S, Teanpaisan R. Reduction of Streptococcus mutans by probiotic milk: a multicenter randomized controlled trial. Clin Oral Investig 2019; 24:2363-2374. [PMID: 31838596 DOI: 10.1007/s00784-019-03095-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To investigate the effects of probiotics, Lactobacillus paracasei SD1, on the quantities of Streptococcus mutans in saliva and plaque samples of preschool children. DESIGN This randomized trial recruited 487 preschool children from eight childcare centers. Participants were assigned to receive a 6-month course of placebo milk daily (group I), probiotic milk either daily (group II) or three days a week (triweekly, group III). The absolute quantities of S. mutans and total lactobacilli in the saliva and plaque samples at baseline (T0), after intervention (T6), and 6 months after discontinuation (T12) were assessed by qPCR. RESULTS Of 487 children, 354 completed all follow-up periods. However, only 268 children (3.2 ± 0.8 years old; groups I = 86, II = 89, and III = 93) provided adequate saliva for qPCR. Whereas the quantities of S. mutans were significantly decreased in groups II and III compared to group I in the saliva and plaque samples at T6 and T12, those of total lactobacilli were significantly increased (p < 0.0167). There was no difference in the quantities of S. mutans or total lactobacilli between groups II and III at any period. Significant changes in the quantities of S. mutans and total lactobacilli lasted until T12 compared to T0 (p < 0.0167). CONCLUSIONS Probiotic administration daily or triweekly reduces S. mutans quantities, whereas it increases total lactobacilli quantities that persists at least 6 months after discontinuation in the saliva and plaque samples of preschool children. CLINICAL RELEVANCE Daily or triweekly consumption of L. paracasei SD1 supplemented in milk may help prevent dental caries in preschool children.
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Affiliation(s)
- Chanika Manmontri
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Oral and Maxillofacial Biology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Areerat Nirunsittirat
- Center of Excellence in Oral and Maxillofacial Biology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.,Division of Community Dentistry, Department of Family and Community Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supatcharin Piwat
- Common Oral Diseases and Epidemiology Research Center, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.,Department of Preventive Dentistry, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Onnida Wattanarat
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Oral and Maxillofacial Biology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nuntiya Pahumunto
- Common Oral Diseases and Epidemiology Research Center, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.,Department of Stomatology, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Anupong Makeudom
- Center of Excellence in Oral and Maxillofacial Biology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Thanapat Sastraruji
- Center of Excellence in Oral and Maxillofacial Biology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Suttichai Krisanaprakornkit
- Center of Excellence in Oral and Maxillofacial Biology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.,Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Rawee Teanpaisan
- Common Oral Diseases and Epidemiology Research Center, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand. .,Department of Stomatology, Faculty of Dentistry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.
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9
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Grippi C, Ahrens W, Buchecker K, Chadjigeorgiou C, De Henauw S, Koni AC, Foraita R, Lissner L, Molnár D, Moreno LA, Pitsiladis Y, Reisch LA, Russo P, Siani A, Veidebaum T, Iacoviello L, Gianfagna F. Association between variants of neuromedin U gene and taste thresholds and food preferences in European children: Results from the IDEFICS study. Appetite 2019; 142:104376. [PMID: 31326439 DOI: 10.1016/j.appet.2019.104376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
AIM The neuropeptide neuromedin U (NMU) known for its role in appetite, feeding and energy balance could be involved in the control of food choice and taste sensitivity. We examined the association between NMU polymorphisms/haplotypes and taste thresholds and food preferences in a population of European children. METHODS A total of 578 subjects from the IDEFICS study (mean age 7.5 ± 0.8 SD, boys 53.6%) with NMU genotype data and food preference (salty, fatty, sweet, flavour and umami food) and taste threshold (salt, fat, sweet, umami) tests available were analysed. Three single nucleotide polymorphisms (SNPs; rs6827359, T:C; rs12500837, T:C; rs9999653, C:T) of NMU gene were analyzed and five major haplotypes were inferred. The associations between genotypes and food preferences or taste thresholds were investigated (odds ratios -OR, adjusted for age, sex and country). A p < 0.05 after false discovery rate adjustment (pFDR) was considered statistically significant. RESULTS The association between NMU genotypes and food preference showed two NMU SNPs associated with preference for food containing sodium glutamate (umami taste; rs6827359C, OR = 1.61, 95% confidence interval (CI):1.20-2.17; rs9999653T, OR = 1.59, 95%CI:1.18-2.13). In the haplotype analysis, the CTT haplotype showed an OR of 1.70 (95%CI:1.16-2.5) for the umami food preference, while CCT haplotype showed an OR of 1.63 (95%CI:1.11-2.40), compared to the most frequent haplotype (TTC). Carriers of CCT/CCT vs subjects with no CCT haplotype showed an OR of 4.78 (95%CI:1.86-12.30). Umami food preference was associated with low values of BMI z-score, arm circumferences, skinfolds and fat mass (pFDR<0.05). No association between NMU genetic variants and taste thresholds was found. CONCLUSIONS This study shows for the first time in children an association between preference for umami food and a NMU haplotype, previously found associated with low BMI values.
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Affiliation(s)
- Claudio Grippi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany; Faculty of Mathematics and Computer Science, University of Bremen, Bremen, Germany
| | | | | | - Stefaan De Henauw
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Anna C Koni
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ronja Foraita
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
| | - Lauren Lissner
- Department of Community Medicine and Public Health, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Denés Molnár
- Department of Paediatrics, Medical School, University of Pécs, Pécs, Hungary
| | - Luis A Moreno
- GENUD (Growth, Exercise, Nutrition and Development) Research Group, University of Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Yannis Pitsiladis
- Collaborating Centre of Sports Medicine, University of Brighton, Brighton, United Kingdom
| | - Lucia A Reisch
- Department of Management, Society and Communication, Copenhagen Business School, Copenhagen, Denmark
| | - Paola Russo
- Unit of Epidemiology & Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
| | - Alfonso Siani
- Unit of Epidemiology & Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
| | - Toomas Veidebaum
- Department of Chronic Diseases, National Institute for Health Development, Tallinn, Estonia
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy; EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Francesco Gianfagna
- EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy; Mediterranea Cardiocentro, Napoli, Italy
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10
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Abstract
Saliva and oral/buccal samples have become increasingly valuable sources of genetic material for clinical applications. The DNA obtained by these samples is of comparable quality to that from blood samples. This, coupled with the ease of collecting saliva and oral/buccal samples, has led to increased numbers of such samples being incorporated into biobanks. This chapter will detail the steps involved in procuring, transporting, and storing saliva, buccal swabs, and oral wash samples for further use in downstream applications.
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11
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Galiana‐Simal A, Muñoz‐Martinez V, Calero‐Bueno P, Vela‐Romero M, Beato‐Fernandez L. Towards a future molecular diagnosis of autism: Recent advances in biomarkers research from saliva samples. Int J Dev Neurosci 2018; 67:1-5. [DOI: 10.1016/j.ijdevneu.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Adrian Galiana‐Simal
- Clínica Centro de Desarrollo Infantil de Ciudad Real (CDICR)Calle Eras del Cerrillo n°813004Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Victoria Muñoz‐Martinez
- Hospital General Universitario de Ciudad Real (HGUCR), Servicio de PsiquiatríaCalle Obispo Rafael Torija s/n13005Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Paloma Calero‐Bueno
- Universidad de Castilla‐La Mancha (UCLM)Facultad de Terapia Ocupacional, Logopedia y EnfermeríaAvda. Real Fábrica de Seda, s/n, 45600Talavera de la ReinaToledoSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Maria Vela‐Romero
- Clínica Centro de Desarrollo Infantil de Ciudad Real (CDICR)Calle Eras del Cerrillo n°813004Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
| | - Luis Beato‐Fernandez
- Hospital General Universitario de Ciudad Real (HGUCR), Servicio de PsiquiatríaCalle Obispo Rafael Torija s/n13005Ciudad RealSpain
- Grupo de Investigación en Trastornos del Neurodesarrollo de Ciudad Real (TNDCR)Ciudad RealSpain
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12
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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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13
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Gianfagna F, Grippi C, Ahrens W, Bailey MES, Börnhorst C, De Henauw S, Foraita R, Koni AC, Krogh V, Mårild S, Molnár D, Moreno L, Pitsiladis Y, Russo P, Siani A, Tornaritis M, Veidebaum T, Iacoviello L. The role of neuromedin U in adiposity regulation. Haplotype analysis in European children from the IDEFICS Cohort. PLoS One 2017; 12:e0172698. [PMID: 28235053 PMCID: PMC5325300 DOI: 10.1371/journal.pone.0172698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/08/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND AND AIMS Neuromedin U (NMU) is a hypothalamic neuropeptide with important roles in several metabolic processes, recently suggested as potential therapeutic target for obesity. We analysed the associations between NMU gene variants and haplotypes and body mass index (BMI) in a large sample of European children. METHODS AND RESULTS From a large European multi-center study on childhood obesity, 4,528 children (2.0-9.9 years, mean age 6.0±1.8 SD; boys 52.2%) were randomly selected, stratifying by age, sex and country, and genotyped for tag single nucleotide polymorphisms (SNPs; rs6827359, T:C; rs12500837, T:C; rs9999653,C:T) of NMU gene, then haplotypes were inferred. Regression models were applied to estimate the associations between SNPs or haplotypes and BMI as well as other anthropometric measures. BMI was associated with all NMU SNPs (p<0.05). Among five haplotypes inferred, the haplotype carrying the minor alleles (CCT, frequency = 22.3%) was the only associated with lower BMI values (beta = -0.16, 95%CI:-0.28,-0.04, p = 0.006; z-score, beta = -0.08, 95%CI:-0.14,-0.01, p = 0.019) and decreased risk of overweight/obesity (OR = 0.81, 95%CI:0.68,0.97, p = 0.020) when compared to the most prevalent haplotype (codominant model). Similar significant associations were also observed using the same variables collected after two years' time (BMI, beta = -0.25, 95%CI:-0.41,-0.08, p = 0.004; z-score, beta = -0.10, 95%CI:-0.18,-0.03, p = 0.009; overweight/obesity OR = 0.81, 95%CI:0.66,0.99, p = 0.036). The association was age-dependent in girls (interaction between CCT haplotypes and age, p = 0.008), more evident between 7 and 9 years of age. The CCT haplotype was consistently associated with lower levels of fat mass, skinfold thickness, hip and arm circumferences both at T0 and at T1, after adjustment for multiple testing (FDR-adjusted p<0.05). CONCLUSIONS This study shows an association between a NMU haplotype and anthropometric indices, mainly linked to fat mass, which appears to be age- and sex-specific in children. Genetic variations within or in linkage with this haplotype should be investigated to identify functional variants responsible for the observed phenotypic variation.
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Affiliation(s)
- Francesco Gianfagna
- Laboratory of Molecular and Nutritional Epidemiology, Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
- EPIMED Research Center, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy
- * E-mail:
| | - Claudio Grippi
- Laboratory of Molecular and Nutritional Epidemiology, Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
- Faculty of Mathematics and Computer Science, Institute of Statistics, Bremen University, Bremen, Germany
| | - Mark E. S. Bailey
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Claudia Börnhorst
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
| | - Stefan De Henauw
- Department of Public Health, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ronja Foraita
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
| | - Anna C. Koni
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Vittorio Krogh
- Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Staffan Mårild
- Dept. of Paediatrics, Inst. of Clinical Sciences, Sahlgrenska Academy at Gothenburg University, Gothenburg, Sweden
| | - Dénes Molnár
- Department of Paediatrics, Medical Faculty, University of Pécs, Pécs, Hungary
| | - Luis Moreno
- GENUD (Growth, Exercise, Nutrition and Development) Research Group, University of Zaragoza, Zaragoza, Spain
| | - Yannis Pitsiladis
- Centre for Sport and Exercise Science and Medicine, University of Brighton, Brighton, United Kingdom
| | - Paola Russo
- Unit of Epidemiology & Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
| | - Alfonso Siani
- Unit of Epidemiology & Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
| | | | - Toomas Veidebaum
- Department of Chronic Diseases, National Institute for Health Development, Tallinn, Estonia
| | - Licia Iacoviello
- Laboratory of Molecular and Nutritional Epidemiology, Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy
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14
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McDonald NM, Baker JK, Messinger DS. Oxytocin and parent-child interaction in the development of empathy among children at risk for autism. Dev Psychol 2016; 52:735-45. [PMID: 26998571 DOI: 10.1037/dev0000104] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This longitudinal study investigated whether variation in the oxytocin receptor gene (OXTR) and early parent-child interactions predicted later empathic behavior in 84 toddlers at high or low familial risk for autism spectrum disorder. Two well-studied OXTR single-nucleotide polymorphisms, rs53576 and rs2254298, were examined. Parent-child interaction was measured at 15 and 18 months of age during free play sessions. Empathy was measured at 24 and 30 months using a response to parental distress paradigm. While there was no direct association between parent-child interaction quality or OXTR and empathy, rs53576 moderated the relation between interaction quality and empathy. Results suggest that the interplay between OXTR and early parent-child interactions predicts individual differences in empathy in children at varying risk for atypical social development. Findings are consonant with a differential susceptibility model in which an OXTR variant may increase the social salience of interaction processes for specific allele carriers. These results increase our understanding of predictors of empathy development in young children with a wide range of social outcomes. (PsycINFO Database Record
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Affiliation(s)
| | - Jason K Baker
- Department of Child and Adolescent Studies, California State University
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15
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Langie SAS, Szarc vel Szic K, Declerck K, Traen S, Koppen G, Van Camp G, Schoeters G, Vanden Berghe W, De Boever P. Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy. PLoS One 2016; 11:e0151109. [PMID: 26999364 PMCID: PMC4801358 DOI: 10.1371/journal.pone.0151109] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/22/2016] [Indexed: 12/17/2022] Open
Abstract
The etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n = 5) compared to healthy controls (n = 5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437 (P<0.05 and |Δβ|>0.1), respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. The absolute levels of methylation in blood and saliva were confirmed for 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes using pyrosequencing analysis. The differential methylation could only be confirmed for DMS in PM20D1 and STK32C genes in saliva. We show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS when comparing RA cases and healthy controls. The results were replicated in blood cells of the same individuals and confirmed by pyrosequencing analysis. This study provides proof-of-concept for the applicability of saliva-based whole-genome methylation analysis in the field of respiratory allergy.
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Affiliation(s)
- Sabine A. S. Langie
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- * E-mail:
| | - Katarzyna Szarc vel Szic
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Sophie Traen
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Gudrun Koppen
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Guy Van Camp
- Laboratory of Cancer Research and Clinical Oncology, Center for Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Greet Schoeters
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
- University of Southern Denmark, Institute of Public Health, Department of Environmental Medicine, Odense, Denmark
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick De Boever
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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16
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Gunderson EP, Hurston SR, Dewey KG, Faith MS, Charvat-Aguilar N, Khoury VC, Nguyen VT, Quesenberry CP. The study of women, infant feeding and type 2 diabetes after GDM pregnancy and growth of their offspring (SWIFT Offspring study): prospective design, methodology and baseline characteristics. BMC Pregnancy Childbirth 2015; 15:150. [PMID: 26177722 PMCID: PMC4504097 DOI: 10.1186/s12884-015-0587-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Breastfeeding is associated with reduced risk of becoming overweight or obese later in life. Breastfed babies grow more slowly during infancy than formula-fed babies. Among offspring exposed in utero to maternal glucose intolerance, prospective data on growth during infancy have been unavailable. Thus, scientific evidence is insufficient to conclude that breastfeeding reduces the risk of obesity among the offspring of diabetic mothers (ODM). To address this gap, we devised the Study of Women, Infant Feeding and Type 2 Diabetes after GDM Pregnancy and Growth of their Offspring, also known as the SWIFT Offspring Study. This prospective, longitudinal study recruited mother-infant pairs from the SWIFT Study, a prospective study of women with recent gestational diabetes mellitus (GDM). The goal of the SWIFT Offspring Study is to determine whether breastfeeding intensity and duration, compared with formula feeding, are related to slower growth of GDM offspring during the first year life. This article details the study design, participant eligibility, data collection, and methodologies. We also describe the baseline characteristics of the GDM mother-infant pairs. METHODS The study enrolled 466 mother-infant pairs among GDM deliveries in northern California from 2009-2011. Participants attended three in-person study exams at 6-9 weeks, 6 months and 12 months after delivery for infant anthropometry (head circumference, body weight, length, abdominal circumference and skinfold thicknesses), as well as maternal anthropometry (body weight, waist circumference and percent body fat). Mothers also completed questionnaires on health and lifestyle behaviors, including infant diet, sleep and temperament. Breastfeeding intensity and duration were assessed via several sources (diaries, telephone interviews, monthly mailings and in-person exams) from birth through the first year of life. Pregnancy course, clinical perinatal and newborn outcomes were obtained from health plan electronic medical records. Infant saliva samples were collected and stored for genetics studies. DISCUSSION This large, racially and ethnically diverse cohort of GDM offspring will enable evaluation of the relationship of infant feeding to growth during infancy independent of perinatal characteristics, sociodemographics and other risk factors. The longitudinal design provides the first quantitative measures of breastfeeding intensity and duration among GDM offspring during early life.
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Affiliation(s)
- Erica P Gunderson
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, 94612-2304, Oakland, CA, USA.
| | - Shanta R Hurston
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, 94612-2304, Oakland, CA, USA.
| | - Kathryn G Dewey
- Department of Nutrition, University of California, Davis, One Shields Ave, 95616, Davis, CA, USA.
| | - Myles S Faith
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.
| | - Nancy Charvat-Aguilar
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, 94612-2304, Oakland, CA, USA.
| | - Vicky C Khoury
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, 94612-2304, Oakland, CA, USA.
| | - Van T Nguyen
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, 94612-2304, Oakland, CA, USA.
| | - Charles P Quesenberry
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, 94612-2304, Oakland, CA, USA.
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Tinker SC, Gilboa S, Reefhuis J, Jenkins MM, Schaeffer M, Moore CA. Challenges in Studying Modifiable Risk Factors for Birth Defects. CURR EPIDEMIOL REP 2015; 2:23-30. [PMID: 26236577 PMCID: PMC4516719 DOI: 10.1007/s40471-014-0028-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conducting research to identify modifiable risk factors for birth defects is difficult for a variety of reasons. While some challenges are familiar to researchers across many disciplines, the confluence of issues affecting birth defects research may not be well understood by those outside of the field. This article describes several methodological challenges to the study of birth defects and ways these challenges might be addressed: (1) ascertainment, definition and classification of birth defects; (2) exposure assessment on modifiable risk factors; (3) analytical challenges related to small numbers and multiple statistical tests; (4) the role of genetics, including the collection of specimens and analysis of genetic data; and (5) challenges in translating research and demonstrating public health impact. Understanding these issues is important for researchers planning studies, reviewers evaluating the scientific merit of results from these studies, and consumers of the research, including fellow researchers, policy makers, health care providers, and families.
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Affiliation(s)
- Sarah C. Tinker
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS E86, Atlanta, GA 30333, Phone: 404-498-3509, Fax: 404-498-3040
| | - Suzanne Gilboa
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS E86, Atlanta, GA 30333, Phone: 404-498-4425, Fax: 404-498-3040
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS E86, Atlanta, GA 30333, Phone: 404-498-3917, Fax: 404-498-3040
| | - Mary M. Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS E86, Atlanta, GA 30333, Phone: 404-498-3889, Fax: 404-498-3550
| | - Marcy Schaeffer
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS E86, Atlanta, GA 30333, Phone: 404-498-0265, Fax: 404-498-3040
| | - Cynthia A. Moore
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS E86, Atlanta, GA 30333, Phone: 404-498-3927, Fax: 404-498-3040
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18
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Samoukina AM, Mikhaĭlova ES, Chervinets VM, Alekseeva IA, Zhmakin IA, Andreeva OV. [Microbiological monitoring of oral fluid of clinically healthy children]. STOMATOLOGIIA 2015; 94:11-13. [PMID: 25909606 DOI: 10.17116/stomat201594111-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The article presents qualitative and quantitative parameters of microbiocenosis of oral fluid and feces of clinically healthy children in different age groups. In most of the cases compensated disbiotic changes were found, which were characterized by reduction in the number of indigenous microflora (lactobacilli and bifidobacteria) and increase of representatives of opportunistic pathogens (Staphylococcus, Bacillus and Candida). Microecological changes in different gastrointestinal biotopes are closely interrelated. Saliva may be considered as a specimen of integral fluid of human environment and can be used for complex assessment of the state of gastrointestinal tract microflora.
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Affiliation(s)
- A M Samoukina
- Tverskaia gosudarstvennaia meditsinskaia akademiia Minzdrava Rossii, 170100, Tver', Rossiia
| | - E S Mikhaĭlova
- Tverskaia gosudarstvennaia meditsinskaia akademiia Minzdrava Rossii, 170100, Tver', Rossiia
| | - V M Chervinets
- Tverskaia gosudarstvennaia meditsinskaia akademiia Minzdrava Rossii, 170100, Tver', Rossiia
| | - Iu A Alekseeva
- Tverskaia gosudarstvennaia meditsinskaia akademiia Minzdrava Rossii, 170100, Tver', Rossiia
| | - I A Zhmakin
- Tverskaia gosudarstvennaia meditsinskaia akademiia Minzdrava Rossii, 170100, Tver', Rossiia
| | - O V Andreeva
- Tverskaia gosudarstvennaia meditsinskaia akademiia Minzdrava Rossii, 170100, Tver', Rossiia
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19
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Yang ZM, Lin J, Chen LH, Zhang M, Chen WW, Yang XR. The roles of AMY1 copies and protein expression in human salivary α-amylase activity. Physiol Behav 2015; 138:173-8. [PMID: 25446200 DOI: 10.1016/j.physbeh.2014.10.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/21/2014] [Accepted: 10/27/2014] [Indexed: 11/11/2022]
Abstract
Salivary α-amylase (sAA) activity has been extensively investigated in nutrition and psychology. But few studies were performed to assess the role played by sAA gene (AMY1) copies and protein expression in basal and stimulus-induced sAA activity. The sAA activity, amount and AMY1 copy number were determined from 184 saliva samples pre- and post-citric acid stimulation. Our findings showed that citric acid could induce significant increase in sAA activity, total sAA amount, and glycosylated sAA amount, among which the glycosylated sAA amount had the largest response. The correlation analysis showed that AMY1 copy number, total sAA amount and AMY1 copy number×total sAA amount had significantly positive and successively increasing correlations with sAA activity in unstimulated and stimulated saliva, respectively, and furthermore, we observed higher correlations in unstimulated saliva when compared with the corresponding correlations in stimulated saliva. We also observed significant correlations between glycosylated sAA amount and sAA activity in unstimulated and stimulated saliva, respectively. Interestingly, the correlations were higher in stimulated saliva than in unstimulated saliva, and the correlations between glycosylated sAA amount and sAA activity were higher than that of between total sAA amount and sAA activity in stimulated saliva. Moreover, total sAA amount ratio and glycosylated sAA amount ratio showed significantly positive correlation with sAA activity ratio. AMY1 copy number had no correlation with sAA activity ratio. These findings suggested that AMY1 copy number and sAA amount played crucial roles in sAA activity; however, the roles were attenuated after stimulation due to fortified release of glycosylated sAA.
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Affiliation(s)
- Ze-Min Yang
- School of Basic Courses, Guangdong Pharmaceutical University, China.
| | - Jing Lin
- School of Basic Courses, Guangdong Pharmaceutical University, China
| | - Long-Hui Chen
- Pi-Wei Institute, Guangzhou University of Chinese Medicine, China
| | - Min Zhang
- Pediatrics of Traditional Chinese Medicine, Haizhu Maternal and Child Health Hospital, China
| | - Wei-Wen Chen
- Pi-Wei Institute, Guangzhou University of Chinese Medicine, China
| | - Xiao-Rong Yang
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, China
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20
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Rahmioglu N, Fassbender A, Vitonis AF, Tworoger SS, Hummelshoj L, D'Hooghe TM, Adamson GD, Giudice LC, Becker CM, Zondervan KT, Missmer SA. World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project: III. Fluid biospecimen collection, processing, and storage in endometriosis research. Fertil Steril 2014; 102:1233-43. [PMID: 25256929 PMCID: PMC4230639 DOI: 10.1016/j.fertnstert.2014.07.1208] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 12/12/2022]
Abstract
Objective To harmonize standard operating procedures (SOPs) and standardize the recording of associated data for collection, processing, and storage of fluid biospecimens relevant to endometriosis. Design An international collaboration involving 34 clinical/academic centers and 3 industry collaborators from 16 countries on 5 continents. Setting In 2013, 2 workshops were conducted, followed by global consultation, bringing together 54 leaders in endometriosis research and sample processing worldwide. Patient(s) None. Intervention(s) Consensus SOPs were based on: [1] systematic comparison of SOPs from 18 global centers collecting fluid samples from women with and without endometriosis on a medium/large scale (publication on >100 cases), [2] literature evidence where available, or consultation with laboratory experts otherwise, and [3] several global consultation rounds. Main Outcome Measure(s) Standard recommended and minimum required SOPs for biofluid collection, processing, and storage in endometriosis research. Result(s) We developed recommended standard and minimum required SOPs for the collection, processing, and storage of plasma, serum, saliva, urine, endometrial/peritoneal fluid, and menstrual effluent, and a biospecimen data-collection form necessary for interpretation of sample-derived results. Conclusion(s) The Endometriosis Phenome and Biobanking Harmonisation Project SOPs allow endometriosis research centers to decrease variability in biofluid sample results, facilitating between-center comparisons and collaborations. The procedures are also relevant to research into other female conditions involving biofluid samples subject to cyclic reproductive influences. The consensus SOPs are based on the best available evidence; areas with limited evidence are identified as requiring further pilot studies. The SOPs will be reviewed based on investigator feedback, and through systematic tri-annual follow-up. Updated versions will be made available at: endometriosisfoundation.org/ephect.
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Affiliation(s)
- Nilufer Rahmioglu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Amelie Fassbender
- Organ Systems, Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium; Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Leuven, Leuven, Belgium
| | - Allison F Vitonis
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Boston Center for Endometriosis, Boston Children's Hospital and Brigham & Women's Hospital, Boston, Massachusetts
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Lone Hummelshoj
- World Endometriosis Research Foundation (WERF), London, United Kingdom
| | - Thomas M D'Hooghe
- Organ Systems, Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium; Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Leuven, Leuven, Belgium
| | - G David Adamson
- World Endometriosis Research Foundation (WERF), London, United Kingdom; Palo Alto Medical Foundation Fertility Physicians of Northern California, Palo Alto, California
| | - Linda C Giudice
- World Endometriosis Research Foundation (WERF), London, United Kingdom; University of California San Francisco, San Francisco, California
| | - Christian M Becker
- Nuffield Department of Obstetrics & Gynaecology, University of Oxford, Oxford, United Kingdom; Endometriosis CaRe Centre Oxford, University of Oxford, Oxford, United Kingdom
| | - Krina T Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Nuffield Department of Obstetrics & Gynaecology, University of Oxford, Oxford, United Kingdom; Endometriosis CaRe Centre Oxford, University of Oxford, Oxford, United Kingdom.
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Boston Center for Endometriosis, Boston Children's Hospital and Brigham & Women's Hospital, Boston, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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21
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Gassó P, Pagerols M, Flamarique I, Castro-Fornieles J, Rodriguez N, Mas S, Curran S, Aitchison K, Santosh P, Lafuente A. The effect of age on DNA concentration from whole saliva: Implications for the standard isolation method. Am J Hum Biol 2014; 26:859-62. [DOI: 10.1002/ajhb.22593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 07/02/2014] [Accepted: 07/17/2014] [Indexed: 11/06/2022] Open
Affiliation(s)
- Patricia Gassó
- Department of Pathological Anatomy; Pharmacology, and Microbiology, University of Barcelona; Barcelona 08036 Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona 08036 Spain
| | - Mireia Pagerols
- Department of Pathological Anatomy; Pharmacology, and Microbiology, University of Barcelona; Barcelona 08036 Spain
| | - Itziar Flamarique
- Department of Child and Adolescent Psychiatry and Psychology; Institute of Neurosciences, Hospital Clinic of Barcelona; Barcelona 08036 Spain
| | - Josefina Castro-Fornieles
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona 08036 Spain
- Department of Child and Adolescent Psychiatry and Psychology; Institute of Neurosciences, Hospital Clinic of Barcelona; Barcelona 08036 Spain
- Department of Psychiatry and Clinical Psychobiology; University of Barcelona; Barcelona 08036 Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM); Madrid 08029 Spain
| | - Natalia Rodriguez
- Department of Pathological Anatomy; Pharmacology, and Microbiology, University of Barcelona; Barcelona 08036 Spain
| | - Sergi Mas
- Department of Pathological Anatomy; Pharmacology, and Microbiology, University of Barcelona; Barcelona 08036 Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona 08036 Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM); Madrid 08029 Spain
| | - Sarah Curran
- MRC Social; Genetic; and Developmental Psychiatry Centre; Institute of Psychiatry, King's College; London SE5 8AF United Kingdom
| | - Katherine Aitchison
- MRC Social; Genetic; and Developmental Psychiatry Centre; Institute of Psychiatry, King's College; London SE5 8AF United Kingdom
- Department of Psychiatry; University of Alberta; Edmonton T6G 2R7 Canada
| | - Paramala Santosh
- Centre for Interventional Paediatric Psychopharmacology (CIPP); South London and Maudsley NHS Foundation Trust; London SE5 8AZ United Kingdom
- Department of Child Psychiatry; Institute of Psychiatry, King's College; London SE5 8AF United Kingdom
| | - Amalia Lafuente
- Department of Pathological Anatomy; Pharmacology, and Microbiology, University of Barcelona; Barcelona 08036 Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona 08036 Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM); Madrid 08029 Spain
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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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23
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Poynter JN, Ross JA, Hooten AJ, Langer E, Blommer C, Spector LG. Predictors of mother and child DNA yields in buccal cell samples collected in pediatric cancer epidemiologic studies: a report from the Children's Oncology group. BMC Genet 2013; 14:69. [PMID: 23937514 PMCID: PMC3751424 DOI: 10.1186/1471-2156-14-69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/03/2013] [Indexed: 11/16/2022] Open
Abstract
Background Collection of high-quality DNA is essential for molecular epidemiology studies. Methods have been evaluated for optimal DNA collection in studies of adults; however, DNA collection in young children poses additional challenges. Here, we have evaluated predictors of DNA quantity in buccal cells collected for population-based studies of infant leukemia (N = 489 mothers and 392 children) and hepatoblastoma (HB; N = 446 mothers and 412 children) conducted through the Children’s Oncology Group. DNA samples were collected by mail using mouthwash (for mothers and some children) and buccal brush (for children) collection kits and quantified using quantitative real-time PCR. Multivariable linear regression models were used to identify predictors of DNA yield. Results Median DNA yield was higher for mothers in both studies compared with their children (14 μg vs. <1 μg). Significant predictors of DNA yield in children included case–control status (β = −0.69, 50% reduction, P = 0.01 for case vs. control children), brush collection type, and season of sample collection. Demographic factors were not strong predictors of DNA yield in mothers or children in this analysis. Conclusions The association with seasonality suggests that conditions during transport may influence DNA yield. The low yields observed in most children in these studies highlight the importance of developing alternative methods for DNA collection in younger age groups.
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24
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Gianfagna F, Cugino D, Ahrens W, Bailey MES, Bammann K, Herrmann D, Koni AC, Kourides Y, Marild S, Molnár D, Moreno LA, Pitsiladis YP, Russo P, Siani A, Sieri S, Sioen I, Veidebaum T, Iacoviello L. Understanding the links among neuromedin U gene, beta2-adrenoceptor gene and bone health: an observational study in European children. PLoS One 2013; 8:e70632. [PMID: 23936460 PMCID: PMC3731254 DOI: 10.1371/journal.pone.0070632] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/20/2013] [Indexed: 01/08/2023] Open
Abstract
Neuromedin U, encoded by the NMU gene, is a hypothalamic neuropeptide that regulates both energy metabolism and bone mass. The beta-2 adrenergic receptor, encoded by the ADRB2 gene, mediates several effects of catecholamine hormones and neurotransmitters in bone. We investigated whether NMU single nucleotide polymorphisms (SNPs) and haplotypes, as well as functional ADRB2 SNPs, are associated with bone stiffness in children from the IDEFICS cohort, also evaluating whether NMU and ADRB2 interact to affect this trait. A sample of 2,274 subjects (52.5% boys, age 6.2±1.8 years) from eight European countries, having data on calcaneus bone stiffness index (SI, mean of both feet) and genotyping (NMU gene: rs6827359, rs12500837, rs9999653; ADRB2 gene: rs1042713, rs1042714), was studied. After false discovery rate adjustment, SI was significantly associated with all NMU SNPs. rs6827359 CC homozygotes showed the strongest association (recessive model, Δ = −1.8, p = 0.006). Among the five retrieved haplotypes with frequencies higher than 1% (range 2.0–43.9%), the CCT haplotype (frequency = 39.7%) was associated with lower SI values (dominant model, Δ = −1.0, p = 0.04) as compared to the most prevalent haplotype. A non-significant decrease in SI was observed in in ADRB2 rs1042713 GG homozygotes, while subjects carrying SI-lowering genotypes at both SNPs (frequency = 8.4%) showed much lower SI than non-carriers (Δ = −3.9, p<0.0001; p for interaction = 0.025). The association was more evident in preschool girls, in whom SI showed a curvilinear trend across ages. In subgroup analyses, rs9999653 CC NMU or both GG ADRB2 genotypes were associated with either lower serum calcium or β-CrossLaps levels (p = 0.01). This study in European children shows, for the first time in humans, a role for NMU gene through interaction with ADRB2 gene in bone strength regulation, more evident in preschool girls.
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Affiliation(s)
- Francesco Gianfagna
- Research Laboratories, Fondazione di Ricerca e Cura “Giovanni Paolo II”, Università Cattolica del Sacro Cuore, Campobasso, Italy
| | | | - Wolfgang Ahrens
- Department of Epidemiological Methods and Etiologic Research, Leibniz-Institute for Prevention Research and Epidemiology - BIPS GmbH, Bremen, Germany
- Department of Mathematics and Computer Sciences, University of Bremen, Bremen, Germany
| | - Mark E. S. Bailey
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Karin Bammann
- Department of Epidemiological Methods and Etiologic Research, Leibniz-Institute for Prevention Research and Epidemiology - BIPS GmbH, Bremen, Germany
- Institute for Public Health and Nursing Research, University of Bremen, Bremen, Germany
| | - Diana Herrmann
- Department of Epidemiological Methods and Etiologic Research, Leibniz-Institute for Prevention Research and Epidemiology - BIPS GmbH, Bremen, Germany
| | - Anna C. Koni
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Yiannis Kourides
- Research and Education Institute of Child Health, Strovolos, Cyprus
| | - Staffan Marild
- Department of Pediatrics, Institute of Clinical Sciences, The Queen Silvia Children’s Hospital, Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Dénes Molnár
- Department of Pediatrics, University of Pécs, Pécs, Hungary
| | - Luis A. Moreno
- GENUD (Growth, Exercise, NUtrition and Development) Research Group, University of Zaragoza, Zaragoza, Spain
| | - Yannis P. Pitsiladis
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Paola Russo
- Epidemiology & Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
| | - Alfonso Siani
- Epidemiology & Population Genetics, Institute of Food Sciences, CNR, Avellino, Italy
| | - Sabina Sieri
- Department of Preventive and Predictive Medicine, Nutritional Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Isabelle Sioen
- Department of Public Health, Ghent University, Ghent, Belgium
- FWO, Research Foundation Flanders, Brussels, Belgium
| | - Toomas Veidebaum
- Center of Health and Behavioral Science, National Institute for Health Development, Tallinn, Estonia
| | - Licia Iacoviello
- Casa di Cura Montevergine, Mercogliano (AV), Italy
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
- * E-mail:
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25
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Küchler EC, Tannure PN, Falagan-Lotsch P, Lopes TS, Granjeiro JM, Amorim LMF. Buccal cells DNA extraction to obtain high quality human genomic DNA suitable for polymorphism genotyping by PCR-RFLP and Real-Time PCR. J Appl Oral Sci 2013; 20:467-71. [PMID: 23032210 PMCID: PMC3881822 DOI: 10.1590/s1678-77572012000400013] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 09/30/2011] [Indexed: 02/05/2023] Open
Abstract
Objective The aim of this study was to evaluate, by PCR-RFLP and Real-time PCR, the yield
and quality of genomic DNA collected from buccal cells by mouthwash after
different storage times at room temperature. Material and Methods A group of volunteers was recruited to collect buccal cells using a mouthwash
solution. The collected solution was divided into 3 tubes, one tube were used for
immediate extraction and the remaining received ethanol and were kept at room
temperature for 4 and 8 days followed by DNA extraction. The concentration, purity
and integrity of the DNA were determined using spectrophotometry and
electrophoresis. DNA quality differences among the three incubation times were
also evaluated for genotyping EGF +61 A/G (rs 4444903) polymorphism by PCR-RFLP
and for IRF6 polymorphism (rs 17015215) using Real-Time PCR. Results There was no significant difference of DNA yield (p=0.75) and purity (p=0.86)
among the three different incubation times. DNA obtained from different incubation
times presented high-molecular weight. The PCR-RFLP and Real time PCR reactions
were successfully performed for all DNA samples, even those extracted after 8 days
of incubation. All samples genotyped by Real-Time PCR presented C allele for IRF6
gene polymorphism (homozygous: CC; heterozygous: CT) and the C allele was used as
a reference for Ct values. The samples presented the same genotype for the
different times in both techniques. Conclusion We demonstrated that the method described herein is simple and low cost, and that
DNA can be extracted and PCR amplified after storage in mouthwash solution at room
temperature.
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Affiliation(s)
- Erika Calvano Küchler
- Cell Therapy Center, Unit of Clinical Research, University Hospital Antonio Pedro, Fluminense Federal University, Niteroi, RJ, Brazil
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26
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Kalyanasundaram D, Kim JH, Yeo WH, Oh K, Lee KH, Kim MH, Ryew SM, Ahn SG, Gao D, Cangelosi GA, Chung JH. Rapid extraction and preservation of genomic DNA from human samples. Anal Bioanal Chem 2013; 405:1977-83. [PMID: 23307121 DOI: 10.1007/s00216-012-6637-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/24/2012] [Accepted: 12/06/2012] [Indexed: 11/29/2022]
Abstract
Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.
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Affiliation(s)
- D Kalyanasundaram
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
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27
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Lauria F, Siani A, Bammann K, Foraita R, Huybrechts I, Iacoviello L, Koni AC, Kourides Y, Marild S, Molnar D, Moreno LA, Pigeot I, Pitsiladis YP, Veidebaum T, Russo P. Prospective analysis of the association of a common variant of FTO (rs9939609) with adiposity in children: results of the IDEFICS study. PLoS One 2012; 7:e48876. [PMID: 23155422 PMCID: PMC3498350 DOI: 10.1371/journal.pone.0048876] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 10/02/2012] [Indexed: 01/11/2023] Open
Abstract
Objectives We investigated cross-sectionally and longitudinally the relationship between FTO rs9939609 and obesity-related characteristics in the European children of the IDEFICS project and the interaction of this variant with a lifestyle intervention. Population and Methods A cohort of 16224 children (2–9 years) was recruited into a population-based survey (T0) from eight European countries. A second survey (T1) reassessed the children two years later. A random sample of 4405 children was extracted for genetic studies. 3168 children were re-examined two years later. Half of them underwent a lifestyle intervention program. The FTO rs9939609 was genotyped. Weight, height, waist circumference, triceps and subscapular skinfolds were measured at T0 and T1. Results At T0, the risk A allele of rs9939609 was significantly associated with higher values of body mass index (BMI), waist circumference and skinfolds (age, sex, and country-adjusted p-values: all p<0.001) and with a statistically significant increased risk of overweight/obesity. Over the two year follow-up, no interaction between genotype and intervention was observed. The A allele was associated to a significantly higher increase in all the anthropometric variables examined at T0 independently from the study group (intervention versus control) (p-values: all p<0.002, adjusted for age, sex, country, intervention/control study group, T0 values, and individual time interval between T0 and T1). Over the two-year follow–up, 210 new cases of overweight/obesity occurred. A statistically significant higher incidence of overweight/obesity was associated to the A allele [ORA = 1.95, 95% CI = (1.29; 2.97)]. Conclusions We confirmed the association between the FTO rs9939609 and body mass and overweight/obesity risk in European children. The main finding of the study is that the A allele carriers present higher increase of body mass and central adiposity over time and higher risk of developing overweight/obesity during growth, independently from intervention measures.
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Affiliation(s)
- Fabio Lauria
- Unit of Epidemiology and Population Genetics, Institute of Food Sciences, Consiglio Nazionale delle Ricerche, Avellino, Italy
| | - Alfonso Siani
- Unit of Epidemiology and Population Genetics, Institute of Food Sciences, Consiglio Nazionale delle Ricerche, Avellino, Italy
- * E-mail:
| | - Karin Bammann
- BIPS-Institute for Epidemiology and Prevention Research, Bremen, Germany
| | - Ronja Foraita
- BIPS-Institute for Epidemiology and Prevention Research, Bremen, Germany
| | - Inge Huybrechts
- Unit Nutrition and Food Safety, Department of Public Health, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Licia Iacoviello
- Fondazione di Ricerca e Cura “Giovanni Paolo II”, Università Cattolica del Sacro Cuore, Campobasso, Italy
| | - Anna C. Koni
- Institute for Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Yannis Kourides
- Research and Education Foundation of Child Health, Strovolos, Cyprus
| | - Staffan Marild
- Department of Paediatrics, Queen Silvia Children's Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Denes Molnar
- Department of Paediatrics, Medical Faculty, University of Pecs, Pecs, Hungary
| | - Luis A. Moreno
- Growth, Exercise, Nutrition and Development (GENUD Research Group), University of Zaragoza, Zaragoza, Spain
| | - Iris Pigeot
- BIPS-Institute for Epidemiology and Prevention Research, Bremen, Germany
| | - Yannis P. Pitsiladis
- Institute for Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Paola Russo
- Unit of Epidemiology and Population Genetics, Institute of Food Sciences, Consiglio Nazionale delle Ricerche, Avellino, Italy
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28
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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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29
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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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30
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Nemoda Z, Horvat-Gordon M, Fortunato CK, Beltzer EK, Scholl JL, Granger DA. Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples. BMC Med Res Methodol 2011; 11:170. [PMID: 22182470 PMCID: PMC3267685 DOI: 10.1186/1471-2288-11-170] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 12/19/2011] [Indexed: 11/10/2022] Open
Abstract
Background Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva. Methods Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP) in the catechol-0-methyltransferase gene (COMT rs4680) and one representative variable number of tandem repeats (VNTR) in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region) were selected for genetic analyses. Results The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days), repeated freeze-thaw cycles (up to 6 cycles), and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible. Conclusions Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using 10 ng of DNA per genotyping reaction, the obtained samples can be used for more than one hundred candidate gene assays. When saliva is collected with an absorbent device, most of the nucleic acid content remains in the device, therefore it is advisable to collect the device separately for later genetic analyses.
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Affiliation(s)
- Zsofia Nemoda
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tuzolto utca, Budapest, Hungary.
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31
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Influence of sample collection and preanalytical sample processing on the analyses of biological markers in the European multicentre study IDEFICS. Int J Obes (Lond) 2011; 35 Suppl 1:S104-12. [PMID: 21483409 DOI: 10.1038/ijo.2011.41] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To evaluate the influence of a standardised sampling protocol and process quality across the different IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) centres on the results of the biochemical measurements. DESIGN Baseline survey within the community-based intervention study. SUBJECTS A total of 16,224 children, aged 2-8 years, enrolled in the IDEFICS baseline survey in 8 European countries. Venous or capillary blood samples were collected from 12,430 children, urine samples from 13,890 children and saliva samples from 14,019 children. METHODS A set of quality indicators was recorded for the biological blood, urine and saliva samples collected during the IDEFICS study. Results of blood and urine measurements were analysed and stratified by selected quality indicators. RESULTS Concentrations of biological markers in blood and urine measured during the IDEFICS baseline survey are associated with several quality indicators assessed in this study. Between-country variations of these biomarkers are described. It was confirmed that fasting has a big influence on the concentration of certain biomarkers. Biomarkers in morning urine samples may be erroneous if the study subjects void during the night or if samples are not taken from the very first morning urine. CONCLUSIONS The analysed data underline that a standardised sampling protocol is of major importance, especially in multicentre studies, but non-compliance is ever present in spite of well-defined standard operation procedures. Deviations from the protocol should therefore always be documented to avoid error pertaining to the concentration of biological markers.
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Page AS, Winklhofer-Roob BM. Five-minutes-to-twelve for implementation of early changes in dietary and lifestyle behaviour across Europe. Int J Obes (Lond) 2011; 35 Suppl 1:S1-2. [PMID: 21483408 DOI: 10.1038/ijo.2011.29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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