DNA yield and quality of saliva samples and suitability for large-scale epidemiological studies in children

Pre-Analytical Factors Affecting Extracellular DNA in Saliva

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.

Novel use of menstrual blood for monitoring glycaemic control in patients with diabetes: a proof-of-concept study

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.

The Use of Saliva as a Biosample in the Light of COVID-19

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.

Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

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.

Measuring attack on self: The need for field-friendly methods development and research on autoimmunity in human biology

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.

Child Salivary SIgA and Its Relationship to Enteric Infections and EED Biomarkers in Maputo, Mozambique

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.

Reduction of Streptococcus mutans by probiotic milk: a multicenter randomized controlled trial

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.

Association between variants of neuromedin U gene and taste thresholds and food preferences in European children: Results from the IDEFICS study

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.

Procurement, Transportation, and Storage of Saliva, Buccal Swab, and Oral Wash Specimens

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.

Salivary DNA Methylation Profiling: Aspects to Consider for Biomarker Identification

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.

The role of neuromedin U in adiposity regulation. Haplotype analysis in European children from the IDEFICS Cohort

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.

Oxytocin and parent-child interaction in the development of empathy among children at risk for autism

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

Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy

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.

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

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.

Challenges in Studying Modifiable Risk Factors for Birth Defects

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.

[Microbiological monitoring of oral fluid of clinically healthy children]

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.

The roles of AMY1 copies and protein expression in human salivary α-amylase activity

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.

World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project: III. Fluid biospecimen collection, processing, and storage in endometriosis research

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.

Simple sequence repeats in the national longitudinal study of adolescent health: an ethnically diverse resource for genetic analysis of health and behavior

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.

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

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.

Understanding the links among neuromedin U gene, beta2-adrenoceptor gene and bone health: an observational study in European children

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.

Buccal cells DNA extraction to obtain high quality human genomic DNA suitable for polymorphism genotyping by PCR-RFLP and Real-Time PCR

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.

Rapid extraction and preservation of genomic DNA from human samples

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.

Prospective analysis of the association of a common variant of FTO (rs9939609) with adiposity in children: results of the IDEFICS study

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 [OR_A = 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.

Quality of DNA extracted from saliva samples collected with the Oragene™ DNA self-collection kit

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.

Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples

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.

Influence of sample collection and preanalytical sample processing on the analyses of biological markers in the European multicentre study IDEFICS

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.