Clinical trial participant characteristics and saliva and DNA metrics

Abstract

BackgroundClinical trial and epidemiological studies need high quality biospecimens from a representative sample of participants to investigate genetic influences on treatment response and disease. Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of saliva biospecimen samples collected through the mail, trial participant demographic and behavioral characteristics, and their association with saliva and DNA quantity and quality.MethodsSaliva biospecimens were collected using the Oragene® DNA Self-Collection Kits from participants in a National Cancer Institute funded smoking cessation trial. Saliva biospecimens from 565 individuals were visually inspected for clarity prior to and after DNA extraction. DNA samples were then quantified by UV absorbance, PicoGreen®, and qPCR. Genotyping was performed on 11 SNPs using TaqMan® SNP assays and two VNTR assays. Univariate, correlation, and analysis of variance analyses were conducted to observe the relationship between saliva sample and participant characteristics.ResultsThe biospecimen kit return rate was 58.5% among those invited to participate (n = 967) and 47.1% among all possible COMPASS participants (n = 1202). Significant gender differences were observed with males providing larger saliva volume (4.7 vs. 4.5 ml, p = 0.019), samples that were more likely to be judged as cloudy (39.5% vs. 24.9%, p < 0.001), and samples with greater DNA yield as measured by UV (190.0 vs. 138.5, p = 0.002), but reduced % human DNA content (73.2 vs. 77.6 p = 0.005) than females. Other participant characteristics (age, self-identified ethnicity, baseline cigarettes per day) were associated with saliva clarity. Saliva volume and saliva and DNA clarity were positively correlated with total DNA yield by all three quantification measurements (all r > 0.21, P < 0.001), but negatively correlated with % human DNA content (saliva volume r = -0.148 and all P < 0.010). Genotyping completion rate was not influenced by saliva or DNA clarity.ConclusionFindings from this study show that demographic and behavioral characteristics of smoking cessation trial participants have significant associations with saliva and DNA metrics, but not with the performance of TaqMan® SNP or VNTR genotyping assays.Trial registrationCOMPASS; registered as NCT00301145 at clinicaltrials.gov.

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

“…The overwhelming majority (4584 out of 4678 or 98%) of samples provided DNA of sufficiently high yield and quality (Table 3) for multiple genotyping assays as evidenced by the high genotyping success rates for both DNA collection methods ( Table 4). The DNA yield differed between the two collection methods, with whole saliva yields being higher than yields from sponges (Table 3) and this is in line with previous reports in the literature (1,2,4,5,(14)(15)(16)(19)(20)(21). Total DNA yield from the 4 ml Oragene DNA/saliva solution fulfilled, on average, the specifications of the manufacturer of above 20 µg (22) for the whole saliva collection method (Table 3).…”

“…Genetic epidemiology studies and clinical trials involving genetic association analysis are highly dependent on collecting, storing and distributing DNA of good quality from a representative sample of participants to examine genetic influences on treatment response and disease risk (1). Genotyping success rates depend on DNA quality and yield (2).…”

Genetic research participation in a young adult community sample

“…Several findings regarding participant characteristics were associated with providing a sample and the storage of the DNA. The findings of the effects of ethnicity, gender, and education on obtaining a DNA sample have been contradictory in the literature (Kozlowski et al 2002;Nishita et al 2009). Often, participation rates of minority groups are lower than other racial/ethnic groups (Chen et al 2005;Kozlowski et al 2002;McQuillan et al 2003;Meisel et al 2012), but we did not detect any racial/ethnicity or gender differences within our study sample.…”

“…This offered those with a fear of needles or seeing blood the opportunity to avoid doing something they disliked. Other studies find participation is higher for less invasive DNA collection options (e.g., saliva or buccal) than those asked to donate a blood sample in population studies (Hansen et al 2007;Johnson et al 2011); saliva return rates often vary between 52-80 % (Etter et al 1998(Etter et al , 2005Nishita et al 2009). Second, providing an incentive also increased the chance of obtaining a biologic sample.…”

“…Despite the non-invasive nature of collecting salivary samples and sending them through the mail, studies using this approach have variable return rates; even if participants express a high agreement to participate, the actual return of saliva samples is often low (Bhutta et al 2013). Furthermore, even though other studies have been able to obtain a second saliva sample from half of their attempted requests, many of the initial low-yield samples also had a lowyield in the second sample too (Nishita et al 2009). Thus, benefits of the recruitment approach for additional samples must be weighed against other factors, such as collection cost and DNA yield and quality.…”