Author:
Nishita Denise M,Jack Lisa M,McElroy Mary,McClure Jennifer B,Richards Julie,Swan Gary E,Bergen Andrew W
Abstract
Abstract
Background
Clinical trial and epidemiological studies need high quality biospecimens from a representative sample of participants to investigate genetic influences on treatment response and disease. Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of saliva biospecimen samples collected through the mail, trial participant demographic and behavioral characteristics, and their association with saliva and DNA quantity and quality.
Methods
Saliva biospecimens were collected using the Oragene® DNA Self-Collection Kits from participants in a National Cancer Institute funded smoking cessation trial. Saliva biospecimens from 565 individuals were visually inspected for clarity prior to and after DNA extraction. DNA samples were then quantified by UV absorbance, PicoGreen®, and qPCR. Genotyping was performed on 11 SNPs using TaqMan® SNP assays and two VNTR assays. Univariate, correlation, and analysis of variance analyses were conducted to observe the relationship between saliva sample and participant characteristics.
Results
The biospecimen kit return rate was 58.5% among those invited to participate (n = 967) and 47.1% among all possible COMPASS participants (n = 1202). Significant gender differences were observed with males providing larger saliva volume (4.7 vs. 4.5 ml, p = 0.019), samples that were more likely to be judged as cloudy (39.5% vs. 24.9%, p < 0.001), and samples with greater DNA yield as measured by UV (190.0 vs. 138.5, p = 0.002), but reduced % human DNA content (73.2 vs. 77.6 p = 0.005) than females. Other participant characteristics (age, self-identified ethnicity, baseline cigarettes per day) were associated with saliva clarity. Saliva volume and saliva and DNA clarity were positively correlated with total DNA yield by all three quantification measurements (all r > 0.21, P < 0.001), but negatively correlated with % human DNA content (saliva volume r = -0.148 and all P < 0.010). Genotyping completion rate was not influenced by saliva or DNA clarity.
Conclusion
Findings from this study show that demographic and behavioral characteristics of smoking cessation trial participants have significant associations with saliva and DNA metrics, but not with the performance of TaqMan® SNP or VNTR genotyping assays.
Trial registration
COMPASS; registered as NCT00301145 at clinicaltrials.gov.
Publisher
Springer Science and Business Media LLC
Subject
Health Informatics,Epidemiology
Reference25 articles.
1. Landi MT, Caporaso N: Sample collection, processing and storage. IARC Sci Publ. 1997, 223-236.
2. Vaught JB: Blood collection, shipment, processing, and storage. Cancer Epidemiol Biomarkers Prev. 2006, 15 (9): 1582-1584. 10.1158/1055-9965.EPI-06-0630.
3. Iwasiow RM, Desbois A, Birnboim HC: Long-term stability of DNA from saliva samples stored in Oragene®DNA. 2004, Ottawa, Ontario, Canada: DNA Genotek, Inc
4. Ng DP, Koh D, Choo S, Chia KS: Saliva as a viable alternative source of human genomic DNA in genetic epidemiology. Clin Chim Acta. 2006, 367 (1-2): 81-85. 10.1016/j.cca.2005.11.024.
5. Hansen TV, Simonsen MK, Nielsen FC, Hundrup YA: Collection of blood, saliva, and buccal cell samples in a pilot study on the Danish nurse cohort: comparison of the response rate and quality of genomic DNA. Cancer Epidemiol Biomarkers Prev. 2007, 16 (10): 2072-2076. 10.1158/1055-9965.EPI-07-0611.
Cited by
34 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献