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

Abstract

Objective: To evaluate two saliva collection methods for DNA yield and quality as applied to a large, integrated, multi-centre, European project involving the collection of biological material from children. Design: Cross-sectional multi-centre comparative study in young children. Methods: Saliva samples were collected from 14,019 children aged 2-9 years from eight European countries participating in the IDEFICS (Identification and prevention of Dietary-and lifestyle-induced health EFfects In Children and infantS) study. This involved either the collection of 2 ml of saliva from children who were able to spit, or using a sponge to collect whole saliva and buccal mucosal cells from the inside of the mouth of younger children unable to spit. Samples were assembled centrally in each participating centre and subsequently dispatched for DNA extraction and biobanking to the University of Glasgow. A subgroup of 4,678samples (approximately 33% of sampled individuals) was chosen for DNA extraction prior to genotyping. Results: The whole saliva collection method resulted in higher DNA yield than the sponge collection method (mean ± SD; Saliva: 20.95 ± 2.35 µg,; Sponge: 9.13 ± 2.25 µg; P<0.001). DNA quality as measured by A 260 /A 280 was similar for the two collection methods. A minimum genotype calling success rate of 95% showed that both methods provide good quality DNA for genotyping using TaqMan® allelic discrimination assays. Conclusions: Our results showed higher DNA yield from the whole saliva collection method compared to the assisted sponge collection. However, both collection methods provided DNA of sufficient quantity and quality for large-scale genetic epidemiological studies.

Saliva Sampling of Alcoholic Participants using Three Saliva Collection Methods

“…Such findings are in line with other reported studies whereby the DNA yield extracted using whole saliva collection method was in the range of 8-30 μg from 1-2 mL of saliva (Koni et al 2011;Nemoda et al 2011;Ng et al 2006). Compared with the whole saliva collection method, the Oragene-DNA saliva collection kit was more efficient as the method yielded much higher DNA (Hansen et al 2007;Philibert et al 2008b;Pulford et al 2013a).…”

“…The whole saliva collection method has been reported to be successful in producing DNA of higher yields with lengthier DNA fragments (Feigelson et al 2001;Heath et al 2001). However, when compared to the use of saliva collection kits that are available commercially, the quantity of DNA extracted from whole saliva samples were often found to be lower (Koni et al 2011;Nemoda et al 2011;Pulford et al 2013a).…”

Polymorphisms of matrix metalloproteinase gene and adiposity indices in European children: results of the IDEFICS study

“…23,24 DNA was successfully extracted in all cases; however, 94 samples were excluded because of improbable high or negative DNA yields and further 44 samples were not correctly genotyped. A total of 4540 samples having at least 1 single nucleotide polymorphism (SNP) successfully genotyped in the MMP3 was used for the final analysis.…”

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

“…A small fraction of samples (0.7%) was found to be dried up, but could all be rehydrated and still extracted with a sufficient yield of DNA. Details on the quality of collected saliva samples and extracted DNA have been described by Koni et al 13 A comprehensive overview of the quality management applied in the IDEFICS study has been provided elsewhere in detail. 14 Feedback on sample quality was given to the centres throughout the survey to continuously improve sample collection.…”