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Updated: Jun 2, 2026
Collection and Extraction of Saliva DNA for Next Generation Sequencing
Published on: August 27, 2014
DNA yield and quality of saliva samples and suitability for large-scale epidemiological studies in children
1College of Medicine, Veterinary and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Scotland, UK.
Insights
Whole saliva collection yielded more DNA than sponge collection in children. Both methods provided sufficient DNA quality for large-scale genetic studies in the IDEFICS project.
Area of Science:
- Pediatric Health Research
- Genetic Epidemiology
- Biobanking and Sample Collection
Background:
- Large-scale European studies require efficient biological sample collection methods.
- Collecting DNA from children presents unique challenges, particularly for younger age groups.
- The IDEFICS study aimed to identify and prevent lifestyle-induced health effects in children.
Purpose of the Study:
- To compare DNA yield and quality from two saliva collection methods in children.
- To determine the suitability of these methods for a large, multicentre European genetic study.
- To inform best practices for biological sample collection in pediatric research.
Main Methods:
- A cross-sectional multicentre study involving 14,019 children aged 2-9 years across eight European countries.
- Two saliva collection techniques were employed: direct spitting and sponge collection for non-spitting children.
- DNA was extracted from a subset of samples (4678) for genotyping.
Main Results:
- Whole saliva collection yielded significantly higher DNA quantity (20.95 μg) compared to sponge collection (9.13 μg).
- DNA quality, assessed by A260/A280 ratios, was comparable between the two methods.
- Both methods achieved a genotype calling success rate of ≥95%, indicating good DNA quality for genotyping.
Conclusions:
- The whole-saliva collection method is superior for maximizing DNA yield in pediatric populations.
- Both saliva and sponge collection methods yield DNA of adequate quality for large-scale genetic epidemiological research.
- These findings support the feasibility of collecting biological samples for genetic studies in large, diverse pediatric cohorts.
Objective:
To evaluate two saliva collection methods for DNA yield and quality as applied to a large, integrated, multicentre, European project involving the collection of biological material from children.
Design:
Cross-sectional multicentre 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 despatched for DNA extraction and biobanking to the University of Glasgow. A subgroup of 4678 samples (∼33% of sampled individuals) were chosen for DNA extraction before genotyping.
Results:
The whole-saliva collection method resulted in a higher DNA yield than the sponge collection method (mean±s.d.; 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 with the assisted sponge collection. However, both collection methods provided DNA of sufficient quantity and quality for large-scale genetic epidemiological studies.
