Dataset Information

Saliva sampling in global clinical studies: the impact of low sampling volume on performance of DNA in downstream genotyping experiments.

ABSTRACT:

Background

The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling methods available. Initial observation in this study suggested a reduced genotyping success rate of some saliva derived DNA samples when compared to blood derived DNA samples prompting further investigation.

Methods

Genotyping success rate was investigated to assess the suitability of using saliva samples in future safety and efficacy pharmacogenetics experiments. The Oragene® OG-300 DNA Self-Collection kit was used to collect and extract DNA from saliva from 1468 subjects enrolled in global clinical studies. Statistical analysis evaluated the impact of saliva sample volume of collection on the quality, yield, concentration and performance of saliva DNA in genotyping assays.

Results

Across 13 global clinical studies that utilized the Oragene® OG-300 DNA Self-Collection kit there was variability in the volume of saliva sample collection with ~31% of participants providing 0.5 mL of saliva, rather than the recommended 2 mL. While the majority of saliva DNA samples provided high quality genotype data, collection of 0.5 mL volumes of saliva contributed to DNA samples being significantly less likely to pass genotyping quality control standards. Assessment of DNA sample characteristics that may influence genotyping outcomes indicated that saliva sample volume, DNA purity and turbidity were independently associated with sample genotype pass rate, but that saliva collection volume had the greatest effect.

Conclusion

When employing saliva sampling to obtain DNA, it is important to encourage all study participants to provide sufficient sample to minimize potential loss of data in downstream genotyping experiments.

SUBMITTER: Pulford DJ

PROVIDER: S-EPMC3698156 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Publications

Saliva sampling in global clinical studies: the impact of low sampling volume on performance of DNA in downstream genotyping experiments.

Pulford David J DJ Mosteller Michael M Briley J David JD Johansson Kelley W KW Nelsen Anita J AJ

BMC medical genomics 20130610

<h4>Background</h4>The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling methods available. Initial observation in this study suggested a reduced genotyping success rate of some saliva derived DNA samples when compared to blood derived DNA samples prompting further investigation.<h4>Methods</h4>Genotyping success rate was investigated to assess ...[more]

PMID: 23759220

Similar Datasets

Project description:The question of whether DNA obtained from saliva is an acceptable alternative to DNA from blood is a topic of considerable interest for large genetics studies. We compared the yields, quality and performance of DNAs from saliva and blood from a mostly elderly study population.Two thousand nine hundred ten DNAs from primarily elderly subjects (mean age ± standard deviation (SD): 65 ± 12 years), collected for the Primary Open-Angle African-American Glaucoma Genetics (POAAGG) study, were evaluated by fluorometry and/or spectroscopy. These included 566 DNAs from blood and 2344 from saliva. Subsets of these were evaluated by Sanger sequencing (n = 1555), and by microarray SNP genotyping (n = 94) on an Illumina OmniExpress bead chip platform.The mean age of subjects was 65, and 68 % were female in both the blood and saliva groups. The mean ± SD of DNA yield per ml of requested specimen was significantly higher for saliva (17.6 ± 17.8 ?g/ml) than blood (13.2 ± 8.5 ?g/ml), but the mean ± SD of total DNA yield obtained per saliva specimen (35 ± 36 ?g from 2 ml maximum specimen volume) was approximately three-fold lower than from blood (106 ± 68 ?g from 8 ml maximum specimen volume). The average genotyping call rates were >99 % for 43 of 44 saliva DNAs and >99 % for 50 of 50 for blood DNAs. For 22 of 23 paired blood and saliva samples from the same individuals, the average genotyping concordance rate was 99.996 %. High quality PCR Sanger sequencing was obtained from ? 98 % of blood (n = 297) and saliva (n = 1258) DNAs. DNA concentrations ?10 ng/?l, corresponding to total yields ? 2 ?g, were obtained for 94 % of the saliva specimens (n = 2344).In spite of inferior purity, the performance of saliva DNAs for microarray genotyping was excellent. Our results agree with other studies concluding that saliva collection is a viable alternative to blood. The potential to boost study enrollments and reduce subject discomfort is not necessarily offset by a reduction in genotyping efficiency. Saliva DNAs performed comparably to blood DNAs for PCR Sanger sequencing.

Dataset Information

Saliva sampling in global clinical studies: the impact of low sampling volume on performance of DNA in downstream genotyping experiments.

Background

Methods

Results

Conclusion

Publications

Saliva sampling in global clinical studies: the impact of low sampling volume on performance of DNA in downstream genotyping experiments.

Similar Datasets

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