Saliva DNA quality and genotyping efficiency in a predominantly elderly population

Abstract

BackgroundThe 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.MethodsTwo 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.ResultsThe 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 μg/ml) than blood (13.2 ± 8.5 μg/ml), but the mean ± SD of total DNA yield obtained per saliva specimen (35 ± 36 μg from 2 ml maximum specimen volume) was approximately three-fold lower than from blood (106 ± 68 μg 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/μl, corresponding to total yields ≥ 2 μg, were obtained for 94 % of the saliva specimens (n = 2344).ConclusionsIn 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-016-0172-y) contains supplementary material, which is available to authorized users.

The utility of DNA extracted from saliva for genome-wide molecular research platforms

“…Advantages including; (1) samples collected using commercial kits are stable at room temperature and transportable, (2) self-collection kits can be sent to participant’s homes with validated self-guided instructions for providing an adequate sample, and (3) samples can be returned at their convenience. Potential disadvantages of saliva collection include lower mean DNA yield and potential contamination from bacterial DNA [ 1 , 2 ].…”

“…A challenge is that saliva samples contain multiple enzymes and antibacterial components, as well as large quantities of nucleated buccal (epithelial) cells, leukocytes and bacterial DNA [ 1 , 6 , 7 ], potentially making interpretation more difficult. While there has been variation in reported DNA yield from saliva compared with blood [ 1 , 2 ] it has been a sufficient template to enable genetic testing and genotype call rates with high concordance [ 1 , 5 , 8 ].…”

Saliva Sampling of Alcoholic Participants using Three Saliva Collection Methods

“…Saliva, like blood, contains an abundance of proteins, nucleic acid molecules, antibodies, hormones, enzymes, growth factors and antimicrobial constituents (de Almeida Pdel et al 2008;Humphrey & Williamson 2001). Based on the preliminary findings of this study, saliva has the potential to be used as a bio diagnostic tool for research purposes as well as for high throughput genotyping studies (Abraham et al 2012;Gudiseva et al 2016;Pulford et al 2013b). …”

Genetic conditionality of strength by the ACE gene in women horse riders

“…The 260/280 nm absorbance ratio between 1.6 and 2.0 for samples were considered pure. Ratio lower than 1.6 testifies to higher protein contaminates [17,18].…”