Related Experiment Video
Updated: Mar 23, 2026
Collection and Extraction of Saliva DNA for Next Generation Sequencing
Published on: August 27, 2014
Saliva DNA quality and genotyping efficiency in a predominantly elderly population
Harini V Gudiseva1, Mark Hansen2, Linda Gutierrez2
1Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
Background:
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.
Methods:
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.
Results:
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 microg/ml) than blood (13.2 ± 8.5 microg/ml), but the mean ± SD of total DNA yield obtained per saliva specimen (35 ± 36 microg from 2 ml maximum specimen volume) was approximately three-fold lower than from blood (106 ± 68 microg 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/microl, corresponding to total yields ≥ 2 microg, were obtained for 94 % of the saliva specimens (n = 2344).
Conclusions:
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.
