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BMC Med Genomics. 2016 Apr 7;9:17. doi: 10.1186/s12920-016-0172-y.

Saliva DNA quality and genotyping efficiency in a predominantly elderly population.

Author information

1
Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
2
Illumina Inc, San Diego, CA, USA.
3
Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA. Joan.O'Brien@uphs.upenn.edu.

Abstract

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 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).

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.

KEYWORDS:

260/280 absorbance; African-Americans; Blood; Call rates; DNA; Elderly; GWAS; Genotyping; Glaucoma; Microarrays; SNPs; Saliva

PMID:
27052975
PMCID:
PMC4823890
DOI:
10.1186/s12920-016-0172-y
[Indexed for MEDLINE]
Free PMC Article

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