title: Saliva DNA quality and genotyping efficiency in a predominantly elderly population.
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.
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Harini V
authors.initials: HV
authors.lastname: Gudiseva
authors.affiliation: Illumina Inc, San Diego, CA, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Hansen
authors.affiliation: Illumina Inc, San Diego, CA, USA.
authors.forename: Linda
authors.initials: L
authors.lastname: Gutierrez
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Collins
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: He
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Lana D
authors.initials: LD
authors.lastname: Verkuil
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Ian D
authors.initials: ID
authors.lastname: Danford
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Sagaser
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Anita S
authors.initials: AS
authors.lastname: Bowman
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Salowe
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Prithvi S
authors.initials: PS
authors.lastname: Sankar
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Eydie
authors.initials: E
authors.lastname: Miller-Ellis
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Lehman
authors.affiliation: Scheie Eye Institute, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA, 19104, USA. Joan.O'Brien@uphs.upenn.edu.
authors.forename: Joan M
authors.initials: JM
authors.lastname: O'Brien
mesh_terms: D000368:Aged; D004247:DNA / Q000097:blood / Q000378:metabolism*; D003710:Demography; D005260:Female; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D012463:Saliva / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: 260/280 absorbance; African-Americans; Blood; Call rates; DNA; Elderly; GWAS; Genotyping; Glaucoma; Microarrays; SNPs; Saliva