Array-based whole-genome survey of dog saliva DNA yields high quality SNP data.
BACKGROUND
Genome-wide association scans for genetic loci underlying both Mendelian and complex traits are increasingly common in canine genetics research. However, the demand for high-quality DNA for use on such platforms creates challenges for traditional blood sample ascertainment. Though the use of saliva as a means of collecting DNA is common in human studies, alternate means of DNA collection for canine research have instead been limited to buccal swabs, from which dog DNA is of insufficient quality and yield for use on most high-throughput array-based systems. We thus investigated an animal-based saliva collection method for ease of use and quality of DNA obtained and tested the performance of saliva-extracted canine DNA on genome-wide genotyping arrays.


RESULTS
Overall, we found that saliva sample collection using this method was efficient. Extractions yielded high concentrations ( approximately 125 ng/ul) of high-quality DNA that performed equally well as blood-extracted DNA on the Illumina Infinium canine genotyping platform, with average call rates >99%. Concordance rates between genotype calls of saliva- versus blood-extracted DNA samples from the same individual were also >99%. Additionally, in silico calling of copy number variants was successfully performed and verified by PCR.


CONCLUSIONS
Our findings validate the use of saliva-obtained samples for genome-wide association studies in canines, highlighting an alternative means of collecting samples in a convenient and non-invasive manner.
Department of Psychiatry and Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.
Jennifer S
JS
Yokoyama
Carolyn A
CA
Erdman
Steven P
SP
Hamilton
D000483:Alleles; D000818:Animals; D033481:Chromosomes, Mammalian / Q000235:genetics; D004247:DNA / Q000097:blood / Q000235:genetics* / Q000302:isolation & purification; D056915:DNA Copy Number Variations / Q000235:genetics; D004285:Dogs / Q000235:genetics*; D005819:Genetic Markers; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012463:Saliva / Q000378:metabolism*; D013048:Specimen Handling
D005819:Genetic Markers; D004247:DNA