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

Abstract

Objective: The study aimed to investigate the suitability of DNA extracted from saliva for high throughput molecular genotyping and DNA methylation platforms by comparing its performance with that of DNA extracted from blood. The genome-wide methylation profile, using the Infinium HumanMethylation450 Beadchip array® (Illumina, San Diego, CA), was measured for 20 DNA samples. Common genetic variation was measured, using the Infinium HumanCore Beadchip® (Illumina, San Diego, CA) for 4 samples (matching samples from 2 people). Results: DNA from blood and saliva returned genotyping call rates and reproducibility frequencies of > 99%. High-quality DNA methylation data was obtained from both saliva and blood DNA, with average detection p-values for each sample ranging from 0.001 to 0.006. Slightly higher global DNA methylation levels were observed in whole blood DNA than saliva DNA. Correlations between individuals for each sample type were generally greater than correlations between two sample types from the same individual (Pearson's correlation, r = 0.9696 in 10 pairs of matched blood and saliva derived DNA, r = 0.9702 between saliva samples, and r = 0.9769 between blood derived DNA). Saliva yields DNA of sufficient quantity and quality to compare favourably with blood as a source of DNA for genetic and epigenetic research purposes.