Saliva and buccal samples are popular for epigenome wide association studies (EWAS) due to their
ease of collection compared and their ability to sample a different cell lineage compared to blood.
As these samples contain a mix of white blood cells and buccal epithelial cells that can vary within
a population, this cellular heterogeneity may confound EWAS. This has been addressed by
including cellular heterogeneity obtained through cytology at the time of collection or by using
cellular deconvolution algorithms built on epigenetic data from specific cell types. However, to
our knowledge, the two methods have not yet been compared. Here we show that the two
methods are highly correlated in saliva and buccal samples (R = 0.84, P < 0.0001) by comparing
data generated from cytological staining and Infinium MethylationEPIC arrays and the EpiDISH
deconvolution algorithm from buccal and saliva samples collected from twenty adults. In addition,
by using an expanded dataset from both sample types, we confirmed our previous finding that
age has strong, non-linear negative correlation with epithelial cell proportion in both sample
types. However, children and adults showed a large within-population variation in cellular
heterogeneity. Our results validate the use of the EpiDISH algorithm in estimating the effect of
cellular heterogeneity in EWAS and showed DNA methylation generally underestimates the
epithelial cell content obtained from cytology.