Don’t brush off buccal data heterogeneity

Buccal epithelial cells are among the most clinically accessible tissues and are increasingly being used to identify epigenetic disease patterns. However, substantial variation in buccal DNA methylation patterns indicates heterogeneity of cell types within and between samples, raising questions of data quality. We systematically estimated cell-type composition for a large collection of buccal and saliva samples from 11 published studies of DNA methylation. In these we identified numerous cases of buccal samples with questionable purity, which may be affected by sampling from individuals with neurodevelopmental disorders, and by the brushes used for sample collection. Further challenges are involved in comparisons with tissues such as saliva, in which buccal component varies widely. We propose a reference-based method of correcting for buccal purity that reduces unwanted variation while preserving cross-tissue differences. Our work demonstrates the wide variation of buccal quality in epigenetic studies and suggests a possible approach to overcome this issue.

口腔上皮细胞（buccal epithelial cells）是临床最易获取的组织之一，正越来越多地被用于鉴定表观遗传疾病相关特征。然而，口腔DNA甲基化模式存在显著差异，这表明样本内部及样本间存在细胞类型异质性，进而对数据质量构成了质疑。我们系统评估了来自11项已发表DNA甲基化研究的大规模口腔及唾液样本队列的细胞类型组成。在此分析中，我们发现多份口腔样本的纯度存疑，该现象可能受到神经发育障碍个体的采样过程以及样本采集所用毛刷的影响。在与唾液等组织进行比对时还存在额外挑战，因为唾液中的口腔组分差异极大。我们提出了一种基于参考的校正口腔样本纯度的方法，该方法可在保留跨组织差异的同时减少非预期的变异。本研究揭示了表观遗传研究中口腔样本质量的广泛差异，并为解决这一难题提供了可行思路。