Background: Tumor purity is of great significance for the study of tumor genotyping and the prediction of recurrence, which is significantly affected by tumor heterogeneity. Tumor heterogeneity is the basis of drug resistance in various cancer treatments, and DNA methylation plays a core role in the generation of tumor heterogeneity. Almost all types of cancer cells are associated with abnormal DNA methylation in certain regions of the genome. The selection of tumor-related differential methylation sites, which can be used as an indicator of tumor purity, has important implications for purity assessment. At present, the selection of information sites mostly focuses on inter-tumor heterogeneity and ignores the heterogeneity of tumor growth space that is sample specificity.Results: Considering the specificity of tumor samples and the information gain of individual tumor sample relative to the normal samples, we present an approach, PESM, to evaluate the tumor purity through the specificity difference methylation sites of tumor samples. Applied to more than 200 tumor samples of Prostate adenocarcinoma (PRAD) and Kidney renal clear cell carcinoma (KIRC), it shows that the tumor purity estimated by PESM is highly consistent with other existing methods. In addition, PESM performs better than the method that uses the integrated signal of methylation sites to estimate purity. Therefore, different information sites selection methods have an important impact on the estimation of tumor purity, and the selection of sample specific information sites has a certain significance for accurate identification of tumor purity of samples.

中文翻译：

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PESM：一种基于样本特异性甲基化位点的肿瘤纯度估计新方法

背景：肿瘤纯度对于肿瘤基因分型研究和复发预测具有重要意义，肿瘤异质性显着影响复发预测。肿瘤异质性是各种癌症治疗中耐药的基础，而DNA甲基化在肿瘤异质性的产生中起着核心作用。几乎所有类型的癌细胞都与基因组某些区域的异常 DNA 甲基化有关。肿瘤相关差异甲基化位点的选择可用作肿瘤纯度的指标，对纯度评估具有重要意义。目前，信息位点的选择多侧重于肿瘤间的异质性，而忽略了肿瘤生长空间的异质性即样本特异性。 结果：考虑到肿瘤样本的特异性和个体肿瘤样本相对于正常样本的信息增益，我们提出了一种方法，PESM，通过肿瘤样本的特异性差异甲基化位点来评估肿瘤纯度。应用于前列腺腺癌（PRAD）和肾透明细胞癌（KIRC）的200多个肿瘤样本，表明PESM估计的肿瘤纯度与其他现有方法高度一致。此外，PESM 的性能优于使用甲基化位点积分信号来估计纯度的方法。因此，不同的信息位点选择方法对肿瘤纯度的估计有重要影响，样本特异性信息位点的选择对于准确鉴定样本的肿瘤纯度具有一定的意义。