Lymphoma is one of the leading causes of cancer and cancer deaths and yet has not been amenable to population screening. The role of methylated DNA markers (MDMs) in the detection of lymphoma has not been extensively studied. We aimed to discover, validate, and test tissue–derived MDMs of lymphoma in archival plasma specimens. Reduced representation bisulfite sequencing (RRBS) was performed on a discovery set of frozen tissues. MDMs identified were converted to methylation–specific PCR assays and validated on independent formalin–fixed, paraffin‐embedded (FFPE) tissues. Target enrichment long–probe quantitative‐amplified signal (TELQAS) assays were developed and assayed in plasma–extracted, bisulfite‐converted DNA from independent treatment‐naïve lymphoma patients and healthy controls. Prediction of cancer status was modeled using random forest model with in silico cross‐validation. After discovery and validation in tissue, 16 TELQAS assays (ZNF503, VWA5B1, HOXA9, GABRG3, ITGA5, MAX.chr17.7190, BNC1, CDK20, MAX.chr4.4069, TPBG, DNAH14, SYT6, CACNG8, FAM110B, ADRA1D, and NRN1) were selected for testing in plasma. These detected 78% (95% CI, 74%–82%) of lymphoma cases at 90% specificity. Excluding marginal zone and T‐cell lymphomas, sensitivity increased to 84% (80%–88%). MDMs in plasma show promise to detect lymphoma and are candidates for inclusion in multi‐cancer detection studies.

中文翻译：

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血浆甲基化 DNA 标志物在淋巴瘤检测中的应用：发现、验证和临床试点


淋巴瘤是导致癌症和癌症死亡的主要原因之一，但尚未接受人群筛查。甲基化 DNA 标志物 （MDM） 在淋巴瘤检测中的作用尚未得到广泛研究。我们旨在在存档血浆标本中发现、验证和测试组织来源的淋巴瘤 MDM。对一组发现的冷冻组织进行减少表示亚硫酸氢盐测序 （RRBS）。将鉴定的 MDM 转换为甲基化特异性 PCR 检测，并在独立的福尔马林固定、石蜡包埋 （FFPE） 组织上进行验证。开发靶向富集长探针定量扩增信号 （TELQAS） 检测，并在来自独立治疗初治淋巴瘤患者和健康对照的血浆提取、亚硫酸氢盐转化的 DNA 中进行检测。使用随机森林模型和计算机交叉验证对癌症状态的预测进行建模。在组织中发现和验证后，选择 16 种 TELQAS 检测 （ZNF503、VWA5B1、HOXA9、GABRG3、ITGA5、MAX.chr17.7190、BNC1、CDK20、MAX.chr4.4069、TPBG、DNAH14、SYT6、CACNG8、FAM110B、ADRA1D 和 NRN1）在血浆中检测。这些检测检测到 78% （95% CI， 74%–82%） 的淋巴瘤病例，特异性为 90%。不包括边缘区和 T 细胞淋巴瘤，敏感性增加到 84% （80%–88%）。血浆中的 MDM 显示出检测淋巴瘤的前景，并且是纳入多癌症检测研究的候选者。