Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection
Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection
复制标题
DOI：
10.1016/j.ygyno.2019.11.028
复制
发表时间：
2020-02-01
影响因子：
4.7
通讯作者：
Bakkum-Gamez, Jamie N.
中科院分区：
文献类型：
--
作者：
Sangtani, Ajleeta;Wang, Chen;Bakkum-Gamez, Jamie N.
Objective.我们旨在通过分析拷贝数、甲基化标记和突变来评估是否可以在阴道分泌物收集的脱落DNA中检测到子宫内膜癌（EC）。在子宫切除术前收集38例EC患者和28例良性适应症妇女的卫生棉条。对提取的ECT 1DNA进行以下操作：1）低覆盖全基因组测序（LCWGS）以评估拷贝数，2）焦磷酸测序以测量HOXA 9、RASSFI和CDH 13的启动子甲基化百分比，和3）下一代测序（NGS）以鉴定通过癌症基因组图谱鉴定的与EC相关的19个基因中的突变。计算每种检测和检测组合的灵敏度和特异性。甲基化分析产生了最高的特异性，但最低的灵敏度（37-40%的灵敏度; HOXA 9，RASSFI和HTR 1B的特异性为100%），而突变分析具有提高的灵敏度（50%的灵敏度; 83%的特异性）。只有一个“假阳性”结果的拷贝数变异被确定为良性手术指征的妇女，这是基于检测拷贝数的变化，并与平滑肌肉瘤，只有在子宫切除术识别。将3种生物标志物类别中的任何一种视为阳性，灵敏度为92%，特异性为86%。突变分析并没有增加拷贝数和甲基化分析组合的敏感性。这项研究证明了子宫内膜癌的非侵入性但精确检测的原理证明。我们建议，通过改进生物标志物测试，有可能开发出一种临床上有用的检测EC的测试。(C)2019爱思唯尔公司All rights reserved.
Objective. We aimed to assess whether endometrial cancer (EC) can be detected in shed DNA collected with vaginal tampon by analyzing copy number, methylation markers, and mutations.Methods. Tampons were collected prior to hysterectomy from 38 EC patients and 28 women with benign indications. Extracted tampon DNA underwent the following: 1) low-coverage whole genome sequencing (LCWGS) to assess copy number, 2) pyrosequencing to measure percent promotor methylation of HOXA9, RASSFI, and CDH13 and 3) next generation sequencing (NGS) to identify mutations in 19 genes associated with EC identified through The Cancer Genome Atlas. Sensitivity and specificity for each test and test combinations were calculated.Results. Methylation analysis yielded the highest specificities but lowest sensitivities (37-40% sensitivity; 100% specificity for HOXA9, RASSFI and HTR1B) while mutation analysis had improved sensitivity (50% sensitivity; 83% specificity). Only one "false positive" result for copy number variants was identified among women with benign surgical indications, which was based on detection of copy number changes, and associated with a leiomyosarcoma that was only recognized at hysterectomy. Considering any of the 3 biomarker classes as a positive, resulted in a sensitivity of 92% and specificity of 86%. Mutation analysis did not add sensitivity to the combination of analysis of copy number and methylation.Conclusions. This study demonstrates a proof-of-principle for non-invasive yet precise detection of endometrial cancer. We propose that with improved biomarker testing, it may be possible to develop a clinically useful test for detecting EC. (C) 2019 Elsevier Inc. All rights reserved.