A systematic evaluation of stool DNA preparation protocols for colorectal cancer screening via analysis of DNA methylation biomarkers

doi:10.1515/cclm-2020-0300

科研成果详情

题名	A systematic evaluation of stool DNA preparation protocols for colorectal cancer screening via analysis of DNA methylation biomarkers
作者	Jin, Shengnan1,2; Ye, Qian 1,2; Hong, Yanping 1,2; Dai, Wenqing 1,2; Zhang, Chengliang 1,2; Liu, Weihao 1,2; Guo, Ying1,2; Zhu, Dewen 1,2; Zhang, Zhengzheng 1,2; Chen, Shiliang 1,2; Wang, Yourong 1,2; Li, Dandan 1,2; Ma, Wen 1,2; Yang, Zhengquan1,2; Li, Jinlei3; Zheng, Zhihai3; Luan, Ju 1,2,4; Wu, Xiaoli5; Jiang, Feizhao3; Xu, Chang 3; Ding, Chunming1,2
发表日期	2021-01
发表期刊	CLINICAL CHEMISTRY AND LABORATORY MEDICINE 影响因子和分区
语种	英语
原始文献类型	Article
关键词	colorectal carcinoma screening DNA methylation fecal DNA extraction NDRG4 SDC2
其他关键词	AMERICAN-COLLEGE ; FECAL DNA ; PERFORMANCE ; COLONOSCOPY ; STATISTICS ; EXTRACTION ; MUTATION ; SAMPLES ; GENE
摘要	Objectives: Colorectal cancer (CRC) screening using stool samples is now in routine use where tumor DNA methylation analysis for leading markers such as NDRG4 and SDC2 is an integral part of the test. However, processing stool samples for reproducible and efficient extraction of human genomic DNA remains a bottleneck for further research into better biomarkers and assays. Methods: We systematically evaluated several factors involved in the processing of stool samples and extraction of DNA. These factors include: stool processing (solid and homogenized samples), preparation of DNA from supernatant and pellets, and DNA extraction with column and magnetic beads-based methods. Furthermore, SDC2 and NDRG4 methylation levels were used to evaluate the clinical performance of the optimal protocol. Results: The yield of total and human genomic DNA (hgDNA) was not reproducible when solid stool scraping is used, possibly due to sampling variations. More reproducible results were obtained from homogenized stool samples. Magnetic beads-based DNA extraction using the supernatant from the homogenized stool was chosen for further analysis due to better reproducibility, higher hgDNA yield, lower non-hgDNA background, and the potential for automation. With this protocol, a combination of SDC2 and NDRG4 methylation signals with a linear regression model achieved a sensitivity and specificity of 81.82 and 93.75%, respectively. Conclusions: Through the systematic evaluation of different stool processing and DNA extraction methods, we established a reproducible protocol for analyzing tumor DNA methylation markers in stool samples for colorectal cancer screening.
资助项目	National Natural Sciences Foundation of ChinaNational Natural Science Foundation of China (NSFC) [81672922]; Medical Health Science and Technology Project of Zhejiang Provincial Health Commission [2017174160]; Wenzhou Science and Technology Bureau [2018ZY005, Y20160044]; High-Level Innovation Team of Universities in Zhejiang Province [604090352/610]; Innovation Discipline of Zhejiang Province in Nucleic Acid Molecular Diagnostics [437201702G]; Key Discipline of Zhejiang Province in Medical Technology (Fist Class, Category A) [437601607]
出版者	WALTER DE GRUYTER GMBH
出版地	BERLIN
ISSN	1434-6621
EISSN	1437-4331
卷号	59 期号:1 页码:91-99
DOI	10.1515/cclm-2020-0300
页数	9
WOS类目	Medical Laboratory Technology
WOS研究方向	Medical Laboratory Technology
WOS记录号	WOS:000599400500017
收录类别	SCIE ; PUBMED ; SCOPUS
URL	查看原文
PubMed ID	32673280
SCOPUSEID	2-s2.0-85088944513
自科自定义期刊分类	T3(B)类
通讯作者地址	[Ding, Chunming]School of Laboratory Medicine and Life Sciences,Wenzhou Medical University,Wenzhou, Zhejiang,China ; [Xu, Chang]Department of Colorectal Surgery,First Affiliated Hospital,Wenzhou Medical University,Zhejiang,China
Scopus学科分类	Clinical Biochemistry;Biochemistry (medical)
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	https://kms.wmu.edu.cn/handle/3ETUA0LF/16454
专题	检验医学院（生命科学学院、生物学实验教学中心）附属第一医院_消化内科附属第一医院_肛肠外科
通讯作者	Xu, Chang; Ding, Chunming
作者单位	1.School of Laboratory Medicine and Life Sciences,Wenzhou Medical University,Wenzhou, Zhejiang,China; 2.Key Laboratory of Laboratory Medicine,Ministry of Education,Wenzhou Medical University,Wenzhou, Zhejiang,China; 3.Department of Colorectal Surgery,First Affiliated Hospital,Wenzhou Medical University,Wenzhou, Zhejiang,China; 4.Innovation Biomedical Co.,Ltd.,Wenzhou, Zhejiang,China; 5.Department of Gastroenterology,First Affiliated Hospital,Wenzhou Medical University,Wenzhou, Zhejiang,China
第一作者单位	检验医学院（生命科学学院、生物学实验教学中心）; 温州医科大学
通讯作者单位	检验医学院（生命科学学院、生物学实验教学中心）; 附属第一医院
第一作者的第一单位	检验医学院（生命科学学院、生物学实验教学中心）
推荐引用方式 GB/T 7714	Jin, Shengnan,Ye, Qian,Hong, Yanping,et al. A systematic evaluation of stool DNA preparation protocols for colorectal cancer screening via analysis of DNA methylation biomarkers[J]. CLINICAL CHEMISTRY AND LABORATORY MEDICINE,2021,59(1):91-99.
APA	Jin, Shengnan., Ye, Qian., Hong, Yanping., Dai, Wenqing., Zhang, Chengliang., ... & Ding, Chunming. (2021). A systematic evaluation of stool DNA preparation protocols for colorectal cancer screening via analysis of DNA methylation biomarkers. CLINICAL CHEMISTRY AND LABORATORY MEDICINE, 59(1), 91-99.
MLA	Jin, Shengnan,et al."A systematic evaluation of stool DNA preparation protocols for colorectal cancer screening via analysis of DNA methylation biomarkers".CLINICAL CHEMISTRY AND LABORATORY MEDICINE 59.1(2021):91-99.