Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms

doi:10.1515/cclm-2022-0511

科研成果详情

题名	Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms
作者	Jin, Shengnan1,2; Huang, Dan1,2; Jin, Weijiang1,2; Wang, Yourong 1,2; Shao, Hengrong 1,2; Gong, Lisha1,2; Luo, Zhenni1,2; Yang, Zhengquan1,2; Luan, Ju 4,5; Xie, Deyao3; Ding, Chunming1,2
发表日期	2022-09-27
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	allelic imbalance copy number alterations heterogeneous DNA loss of heterozygosity matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) mass spectrometry
其他关键词	ALLELIC IMBALANCE ; HETEROZYGOSITY ANALYSIS ; SNP ARRAYS ; CANCER ; GENE ; ALLELOTYPE ; EXPRESSION ; ONCOGENE ; ERBB-2 ; P16
摘要	Objectives Copy number alterations (CNAs) are frequently found in malignant tissues. Different approaches have been used for CNA detection. However, it is not easy to detect a large panel of CNA targets in heterogenous tumors. Methods We have developed a CNAs detection approach through quantitatively analyzed allelic imbalance by allelotyping single nucleotide polymorphisms (SNPs) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, the copy number changes were quantified by real-competitive PCR (rcPCR) to distinguish loss of heterozygosity (LOH) and genomic amplification. The approach was used to validate the CNA regions detected by next generation sequencing (NGS) in early-stage lung carcinoma. Results CNAs were detected in heterogeneous DNA samples where tumor DNA is present at only 10% through the SNP based allelotyping. In addition, two different types of CNAs (loss of heterozygosity and chromosome amplification) were able to be distinguished quantitatively by rcPCR. Validation on a total of 41 SNPs from the selected CNA regions showed that copy number changes did occur, and the tissues from early-stage lung carcinoma were distinguished from normal. Conclusions CNA detection by MALDI-TOF MS can be used for validating potentially interesting genomic regions identified from next generation sequencing, and for detecting CNAs in tumor tissues consisting of a mixture of neoplastic and normal cells.
资助项目	Zhejiang Provincial Natural Science Foundation of China [LY19H160027]; High-Level Innovation Team of Universities in Zhejiang Province [604090352/610]; 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	60 期号:10 页码:1543-1550
DOI	10.1515/cclm-2022-0511
页数	8
WOS类目	Medical Laboratory Technology
WOS研究方向	Medical Laboratory Technology
WOS记录号	WOS:000837326500001
收录类别	SCIE ; PUBMED ; SCOPUS
URL	查看原文
PubMed ID	35938948
SCOPUSEID	2-s2.0-85136243569
通讯作者地址	[Ding, Chunming]School of Laboratory Medicine and Life Sciences,Wenzhou Medical University,Zhejiang,Wenzhou,325035,China
Scopus学科分类	Clinical Biochemistry;Biochemistry (medical)
引用统计	被引频次[WOS]：0 [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/154257
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_心胸外科
通讯作者	Ding, Chunming
作者单位	1.School of Laboratory Medicine and Life Sciences,Wenzhou Medical University,Zhejiang,Wenzhou,China; 2.Key Laboratory of Laboratory Medicine,Ministry of Education,Wenzhou Medical University,Zhejiang,Wenzhou,325035,China; 3.Department of Thoracic Surgery,The First Affiliated Hospital of Wenzhou Medical University,Zhejiang,Wenzhou,China; 4.Key Laboratory of Laboratory Medicine,Ministry of Education,Wenzhou Medical University,Zhejiang,Wenzhou,China; 5.InnoMed Diagnostics Inc.,Wenzhou,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）
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,Huang, Dan,Jin, Weijiang,et al. Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms[J]. CLINICAL CHEMISTRY AND LABORATORY MEDICINE,2022,60(10):1543-1550.
APA	Jin, Shengnan., Huang, Dan., Jin, Weijiang., Wang, Yourong., Shao, Hengrong., ... & Ding, Chunming. (2022). Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms. CLINICAL CHEMISTRY AND LABORATORY MEDICINE, 60(10), 1543-1550.
MLA	Jin, Shengnan,et al."Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms".CLINICAL CHEMISTRY AND LABORATORY MEDICINE 60.10(2022):1543-1550.