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Jin S, Huang D, Jin W, Wang Y, Shao H, Gong L, Luo Z, Yang Z, Luan J, Xie D, Ding C. Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms. Clin Chem Lab Med 2022; 60:1543-1550. [PMID: 35938948 DOI: 10.1515/cclm-2022-0511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Shengnan Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Dan Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Weijiang Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Yourong Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Hengrong Shao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Lisha Gong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Zhenni Luo
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Zhengquan Yang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Ju Luan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; and InnoMed Diagnostics Inc., Wenzhou, P.R. China
| | - Deyao Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
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Lin XC, Zhang T, Liu L, Tang H, Yu RQ, Jiang JH. Mass Spectrometry Based Ultrasensitive DNA Methylation Profiling Using Target Fragmentation Assay. Anal Chem 2016; 88:1083-7. [DOI: 10.1021/acs.analchem.5b04247] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiang-Cheng Lin
- State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ting Zhang
- State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Lan Liu
- State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hao Tang
- State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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Fujishima K, Yamamoto S, Tsukagoshi K, Hashimoto M. A Microbead-based Single Base Extension Assay for the Detection of Known Single-base Changes in Genomic DNA. CHEM LETT 2015. [DOI: 10.1246/cl.150014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kohei Fujishima
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Shunsuke Yamamoto
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Doshisha University
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Zhu J, Qiu C, Palla M, Nguyen T, Russo JJ, Ju J, Lin Q. A Microfluidic Device for Multiplex Single-Nucleotide Polymorphism Genotyping. RSC Adv 2014; 4:4269-4277. [PMID: 26594354 PMCID: PMC4651459 DOI: 10.1039/c3ra44091e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most abundant type of genetic variations; they provide the genetic fingerprint of individuals and are essential for genetic biomarker discoveries. Accurate detection of SNPs is of great significance for disease prevention, diagnosis and prognosis, and for prediction of drug response and clinical outcomes in patients. Nevertheless, conventional SNP genotyping methods are still limited by insufficient accuracy or labor-, time-, and resource-intensive procedures. Microfluidics has been increasingly utilized to improve efficiency; however, the currently available microfluidic genotyping systems still have shortcomings in accuracy, sensitivity, throughput and multiplexing capability. To address these challenges, we developed a multi-step SNP genotyping microfluidic device, which performs single-base extension of SNP specific primers and solid-phase purification of the extension products on a temperature-controlled chip. The products are ready for immediate detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), providing identification of the alleles at the target loci. The integrated device enables efficient and automated operation, while maintaining the high accuracy and sensitivity provided by MS. The multiplex genotyping capability was validated by performing rapid, accurate and simultaneous detection of 4 loci on a synthetic template. The microfluidic device has the potential to perform automatic, accurate, quantitative and high-throughput assays covering a broad spectrum of applications in biological and clinical research, drug development and forensics.
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Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - Chunmei Qiu
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - James J. Russo
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
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Radisavljević M, Kamceva T, Vukićević I, Nisavić M, Milovanović M, Petković M. Sensitivity and accuracy of organic matrix-assisted laser desorption and ionisation mass spectrometry of FeCl3 is higher than in in matrix-free approach. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:77-89. [PMID: 24261080 DOI: 10.1255/ejms.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We compare the quality and reliability of laser desorption and ionisation mass spectra of FeCl3 acquired without the assistance of the matrix with the spectra acquired with different organic matrix molecules. Generally, inorganic salts tend to form clusters upon laser irradiation, the signals of which can be easily distinguished from ions arising from the matrix. In the presence of a matrix, cluster ions are, however, mostly suppressed. We have compared the number of analyte signals, accuracy of determination of isotope composition of the analyte and the sensitivity of FeCl3 detection between different approaches. The results obtained imply that the sensitivity of mass spectrometric analysis of FeCl3 is somewhat higher when matrices are applied than in the matrix-free approach. Among all matrices tested in this work, F20TPP seems to be the most promising for further applications as a matrix for mass spectrometry of inorganic salts.
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Affiliation(s)
- Maja Radisavljević
- Laboratory of Physical Chemistry, Vinća, Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia.
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