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.
Funding source: High-Level Innovation Team of Universities in Zhejiang Province
Award Identifier / Grant number: 604090352/610
Funding source: Key Discipline of Zhejiang Province in Medical Technology (Fist Class, Category A)
Award Identifier / Grant number: 437601607
Funding source: Zhejiang Provincial Natural Science Foundation of China
Award Identifier / Grant number: LY19H160027
Acknowledgments
The authors thank all patients for participating in the study and the doctors and nurses for clinical support.
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Research funding: This work was supported by Zhejiang Provincial Natural Science Foundation of China (DX: Grant No. LY19H160027), High-Level Innovation Team of Universities in Zhejiang Province (CD: Grant No. 604090352/610), and Key Discipline of Zhejiang Province in Medical Technology (Fist Class, Category A) (Grant No. 437601607).
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Author contributions: Chunming Ding, Shengnan Jin and Deyao Xie design of the project, and led the writing of the manuscript. Chunming Ding, Shengnan Jin, Dan Huang, Weijiang Jin, Yourong Wang participated in study design and data interpretation; Hengrong Shao, Lisha Gong, Zhenni Luo, Zhengquan Yang, Ju Luan analyzed the data; Deyao Xie provided clinical expertise. All authors have accepted responsibility for the entire content of this manuscript and approved its submission.
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Competing interests: The authors declare no competing interests.
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Informed consent: Informed consent was obtained from all individuals included in this study.
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Ethical approval: The study was approved by the Clinical Research Ethics of the First Affiliated Hospital of Wenzhou Medical University (2019-ky-50).
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