Journal
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
Volume 60, Issue 10, Pages 1543-1550Publisher
WALTER DE GRUYTER GMBH
DOI: 10.1515/cclm-2022-0511
Keywords
allelic imbalance; copy number alterations; heterogeneous DNA; loss of heterozygosity; matrix-assisted laser desorption; ionization time-of-flight mass spectrometry (MALDI-TOF) mass spectrometry
Categories
Funding
- 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]
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The study developed a method for CNAs detection through SNP allelotyping and rcPCR, successfully detecting CNAs in heterogeneous DNA samples and quantitatively distinguishing different types of CNAs. This approach can validate CNA regions identified by NGS and detect CNAs in tumor tissues consisting of a mixture of neoplastic and normal cells.
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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