杂合子丢失
单核苷酸多态性
生物
分子生物学
基因组DNA
拷贝数变化
DNA测序
SNP阵列
质谱法
DNA
遗传学
癌症研究
化学
等位基因
基因
基因型
基因组
色谱法
作者
Shengnan Jin,Dan Na Huang,Weijiang Jin,Yourong Wang,Hengrong Shao,Liang Gong,Zhenni Luo,Zhining Yang,Ju Luan,Deyao Xie,Chunming Ding
标识
DOI:10.1515/cclm-2022-0511
摘要
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.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.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.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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