利用单核苷酸多态性芯片全基因组检测人大细胞肺癌细胞株的杂合性缺失和拷贝数变异

背景和目的DNA序列的杂合性缺失(LOH)和拷贝数变异(CNV)普遍存在于肿瘤基因组,并认为与肿瘤发生发展相关。高密度单核苷酸多态性(SNP)芯片能够检测全基因组的LOH和CNV适用于研究肿瘤遗传变异。本研究运用该技术寻找人大细胞肺癌细胞株NL9980全基因组的LOH和CNV。方法提取细胞株总DNA并应用500K SNP芯片进行检测。芯片获得的500000位点的杂交信号强度数据使用Affymetrix专利软件估算各SNP位点基因型和拷贝数。进一步分析获得NL9980全基因组LOH和CNV。结果芯片的SNP位点检测率超过了93%的主要质控标准。NL9980细胞中LOH散布在所有染色体,CNV主要分布在2,3,4,5,7,10,11和18号等染色体。结论研究表明NL9980基因组存在复杂的遗传变异。SNP芯片高分辨率和提供等位基因型信息等优势极大地提高了肺癌遗传变异研究的能力。

Genome-wide detection of loss of heterozygosity and copy number variation in a human lung large cell carcinoma cell line by affymetrix single-nucleotide polymorphism array 500K

Background and objective Loss of heterozygosity (LOH) and Copy number copy number variation (CNV) of DNA sequences is a common feature of cancer genomes, which is thought to be linked to tumorigenesis and progression. High-density single- nucleotide polymorphism (SNP) genotyping array are able to provided a genotype and copy number information with genome-wide coverage, which is suitable for the analysis of complex genetic alterations present in cancer. Thus a human lung large cell carcinoma cell line NL9980 was assayed for the global profile of LOH and CNV. Methods Genomic DNA from the cell line was screened for LOH and CNV using Affymetrix GeneChip? Human Mapping array 500K Set. The hybridization intensity data of 500 000 SNP loci was analyzed using Affymetrix proprietary software for genotyping and copy number of each locus, and a genome-wide map of LOH and CNV of the cell line was constructed. Results The SNP call rate of array Nsp I (-262K) was 95.14%, and the rate of Sty I (-238K) was 97.15%. The both call rates of the components of 500K array set were in excess of 93%, the cardinal quality control standard. LOH profiles of the sample were across all chromosomes, and most of CN gains and losses regions were found on chromosomes such as 2, 3, 4, 5, 7, 10, 11, and 18. Conclusion The results have shown that there were complex genetic alterations present in NL9980. And it is possible to achieve high performance outcomes using Affymetrix SNP array 500K to interrogate LOH and CNV in lung cancer genome. This advance of high- resolution with allelic information should substantially improve the ability to further understanding of the genetic basis of lung cancers.