Copy number estimation algorithms and fluorescence in situ hybridization to describe copy number alterations in human tumors
Copy number estimation algorithms and fluorescence in situ hybridization to describe copy number alterations in human tumors
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DOI：
10.1111/j.1440-1827.2009.02354.x
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发表时间：
2009-04-01
影响因子：
2.2
通讯作者：
Sugimura, Haruhiko
中科院分区：
文献类型：
--
作者：
Suzuki, Masaya;Nagura, Kiyoko;Sugimura, Haruhiko
人类肿瘤的高分辨率遗传分析平台已经变得流行，并且已经将几种拷贝数估计算法应用于单核苷酸多态性微阵列产生的数据。尽管已经在几种不同的平台或方法之间进行了比较，但从未对不同的拷贝数估计算法进行过稳健的比较，并且与肿瘤中的多重荧光原位杂交（FISH）数据相比，估计的有效性很少得到解决。在本研究中，使用Affyoung 250K Nsp阵列在两个癌症病例中生成的数据集来比较用于估计拷贝数改变（CNA）的两种广泛使用的算法：基于基因分型微阵列的拷贝数变异（CNV）分析（GEMCA）算法和用于Affyoung基因芯片作图的拷贝数分析仪（CNAG）算法。注意到这两种算法的估计值之间存在相当大的差异，因为用于计算阈值的公式不同。两种算法都产生了与FISH结果高度一致的数据，但CNAG在检测丢失方面更为严格。两种算法在某些领域都有所提高，但FISH没有显示出任何变化。探讨这些剩余差异的原因将是有意义的。
The platforms of high-resolution genetic analysis of human tumors have become popular, and several copy number estimation algorithms have been applied to the data generated by single-nucleotide polymorphism microarrays. Although comparisons have been made between several different platforms or methodologies, there has never been a robust comparison of different copy number estimation algorithms, and the validity of the estimations in comparison with multiple fluorescence in situ hybridization (FISH) data in tumors has rarely been addressed. In the present study the dataset that the Affymetrix 250K Nsp array generated in two cancer cases was used to compare the two widely used algorithms for estimating copy number alterations (CNA): the genotyping microarray-based copy number variation (CNV) analysis (GEMCA) algorithm and the copy number analyzer for Affymetrix Genechip mapping (CNAG) algorithm. Considerable differences were noticed between the estimations by these two algorithms, because of the difference in the formula used to calculate the threshold values. Both algorithms yielded highly consistent data with the FISH results, but CNAG was more stringent for detecting loss. There were areas in which both algorithms provided gains, but FISH showed no change. It will be interesting to pursue the reasons for these remaining discrepancies.