Performance Comparison of Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-Genome Microarrays in Complex Cancer Samples
Performance Comparison of Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-Genome Microarrays in Complex Cancer Samples
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DOI：
10.1159/000345125
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发表时间：
2013-01-01
影响因子：
1.7
通讯作者：
Nyegaard, M.
中科院分区：
文献类型：
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作者：
Bodker, J. S.;Gyrup, C.;Nyegaard, M.
Affytelium细胞遗传学2.7M全基因组微阵列（Cyto2.7M）检测基因组畸变。Cyto2.7M阵列增加了癌症相关基因区域的覆盖率，与常用的AffytoSNP 6.0全基因组微阵列（SNP 6.0）相比，处理时间减少了4倍，输入要求减少了5倍（100 ng）。我们着手比较这些微阵列在含有复杂基因组变化的癌症样本上的性能。我们使用SNP 6.0和Cyto2.7M微阵列分析了8个淋巴瘤样本和1个血液样本的基因组DNA。我们比较了阵列的4个参数，包括拷贝数变异（CNV）检测、CNV边界、分配给畸变的实际拷贝数（CN）和杂合性丢失。通过定量PCR验证所选区域的CN状态。观察到阵列之间在所有测试参数上的非常高的一致性，因此224个畸变中只有30个在CN状态上不一致，对应于总共相似的12 Mb或分析的碱基对的0.06%。因此，SNP6.0和Cyto2.7M阵列同样适用于检测复杂样品（如癌症样品）中的基因组畸变。Cyto2.7M阵列缩短了处理时间，降低了输入要求，可在只有有限DNA的情况下对样本进行基因组分析。版权所有（c）2012 S. Karger AG，巴塞尔
The Affymetrix cytogenetic 2.7M whole-genome microarray (Cyto2.7M) detects genomic aberrations. The Cyto2.7M array has increased coverage in regions with cancer-related genes, similar to 4-fold reduced processing time, and 5-fold reduced input requirements (100 ng) compared to the commonly used Affymetrix SNP6.0 genome-wide microarray (SNP6.0). We set out to compare the performance of these microarrays on cancer samples containing complex genomic changes. We analyzed genomic DNA from 8 lymphoma samples and 1 blood sample using both SNP6.0 and Cyto2.7M microarrays. We compared the arrays with respect to 4 parameters, including detection of copy number variations (CNV), CNV boundaries, the actual copy number (CN) assigned to the aberrations, and loss of heterozygosity. The CN state of selected regions was validated by quantitative PCR. Very high consistency between arrays on all parameters tested was observed, hence only 30 of 224 aberrations disagreed on the CN state, corresponding to a total of similar to 12 Mb or 0.06% of the analyzed base pairs. Thus, the SNP6.0 and Cyto2.7M arrays are equally well suited to detect genomic aberrations in complex samples such as cancer samples. With reduced processing time and lower input requirements, the Cyto2.7M array enables genomic analysis of samples where only limited DNA is available. Copyright (c) 2012 S. Karger AG, Basel