Staaf Johan, Vallon-Christersson Johan, Lindgren David, Juliusson Gunnar, Rosenquist Richard, Höglund Mattias, Borg Ake, Ringnér Markus
Department of Oncology, Clinical Sciences, Lund University, SE-22185 Lund, Sweden.
BMC Bioinformatics. 2008 Oct 2;9:409. doi: 10.1186/1471-2105-9-409.
Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples.
We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The asymmetry is caused by a remaining bias between the two dyes used in the Infinium II assay after using the normalization method in Illumina's proprietary software (BeadStudio). We propose a quantile normalization strategy for correction of this dye bias. We tested the normalization strategy using 535 individual hybridizations from 10 data sets from the analysis of cancer genomes and normal blood samples generated on Illumina Infinium II 300 k version 1 and 2, 370 k and 550 k BeadChips. We show that the proposed normalization strategy successfully removes asymmetry in estimates of both allelic proportions and copy numbers. Additionally, the normalization strategy reduces the technical variation for copy number estimates while retaining the response to copy number alterations.
The proposed normalization strategy represents a valuable tool that improves the quality of data obtained from Illumina Infinium arrays, in particular when used for LOH and copy number variation studies.
Illumina Infinium全基因组基因分型（WGG）阵列越来越多地应用于癌症基因组学研究，以研究基因拷贝数改变和等位基因特异性畸变，如杂合性缺失（LOH）。为WGG阵列标准化开发的方法大多集中在二倍体正常样本上。然而，对于癌症样本，基因组畸变可能会混淆标准化和数据解释。因此，我们研究了Illumina Infinium阵列常用的标准化方法应用于癌症样本时的效果。
我们证明了每个单核苷酸多态性（SNP）的两个等位基因检测存在不对称性，这对等位基因比例和拷贝数估计都有有害影响。这种不对称性是由于在Illumina专有软件（BeadStudio）中使用标准化方法后，Infinium II检测中使用的两种染料之间仍存在偏差。我们提出了一种分位数标准化策略来校正这种染料偏差。我们使用来自10个数据集的535次个体杂交测试了标准化策略，这些数据集来自对癌症基因组和正常血液样本的分析，样本在Illumina Infinium II 300 k版本1和2、370 k和550 k BeadChip上生成。我们表明，所提出的标准化策略成功消除了等位基因比例和拷贝数估计中的不对称性。此外，标准化策略减少了拷贝数估计的技术变异，同时保留了对拷贝数改变的响应。
所提出的标准化策略是一种有价值的工具，可提高从Illumina Infinium阵列获得的数据质量，特别是在用于LOH和拷贝数变异研究时。
