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Figure 1 | BMC Bioinformatics

Figure 1

From: Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

Figure 1

Occurrence of asymmetrical B allele frequencies and copy number estimates. Urothelial tumor UC152_I hybridized on an Infinium 370 k BeadChip is shown. CNV probes have been removed. (a) B allele frequency for chromosome 1. (b)Mirrored B allele frequency (mBAF) for chromosome 1, with individual SNPs colored according to BAF values: less than 0.5 (orange), above 0.5 (blue) showing the asymmetry of BAF values around 0.5. (c) BAF profile of chromosome 1, with individual SNPs colored according to genotype calls: AA (green), AB (yellow), BB (red) and no calls (gray). The cause of the BAF asymmetry also affects genotyping as seen for SNPs not assigned to a genotype (gray), which in the region 1q32.1 to qter (highlighted with a light blue background) predominantly are present with BAF < 0.5. (d) Copy number estimates (Log R ratio) for chromosome 1, with individual SNPs colored according to genotype. The cause of the BAF asymmetry also affects copy number estimates as seen for regions of gain and loss, where AA and BB SNPs do not overlap. (e) Scatter plot of normalized allele intensities X and Y with individual SNPs colored according to genotype. A lowess regression line (solid) for heterozygous SNPs and the expected X = Y line (dashed) are superimposed. (f) Boxplots of the distributions of allele intensities X (green) and Y (red).

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