Figure 1.

Transformation of B allele frequency data for a paired tumor sample. (a) BAF for chromosome 8 of breast tumor 2 (data set 1). (b) Copy number profile of chromosome 8 with CBS segmentation profile superimposed in red. Gains (red bars) and losses (green bars) are called by comparison of the CBS profile to log2-ratio thresholds (± 0.15). (c) B allele frequency for chromosome 8 with SNPs homozygous in the matched normal sample removed. Horizontal dashed lines indicate positions of 0.97, 0.9, 0.1, 0.03 and 0.5 in BAF. (d) Transformation of BAF into mBAF for chromosome 8. SNPs homozygous in the matched normal sample removed. Horizontal dashed lines indicate positions of 0.97, 0.9 and 0.5 in mBAF. (e) Segmentation of a paired breast cancer mBAF profile. CBS was applied to mBAF data for chromosome 8 of breast tumor 2 (data set 1) after removal of SNPs homozygous in the matched normal sample. CBS segmentation profile is superimposed in orange. Horizontal dashed lines indicate positions of 0.97, 0.9 and 0.5 in mBAF.

Staaf et al. Genome Biology 2008 9:R136   doi:10.1186/gb-2008-9-9-r136
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