Figure 4

Comparison of BAF asymmetry for regions of allelic imbalance before and after tQN across different Infinium II platforms. BAF profiles for 35 tumor samples were divided into an upper (BAF > 0.5) and lower (BAF < 0.5) part, transformed to mBAF and separately segmented. For a defined genomic region, the average difference in segmented mBAF between the upper and lower part is expected to be zero if no asymmetry is present. Genomic regions were based on segmentation breakpoints of the upper BAF part. Only regions > 30 SNPs and with a segmented mBAF value > 0.6 in the upper and/or lower part were used in the comparisons. Black squares correspond to BeadStudio data and red triangles correspond to tQN data. Error bars for each sample and normalization method show the interquartile range (IQR). (a) BAF asymmetry for 14 matched tumor-normal samples. The black bar denotes 11 paired urothelial tumors from data set 4 and the white bar denotes the paired tumor samples from data set 8. tQN data systematically show less difference between the upper and lower BAF part compared to BeadStudio for the 14 matched tumors. (b) BAF asymmetry for 21 unmatched urothelial, breast and CLL tumor samples. The black bar denotes the 5 unpaired urothelial tumors from data set 4, the blue bar denotes CLL tumors from data set 7 and the red bar denotes breast tumors from data set 6. tQN data systematically show less difference between the upper and lower BAF part compared to BeadStudio for the 21 unmatched tumors.