Additional data file 1 Figure S1 Triplet filtering for
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Additional data file 1 Figure S1 Triplet filtering for
Figure S1. Triplet filtering for removal of non-informative homozygous SNPs after applying a fixed mBAF threshold. (a) Principle of triplet filtering. (b) Histogram of ...
Additional data file 1 Figure S1 Triplet filtering for removal of non-informative homozygous SNPs after applying a fixed mBAF threshold. (a) Principle of triplet filtering. (b) Histogram of triplet sums for SNPs homozygous in the matched blood and not removed by the used mBAF threshold of 0.97 for 15 urothelial carcinomas (data set 2). Vertical red dashed line corresponds to a triplet sum of 0.8. (c) Boxplot of triplet sums for SNPs homozygous in the matched blood and not removed by mBAF cut-off 0.97 for 15 urothelial carcinomas. Vertical red dashed line corresponds to a triplet sum of 0.8. (d) mBAF profile of chromosome 8 in breast tumor 2 (data set 1) after removal of SNPs with mBAF > 0.97. SNPs colored in red have triplet sums > 0.8. (e) Triplet sums for SNPs on chromosome 8 in breast tumor 2 after removal of SNPs with mBAF > 0.97. SNPs colored in red have triplet sums > 0.8. (f) mBAF profile of chromosome 8 in breast tumor 2 after removal of SNPs with mBAF > 0.97 and SNPs with triplet sums > 0.8. Figure S2 Comparison of sensitivity for detecting ten simulated allelic imbalances for five methods. SNPs called as AB in NA06991 were used to estimate the sensitivity for the methods in detecting allelic imbalances in the simulated data set with increasing normal cell contamination. Sensitivity was calculated for each method based on the number of correct calls of the type of allelic imbalance for each region (gain is identified as gain). Lines correspond to sensitivity for PennCNV (black), QuantiSNP (green), unpaired segmentation (red), paired segmentation (orange), and SOMATICs (blue). Figure S3 Difference in technical variation between Affymetrix SNP arrays and Illumina BeadChips for an urothelial carcinoma. Urothelial carcinoma UC199_I (data set 2) was hybridized on an Illumina 370k BeadChip and an Affymetrix 250k Nsp Mapping array. (a) Illumina BAF estimates for chromosome 9. (b) Affymetrix BAF estimates for chromosome 9. (c) Illumina BAF estimates for chromosome 9 after removal of SNPs homozygous in the matched normal blood. (d) Affymetrix BAF estimates for chromosome 9 after removal of SNPs homozygous in the matched normal blood. Figure S4 Modifications of the segmentation strategy to better handle Affymetrix WGG data. Urothelial tumor UC3 (data set 2) was hybridized on an Affymetrix 250k Nsp Mapping array. Red line represents the CBS segmentation profile. Chromosome 5 is displayed. Horizontal dashed lines indicate positions of 0.97 and 0.9 in mBAF. (a) Identical parameters as for Illumina data. (b) mBAF cut-off lowered to 0.9, triplet filtering lowered to 0.6 and median used for estimation of the segmented value in the CBS algorithm.
