Additional file 2 of Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies

Additional file 2:Evidence of subclonal heterogeneity from RNA-Seq data across a collection of melanoma samples. Allelic imbalance along each gene demonstrates subclonal heterogeneity. The score of the non-reference nucleotide has been calculated as 0.5- | 0.5 - (#B/(#B+#A)) |, where #A and #B are the numbers of reads hosting the reference and non-reference nucleotide respectively. However, all the reported genes have a multimodal distribution of B-allele frequencies along at least one exon. The B-allele frequencies close to 0.5 have been marked in grey, B-alleles that significantly deviate from this cluster are considered acquired somatic mutations (black) and can be explained by subclonal heterogeneity. Vertical bars represent 95% confidence intervals. All non-reference nucleotides shown are supported by at least 100 reads. Vertical dashed lines mark the boundaries between exons in the transcript. (PDF 46 KB)