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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)

Additional file 1:Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies. Comparing the M-Measure-based approach to a state-of-the-art CNA algorithm by testing their ability to identify de novo aberrations in SNP-array signals from an evolving tumor at two time points. (DOC 820 KB)

Assessments of physiological parameters before, during and after ischemia (MCAO) in control and PSR pre-treated rats. Figure S1. Representative TTC-stained brain slices for sham and MCAO rats, with the latter animals divided into 4 groups that were pre-treated with vehicle, 1.1 g/kg, 2.2 g/kg or 5.5 g/kg PSR. Figure S2. Representative TTC-stained brain slices for sham and MCAO rats, with the latter animals divided into 4 groups that were post-treated with vehicle, 1.1 g/kg, 2.2 g/kg or 5.5 g/kg PSR. (DOCX 3065 kb)

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

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