Additional file 1: of Substantial batch effects in TCGA exome sequences undermine pan-cancer analysis of germline variants

Figure S1. Number of variants in exomes per sample across ethnic groups and cancer types. Figure S2. Variability in called variants across TCGA sequencing centers for variants that are in consensus (at least two different variant calling tools.). Figure S3. Average number of variants per sample based on an alternative variant calling pipeline (for all 33 cancer types). Figure S4. Germline variant distribution plots for representative genes by cancer types. Table S1. Number of variants in exomes per sample across ethnic groups and cancer types. Table S2. Cancer-type statistics derived from TCGA. Table S3. Kolmogorov-Smirnov P-value per gene across all pairs of the 6 analyzed cancer types. A measure of the batch distinctive variant distribution pattern is shown for the 104 CPG annotated by COSMIC (named “104 CPG”) and the entire genes (named “all genes”). The table lists all genes with at least a single variant among the compared groups. (ZIP 5414 kb)