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Fig. 3 | Genome Medicine

Fig. 3

From: OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

Fig. 3

Schematic of an OncoGEMINI workflow for filtering variants. Variants are filtered using a combination of OncoGEMINI tools and included annotations as filter requirements. For each set of numbers, those listed on the left belong to patient #1, and those on the right are from patient #3. On the leftmost side of the figure, the total number of variants for each patient is listed with an increasing number of cancer annotation filter requirements being added from top to bottom, and the corresponding number of variants that meet those requirements, being specified as individual rows. Below each of these values, colored in orange, are the total number of variants that are flagged as somatic for that given combination of annotation filters. For each row, the number of variants is further restricted by individual OncoGEMINI tools listed towards the right side of the figure, highlighted in light gray boxes. The number of variants returned by different combinations of OncoGEMINI tools and cancer annotation filters are continued as rows within each of the gray boxes corresponding to different tool types. All variant counts listed in the gray boxes correspond to the total number of somatic and inherited variants. However, the majority of returned variants are somatic in the bottleneck and truncal boxes, especially as more annotation filters are used. Given that LOH variants are present in the germline, they are not labeled as somatic mutations in the same manner as bottleneck or truncal variants. Thus, variants identified in the loh box are not necessarily labeled as somatic. Any combinations of OncoGEMINI tools and cancer annotation filters that return any of the previously identified somatic variants are specified with the genes in which the variants were found and their specific mutations

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