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Fig. 1 | Genome Medicine

Fig. 1

From: Rational design of cancer gene panels with OncoPaD

Fig. 1

Illustration of the rationale of OncoPaD and its use. Left: Information required to start the design of a panel. It consists of two mandatory parameters: (1) cancer type(s) of the panel (top) and (2) genes of interest: (a) cancer driver genes (CDs), (b) CDs with drug biomarkers, or (c) a list provided by the user (middle). Some advanced parameters are configurable to design the panel (bottom). Right: OncoPaD algorithm. OncoPaD filters a pan-cancer cohort (7298 samples) by the cancer type(s) selected by the user (1), thus producing the cohort relevant for the panel; next, the genes relevant to tumorigenesis in the panel cohort are chosen from those selected by the user (2); the mutational hotspots of these genes are identified (details in Additional file 2: Figure S1 and the "Methods" section) (3); the cumulative distribution of mutations (or coverage) of selected genes and/or hotspots in the panel cohort is built and those that contribute the most to this coverage (Tiers 1 and 2) are selected (4); finally OncoPaD generates reports of the main features of the designed panel, with additional ancillary information of all genes and/or mutational hotspots in the panel (5)

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