Table 1 Comparison of OncoPaD with other resources. Six different features are included: (1) the input genes for panel design; (2) whether the resource allows to estimate (and fine-tune) the cost-effectiveness of the designed panel; (3) whether the resource provides additional ancillary annotations for mutations included in the panel; (4) whether the tool is a web service easy to maintain, evolve and use or a static resource; (5) the type of output provided to the user; and (6) the level of customization of the panel that the user can attain
TEAM [15] | Martinez et al. [16] | Design studio | OncoPaD | |
|---|---|---|---|---|
Input genes | • Genes with HIMs from COSMIC • User’s mutation list | Genes with NSMs in at least 4 % of samples in cohort 1 | User’s gene list | • Driver genes in 28 cancer types • Genes with drug biomarkers • User’s gene list |
In silico performance | Fraction of tumors from cohort 1 with NSMs | Kbps included in the panel | • Fraction of tumors from cohort 2 with PAMs • Kbps included in the panel | |
Metadata of panel mutations | Functional impact (SIFT and Polyphen) | • Validated oncogenic mutations • Drug biomarker mutations | ||
Type of resource | Web service | Static panels | Web service | Web service |
Output | Json file with selection of genes | List of ranked pan-cancer and per cancer type genes | • Bed file • Panel primers | • Reports with information on mutations included in the panel and performance (interactive HTML/PDF/Excel/Bed file) |
User customization options | • Filter by genes with HIMs • Filter by genes found in COSMIC • Add/remove genes | Input gene list | • Cancer type(s) to design the panel • Panel input genes (pre-compiled lists of drivers/biomarkers and/or user defined). • Fine-tune the design of the panel |