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

cohort 1: 3192 samples from ten cancer types; cohort 2: 7298 samples from 28 cancer types

HIM high impacting mutation, PAM protein-affecting mutation, NSM non-synonymous mutation