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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

From: Rational design of cancer gene panels with OncoPaD

  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
  1. cohort 1: 3192 samples from ten cancer types; cohort 2: 7298 samples from 28 cancer types
  2. HIM high impacting mutation, PAM protein-affecting mutation, NSM non-synonymous mutation