Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations

Table 1 Single nucleotide variants included in this study stratified according to the evidence supporting their impact on protein function

A total of 3,591 single nucleotide variants (SNVs) in six bona fide oncogenes, six new cancer genes and three bona fide tumor suppressor genes were assessed for the evidence supporting a functional role for each of the mutations. These SNVs were classified as non-neutral, neutral or uncertain based on direct experimental/functional data in the literature and/or on the basis of causation of Li-Fraumeni syndrome and Li-Fraumeni-like syndrome (for TP53) or early onset breast and ovarian cancer syndrome (for BRCA1 and BRCA2), as recorded in dedicated mutation databases [28-30]. For a detailed list, see Additional file 2.

ISSN: 1474-760X