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Breast cancer simple somatic mutation data include single base substitutions, multiple base substitutions and short indels.
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SNAP (Screening for Non-Acceptable Polymorphisms) is a neural-network based computational tool trained on a large set of mutation data, including PMD data, that performs well in distinguishing neutral from non-neutral amino acid substitutions [6].
This makes one question whether the authors took into account the regulatory interactions, that is, protein-DNA interactions that are depicted as edges in the KEGG pathways and maintained the fusion or other mutation data included from KEGG.
Myriad, Prevention Genetics and Medical Neurogenetics are the only three laboratories not agreeing to contribute data on human genetic variants to MutaDATABASE, in contrast to over 100 services that have agreed to contribute mutation data (including GeneDx, Quest/Athena, LabCorp and other large commercial testing services).
Data include mutation status, copy number variations and clinical data, only cases with complete data were included in current analysis (n = 542).
The rationale was that sequence data include the causal mutations that underlie QTL and that the effects of these mutations are estimated directly and not via effects of associated SNPs.
In vivo efficacy and mutation data were included if they were sampled within 2 years from the time of the SP-IPTi study and within a 50km radius.
The Catalogue of Somatic Mutations in Cancer (COSMIC) (Bamford et al., 2004) is an online repository of somatic mutation data, which includes amino acid substitutions (AASs).
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