Identification of 33 candidate oncogenes by screening for base-specific mutations.

The functional effect of somatic mutations can sometimes be predicted from mutation patterns. Inactivating mutations often truncate the protein product, and frequent occurrence of such changes in a gene is a sign of a possible tumour suppressor function, as exemplified by the APC gene in colorectal cancer (CRC; Fearon, 2011). The most pathognomonic feature of mutations activating a gene product is recurrent occurrence in one or few codons. Such a signal is a strong indicator of selective value. Importantly, these types of changes also provide possibilities for therapeutic approaches through tackling the abnormal activity of the specific mutant protein product. Examples of successful utilisation of such a strategy include, but are not limited to, inhibitors of BRAF Val600Glu and activated EGFR (Lynch et al, 2004; Bollag et al, 2010). This success is in many cases marred by the fact that targeted monotherapies often fail to cure a patient because of pre-existing resistant subclones. Whereas the most common mutation hotspots may at present be largely known, any additional hotspots would provide a valuable platform for cancer biology in pinpointing relevant genes and domains to study, as well as for development of potentially curative combination therapies for stratified cancer care. Colorectal cancer with microsatellite instability (MSI) defines a subgroup of CRCs with distinct clinical characteristics. These hypermutable CRCs may represent a sensitive system for generation, selection and detection of mutation hotspots. Indeed, in MSI CRC multiple well-established oncogenes, in particular BRAF, KRAS, PIK3CA and CTNNB1, are known to display very specific mutation hotspots (Fearon, 2011). We have previously mined exome-sequencing data of 25 MSI CRCs for hotspot point mutations (Gylfe et al, 2013). That study did not consider identical base-specific mutations in the discovery set. The rationale for exclusion of this important mutation type was that such mutation signals, according to our early experience with exome data, typically arose from uncalled polymorphic germline variants. Expansion of control data as well as developments in analysis pipeline currently enable much more robust calling of somatic mutations. Thus, we have here taken the study forward to search for novel recurrent somatic cancer mutations hitting exactly the same base position.