For the 15 tumors and 3 normal controls, we obtained 400,000 sequences per sample on average (350× mean target coverage). At the exonic regions, four out of the four identified missense alterations were validated. None of the 37 identified indels could be confirmed, probably due to indel errors generated by the Ion PGM platform [
2]. Three of the four missense alterations were not identified in any of the 99 controls, and therefore were classified as possibly associated with WT: two at
APC (Ile2541Val and Met1413Val) and one at
PLCG2 (Asn946Ser). No point mutation was observed for
WT1 and
CTNNB1 genes. In the intronic regions, the somatic substitution pattern was evaluated by classifying the tumor's substitutions in two groups: single nucleotide polymorphisms (SNPs) (alterations also present in normal samples, dbSNP and 1000genomes) and somatic substitutions (remaining alterations). A general trend in the somatic base substitution pattern was observed, with the tumors presenting an over-representation of G:C>A:T changes (
P >0.001) and a reduction of A:T>G:C changes (
P >0.001) when compared to the SNP variants. Regarding the frequency of the other classes of somatic substitutions, a wide variation was observed among the different tumors.