KIT-R49C) shows that neither of them has evidence of presence in the xenograft (Figure 2). In the matching colon xenograft sample, we identified 11 somatic mutations, of which 8 are shared with the primary (Figure 2, Table 1). Examination of the three xenograft-specific mutations revealed that two were well covered in the primary without evidence of the mutant allele, but one (STK11-R304W) was a false negative in the primary (filtered due to relatively low coverage) and validated by an independent assay at 23% prevalence (Table S9 in Additional file 2). Interestingly, this mutation has been identified in patients with Peutz-Jeghers syndrome, an inherited cancer syndrome associated with intestinal polyps and cancer risk [17]. Both STK11-R304W and APC-R283X show significant and similar prevalence differences in the primary (22 to 23%) and xenograft (49%), suggesting that they may be present in the same populations of cells, and were selected for in the xenograft.
