Fumagalli et al. BMC Cancer 2010, 10:101 http://www.biomedcentral.com/1471-2407/10/101 Table 1: Mutations detected with OncoCarta (Continued) EGFR-P772_H773insV EGFR-H773>NPY EGFR-H773_V774insNPH/H773_V774insPH/H773_V774insH EGFR-V774_C775insHV EGFR-T790 M EGFR-L858R EGFR-L861Q EGFR-L747_T750del, P ins/E746_A750del, T751A EGFR-E746_T751del, I ins/S752_I759del KIT-K550_K558del KIT-K558_V560del KIT-K558_E562del KIT-V559del KIT-V559_V560del KIT-V560del KIT-Y570_L576del KIT-E561K KIT-L576P Page 6 of 14 PIK3CA-G1049R PIK3CA-R38H PIK3CA-C901F PIK3CA-M1043I/M1043I RET-C634R RET-C634W/Y RET-E632_L633del RET-M918T RET-A664D dilutes the number of tumor cells. This is of particular concern when profiling lymph nodes, which may con- tain a minority of tumor cells. Frequencies of C-07 mutations in KRAS, NRAS, PIK3CA, and BRAF detected with OncoCarta and the Sequenom platform were similar to previous reports In this preliminary assessment of the feasibility of using the Sequenom platform to do large-scale mutation profil- ing of colon cancer samples isolated from FFPET, it was essential to determine if our data yielded frequencies typical of what has been seen previously. Table 2 shows the mutation frequencies obtained here and from the COSMIC (Catalog of Somatic Mutations in Cancer) database [21]. The COSMIC frequencies seen in Table 2 are based only on those mutations that are detectable with OncoCarta. OncoCarta assays interrogate 99%, 98%, and 78% of the known colon cancer mutations in BRAF, KRAS, and PIK3CA, respectively, based on a large num- ber of colon cancer samples that have been sequenced in BRAF (n = 4628), KRAS (n = 858) and PIK3CA (n = 247). The OncoCarta panel found that the most frequent mutations in C-07 were KRAS (43.5%), PIK3CA (20.1%), and BRAF (12.1%), which are similar to what is seen in COSMIC. NRAS mutations, while infrequent, were detected in codons 12, 13 and 61 and represent a sizable minority of the C0-7 samples (3.8%). These data suggest Figure 2 Spectra for cell lines UACC-893 and A2058. The expected positions for the unexteneded primer (UEP), and the extension products (Mutant and WT) from assays PIK3CA_9 and BRAF_15 in cell lines UACC-893 and A2058, respectively, are indicated with red dashed lines. The proportion of peak areas and the specific base is also shown. Assays PIK3CA_9 and BRAF_15 detected mutations in PIK3CA at amino acid position 1047 and in BRAF at amino acid position 600, respectively. Other peaks included in these spectra as result of multiplexing but not part of the designated assays are indicated as grey dashed lines.