Figure 2

GEP gene copy number by FISH analysis with reference to centromere 17 (CEN17) and centromere 3 (CEN3). GEP gene (green) was detected by two flanking probes, RP11-436 J4 (left) and RP11-52 N13 (right), respectively. Control probes (red) included the centromere 17 (CEN17) and centromere 3 (CEN3). DNA copy number for each set was quantified for 100 cells and the scores (signals per cell) presented in Table 1. This case HCC801 showed CEN17 scores ranged 3.37 to 3.51, and GEP scores 3.66 to 3.80. The data indicated an increased chromosome 17 copy number at centromere and GEP locus at 17q21. Nonetheless, CEN3 scores ranged 1.97 to 2.17, indicating approximately two copies of chromosome 3 (diploid) with reference to GEP scores 3.73 by different probes flanking the gene region. GEP copy number for this case HCC801 was 3.60 by FISH analysis (reference to CEN3) compared to 2.56 by QuMA (reference to D3S1609). QuMA is a PCR-based assay method and the extend of underestimation would depend on the percentage of non-tumor cells, e.g. infiltrating lymphocytes etc., within the tumor mass. Details have also been described in Discussion.