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Figure 6 | Genome Biology

Figure 6

From: GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

Figure 6

GeneCount analyses in cervical cancers. (a) Frequency histogram (number of tumors) of smoothed aCGH ratios (GLAD) for MRPS23 (BAC clone ID RP11-19F16). Dotted lines indicate the cut off ratio levels of ± 0.2, identifying 5 tumors with genetic gain and 3 tumors with loss. (b) Frequency histogram (number of tumors) of MRPS23 copy number calculated by GeneCount. The GLAD ratio levels, the DI measured by flow cytometry, and the tumor cell fraction estimated by GeneCount were used in the calculation. Similar results were achieved based on the CGH-Explorer ratio levels. (c) Plot of gene expressions against gene dosage; that is, the MRPS23 copy number divided by the total DNA content (N/(2·DI)). Increased gene dosage with more than 15% of the total DNA content (log2 transformed gene dosage of at least 0.2) were seen in 15 tumors (red and blue symbols). Red symbols represent the five tumors with gain in (a), whereas blue symbols represent the remaining ten tumors with increased gene dosage that were not identified in (a). The correlation coefficient and P-value from Pearson product moment correlation analysis are indicated. (d) Kaplan Meier analysis based on GeneCount results for MRPS23. Plots of the survival probability are shown for 5 patients with high gene dosage in (c), who also had gain in (a) (red line), 10 patients with high gene dosage in (c) and without gain in (a) (blue line), and 78 patients with low gene dosage in (c). (e) Kaplan Meier analysis based on the MRPS23 ratio levels. The survival probability of 5 patients with gain in (a) (red line) and 88 patients without gain in (a) (black line) is plotted. Only five high risk patients were identified in (e), whereas ten more patients were identified by GeneCount in (d). P-value in log-rank test is indicated in (d,e). Panels (a,b,d) are based on 93 tumors, for which the tumor cell fraction could be estimated by GeneCount. Panel (c) is based on 89 of these tumors, for which both DNA copy number and gene expression were available.

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