Figure 4

Loss of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) DNA copy-number (CN) in human basal-like breast cancers. (a) Basal-like carcinomas (BLCs) and human epidermal growth factor receptor overexpressing (HER2+) carcinomas behaved differently for PTEN CN in a significant manner. Recurrent DNA CN alterations were observed around the PTEN gene (between 72,260,000 and 93,93,000 bp of chromosome 10) in BLCs compared with HER2+ carcinomas. Frequencies of genome CN gain (red) and loss (green) were calculated using the FrAGL (Frequency of Amplicon, Gain and Loss) option of VAMP software (Visualisation and Analysis of array-CGH, transcriptome and other Molecular Profiles) [63]. The vertical blue bar represents PTEN position from 89,613,175 to 89,718,511 bp. Percentages of tumours with loss, normal or gain of PTEN CN are presented within the two populations in the table. p value is shown (** p < 0.01, fisher exact test). (b) Correlation between PTEN protein level and PTEN DNA CN. PTEN protein level was quantified as in Figure 3a. Linear regression, Spearman correlation c and p value (* p < 0.05) are presented. BLCs (solid circles) and HER2+ carcinomas (open circles) are shown. The two vertical black lines (X = 2 ± 0.28) separate loss/normal/gain PTEN CN (forceGL parameter: 0.28).