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. Author manuscript; available in PMC: 2010 Sep 15.
Published in final edited form as: Cancer Res. 2009 Aug 25;69(18):7357–7365. doi: 10.1158/0008-5472.CAN-09-0064

Figure 1. DNA copy number analysis of 161 primary breast tumors identified novel gene amplification events.

Figure 1

We used the Affymetrix SNP arrays to identify potential oncogenes in regions of focal amplification. A) Copy number estimation of ERBB2 by SNP array and qPCR were conducted using 76 tumors that are the subset of the 161 tumors. The regression line is described by y = 0.1635x + 0.7479 with R2 = 0.7965. B) Examples of three loci exhibiting gene amplification listed in Table 1 are shown here, including TBL1XR1, IRX2, and NOTCH3/BRD4. Two tumor samples are shown for each locus. The graphs were generated by the Partek Genomics Suite. Genomic position is displayed on x-axis and log2ratio (tumor hybridization intensity divided by normal reference samples from HapMap project) is on y-axis. The red lines highlight gene amplification regions. Gene annotation encompassing each amplification region is provided at the top of the graphs. C) Gene expression measured by RT-qPCR is shown. Gene expression was measured in 14 tumors. For 7 of the tumors, adjacent normal samples were also analyzed. The expression values of tumors are normalized by the average value of the seven normal samples; hence, gene expression is indicated on the y-axis relative to this average value. The matched normal sample is connected to each corresponding tumor from the same patient by a straight line. The matched normal and tumor samples are represented by filled diamonds, whereas tumors without matched normal are indicated by open squares. The tumors showing amplification and their adjacent normal samples are indicated by red symbols and lines.