Jung et al. BMC Cancer 2012, 12:382 http://www.biomedcentral.com/1471-2407/12/382 Page 8 of 11 Figure 4 Kaplan–Meier curves by RAR status in the discovery set. (A) RAR-G12 (16p11.2) positives vs. negatives, (B) RAR-G13 (17q12) positives vs. negatives, and (C) RAR-G12/G13 double-positives vs. others. The curves show overall survival. explore this possibility, we defined RARs in a discovery set of EBC and examined their associations with progno- sis. A total of 23 RARs were defined, and all of them were found to overlap at least one of the recently reported CNAs in breast cancer including EBC, suggest- ing the reliability of our data [14-17]. The nature of RARs (gain or loss) was also largely consistent with the previous observations. For example, RAR-L3 (8p21.2) and RAR-L5 (17p12), where PPP2R2A and MAP2K4 are located, respectively, and RAR-G13 (17q12), where ERBB2 is located, were consistently detected in a recent large-scale breast cancer genetic subgroup study [14]. In particular, 21 of the 23 RARs overlap recurrent copy number alterations identified in EBCs (stage I and II) from whites, blacks, and Hispanics by Thompson et al.’s recent study [15]. However, the recurrent gain on 14q11.2 in Thompson et al.’s report was not detected in our array-CGH analysis. This difference, which requires further investigation, may be due to a Korean EBC- specific feature or to the probe design of the array- platform used in this study. We validated the association of RARs with prognosis in the larger independent repli- cation set of 97 EBCs. In addition to RARs, some entire chromosomal arm changes were also commonly observed (> 30% of the samples) in this study (Additional file 1: Table S7), and are largely consistent with previous ob- servations in breast cancer of diverse ethnic groups [11,25]. Of the RARs identified in this study, 15 were com- monly detected in both stages I and II, which suggests Figure 5 Kaplan–Meier curves by RAR status in the replication set. (A) Genomic qPCR system targets; NUPR1 gene located in RAR-G12; ERBB2 gene located in RAR-G13. (B) NUPR1 (RAR-G12) positives vs. negatives. (C) ERBB2 (RAR-G13) positives vs. negatives. (D) NUPR1-ERBB2 double-positives vs. others. (E) Survival curves by subgroup; RAR-G12/13 double-positives, positive for either RAR-G12 or G-13, and double-negatives. The curves show overall survival.