Jung et al. BMC Cancer 2012, 12:382 http://www.biomedcentral.com/1471-2407/12/382 There are several limitations in this study. First, due to the limited sample size of subtypes, we could not see the prognostic implications of the RARs in the four molecular subtypes properly. Second, we did not examine the molecular mechanisms of the synergistic effect of the ERBB2-NUPR1 co-occurrence. Further studies will be required to delineate the roles of NUPR1 gain and the simultaneous ERBB2-NUPR1 gains in early breast tumorigenesis. Third, we used single reference DNA in this study, so it is possible that some of the CNAs identified in this study are CNVs, especially small- sized CNAs overlapping previously reported CNVs. Conclusion In this study, we found six highly common RARs in EBCs and determined the potential of simultaneous alterations of ERBB2 (17q12) and NUPR1 (16p11.2) as significant predictors of poor prognosis in EBC. Our study will help to elucidate the molecular mechanisms underlying early-stage tumorigenesis in breast cancer. In addition, our study shows the potential for combinations of copy number alterations to be used as prognosis pre- dictors for early-stage breast cancer. Additional file Additional file 1: Figure S1. Genome-wide frequency plots of chromosomal alterations for each breast cancer subtype. Table S1. Primer sequences for target and diploid control regions. Table S2. Copy number alterations significantly more frequent in stage II than in stage I. Table S3. High copy number changes in the discovery set of early breast cancers. Table S4. Correlation between RARs and clinicopathologic features. Table S5. RARs in 48 breast cancers by molecular subtype. Table S6. RAR combination rules associated with death events. Table S7. Frequency of chromosomal arm changes in 48 breast cancers. Abbreviations EBC: Early-stage breast cancer; CNA: Copy number alteration; RAR: Recurrently altered region; array-CGH: Oligoarray-comparative genomic hybridization. Competing interests The authors declare that they have no competing interests. Authors’ contribution SHJ executed most experiments and drafted the manuscript. AWL collected the patient specimens and was involved in data analysis. SHY participated in the design of this study, performed statistical analysis and wrote the manuscript. HJH performed an association rule mining and drafted the manuscript. CC was involved in data analysis and preparing the figures. YJC proposed this study, organized the research team, interpreted all the data, and participated in writing the manuscript. All authors read and approved the final manuscript. Acknowledgements This study was supported by a grant from the Korea Healthcare technology R&D Project (A092258), Korea Health 21 R&D Project (A040002) and MRC for Cancer Evolution Research Center (2012047939), Republic of Korea. The authors wish to thank Dr HH Song for statistical comments. Page 10 of 11 Author details 1Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Socho-gu, Seoul 137-701, Republic of Korea. 2Department of Microbiology, The Catholic University of Korea, Seoul, South Korea. 3Department of Hospital Pathology, Humanities and Social Sciences, The Catholic University of Korea, Seoul, South Korea. 4Department of Medical Humanities and Social Sciences, The Catholic University of Korea, School of Medicine, 505 Banpo-dong, Seocho-gu, Seoul 137-701, South Korea. Received: 13 November 2011 Accepted: 9 August 2012 Published: 31 August 2012 References 1. 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