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Background  HER2 positive (HER2+) breast cancers involve chromosomal structural alterations that act as oncogenic driver events.    Methods  We interrogated the genomic structure of 18 clinically-defined HER2+ breast tumors through integrated analysis of whole genome and transcriptome sequencing, coupled with clinical information.    Results   ERBB2  overexpression in 15 of these tumors was associated with  ERBB2  amplification due to chromoanasynthesis with six of them containing single events and the other nine exhibiting multiple events. Two of the more complex cases had adverse clinical outcomes. Chromosomes 8 was commonly involved in the same chromoanasynthesis with 17. In ten cases where chromosome 8 was involved we observed  NRG1  fusions (two cases),  NRG1  amplification (one case),  FGFR1  amplification and  ADAM32  or  ADAM5  fusions.  ERBB3  over-expression was associated with  NRG1  fusions and  EGFR  and  ERBB3  expressions were anti-correlated. Of the remaining three cases, one had a small duplication fully encompassing  ERBB2  and was accompanied with a pathogenic mutation.    Conclusion  Chromoanasynthesis involving chromosome 17 can lead to  ERBB2  amplifications in HER2+ breast cancer. However, additional large genomic alterations contribute to a high level of genomic complexity, generating the hypothesis that worse outcome could be associated with multiple chromoanasynthetic events.    Electronic supplementary material  The online version of this article (10.1186/s12885-018-4594-0) contains supplementary material, which is available to authorized users.

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples