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Open Access Research article

A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications

Michael Marotta1, Xiongfong Chen4, Ayako Inoshita1, Robert Stephens4, G Thomas Budd2, Joseph P Crowe3, Joanne Lyons3, Anna Kondratova1, Raymond Tubbs5 and Hisashi Tanaka16*

Author Affiliations

1 Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA

2 Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA

3 Department of General Surgery, Cleveland Clinic, Cleveland, OH 44195, USA

4 Advanced Biomedical Computing Center, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA

5 Department of Molecular Pathology, Cleveland Clinic, Cleveland, OH 44195, USA

6 Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA

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Breast Cancer Research 2012, 14:R150  doi:10.1186/bcr3362

Published: 26 November 2012

Abstract

Introduction

Segmental duplications (low-copy repeats) are the recently duplicated genomic segments in the human genome that display nearly identical (> 90%) sequences and account for about 5% of euchromatic regions. In germline, duplicated segments mediate nonallelic homologous recombination and thus cause both non-disease-causing copy-number variants and genomic disorders. To what extent duplicated segments play a role in somatic DNA rearrangements in cancer remains elusive. Duplicated segments often cluster and form genomic blocks enriched with both direct and inverted repeats (complex genomic regions). Such complex regions could be fragile and play a mechanistic role in the amplification of the ERBB2 gene in breast tumors, because repeated sequences are known to initiate gene amplification in model systems.

Methods

We conducted polymerase chain reaction (PCR)-based assays for primary breast tumors and analyzed publically available array-comparative genomic hybridization data to map a common copy-number breakpoint in ERBB2-amplified primary breast tumors. We further used molecular, bioinformatics, and population-genetics approaches to define duplication contents, structural variants, and haplotypes within the common breakpoint.

Results

We found a large (> 300-kb) block of duplicated segments that was colocalized with a common-copy number breakpoint for ERBB2 amplification. The breakpoint that potentially initiated ERBB2 amplification localized in a region 1.5 megabases (Mb) on the telomeric side of ERBB2. The region is very complex, with extensive duplications of KRTAP genes, structural variants, and, as a result, a paucity of single-nucleotide polymorphism (SNP) markers. Duplicated segments are varied in size and degree of sequence homology, indicating that duplications have occurred recurrently during genome evolution.

Conclusions

Amplification of the ERBB2 gene in breast tumors is potentially initiated by a complex region that has unusual genomic features and thus requires rigorous, labor-intensive investigation. The haplotypes we provide could be useful to identify the potential association between the complex region and ERBB2 amplification.