While our understanding of functional rearrangements in breast cancer is emerging, other overarching challenges remain. These challenges include how to ensure the quality and depth of sequencing reads, standardized reporting and validation across studies, tumor sample purity, clonal heterogeneity, and multifocality. Less well-understood transposable elements such as LINE1 and Alu, which have not been addressed in this review, are also being investigated to define their role in genomic instability and cancer.128,129 Newer techniques of genome editing such as CRISPR, which allow precise manipulation of the genome at a desired location, are under study to model genomic alterations more efficiently and also to develop gene therapy.130–132 Nevertheless, as our understanding grows with affordable, but sophisticated, sequencing strategies and metagenomic approaches, rearrangement-based biomarkers will be pivotal for the practice of precision medicine in breast cancer.

Bhavna S. Paratala,1,2 Sonia C. Dolfi,1 Hossein Khiabanian,3 Lorna Rodriguez-Rodriguez,4 Shridar Ganesan,1 and Kim M. Hirshfield1

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1Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.

2Department of Cellular and Molecular Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA.

3Department of Pathology, Division of Medical Informatics, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.

4Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.

Correspondence: E-mail: [email protected] 


We would like to acknowledge Ms. Jacqueline Harris for her support and assistance.


ACADEMIC EDITOR: Barbara Guinn, Editor in Chief

PEER REVIEW: Seven peer reviewers contributed to the peer review report. Reviewers’ reports totaled 1324 words, excluding any confidential comments to the academic editor.

FUNDING: This research was supported by a generous gift to the Genetics Diagnostics to Cancer Treatment Program of the Rutgers Cancer Institute of New Jersey and RUCDR Infinite Biologics, The Val Skinner Foundation, NIH/NCI P30CA072720, AHEPA Foundation, and The Ruth Estrin Goldberg Memorial for Cancer Research. The authors confirm that the funder had no influence over the study design, content of the article, or selection of this journal.

COMPETING INTERESTS: Authors disclose no potential conflicts of interest.

Paper subject to independent expert blind peer review. All editorial decisions made by independent academic editor. Upon submission manuscript was subject to anti-plagiarism scanning. Prior to publication all authors have given signed confirmation of agreement to article publication and compliance with all applicable ethical and legal requirements, including the accuracy of author and contributor information, disclosure of competing interests and funding sources, compliance with ethical requirements relating to human and animal study participants, and compliance with any copyright requirements of third parties. This journal is a member of the Committee on Publication Ethics (COPE).

Author Contributions

Wrote the first draft of the manuscript: BSP and KMH. Contributed to the writing of the manuscript: BSP, SCD, HK, SG, and KMH. Jointly developed the structure and arguments for the paper: BSP and KMH. Made critical revisions and approved final version: BSP, SCD, HK, LRR, SG, and KMH. All authors reviewed and approved of the final manuscript.


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