Research Papers: Pathology:

Genome-wide copy number aberrations and HER2 and FGFR1 alterations in primary breast cancer by molecular inversion probe microarray

Hui Chen, Rajesh R. Singh, Xinyan Lu, Lei Huo, Hui Yao, Kenneth Aldape, Ronald Abraham, Shumaila Virani, Meenakshi Mehrotra, Bal Mukund Mishra, Alex Bousamra, Constance Albarracin, Yun Wu, Sinchita Roy-Chowdhuri, Rashmi Kanagal Shamanna, Mark J. Routbort, L. Jeffrey Medeiros, Keyur P. Patel, Russell Broaddus, Aysegul Sahin and Rajyalakshmi Luthra _

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Oncotarget. 2017; 8:10845-10857. https://doi.org/10.18632/oncotarget.14802

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Hui Chen1, Rajesh R. Singh2, Xinyan Lu2, Lei Huo1, Hui Yao3, Kenneth Aldape1,5, Ronald Abraham2, Shumaila Virani2, Meenakshi Mehrotra2, Bal Mukund Mishra2, Alex Bousamra1,4, Constance Albarracin1, Yun Wu1, Sinchita Roy-Chowdhuri1, Rashmi Kanagal Shamanna2, Mark J. Routbort2, L. Jeffrey Medeiros2, Keyur P. Patel2, Russell Broaddus1, Aysegul Sahin1 and Rajyalakshmi Luthra2

1 Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

2 Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

3 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

4 Allegheny Health Network, Pittsburgh, PA, USA

5 Department of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Canada

Correspondence to:

Rajyalakshmi Luthra, email:

Hui Chen, email:

Keywords: breast cancer, SNP microarray, molecular inversion probe microarray, chromothripsis, HER2, Pathology Section

Received: September 16, 2016 Accepted: January 10, 2017 Published: January 24, 2017


Breast cancer remains the second leading cause of cancer-related death in women despite stratification based on standard hormonal receptor (HR) and HER2 testing. Additional prognostic markers are needed to improve breast cancer treatment. Chromothripsis, a catastrophic genome rearrangement, has been described recently in various cancer genomes and affects cancer progression and prognosis. However, little is known about chromothripsis in breast cancer. To identify novel prognostic biomarkers in breast cancer, we used molecular inversion probe (MIP) microarray to explore genome-wide copy number aberrations (CNA) and breast cancer-related gene alterations in DNA extracted from formalin-fixed paraffin-embedded tissue. We examined 42 primary breast cancers with known HR and HER2 status assessed via immunohistochemistry and FISH and analyzed MIP microarray results for correlation with standard tests and survival outcomes. Global genome-wide CNA ranged from 0.2% to 65.7%. Chromothripsis-like patterns were observed in 23/38 (61%) cases and were more prevalent in cases with ≥10% CNA (20/26, 77%) than in cases with <10% CNA (3/12, 25%; p<0.01). Most frequently involved chromosomal segment was 17q12-q21, the HER2 locus. Chromothripsis-like patterns involving 17q12 were observed in 8/19 (42%) of HER2-amplified tumors but not in any of the tumors without HER2 amplification (0/19; p<0.01). HER2 amplification detected by MIP microarray was 95% concordant with conventional testing (39/41). Interestingly, 21% of patients (9/42) had fibroblast growth factor receptor 1 (FGFR1)amplification and had a 460% higher risk for mortality than those without FGFR1 amplification (p<0.01). In summary, MIP microarray provided a robust assessment of genomic CNA of breast cancer.

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