Breast Cancer Research and Treatment

, Volume 127, Issue 1, pp 297–308 | Cite as

Genome-wide copy number alterations in subtypes of invasive breast cancers in young white and African American women

  • Lenora W. M. Loo
  • Yinghui Wang
  • Erin M. Flynn
  • Mary Jo Lund
  • Erin J. Aiello Bowles
  • Diana S. M. Buist
  • Jonathan M. Liff
  • Elaine W. Flagg
  • Ralph J. Coates
  • J. William Eley
  • Li Hsu
  • Peggy L. Porter
Brief Report


Genomic copy number alterations (CNA) are common in breast cancer. Identifying characteristic CNAs associated with specific breast cancer subtypes is a critical step in defining potential mechanisms of disease initiation and progression. We used genome-wide array comparative genomic hybridization to identify distinctive CNAs in breast cancer subtypes from 259 young (diagnosed with breast cancer at <55 years) African American (AA) and Caucasian American (CA) women originally enrolled in a larger population-based study. We compared the average frequency of CNAs across the whole genome for each breast tumor subtype and found that estrogen receptor (ER)-negative tumors had a higher average frequency of genome-wide gain (P < 0.0001) and loss (P = 0.02) compared to ER-positive tumors. Triple-negative (TN) tumors had a higher average frequency of genome-wide gain (P < 0.0001) and loss (P = 0.003) than non-TN tumors. No significant difference in CNA frequency was observed between HER2-positive and -negative tumors. We also identified previously unreported recurrent CNAs (frequency >40%) for TN breast tumors at 10q, 11p, 11q, 16q, 20p, and 20q. In addition, we report CNAs that differ in frequency between TN breast tumors of AA and CA women. This is of particular relevance because TN breast cancer is associated with higher mortality and young AA women have higher rates of TN breast tumors compared to CA women. These data support the possibility that higher overall frequency of genomic alteration events as well as specific focal CNAs in TN breast tumors might contribute in part to the poor breast cancer prognosis for young AA women.


Breast cancer Triple negative Genomic alteration Array comparative genomic hybridization Young women 



The authors would like to thank Stephanie Stafford for assistance with data management and analysis, the leadership and staff of the FHCRC DNA Array Facility and Jeri Glogovac for flow sorting of tumor samples. The study was supported by funding from NCI RO1 CA64292, P. I. William Eley; NCI R01 CA098415, P. I. Peggy Porter.

Conflict of interest

All authors report no conflict of interest associated with this study.

Supplementary material

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Supplementary material 1 (DOC 46 kb)
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Supplementary material 2 (XLS 30 kb)
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Supplementary material 3 (XLSX 48 kb)
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Supplementary material 4 (XLS 25 kb)


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Copyright information

© Springer Science+Business Media, LLC. 2011

Authors and Affiliations

  • Lenora W. M. Loo
    • 1
    • 9
  • Yinghui Wang
    • 2
  • Erin M. Flynn
    • 1
  • Mary Jo Lund
    • 4
    • 8
  • Erin J. Aiello Bowles
    • 5
  • Diana S. M. Buist
    • 5
  • Jonathan M. Liff
    • 4
  • Elaine W. Flagg
    • 6
  • Ralph J. Coates
    • 7
  • J. William Eley
    • 8
  • Li Hsu
    • 2
  • Peggy L. Porter
    • 1
    • 2
    • 3
  1. 1.Division of Human BiologyFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Division of Public Health SciencesFred Hutchinson Cancer Research CenterSeattleUSA
  3. 3.Department of PathologyUniversity of WashingtonSeattleUSA
  4. 4.Department of EpidemiologyRollins School of Public Health, Emory UniversityAtlantaUSA
  5. 5.Group Health Research Institute, Group Health CooperativeSeattleUSA
  6. 6.Division of STD PreventionNational Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and PreventionAtlantaUSA
  7. 7.National Office of Public Health Genomics, Centers for Disease Control and PreventionAtlantaUSA
  8. 8.Hematology and Medical OncologyEmory University School of MedicineAtlantaUSA
  9. 9.Epidemiology ProgramCancer Research Center of Hawaii, University of HawaiiHonoluluUSA

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