TY - JOUR
T1 - Genome-wide copy number aberrations and HER2 and FGFR1 alterations in primary breast cancer by molecular inversion probe microarray
AU - Chen, Hui
AU - Singh, Rajesh R.
AU - Lu, Xinyan
AU - Huo, Lei
AU - Yao, Hui
AU - Aldape, Kenneth
AU - Abraham, Ronald
AU - Virani, Shumaila
AU - Mehrotra, Meenakshi
AU - Mishra, Bal Mukund
AU - Bousamra, Alex
AU - Albarracin, Constance
AU - Wu, Yun
AU - Roy-Chowdhuri, Sinchita
AU - Shamanna, Rashmi Kanagal
AU - Routbort, Mark J.
AU - Medeiros, L. Jeffrey
AU - Patel, Keyur P.
AU - Broaddus, Russell
AU - Sahin, Aysegul
AU - Luthra, Rajyalakshmi
N1 - Funding Information:
RRB is supported in part by the National Institutes of Health Specialized Program of Research Excellence in Uterine Cancer (NIH 2P50 CA098258-08).
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
KW - Breast cancer
KW - Chromothripsis
KW - HER2
KW - Molecular inversion probe microarray
KW - Pathology Section
KW - SNP microarray
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U2 - 10.18632/oncotarget.14802
DO - 10.18632/oncotarget.14802
M3 - Article
C2 - 28125801
AN - SCOPUS:85012921714
SN - 1949-2553
VL - 8
SP - 10845
EP - 10857
JO - Oncotarget
JF - Oncotarget
IS - 7
ER -