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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals
Shelly Gunn1, I-Tien Yeh, Irina Lytvak
1Combimatrix Molecular Diagnostics, 310 Goddard, Irvine, California 92618, USA. gunn@uthscsa.edu
Background:
HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin), remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods.
Methods:
In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE) tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms.
Results:
Array-based comparative genomic hybridization (array CGH) analysis of chromosome 17 resolved HER2 gene status in [20/20] (100%) of cases and revealed additional chromosome 17 copy number changes in [18/20] (90%) of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to "ratio skewing" caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability.
Conclusions:
These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17 abnormalities in these cases suggests that the two probe FISH interphase analysis is inadequate and results interpreted using the HER2/CEP17 ratio should be reported "with caution" when the presence of centromeric amplification or monosomy is suspected by FISH signal gains or losses. The presence of these pericentromeric copy number changes may result in artificial skewing of the HER2/CEP17 ratio towards false negative or false positive results in breast cancer with chromosome 17 complexity. Full genomic analysis should be considered in all cases with complex chromosome 17 aneusomy as these cases are likely to have genome-wide instability, amplifications, and a poor prognosis.
Insights
Array-based genomic analysis resolves equivocal HER2 gene status in breast cancer, identifying chromosome 17 abnormalities missed by traditional methods. This advanced technique improves diagnostic accuracy for targeted therapy decisions.
Area of Science:
- Genomic medicine
- Oncology
- Molecular diagnostics
Background:
- HER2 gene status is crucial for targeted breast cancer therapy with trastuzumab.
- Equivocal HER2 results from IHC and FISH pose treatment challenges.
- Array-based genomic analysis offers an alternative for unresolved HER2 status.
Purpose of the Study:
- To evaluate array-based comparative genomic hybridization (array CGH) for resolving equivocal HER2 gene status.
- To assess the utility of array CGH in identifying chromosome 17 copy number changes.
- To compare array CGH findings with traditional FISH analysis in breast cancer cases.
Main Methods:
- DNA from 20 formalin-fixed paraffin-embedded (FFPE) invasive breast cancer tissues with unresolved HER2 status was analyzed.
- A clinically validated genomic array with 127 probes targeting the HER2 amplicon and chromosome 17 was used.
- Array CGH was performed to determine HER2 gene copy number and identify chromosomal abnormalities.
Main Results:
- Array CGH successfully resolved HER2 gene status in 100% of cases.
- Additional chromosome 17 copy number changes were detected in 90% of cases.
- FISH analysis yielded false positives and negatives due to ratio skewing from centromeric region abnormalities.
Conclusions:
- Array-based genomic analysis is a powerful tool for resolving equivocal HER2 status in breast cancer.
- Complex chromosome 17 abnormalities necessitate caution when interpreting FISH HER2/CEP17 ratios.
- Full genomic analysis is recommended for cases with complex chromosome 17 aneusomy, indicating potential instability and poor prognosis.
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