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HER2 presented the highest level of amplification.
Using the GISTIC algorithm, the 17q12-q21-amplicon exhibited the highest score index because it was the most frequently amplified with the highest level of amplification.
HER2 presented the highest level of amplification (mean, 6.4; range, 2 to 32), whereas the frequency of amplification of the other genes decreased according to the distance of the gene from HER2.
If, as the array CGH data suggests, the highest level of amplification in BT-20 lies outside the region amplified in MDA-MB-134, there may be multiple targets of amplification in this region.
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The highest levels of amplification were found for the outer mixture enrichment followed in decreasing order by uniform and inner mixture gradient cases.
One of the primer pairs and the corresponding probe displayed a high level of amplification efficiency on which a real-time RT-PCR method was established.
There was no significant difference in DFS between tumours with low-level amplification (five or six copies per nucleus) and tumours with a higher level of amplification.
There was no significant difference in OS between tumours with low-level amplification (five or six copies per nucleus) and tumours with a higher level of amplification.
Additionally, we compared tumours with low-level amplification (five or six signals per nucleus) against tumours with a higher level of amplification (more than six signals per nucleus).
However, in our study tumours with five or six copies of HER-2/ neu had a survival comparable to that of tumours with a higher level of amplification.
The L4417 template positive control was excluded from Fig. 2b because as expected it showed an extremely high level of amplification and PCR product.
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