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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.
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.
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).
Of the amplified cases, five tumours showed five or six signals per nucleus, indicating low-level amplification, and 12 tumours showed more than six signals per nucleus (evidence of a higher level of amplification).
It is possible that some of the copy-number increases in these populations are due to a higher level of amplification (more than two copies per chromosome) than a single duplication.
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Higher levels of amplification are reasonably common in tumour samples, e.g. around oncogenes such as ERBB2 and MYC.
Using SiDCoN one can demonstrate that the allelic mixtures for higher levels of amplification (>6n) are difficult to distinguish, especially in the presence of stroma (data now shown).
We show that with higher levels of amplification, most events result in non-identifiable models, meaning that most regions with high levels of amplifications cannot be timed in this way.
We proceeded through optimisation as in Figure 2. Analysis using our assay indicated slightly higher levels of amplification (black bars) than previously reported (open bars) [ 18].
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.
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