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Quality of the hybridization, as defined by Affymetrix in the Genotyping Console as a contrast QC <0.4, was assessed and 1 Ctrl sample failed prior to copy number analysis.
For instance, a mere 8% of Scanlon and Neumann's [2002, p. 380] sample admitted to copying a text from the Internet without citation, but perceived that over 50% of their peers did so (Walker 2010, p. 2).
To determine if treatment with letrozole is associated with changes in the copy number profiles of ER-positive breast carcinomas, DNA from 19 matched pairs of pre- and post-treatment breast carcinoma samples were subjected to copy number profiling as described above.
In contrast, there was a high proportion of samples exhibiting LOH in conjunction with copy number loss at the MAP2K4 locus [ 18]. 56% of samples with LOH (38% of samples overall) were subject to copy number loss, indicating that MAP2K4 may be targeted by this genetic mechanism.
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Copy numbers obtained for 18s were used to generate a correction factor for normalization of target genes using the equation: (maximum 18s copy number)/(18s copy number for each individual sample), and the correction factor was then multiplied by the copy number for each target gene for each sample to give copy number of target gene normalized to 18s per 100 ng of cDNA.
PCR sensitivity (limit of detection) was determined by using DNA from pMHUL28 and 2 confirmed-positive samples by diluting the DNA to copy numbers of 2.71 × 10 for pMHUL28 and 1.59 × 10 for the samples.
The strength of this study in having a large number of samples provides numerous additional insights to copy number features of ovarian cancer.
Copies of target DNA were quantified by converting the mean Ct value generated for each sample to DNA copies using the standard curve generated by MX3000P software from the quantified DNA standards included in each run.
