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The number was similar across epithelial markers, but twice as many benign as malignant samples were missing.
Thus, the tissue origins of all 5,577 individual malignant samples were analyzed by reconstructing cancer-specific gene density estimates without the sample in question.
The 38 malignant samples were comprised of IDC (n = 22), DCIS (n = 12), LCIS (n = 3), and ILC (n = 1) (Table 1).
To focus discovery on differentially expressed candidate markers, peptide levels measured in surgically resected malignant samples were compared with adjacent normal tissue.
The contents of both total collagen and the cross-linked type I and type III collagens in the malignant samples were only about 20% of those in the benign tumours.
Consequently these two potential biomarkers with a higher expression among the malignant samples were selected for further validation with an independent method in both ovarian cyst fluid and serum.
Similar(48)
For each candidate biomarker, the statistical difference between the pre-malignant and malignant samples was compared using the two-sample t-test with the Welch-Satterwaite method for samples of different variances.
The entire training set (including Benign, Normal and Malignant samples) was used to generate factors.
The median expression level of older miRNAs in malignant samples is significantly higher than in normal samples, and there is no distinct difference in the median expression level of young miRNAs between malignant and normal samples (Table 3).
Non-malignant samples were collected from areas >2 cm away from the tumor.
Tumor samples which segregated with non-malignant samples were also removed from further analysis.
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