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The comparison of the first and second rows in Table 1 ("Currently unemployed" and "Valid matches") illustrates the combined impact of attrition, nonresponse, and the matching validation screen based on demographic characteristics.
Here, the 74% reproducibility rate is comparable to the average reproducibility rate observed for the validation screen when the same collection of dsRNA was used to self-validate, which clearly demonstrates a limitation of experimental validation [ 26].
For example, one sample in the Validation Screen, 4198, exhibited nine coding region mutations and another, 6985, six mutations.
Luciferase intensity was normalized by comparison with plate median in the primary screen and by comparison with a control siRNA in the validation screen (Figure-2).
We observed coding region mutation frequencies of 47.8% and 20.4% respectively for BRAF and TP53 in the samples in the Validation Screen (Table S2).
Based on our finding of MAGE mutations in the melanoma cell line samples, a Validation Screen was undertaken in which we sequenced the same MAGE genes in 111 fresh tumor samples collected from 86 melanoma patients who had undergone surgical intervention at the Melanoma Clinic at Austin Health, Melbourne, Australia (Table 2).
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All DMRs positively validated in the microarray validation experiments were subjected to initial clinical validation screening.
Table S1 provides comprehensive data from both the primary and validation screens, and Table S2 provides a list of the 128 validated genes with descriptions.
A secondary functional validation screening revealed that the potential oncogenes participate in different cellular processes affecting proliferation, cell viability, apoptosis or differentiation.
In addition, PMM can potentially be used to gain power for secondary validation screens.
Primers used for the validation screens of ELF3, GNAS, KLF5 and ERBB3.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com