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Due to this discordance, Ge et al. (1999) recommended the use of additional genes in future phylogenetic studies.
Use of additional genes in the MRD assay correctly reclassified patients assigned by WT1 testing to a 'low risk' MRD-negative category into a 'high risk' MRD-positive category.
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As a measure of explainability, we used the number of additional genes, which were needed to connect significant members of a set to a regulatory network.
Commercial, academic and non-profit laboratories are using the availability of additional genes in a single panel as a marketing tool - a 'more is better' approach.
qPCR was also used to examine the expression of additional genes known to be important in the adaptive immune response.
The genome sequence was translated into potential protein sequences in six frames and compared with sequences in the UniProt database using the BLASTP program for identification of additional genes not predicted by other methods and genes <150 bp, especially in the predicted intergenic regions.
There are two reasons for this observed accuracy gain: (1) the set of informative genes could be odd numbered but k-TSP can only use even number of genes; (2) selection of additional genes after the top pair by the TSG classifier considers the joint effect of all selected genes on differentiating the cancer classes whereas the k-TSP classifier only consider the marginal effect of pairs.
A subset of additional genes differentially expressed using the NGS approach were also validated by qRT-PCR.
Based on a recommended cut-off V value of 0.15; ubiquitin was selected as a single standard reference gene for these experiments as the use of additional reference genes did not contribute to a more accurate normalization factor.
For that purpose, researchers have applied a further layer of analysis to the results of clustering, making use of additional data containing annotations of genes being analyzed.
More genomic resources coupled with better methods that account for systematic biases [ 15] and the use of additional characters such as presence/absence of genes [ 10] could soon provide us with a robust phylogeny including all major metazoan lineages [ 4, 53].
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