Platform evaluation and analysis method selection using quality control samples.
Reference standards to facilitate platform evaluation and comparability are needed.
Members of the Knowledge-Translation (KT) Platform Evaluation Team include (in addition to named authors): Pierre Ongolo-Zogo (Cameroon), Tomas Pantoja (Chile), and Nordin Saleh (Malaysia).
In order not to assess the platforms at the brink of their sensitivity it was decided that for the platform evaluation the input per cDNA synthesis should be 1/6 of the RNA from 250 μl plasma.
The similarity of results in the cross platform evaluation and within tissue repeatability was instrumental in the selection of the NanoString nCounter Dx Analysis System as the platform for development and training of the in vitro diagnostic version of the PAM50 classifier.
To date, a number of cross-platform evaluations (including a few studies using SAGE and Affymetrix GeneChips) have been conducted showing a variable, but overall low, concordance.
To date, only a few cross-platform evaluations have been published and unfortunately, no guidelines have been established on the best methods of making such correlations.
Note that, as was reported in previous studies, it is reasonable to assume that the mappable SGM set SGM will suffer from decreased performance rates in cross-platform evaluations (Chuang et al., 2007; Ein-Dor et al., 2006) whereas such effects have not been reported for subnetwork marker approaches.
Some of the on-platform evaluation tools delivered by some manufacturers do already fulfill this requirement.
In 2003, discrepancies in the literature led us to carry out our own cross-platform evaluation [ Yauk et al., 2004].
Among those six external gene sets, except the PGDB gene set, none were found to be significant in the cross-platform evaluation.
