Protocol detail

FFPE Gene Expression Profiling Protocol

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Total RNA was extracted from 25 formalin-fixed, paraffin-embedded (FFPE) tissue blocks using the High Pure RNA Extraction Kit (Roche Applied Science) and subjected to gene expression profiling (GEP) as has been described [20 (link)]. For data analysis and classification, we used the DQN algorithm, which is the noncentral trimmed mean of differences between perfect match and mismatch intensities with quantile normalization [21 (link)]. DQN was normalized with beta distribution and a Bayesian model was used to determine the classification probability.

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Ok C.Y., Ye Q., Li L., Manyam G.C., Deng L., Goswami R.R., Wang X., Montes-Moreno S., Visco C., Tzankov A., Dybkaer K., Zhang L., Abramson J., Sohani A.R., Chiu A., Orazi A., Zu Y., Bhagat G., Richards K.L., Hsi E.D., Choi W.W., van Krieken J.H., Huh J., Ponzoni M., Ferreri A.J., Zhang S., Parsons B.M., Xu M., Møller M.B., Winter J.N., Piris M.A., Xu-Monette Z.Y., Medeiros L.J, & Young K.H. (2015). Age cutoff for Epstein-Barr virus-positive diffuse large B-cell lymphoma–is it necessary?. Oncotarget, 6(16), 13933-13945.

Publication 2015

High Pure RNA Extraction Kit

Embedded paraffin Formalin

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Variable analysis

independent variables

RNA extraction method (High Pure RNA Extraction Kit)
Data analysis and classification algorithm (DQN)

dependent variables

Gene expression profiling (GEP)

control variables

Formalin-fixed, paraffin-embedded (FFPE) tissue blocks
Quantile normalization
Beta distribution normalization
Bayesian model for classification probability

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