NOTE: The LIHC RPPA data submitted by MDACC early in 2016 were discovered to be mislabelled MESO samples. Thus the 2016_01_28 analyses and standard data pipelines for LIHC have been re-run using the corrected samples submitted in March, and the nozzle reports now contain notices of the discrepancies.
The following table shows the changes in sample counts for RPPA data as a result of this patch:
for the following 6 disease studies (which presently have MAFs with GAF 3.0 annotations deposited at the TCGA DCC): KICH, KIRP, LGG, PAAD, SKCM, THCA
Rather than completely remove the affected analyses, we felt it would be valuable diagnostically to have these mutation results available for inspection. Towards that end, here is a comparison of the top 10 significant genes found by MutSig for disease studies that used a GAF 2.1 MAF in the last analyses run (2013_05_23), versus a GAF 3.0 MAF in this run:
The latter two employ the full/scatter-gather version of Paradigm; the previous Pathway_Paradigm version has been renamed to Pathway_Paradigm_Lite, and will continue to be run in our Analyses workflow until all are satisfied it can be deprecated.