Dear TCGA Colleagues,

The Dec 2012 Firehose analysis run has been uploaded and will be available in
the protected data tree pending internal mirroring by the DCC.  This analysis
run was based upon version 2012_12_21 of the Firehose stddata package, and is
described in more detail on our site at

			http://gdac.broadinstitute.org

The highlights of this run are given below and in the dashboard release notes.
If you have any questions or comments please do not hesitate to send them to
our gdac@broadinstitute.org mailing list.


Regards,
Michael S. Noble
Broad Institute of MIT & Harvard

-----------------------------------------------------------------------------------

*  New samples since last analysis run:

	BCR				+164	(7287 total)
	Clinical		+111	(5909 total)
	CN				+218	(6430 total)
	LowP			+100	(601 total)
	Methylation		+51		(6522 total)
	mRNA			-1		(2224 total)
	mRNAseq			+309	(4680 total)
	miRseq			-17		(5627 total)
	MAF				+615	(3798 total)

*  New mutation analyses (and MAFs) for: HNSC, KIRP, LGG, PAAD, SKCM
*  Updated mutation analyses (and MAFs) for: GBM and KIRC
*  New PANCAN12 and PANCAN18 cohorts, with a small handful of analyses
*  2 new kinds of Paradigm runs, against RNASeq and RNASeqWithCopyNumber

*  Correlations against several new clinical data elements, including smoking-
   related (where applicable).  For more details see the stddata run notes at
   https://confluence.broadinstitute.org/display/GDAC/Standardized+Data+Run+Release+Notes

*  Avoid over-interpretation of survival events in the presence of low-count statistics,
   by assigning P value of 100; this prevents clinical correlations from interpreting
   those events as significant when generating survival curves.

*  Due to an internal configuration error, LAML analyses were reduced from 26 to
   12.  This will be corrected in the next run.