Dear TCGA Colleagues,

The September 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_09_13 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

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* Sample Changes:

	BCR				+71		(6952 total)
	Clinical		+8		(5679 total)
	CN				+4		(5814 total)
	Methylation		+118	(5589 total)
	miRseq			+684	(4793 total)
	mRNAseq			+36		(3563 total)
	RPPA			+442	(3173 total)

* Updated Pipelines:

  Aggregate_Clusters & Correlate_Clinical_vs_Molecular_Signatures:
        Now incorporate copy number cNMF and RPPA clustering results, too
  Mutation_Assessor:
        Now handles headers as per the MAF Spec
  Methylation:
		Major optimizations to improve clustering & expression correlation
  MutSig :
	Changed from GenePattern pipeline to Firehose workflow, yielding:
		. more transparency & job-avoidance on intermediate processing steps
		. changed output archive names, from  gdac*Mutation_Significance* to:
			MutSigPreprocess2.0, ProcessCoverageForMutSig2.0, MutSigRun2.0,
			MutSigNozzleReport2.0, MutSigNozzleReportS2N
	Current implementation of v2.0 is not computing a clustered mutations
	result--this will be fixed in next October 2012 analysis run.
	. New version of MutSig (S2N) added to our analysis run: see dashboard for more details.

  Correlate_Clinical_vs_Methylation:
	Given that it executes on one meth probe per gene, chosen by negative correlation
	with expression data (mRNA/mRNAseq), this pipeline is currently not run when
	insufficient expression data exist; in the future, in such cases it will instead
	be it will be run on mean probe values per gene.

* firehose_get v0.3.7: reflect addition of PANCAN8 disease cohort, and resumption of
					   COAD and READ cohorts (on top of existing COADREAD aggregate)