Dear TCGA Colleagues,

The August 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_08_25 of the Firehose stddata package, and is
described in more detail in the dashboards on our site at

			http://gdac.broadinstitute.org

This was a big release with many new samples & algorithm updates, as highlighted
below and in more detail in our online 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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*  New Samples:

   BCR         +35  (6881 total)
   Clinical    +38  (5671 total)
   CN          +424 (5810 total)
   LowP        +402 (478  total)
   Methylation +6   (5471 total)
   miR         +6   (1061 total)
   miRseq      +133 (4109 total)
   mRNA        +6   (2224 total)
   mRNAseq     +67  (3527 total)
   RPPA        +644 (2731 total)

   102 COADREAD samples missing from prior Mutation Significance run have been
   re-included.  See this entry

          https://confluence.broadinstitute.org/display/GDAC/mail/46532198

   in our email archive for an explanation of this issue.

*  111 new reports, for a total of 395 in this run

*  New Pipelines:

   Aggregate_Gene_Status
   CopyNumber_Clustering_CNMF
   CopyNumber_Gistic2_Postprocess_Focal
   Correlate_Clinical_vs_Methylation
   Correlate_Clinical_vs_RPPA
   Correlate_Clinical_vs_mRNAseq
   Correlate_Clinical_vs_miRseq

*  Updated Pipelines:

   - Mutation Assessor: discontinued use of (less-reproducible) web service in
     favor of fully reproducible, locally-installed v2.0 hg18/19 scores files

   - Clustering_CNMF: corrected issue that caused Nozzle reports to randomly
     have tables with the first data row as a header

   - Updated default GISTIC2 parameters: see the Methods & Data Input Description
     section of any GISTIC nozzle report created in our 06/23/2012 analyses run
	 or later.  These are described in detail in the release notes on our site.

   - MutSig report updated to include stick figures depicting the distribution of
	 mutations and mutation types across each significant gene.  Click on any
	 significant gene that appears as a link to display the figure.

*  firehose_get v0.3.5 released: to support AWG runs such as awg_pancan8__2012_08_25

*  stddata runs from April through Aug 2012 have been loaded into IGV, partitioned
   by hg18/hg19.  With Human hg18/hg19 selected in IGV, navigate to

            File->Load from Server... ->The Cancer Genome Atlas->TCGA Broad GDAC

   Future stddata runs will be immediately visible in IGV upon public release.