Dear TCGA Colleagues,

Version 2012_05_15 of the Firehose stddata package has been released and will
be available in the protected data tree pending internal mirroring by the DCC.
Highlights of this run are given below, and in our dashboard release notes at

			http://gdac.broadinstitute.org

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 RPPA_AnnotateWithGene pipeline, which:
  .	Maps antibody proteins to gene symbols, to simplify downstream analyses.  The
	gene symbols come from the MDA_RPPA_Core.antibody_annotation.txt file packaged
	in the mage-tab archive of each RPPA submission.
  .	Includes a figure showing the protein expression levels per sample.

- Mutation_Packager split into two files, Mutation_Packager_Calls and
  Mutation_Packager_Coverage, for smaller downloads if all one wants are MAFs.

- PRAD mutation data now present (83 samples)

- Per Program Office, all clinical and mutation data are now public, so we no longer
  cull them prior to hosting on Broad GDAC site.

- New Broad GCC SNP6 data format, in which all samples from the single platform

	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg

  have been reprocessed in 4 distinct ways (each containing the full complement of samples):

        Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg
        Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
        Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
        Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg

  Please contact the Broad Institute GCC at www.broadinstitute.org/gcc for more details.

- Two BCGSC platforms have been manually deleted for LAML disease type:
	mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__isoform_expression__data
	mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__mirna_expression__data