Dear TCGA Colleagues,

The May 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_05_25 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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. Increased number of pipelines in workflow from 27 to 33, adding:

	Correlate_Clinical_vs_Molecular_Signatures
	Correlate_Clinical_vs_mRNA
	Correlate_Clinical_vs_Mutation
	Correlate_Clinical_vs_miR
	Correlate_CopyNumber_vs_mRNAseq
	RPPA_Clustering_CNMF
	RPPA_Clustering_Consensus

  and removing

	Paradigm_Lite

. Increased number of analysis output reports from 167 to 227
. Increased number of tumorsets with 100% success from 12 to 17

. As noted in the 2012_05_15 data run, Broad GCC SNP6 data has been reprocessed from the single platform

	Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg

  into 4 distinct platforms (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

  Gistic in our GDAC pipeline now operates upon the last of these: scna_minus_germline_cnv_hg19__seg
  Please contact the Broad Institute GCC at www.broadinstitute.org/gcc for more details.

. Internal support for analyses of meth450 platform is underway but incomplete: the data have increased
  more than an order of magnitude in size, which necessitated algorithmic refactoring and additional
  testing.  Look for meth450-based analyses in June.