Dear TCGA Colleagues,

Version 2013_02_22 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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Sample Changes:
   BCR         -8   (7460 total)
   Clinical    +68  (6107 total)
   MAF         +266 (4200 total)
   Methylation +23  (6759 total)
   miRseq      -2   (6060 total)
   mRNAseq     +85  (5018 total)

Clinical parameter update for THCA
   * Additional 9 clinical parameters are included for THCA.
      - 5 parameters for tumor aggressiveness (distant.metastasis,
        extrathyroidal.extension, lymph.node.metastasis,
        completeness.of.resection, number.of.lymph.nodes)
      - 4 parameters for tumor staging systems for THCA
        (tumor.stagecode, neoplasm.diseasestage, multifocality, tumor.size)
         . tumor.size = max(dimension.depth, dimension.length,
	   dimension.width).

MAFs updated to sync with DCC:
   * BLCA v1.3
   * BRCA v5.2 (+265 Tumor Samples)
   * CESC v1.4 (+3 Tumor Samples)
   * LAML v2.12 (-2 Tumor Samples)
   * LUSC v1.5
   * PRAD v1.3
   * UCEC v1.4

hg19 WIGs added:
   * BRCA
   * UCEC
   * GBM

Addressed UUID uppercase bug in our dicer which accidently removed 63
COAD RPPA samples; fix will be evident in data stream after SDRF is
updated at DCC.

Added Firehose AWG Runs page to the AWG section of the NCI wiki

	https://wiki.nci.nih.gov/display/TCGAM/Firehose+AWG+Runs

as a central point of reference for custom Firehose runs done on behalf of
active analysis working groups.  This effort has several aims:

   * Currency: pipelines can be run on the latest daily snapshot of data
     from the DCC, avoiding the time & sample lag of monthly runs
   * Flexibility:  additional runs can be easily performed on AWG-curated
     disease subtypes, and even include custom analyses
   * Speed:  custom AWG runs can be executed in only a few days time
     (excluding computationally intensive codes that may take >1 week)
   * Familiarity:  using the same internal Firehose machinery, and external-
     facing dashboards, Nozzle reports etc, already known to the community
   * Scope: is a stepping stone to open-access Firehose, that can be manipulated
     directly by TCGA researchers, instead of runs curated only at the Broad