Dear TCGA Colleagues,

Version 2012_09_13 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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* No significant sample changes 26 Aug - 06 Sept (see
  https://docs.google.com/spreadsheet/ccc?key=0AqFTJjV2VzMEdHNMX0hqOTd3MGU2Rmo2TXpISktzZGc)

* To assist the melanoma AWG we delayed the first stddata run of Sept 2012 to
  incorporate pending submission of RPPA samples for SKCM, which appeared in
  our mirror as of 9/13.  As this was essentially the midpoint of September,

  ************************************************************************
  ***    stddata__2012_09_13 WAS THE ONLY STDDATA RUN for SEPT 2012    ***
  ************************************************************************

  This simplified our work somewhat without appreciably reducing sample flow,
  while also allowing us to re-sync to our desired target stddata run schedule
  of the 1st and 15th of each month.

* 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)

* The past 5 months of Standardized Data have been loaded into IGV:

   . Partitioned by reference genome - When choosing "Load from
     Server...", only the data for the currently selected reference
     (Human hg18/Human hg19) will be available via the menu.
   . Copy Number data available for both hg18 and hg19, both with and
     without germline samples
   . Meth450 data now available
   . To access, open IGV, and with Human hg18/hg19 selected as the
     reference, navigate:
     File -> Load from Server... -> The Cancer Genome Atlas
     -> TCGA GDAC -> Firehose Standard Data

* RPPA samples newly available for three tumor types:
   . BLCA
   . SKCM
   . THCA

* Potential RPPA issues (waiting on confirmation from M.D. Anderson)
   . Results may be reporting KDR rather than XIAP for KIRC and UCEC
     when converting using the supplied antibody annotations
   . LKB1 antibody may be reported as LBK1 for BRCA and OV

* PANCANCER aggregate set (of 20+ disease types) has been replaced with
  PANCAN8 (containing only 8: BRCA COAD READ KIRC GBM LUSC OV UCEC)

* COAD and READ reintroduced as core disease types, by request of the
  PANCAN8 AWG (COADREAD aggregate continues to be available).  This
  should also assist QCLive automated ingestion by DCC.