Dear TCGA Colleagues,

The June 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_06_23 of the Firehose stddata package, and is
described in more detail in the Release Notes on our site at

			http://gdac.broadinstitute.org

We apologize for the delayed availability of this run:  as evident in our notes,
we've made a considerable number of improvements, in terms of algorithms, archives
submitted, new samples and data types, while also wrestling with a fair share of
snafus.  If you have any further 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

-----------------------------------------------------------------------------------

Release Highlights

*  Increased number of archives generated from 777 to 993
*  Increased number of reports from 227 to 252
*  2,244 new samples since May analyses run: more data & better counting

    76 LowP (new sample type - Low Pass DNAseq)
    230 BCR
    307 Clinical
    618 mRNAseq
    937 miRseq
    76 MAF

*  Methylation:

    Ensure inclusion of meth450 platform, preferentially over meth27 when both
	are present (methods to combine 450 & 27 analytically are not in Firehose,
	but it would be nice for AWGs to provide if possible).

    This greatly increases # meth samples in analyses (e.g. UCEC 117 -> 363)

    Most clusterings show similar results, but some are discordant with previous
	runs:  we could use AWG help to evaluate, and will post comparative analysis
	online towards that end.

*  Clinical correlation improvements:

    Use try/catch to avoid needless failures when params moved in XML schema
	Towards aim of having survival curves ALWAYS generated for ALL disease types
	Archives now generated for clinical correlations:  33 in this run alone
	(versus zero in previous runs)

Many more more details available in our online Release Notes at
	https://confluence.broadinstitute.org/display/GDAC/Analysis+Run+Release+Notes