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  Release notes for the standardized data upon which these analysis runs are based are available here

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2016_01_28__patch

 

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titlePatch: October 2016

NOTE: The LIHC RPPA data submitted by MDACC early in 2016 were discovered to be mislabelled MESO samples. Thus the 2016_01_28 analyses and standard data pipelines for LIHC have been re-run using the corrected samples submitted in March, and the nozzle reports now contain notices of the discrepancies.

The following table shows the changes in sample counts for RPPA data as a result of this patch:

HNSC

+145

(357 total)

LIHC

+121

(184 total)

THCA

+146

(368 total)

 

 

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Spring_2016

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titleSpring 2016 Analysis Run
  1. This is likely to be either the penultimate or perhaps even final standard Firehose analysis run of the TCGA project. Custom AWG runs will continue for TCGA as needed.

  2. This analysis run was based upon the 2016_01_28 data run and includes 1528 analysis reports.

  3. Summary of sample changes (see the comprehensive samples report for more details) since the Fall 2015 analysis run:

    BCR

    +1

    (11368 total)

    Clinical

    +32

    (11196 total)

    CN

    +2

    (10987 total)

    MAF

    +313

    (7099 total)

    Methylation

    +1

    (10972 total)

    miRSeq

    +2

    (10156 total)

    mRNASeq

    +164

    (10267 total)

    rawMAF

    +2072

    (6322 total)

    RPPA

    +627

    (7429 total)

  4. APOBEC pipelines updated: 
    1. used median filtering in primary APOBEC analysis
    2. in downstream clinical correlations, corrected names of categorical variables and descriptions of how they were utilized
  5. cNMF clustering improvement: new criteria used to select best cluster, identical to that describe in Summer 2014 run (see below) for consensus hierarchical clustering:
    The cophenetic correlation coefficients and average silhouette values are used to determine the k with the most robust clusterings. From the plot of cophenetic correlation versus k, we select modes and the point preceding the greatest decrease in cophenetic correlation coefficient, and from these choose the k with the highest average silhouette value.
  6. Survival analysis: for all clinical correlations
    1. Modified the p-value calculation of survival analysis with continuous data. It now uses the quantile interval categorical values instead of continuous values.
    2. Previously it had one hazard ratio value for one continuous value, but now has multiple hazard ratio values for quantile interval curves (and are now reflected in the plot legends)

  7. FireBrowse:
    1. Updated to v1.1.28 to reflect these run results
    2. iCoMut:
      1. loaded 4 additional disease cohorts: DLBC, ESCA, SARC, and THYM
      2. Completed most of work for major new release, stay tuned for announcement next week, incorporating many graphical and data exploration enhancements

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titleJuly 2012 (2012_07_25)
  • New Samples:

    BCR+160(6846 total)
    Clinical+55(5633 total)
    Methylation+140(5465 total)
    mRNAseq+306(3460 total)
    miRseq+195(3976 total)
  • 32 new reports, for a total of 284 in this run
  • New Pipelines:
    • Correlate_Clinical_vs_CopyNumber_Focal
    • Correlate_Clinical_vs_CopyNumber_Arm
  • MutSig:
    • To address item (9) from 2012_06_23 Analysis Run Release Notes, input WIGs (from stddata__2012_07_25) updated to hg19 for:
      • BLCA
      • BRCA
      • CESC
      • KIRC
      • LUSC
      • LUAD
      • PRAD
      • STAD
      • UCEC
    • STAD failing due to memory exhaustion - ignoring for this release as there is no currently active AWG
    • COADREAD analysis is missing 102 samples. Please see explanation in our email archive.
  • Gistic2
    • Failed for PANCANCER due to memory exhaustion; ignored because it is the large 23-tumor cohort, not yet the 8-tumor cohort defined by AWG.

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