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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)

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It now uses the quantile interval categorical values instead of continuous values.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"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)","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"FireBrowse:","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Updated to v1.1.28 to reflect these run results","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"iCoMut:","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"loaded 4 additional disease cohorts: DLBC, ESCA, SARC, and 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BCR	+15	(11367 total)
Clinical	+219	(11164 total)
CN	-2	(10985 total)
LowP	+120	(1211 total)
MAF	+202	(6786 total)
Methylation	+16	(10971 total)
miRSeq	-6	(10154 total)
mRNASeq	+8	(10103 total)
rawMAF	+213	(4250 total)
RPPA	+1346	(6802 total)

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","type":"text"},{"text":"This is due to our new policy of lifting over these MAFs from hg18 to hg19, which all other TCGA MAFs are currently based on, while we have not performed lliftovers on the ","type":"text"},{"text":"accompanying","type":"text"},{"text":" coverage files, which MutSig_2.0 requires.","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"APOBEC analysis now run on COAD/READ, OV, LAML due to new policy of lifting over to hg19","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Clinical analyses:","type":"text"},{"text":" names of some C","type":"text"},{"text":"linical Data Elements (CDEs) have changed. 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BCR	+38	(11352 total)
Clinical	+1352	(10945 total)
CN	+1	(10987 total)
MAF	+523	(6584 total)
Methylation	+533	(10955 total)
miRSeq	+109	(10160 total)
mRNASeq	+365	(10095 total)
rawMAF	+4250	(4250 total)
RPPA	+1120	(5456 total)

"}}}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New rawMAF data type","type":"text","marks":[{"type":"strong"}]},{"text":": f","type":"text"},{"text":"or some disease studies, mutation samples continued to be collected and sequenced after the respective marker paper data freeze. Until now Firehose has packaged and run analyses only on the mutations in the data freeze for the submitted paper. However, since it's in the best interests of the community to have as many samples as possible for analysis, as of this run we are excited to announce that Firehose now includes MAFs that have accumulated post-publication; we introduce the term ","type":"text"},{"text":"rawMAF","type":"text","marks":[{"type":"em"}]},{"text":" to describe such samples, connoting that they have not necessarily been curated by a TCGA analysis working group. 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The search criterion is YYYY_MM_DD datestamp.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Many recent enhancements as described in ","type":"text"},{"text":"April 2015 stddata run notes","type":"text","marks":[{"type":"link","attrs":{"href":"https://confluence.broadinstitute.org/display/GDAC/Standardized+Data+Run+Release+Notes#StandardizedDataRunReleaseNotes-20150402"}}]},{"text":".","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Issues","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The new raw MAF COAD samples contain many InDels, which increased the number of SMGs identified for COAD[READ]: for signficance analysis we internally perform liftover of the COAD[READ] MAFs from hg18 to hg19. 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Clinical	+899	(9593 total)
CN	+1512	(10986 total)
MAF	+143	(6061 total)
Methylation	+513	(10422 total)
miRSeq	+1176	(10051 total)
mRNASeq	+1182	(9730 total)
RPPA	+303	(4336 total)

"}}}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Number of analyses & reports increased from 1008 to 1164","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Including 52 analyses for 3 previously unanalyzed disease cohorts: CHOL, TGCT, and THYM (Cholangiocarcinoma, Testicular Germ Cell Tumors, Thymoma)","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New Analysis Pipelines:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Mutation_APOBEC : determines the level of APOBEC signature activity within mutations (","type":"text"},{"text":"Roberts et al 2013","type":"text","marks":[{"type":"link","attrs":{"href":"http://dx.doi.org/10.1038/ng.2702"}}]},{"text":"). 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BCR	+1143	(11314 total)
Clinical	+604	(8694 total)
CN	+308	(9474 total)
MAF	+380	(5918 total)
Methylation	+681	(9909 total)
miRSeq	+674	(8875 total)
mRNASeq	+524	(8548 total)
RPPA	+1	(4033 total)

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Methylation	+489	(8514 total)
miR	+74	(1135 total)
miRSeq	+306	(7470 total)
mRNA	-2	(2217 total)
mRNASeq	+588	(7478 total)
RPPA	+1	(4033 total)

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Notes","type":"text","marks":[{"type":"link","attrs":{"href":"https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844333808/Standardized+Data+Run+Release+Notes#StandardizedDataRunReleaseNotes-2014_01_15"}}]}]}]}]}]}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"September_2013"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"bgColor":{"value":"white"},"titleBGColor":{"value":"lightblue"},"title":{"value":"September 2013"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Summary of sample changes (see ","type":"text"},{"text":"the comprehensive samples report","type":"text","marks":[{"type":"link","attrs":{"href":"http://gdac.broadinstitute.org/runs/stddata__2013_09_23/samples_report/index.html"}}]},{"text":" for more details):","type":"text"}]},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"legacy-content","text":"","parameters":{"nestedContent":{"type":"doc","content":[{"type":"table","attrs":{"layout":"align-start"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"BCR","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+281","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(8548 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BCR	+281	(8548 total)
Clinical	+804	(7335 total)
CN	+563	(7966 total)
LowP	-12	(859 total)
MAF	+263	(4668 total)
Methylation	+759	(8025 total)
miRseq	+842	(7164 total)
mRNAseq	+1072	(6890 total)
RPPA	+797	(4032 total)

"}}}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Introduced CHASM Analyses for 10 disease cohorts:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Machine learning method to distinguish between driver and passenger somatic missense mutations","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Driver mutations are curated from the COSMIC database","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Passenger mutations are based on background base substitution frequencies observed for the specific tumor type","type":"text"},{"type":"hardBreak"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Introduced GISTIC2 analyses for each of the 13 disease studies containing Low-Pass Copy Number data (cna__illuminahiseq_dnaseqc__hms_harvard_edu)","type":"text"}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Mutation Assessor:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Primary script updated such that runtime is vastly decreased for large MAF files","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New report added summarizing the functional impact of missense mutations at the gene level","type":"text"}]}]}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"GISTIC2 updated to v2.0.19 to fix minor bugs","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Limit absurdly high CN values to +/- 1e6","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Fix line numbers reported when segment shortened to 0 markers","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Allow single- and zero-marker arms for broad analysis","type":"text"}]}]}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Analysis Reports:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased in number to 886","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Enhanced download section of every report to note that ","type":"text"},{"text":"firehose_get","type":"text","marks":[{"type":"link","attrs":{"href":"http://gdac.broadinstitute.org/runs/code/firehose_get.html"}}]},{"text":" can be used, or Broad or TCGA sites (including URLs to each)","type":"text"}]}]}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"IMPORTANT:","type":"text","marks":[{"type":"strong"}]},{"text":" issues with gene annotation in GAF 3.0 have impacted mutation analyses in this run. The GAF 3.0 annotation issue has been discussed in the TCGA sequencing working group and corrective action is underway, but until then we ","type":"text"},{"text":"strongly advise caution","type":"text","marks":[{"type":"em"},{"type":"strong"}]},{"text":" in the interpretation of mutation analyses based upon GAF 3.0. ","type":"text"},{"text":"The following mutation analyses are affected in this run ","type":"text"}]}]}]},{"type":"mediaSingle","attrs":{"layout":"align-start","width":500,"widthType":"pixel"},"content":[{"type":"media","attrs":{"width":833,"id":"67f6ea0b-cc7d-4ebb-9a32-4ef487efe0a1","collection":"contentId-844334195","type":"file","height":410}}]},{"type":"paragraph","content":[{"text":"for the following 6 disease studies (which presently have MAFs with ","type":"text"},{"text":"GAF 3.0 annotations deposited at the TCGA DCC): ","type":"text"},{"text":"KICH, KIRP, LGG, PAAD, SKCM, THCA","type":"text","marks":[{"type":"em"}]}]},{"type":"paragraph","content":[{"text":"Rather than completely remove the affected analyses, we felt it would be valuable diagnostically to have these mutation results available for inspection. Towards that end, here is a comparison of the top 10 significant genes found by MutSig for disease studies that used a ","type":"text"},{"text":"GAF ","type":"text"},{"text":"2.1 MAF in the last analyses run (","type":"text"},{"text":"2013_05_23","type":"text","marks":[{"type":"link","attrs":{"href":"http://gdac.broadinstitute.org/runs/analyses__2013_05_23/"}}]},{"text":"), versus a ","type":"text"},{"text":"GAF ","type":"text"},{"text":"3.0 MAF in this run:","type":"text"}]},{"type":"mediaSingle","attrs":{"layout":"align-start","width":1164,"widthType":"pixel"},"content":[{"type":"media","attrs":{"width":1164,"id":"f4d4963b-8438-4270-aa96-ac42693222fc","collection":"contentId-844334195","type":"file","height":346}}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"May_2013"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"bgColor":{"value":"white"},"titleBGColor":{"value":"lightblue"},"title":{"value":"2013_05_23"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"IMPORTANT:","type":"text","marks":[{"type":"strong"}]},{"text":" this will be the final installment of our monthly cycle of Firehose analyses results. 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Our next Firehose analysis run will therefore be released in September 2013.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Summary of sample changes (see ","type":"text"},{"text":"the comprehensive samples report","type":"text","marks":[{"type":"link","attrs":{"href":"http://gdac.broadinstitute.org/runs/stddata__2013_05_23/samples_report/index.html"}}]},{"text":" for more details):","type":"text"}]},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"legacy-content","text":"","parameters":{"nestedContent":{"type":"doc","content":[{"type":"table","attrs":{"layout":"align-start"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"BCR","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+424","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(8267 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Clinical","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+133","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(6531 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"CN","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+208","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(7403 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"LowP","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+235","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(871 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"MAF","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+116","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(4405 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Methylation","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+120","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(7266 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"miRseq","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+102","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(6322 total)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"mRNAseq","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"+162","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"(5818 total)","type":"text"}]}]}]}]}],"version":1},"reason":"A table in list item can't be created or edited in the new editor.","cxhtml":"

BCR	+424	(8267 total)
Clinical	+133	(6531 total)
CN	+208	(7403 total)
LowP	+235	(871 total)
MAF	+116	(4405 total)
Methylation	+120	(7266 total)
miRseq	+102	(6322 total)
mRNAseq	+162	(5818 total)

"}}}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Analysis Reports:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased from 690 to 774","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Moved Clinical correlations near top of aggregate reports, to promote greater visibility for potential therapeutic discovery","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Corrected outgoing URLs in clinical reports, to remove ","type":"text"},{"text":"__ and |","type":"text","marks":[{"type":"code"}]},{"text":" suffixes from gene or miR names; these suffixes are added during analysis to uniquely identify each instance when a given gene/miR appears multiple times (e.g. ","type":"text"},{"text":"for more than 1 methylation probe","type":"text","marks":[{"type":"link","attrs":{"href":"https://confluence.broadinstitute.org/display/GDAC/Methylation+Preprocessor"}}]},{"text":"), but having them in URL was breaking lookups in ","type":"text"},{"text":"GeneCards","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.genecards.org/"}}]},{"text":" or ","type":"text"},{"text":"miRbase","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.mirbase.org/"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Simpler navigation to similar analysis results across disease cohort types, which is especially useful for comparing subtype results in AWG 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downstream analyses PARADIGM Updated reports to include significance calculation Custom AWG runs since last posted analysis snapshot run: Thyroid 2013_06_06 (preliminary to workshop) Thyroid 2013_06_20 (for analysis workshop) Stomach 2013_06_18 Melanoma 2013_05_02 Released firehose_get version 0.3.13: now with 15% kinder messages than before, enhanced the online documentation and examples, and new -only option","parameters":{"nestedContent":{"type":"doc","content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Pathway_Hotnet:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Parallelized HotNet task, improving performance by factor 3-5X, which should shrink turnaround time of future analysis runs","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"We are in 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- Pathway_Hotnet:
  - Parallelized HotNet task, improving performance by factor 3-5X, which should shrink turnaround time of future analysis runs
  - We are in ongoing discussions with Raphael Lab at Brown to converge our analyses results with theirs, using THCA as testbed
- miRseq_Mature_Clustering:
  - Clustering of miRseq mature expression
- LegoPlotter:
  - Generate Lego plots for MutSig generated MAF files
- MergeMutSigRunResults:
- PARADIGM
  - Updated reports to include significance calculation
Custom AWG runs since last posted analysis snapshot run:
- Thyroid 2013_06_06 (preliminary to workshop)
- Thyroid 2013_06_20 (for analysis workshop)
- Stomach 2013_06_18
- Melanoma 2013_05_02
Released version 0.3.13: now with 15% kinder messages than before, enhanced the online documentation and examples, and new -only option

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BCR	+161	(7468 total)
Clinical	+40	(5949 total)
CN	+122	(6552 total)
MAF	+136	(3934 total)
Methylation	+96	(6618 total)
mRNA	-2	(2222 total)
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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)

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This will be fixed in the next analysis run.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New version of MutSig (S2N) added to our analysis run","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Please note that this version is still in active development and as a result, the significant genes list contains false positives. The algorithm will continue to be refined to eliminate these false positives. In the meantime, an intersection of significant genes found by this version and MutSig v2.0 is suggested to eliminate false positives.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]},{"type":"hardBreak"}]}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"firehose_get v0.3.7: reflect addition of PANCAN8 disease cohort, and resumption of COAD and READ cohorts (on top of existing COADREAD aggregate)","type":"text"},{"type":"hardBreak"},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_Methylation currently runs on one methylation probe per gene chosen by negative correlation with corresponding expression data (mRNA/mRNAseq). When insufficient expression data exists, methylation correlation pipelines do not run. In future iterations, when there is insufficient expression data, ","type":"text"},{"text":"Correlate_Clinical_vs_Methylation","type":"text"},{"text":" will run on mean probe values per gene.","type":"text"}]},{"type":"mediaSingle","attrs":{"layout":"center","width":500,"widthType":"pixel"},"content":[{"type":"media","attrs":{"type":"external","url":"http://gdac.broadinstitute.org/runs/analyses__2012_09_13/ingested_data.png"}}]}]}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"August_2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"title":{"value":"2012_08_25"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The past 5 months of Standardized Data have been loaded into IGV:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"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.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Copy Number data available for both hg18 and hg19, both with and without germline samples","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Meth450 data now available","type":"text"}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To acces, open IGV, and with Human hg18/hg19 selected as the reference, navigate:","type":"text"},{"type":"hardBreak"},{"text":"File -> Load from Server... -> The Cancer Genome Atlas -> TCGA Broad GDAC -> Firehose Standard Data","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New Pipelines:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Aggregate_Gene_Status","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"CopyNumber_Clustering_CNMF","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"CopyNumber_Gistic2_Postprocess_Focal","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_Methylation","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_RPPA","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_mRNAseq","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_miRseq","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Updated Pipelines:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Methylation","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Changed how gene-level data is selected from probe-level data. 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BCR	+35	(6881 total)
Clinical	+38	(5671 total)
CN	+424	(5810 total)
LowP	+402	(478 total)
Methylation	+6	(5471 total)
miR	+6	(1061 total)
miRseq	+133	(4109 total)
mRNA	+6	(2224 total)
mRNAseq	+67	(3527 total)
RPPA	+644	(2731 total)

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BCR	+160	(6846 total)
Clinical	+55	(5633 total)
Methylation	+140	(5465 total)
mRNAseq	+306	(3460 total)
miRseq	+195	(3976 total)

"}}}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"32 new reports, for a total of 284 in this run","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New Pipelines:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_CopyNumber_Focal","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_CopyNumber_Arm","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"MutSig:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To address item (9) from ","type":"text"},{"text":"2012_06_23 Analysis Run Release Notes","type":"text","marks":[{"type":"link","attrs":{"href":"#AnalysisRunReleaseNotes-June_2012"}}]},{"text":", input WIGs (from ","type":"text"},{"text":"stddata__2012_07_25","type":"text","marks":[{"type":"link","attrs":{"href":"https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844333808/Standardized+Data+Run+Release+Notes#StandardizedDataRunReleaseNotes-2012_07_25"}}]},{"text":") updated to hg19 for:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"BLCA","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"BRCA","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"CESC","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"KIRC","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"LUSC","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"LUAD","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"PRAD","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"STAD","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"UCEC","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"STAD failing due to memory exhaustion - ignoring for this release as there is no currently active AWG","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"COADREAD analysis is missing 102 samples. Please see explanation in our ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]},{"text":"email archive","type":"text","marks":[{"type":"link","attrs":{"href":"https://confluence.broadinstitute.org/display/GDAC/mail/46532198"}},{"type":"textColor","attrs":{"color":"#222222"}}]},{"text":".","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Gistic2","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"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.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]}]}]}]}]}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"June_2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"title":{"value":"June 2012 (2012_06_23)"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased number of archives generated from 777 to 993","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased number of reports from 227 to 252","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"2,244 new samples reflected since May analyses run, due to more data and better counting:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"76 LowP (new sample type - Low Pass DNAseq)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"230 BCR","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"307 Clinical","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"618 mRNAseq","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"937 miRseq","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"76 MAF","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"GISTIC2 report now includes a description of both the input and output files in the ","type":"text"},{"text":"Methods & Data","type":"text","marks":[{"type":"em"}]},{"text":" section","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Methylation data:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Rewired pipelines to include meth450 platform, and also give it preference over meth27 when both are present.","type":"text"},{"type":"hardBreak"},{"text":"(Methods to combine 450 & 27 analytically are not in Firehose: would be nice for AWGs to provide if possible)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"This greatly increases count of methylation samples flowing through analyses (e.g. UCEC 117–>363)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"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","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New clustering pipelines heuristic: a sample will be dropped from analyses when 80% or more genes are absent.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"mRNAseq: we now utilize rnaseqv2 archives, but fall back to v1 rnaseq when v2 is not available for a given tumor type","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RSEM estimation used for downstream clustering & correlation analysis, when available, otherwise RPKM estimation will used","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RSEM is used to estimate gene and transcript abundances (","type":"text"},{"text":"http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html"}}]},{"text":"); values are normalized to a fixed upper quartile value of 1000 for gene and 300 for transcript level estimates, and the normalized values are placed in a separate file (From the DCC document).","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The following showed the boxplot of BRCA mRNAseq samples with log2 transformed RESM (left) and RPKM (right). 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Alas, we did not correct for hg19 in time for the run, so ","type":"text"},{"text":"results for all tumor data based upon hg19 (","type":"text"},{"text":"BLCA, BRCA, CESC, KIRC, LUSC, LUAD, PRAD, STAD, and UCEC)","type":"text","marks":[{"type":"textColor","attrs":{"color":"#222222"}}]},{"text":" SHOULD NOT BE USED; archives were not posted to DCC, but the reports will remain online for inspection.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Nozzle report now includes visually compelling, integrative\"CoMut\" plot.","type":"text"}]}]}]}]}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"May_2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"title":{"value":"May 2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased number of pipelines in workflow from 27 to 33, adding:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_Molecular_Signatures","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_mRNA","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_Mutation","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_Clinical_vs_miR","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Correlate_CopyNumber_vs_mRNAseq","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RPPA_Clustering_CNMF","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RPPA_Clustering_Consensus","type":"text"}]}]}]},{"type":"paragraph","content":[{"text":"and removing","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Paradigm_Lite","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased number of analysis output reports from 167 to 227","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Increased number of tumorsets with 100% success from 12 to 17","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"As noted in the ","type":"text"},{"text":"2012_05_15 data run","type":"text","marks":[{"type":"link","attrs":{"href":"https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844333808/Standardized+Data+Run+Release+Notes#StandardizedDataRunReleaseNotes-2012_05_15"}}]},{"text":", Broad GCC SNP6 data has been reprocessed from the single platform","type":"text"}]},{"type":"paragraph","content":[{"text":" Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":"into 4 distinct platforms (each containing the full complement of samples):","type":"text"}]},{"type":"paragraph","content":[{"text":" Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":" Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":" Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":" Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"type":"hardBreak"},{"text":" Gistic in our GDAC pipeline now operates upon the last of these: ","type":"text"},{"text":"scna_minus_germline_cnv_hg19__seg","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"type":"hardBreak"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"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.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Mutation significance & assessor results for lung cancer (LUSC and LUAD tumor types) continue to be removed, as described below.","type":"text"}]}]}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"April_2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"title":{"value":"April 2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Doubled our 100% success rate by eliminating vacuous failures due to having zero data of given 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so methylation analyses will still refect only 1 platform and thus lower counts","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New MAFs: BLCA (28 samples), CESC (36), and STAD (133)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Initial Mutation_Signficance analyses and Mutation_Assessor annotations for CESC and STAD","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Mutation assessor module updated to reflect newer web service version and correct Mutation_Status column etc in outputs","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Reflect individual RNA-Seq expression clustering reports in top-level aggregate report","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"New ","type":"text"},{"text":"firehose_get utility,","type":"text","marks":[{"type":"link","attrs":{"href":"https://confluence.broadinstitute.org/display/GDAC/FirehoseArchiveDownloads"}}]},{"text":" for simpler downloads","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Mutation significance results for lung cancer (LUSC and LUAD tumor types) continue to be removed, as described below","type":"text"}]}]}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"February_2012"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"title":{"value":"February 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dashboard","type":"text","marks":[{"type":"link","attrs":{"href":"https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334294"}}]},{"text":", sans login credentials; alone, this run contains 138 reports, each accessible by a single web-click. We hope this furthers the ","type":"text"},{"text":"TCGA mission","type":"text","marks":[{"type":"link","attrs":{"href":"http://cancergenome.nih.gov/abouttcga/overview"}}]},{"text":" by lowering the entry barrier to use, thereby helping to broaden the impact of TCGA data and analyses.","type":"text"}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Six new analysis pipelines:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"mRNAseq_Clustering_CNMF","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"mRNAseq_Clustering_Consensus","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"miRseq_Clustering_CNMF","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"miRseq_Clustering_Consensus","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Pathway_Paradigm_Expression","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Pathway_Paradigm_Expression_CopyNumber","type":"text"}]}]}]}]}]},{"type":"paragraph","content":[{"text":"The latter two employ the full/scatter-gather version of Paradigm; the previous Pathway_Paradigm version has been renamed to Pathway_Paradigm_Lite, and will continue to be run in our Analyses workflow until all are satisfied it can be deprecated.","type":"text"},{"text":" ","type":"text"}]}]},{"type":"paragraph","content":[{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"anchor","parameters":{"macroParams":{"":{"value":"December_2011"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Anchor"}}}}]},{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"panel","parameters":{"macroParams":{"title":{"value":"December 2011"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Panel"}}},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To simplify data retrieval, the ","type":"text"},{"text":"Tumor Type","type":"text","marks":[{"type":"em"},{"type":"strong"}]},{"text":" cells in our dashboard now link directly to the DCC locations from which the corresponding archives may be downloaded.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"MutSig results for LUSC and LUAD are removed from this run, due to a discrepancy in the set of genes identified as most significant by Mutsig v1.5 versus the set manually curated by the TCGA lung AWG. ","type":"text"},{"text":"New LUSC and LUAC MutSig results will be available once MutSig is upgraded to v2.0 in the Broad GDAC pipeline.","type":"text"}]}]}]}]}],"version":1}