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Data Set NameResponsible WGExpected Availability as of OctoberComment as of OctoberStatusComments
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Basic Information
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Excluded/Included/GraylistPCAWG-TechAVAILABLEAVAILABLE
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Donor clinical dataPCAWG-10/13AVAILABLEAVAILABLE
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Specimen histopathological dataPCAWG-10/13AVAILABLEAVAILABLE
Clinical sex updated in mid Nov: 8 previously missing have been filled, 2 revised
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Specimen QC (stars)PCAWG-QCAVAILABLEAVAILABLEComplete and Final (not changed since 2016/06/01)
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WGS alignmentsPCAWG-TechAVAILABLEAVAILABLE
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RNAseq alignmentsPCAWG-3AVAILABLEAVAILABLE
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ID Mapping for miRNA specimensPCAWG-TechADD methylation & miRNA specimensAVAILABLEMapping to be posted
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ID Mapping for methylation specimensPCAWG-TechTBDPending completion of methylation analysis by PCAWG-4
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Variant Calls
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SNV & Indel calls from 3 core pipelinesPCAWG-TechAVAILABLEAVAILABLE
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Merged SNVs and indelsPCAWG-1AVAILABLEAVAILABLE
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Merged SVsPCAWG-6AVAILABLEretrotransposons are removedAVAILABLE
Revised in mid Nov to remove additional artifacts; low impact
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Merged CNAsPCAWG-11End of October (Clonal)
Subclonal copy number estimates end of November (pcawg-11)
AVAILABLE
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Germline SNP callsPCAWG-8Early Novemberincluding phasingEarly AprilRecommend to use Broad/HaplotypeCaller germline callset interim; repeat analyses when integrated haplotype-phased callset becomes available
Latest update from Jan Korbel 20 February 2017
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Germline CNVsPCAWG-8AVAILABLEDeletions onlyAVAILABLEDeletions only
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Cell Line SNVs and IndelsPCAWG-TechEnd of OctoberAVAILABLEPending filtering and consensus merge
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Methylation
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450k ArrayPCAWG-4mid NovemberAVAILABLE
RnB normalized data uploaded to sftp site: /pancan/pcanwg4/450KData_normalized
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Bisulfite modified sitesPCAWG-4mid NovemberAVAILABLEData uploaded to sftp site: /pancan/pcanwg4/WGBS
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Differentially-methylated regionsPCAWG-4f/u neededAVAILABLE
Data uploaded to sftp site: /pancan/pcanwg4/WGBS_ICGC_Data & WGBS_ICGC_FL_Data
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RNA/Expression Calls
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mRNA expression levelsPCAWG-3AVAILABLEAVAILABLEUpdated on Nov. 22
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miRNA expressionPCAWG-14AVAILABLEAVAILABLE
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lincRNA expressionPCAWG-14AVAILABLEAVAILABLE
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Reference Annotations
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Standard colors and terminologyPCAWG-10/13AVAILABLER library pendingAVAILABLE
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References genes & elementsEkta KhuranaAVAILABLENeeds to be added to Data Set PageAVAILABLE
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Pathogen validation setPCAWG-16AVAILABLENeeds to be added to Data Set PageAVAILABLENeeds to be added to Data Set Page
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Gene sets and pathwaysPCAWG-5AVAILABLENeeds to be added to Data Set PageAVAILABLENeeds to be added to Data Set Page
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Drivers
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Coding driver element cataloguePCAWG-9mid-NovemberAVAILABLEReleased April 21
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Non-coding driver element cataloguePCAWG-2mid-NovemberAVAILABLEReleased April 21
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ncRNA driver cataloguePCAWG-14mid-NovemberAVAILABLEReleased April 21
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SV driver eventsPCAWG-6mid-NovemberAVAILABLEReleased April 21
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CNA driver eventsPCAWG-6mid-NovemberClonal events earlierAVAILABLEReleased April 21
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Germline driver variantsPCAWG-8mid-NovemberAVAILABLEReleased April 21
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Sigificantly mutated genesPCAWG-9AVAILABLE
Coding driver genes per tumor type based on previous knowledge
AVAILABLE
Coding driver genes per tumor type based on previous knowledge
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Patient-centric driver catalogue - Noncoding
PCAWG-9mid-Novemberconservative; TERT onlyApril 28Pending driver catalogue completion
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Patient-centric driver catalogue - Coding
PCAWG-9AVAILABLEconservativeAVAILABLEconservative
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Expression
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eQTLsPCAWG-3DelayedReproducibility issuesAVAILABLE
Final call sets based on Broad GATK germline calls depend on final germline set
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Allele-specific expressionPCAWG-3end of November?Depends on consensus CNV
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mRNA splicingPCAWG-3AVAILABLEAVAILABLE
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Fusion transcriptsPCAWG-3AVAILABLEAVAILABLE
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Alternative promoter usagePCAWG-3AVAILABLEAVAILABLE
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RNA EditingPCAWG-3AVAILABLEAVAILABLE
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Subclones & evolution
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Purity & ploidyPCAWG-11mid-NovemberAVAILABLE
Final ploidy available; purity of copy number quiet cases will be patched
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Per-variant clonality/timing statusPCAWG-11mid-DecemberAVAILABLE"Beta 1"
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Per-variant cancer cell fractionPCAWG-11end of NovemberAVAILABLE"Beta 1"
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Signatures
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Conservative Mutational Signature Catalogue
PCAWG-7end of Octoberf/u neededAVAILABLE2 March - going up on Synapse; available via DropBox
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Per-sample signature compositionPCAWG-7end of Octoberf/u neededAVAILABLE2 March - going up on Synapse; available via DropBox
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Per-mutation signature attributionPCAWG-7end of Octoberf/u needed?Last update from Mike Stratton 1 March
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Others
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Significantly mutated pathwaysPCAWG-5f/u needed?f/u needed
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Pathogen predictionsPCAWG-16beginning of Decembermid December
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HLA & KIR haplotypingPCAWG-15AVAILABLEAVAILABLE
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Neo-antigen predictionsPCAWG-15end of Octoberf/u neededAVAILABLE
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MSI predictionsPCAWG-7end of Octoberf/u neededAVAILABLE
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Molecular subtypesmany groups?
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APOBEC mutagenesisPCAWG-7AVAILABLEon Synapse; November 8, 2016
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