{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn8042988, https://www.synapse.org/#!Synapse:syn8042880","dataSubType":"copy number","label":"consensus copy number","name":"20170119_final_consensus_copynumber_donor","assembly":"hg19","type":"genomicSegment","version":"2017-01-19","unit":"total copy number","colnormalization":"normal2","description":"PCAWG-11 consensus segmented copy number. These profiles contain clonal copy number for nearly the complete genomes and are the result of a bespoke procedure that combines output from 6 different copy number callers: ABSOLUTE, ACEseq, Battenberg, CloneHD, JaBbA and Sclust.  PCAWG-11 working group first ran all methods across all samples with the consensus SVs included and applied an algorithm across the segmentations to obtain consensus breakpoints. With these mandatory breakpoints the methods were rerun without calling any additional breakpoints.<br><br>Samples for which the methods disagreed on the ploidy have gone through an adjustment algorithm that applies various ploidy adjustments in order to maximise the agreement and were assessed through a rigorous review procedure. After obtaining consensus on the ploidy segments are considered individually to assign copy number states: Clonal agreement (3 stars), majority vote agreement and agreement after rounding subclonal copy number (2 stars) and a call from the best method on that sample (1 star). This finally yields a complete, clonal copy number profile.<br><br>"}

{"name":"consensus.20170217.purity.ploidy_donor","type":"clinicalMatrix","cohort":"PCAWG (donor centric)","version":"2017-02-22","url":"https://www.synapse.org/#!Synapse:syn8272483, https://www.synapse.org/#!Synapse:syn8042880","label":"tumor purity and ploidy","description":"PCAWG-11 group pooled purity calls across 10 different methods to form a consensus, using both copy number alterations and SNVs. Purities are assigned a confidence by means of the MAD across the available raw purities, where a low value represents high agreement across the purity callers. The ploidy has an additional annotation that denotes the whole genome duplication status of the tumour. A tumour is either duplicated (wgd) or not (no_wgd). <br><br>purity : estimated median purity<br>ploidy : calculated ploidy of the consensus profile<br>purity_conf_mad : confidence in the purity call by means of taking the median absolute deviation across all available raw purity calls<br>wgd_status : whole genome duplication status determined from the consensus copy number profile. A sample is whole genome doubled (wgd) or not (no_wgd)<br>wgd_uncertain : a boolean denoting whether the whole genome duplication is uncertain. Interpret the copy number of these profiles with caution<br><br>","wrangling_procedure":"Purity and ploidy data are mapped from aliquote uuid to ICGC donor ids using http://pancancer.info/data_releases/may2016/pcawg_sample_sheet.v1.4.2016-09-14.tsv from https://wiki.oicr.on.ca/display/PANCANCER/Available+PCAWG+Data#AvailablePCAWGData-May2016Dataset,Version1.4 . When multiple tumor specimens are available per donor, the avarage is used as the value for the donor.","dataSubType":"purity and ploidy"}