Structural Variation data of ICGC/PCAWG: 2,658 cancers across 38 tumour types

Question

[Shicheng Guo]

Hi All,

Anyone has download structural Variation data of ICGC/PCAWG: 2,658 cancers across 38 tumor types? I am very confused that I have download several different version of these data, but none of them have 2658 samples? I am wondering anyone tried to download ICGC data? and whether the samples are same as the paper claimed?

https://www.nature.com/articles/s41586-019-1913-9#Sec2

Thanks.

Shicheng

Answer 1

[d-cameron]

I've been using the calls from the PCAWG final public release:

https://dcc.icgc.org/releases/PCAWG/consensus_sv

https://dcc.icgc.org/releases/PCAWG/consensus_cnv

At 2749 SV call sets and 2778 CNV call sets across ICGC and TCGA, that's more than the claimed 2,658 and means some samples are missing SV calls. I haven't reconciled these against the 2,658 samples to determine the extent of the overlap.

[jueritation]

Hi Cameron,

I tried your link but failed to open the website. I also tried other ways (e.g. synapse) but it seems there is still no responding for the connection.

Bests,

Jue