Planned Analysis: Somatic Structural Variant and Chromothripsis Analysis

[jharenza]

The goal of this analysis is to identify recurring, putative oncogenic SV lesions/genes with recurrent lesions within and/or across brain tumor subtypes. Coupled to this, investigation of chromothripsis and correlations with survival should be done. See this paper for chromothripsis analysis using WGS.

[gonzolgarcia]

Another example studying structural variants and chromothripsis in our recent paper
Note: in order to study chromothripsis both CNV calls and Str. variant calls are required

[kgaonkar6]

R package for Chromothripsis analysis https://github.com/parklab/ShatterSeek; used in [Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing] https://www.biorxiv.org/content/10.1101/333617v1

[gonzolgarcia]

R package for Chromothripsis analysis https://github.com/parklab/ShatterSeek; used in [Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing] https://www.biorxiv.org/content/10.1101/333617v1

I have been using this package lately and it is not straight forward. In their manuscript they recognize that eventually it requires visual inspection... Another method implemented as a perl module: https://metacpan.org/release/SGOVIND/Shatterproof-0.13

[kgaonkar6]

Ah ok good to know, I've not used the package yet just found it while reading up on SVs.

[gonzolgarcia]

I will be running some of the analyses implemented in our recent paper; including analyses of recurrent SVs and CNVs but also chromothripsis.

[jharenza]

merge with and rename #27