Re: Integrative pipeline for profiling DNA copy,number and inferring tumor phylogeny and Canopy

[Jiang, Yuchao]

Hi Kay,

Thanks for your interest in Canopy. Do you have normal controls for the tumor samples? If so, you can use FALCON to call allele-specific copy numbers. The point mutations are stored in your VCFs. However, you should adopt stringent QC and functional annotations on these mutations. Then the ASCNs and point mutations can be fed into Canopy to infer tumor phylogeny. CODEX is for total copy number analysis and doesn’t apply to the goal you mentioned in your email.

Hope this is helpful,
Yuchao

> On Nov 17, 2017, at 6:49 AM, Pornpimol Charoentong <Pornpimol....@nct-heidelberg.de> wrote:
>
> Dear Dr. Yuchao Jiang,
>
> My name is Pornpimol Charoentong. I'm a postdoctoral research fellow at the National Center for Tumor Disease Heidelberg, Germany. Your recently publication in Biorxiv and Canopy are very interesting. We would like to apply your tool with our 3 projects.
>
> Currently we have exome-sequencing of colorectal cancer (n=50, response and non-response with aPD-L1). We would like to study tumor allele-specific copy number and tumor clonality of our patients. May I ask you some questions regarding to your pipeline?
>
> At the moment we have WES (matched normal tissue) of 2 different locations in tumor region for each sample. We obtain only bam/vcf files from sequencing core facility. Could you please suggest me where should we start in supplementary R script? You provided:
>
> R script for CODEX -> iCNV pipeline
> R script for CODEX -> FALCON-X pipeline
> R script for FALCON -> Canopy pipeline
>
> If we succeed to apply your pipeline with our first set of patients, we plan to apply through all 3 different cancer entities (Ovarian, Breast and Lung, n > 2,000).
>
> Thank you so much in advance for all support and suggestions.
>
> Best regards,
>
> Kay
>
>
> --
> Pornpimol Charoentong, PhD
> National Center for Tumor Diseases
> Tumor Immunology
> Im Neuenheimer Feld 267,
> Room Nr. 106, 69120 Heidelberg
> Phone: +49 6221 5451235
> URL: http://www.nct-heidelberg.de
>

[Yuchao Jiang]

https://github.com/yuchaojiang/Canopy

See under “Common questions” for more details.

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