Running Canopy on Amplicon Sequencing

[Lara Luis]

Hi Yuchao,

Is it possible to run Canopy on tumour only amplicon sequencing ?

I have around 450 patients from the BIG 1-98 clinical trial, it would be amazing to use your tool on them.

Cheers,
Luis
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[Gene Urrutia]

Hi Luis,

Thank you for your interest in Canopy and the MARATHON pipeline.

The inputs for Canopy tumor phylogeny are:
- variant allele frequency of single nucleotide alterations and
- allele specific coverage ratios between tumor and matched normal samples for somatic copy number alterations.

You certainly have sufficient sample size, and amplicon sequencing can be used in CODEX provided it is target-capture based and if it introduces low-rank noise in the sequencing depth.

However for tumor phylogeny, we recommend to use matched tumor and normal samples for analysis. This is in order to detect differences between germline and somatic point mutations and allele-specific copy number.

Also, Canopy needs multiple dissections of tumor from the same patient to infer intra-tumor heterogeneity. If each sample is from a different patient, inter-tumor heterogeneity cannot be estimated by Canopy.

Please see figure 1 and table 1 in the MARATHON pipeline for a summary of available methods and inputs.  https://github.com/yuchaojiang/MARATHON

Thanks,
Gene

[Yuchao Jiang]

Hi Luis,

See below just in case you haven’t got it.

Yuchao

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[Lara Luis]

Thanks Gene and Yuchao, very informative reply.

Cheers,
Luis
________________________________________
From: Yuchao Jiang [yj...@cornell.edu]
Sent: Wednesday, April 11, 2018 6:04 AM
To: Gene Urrutia; Lara Luis
Cc: canopy_phylogeny
Subject: Re: [canopy_phylogeny] Re: Running Canopy on Amplicon Sequencing

Hi Luis,

See below just in case you haven’t got it.

Yuchao

On Apr 10, 2018, at 1:31 PM, Gene Urrutia <gene.u...@gmail.com<mailto:gene.u...@gmail.com>> wrote:

Hi Luis,

Thank you for your interest in Canopy and the MARATHON pipeline.

The inputs for Canopy tumor phylogeny are:
- variant allele frequency of single nucleotide alterations and
- allele specific coverage ratios between tumor and matched normal samples for somatic copy number alterations.

You certainly have sufficient sample size, and amplicon sequencing can be used in CODEX provided it is target-capture based and if it introduces low-rank noise in the sequencing depth.

However for tumor phylogeny, we recommend to use matched tumor and normal samples for analysis. This is in order to detect differences between germline and somatic point mutations and allele-specific copy number.

Also, Canopy needs multiple dissections of tumor from the same patient to infer intra-tumor heterogeneity. If each sample is from a different patient, inter-tumor heterogeneity cannot be estimated by Canopy.

Please see figure 1 and table 1 in the MARATHON pipeline for a summary of available methods and inputs. https://github.com/yuchaojiang/MARATHON

Thanks,
Gene

On Tuesday, April 10, 2018 at 2:54:30 AM UTC-4, Lara Luis wrote:
Hi Yuchao,

Is it possible to run Canopy on tumour only amplicon sequencing ?

I have around 450 patients from the BIG 1-98 clinical trial, it would be amazing to use your tool on them.

Cheers,
Luis
Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.


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