Infer phylogeny from continuous, segmented CNV data from methylation array
0
0
Entering edit mode
11 months ago
Fynn • 0

Hi,

I have methylation data (Illumina HumanMethylationEPIC) from multiple sites in a single tumor and I want to infer a phylogenetic tree for these samples. Using the R package conumee, I can generate segmented copy number profiles for each sample. These segments each have a continuous copy number value that is relative to a normal tissue reference.

Screenshot-2020-10-20-at-12-28-57

I am now looking for a way to get a phylogenetic tree out of this data. So far I plan on converting the continuous CN values into discrete ones (using ABSOLUTE algorithm, as suggested here) and then putting this data into TuMult algorithm (skipping TuMult's own segmentation step).

However, I'm wondering if there might be better methods, more tailored specifically to microarray methylation data. Do you know of any other algorithms or methods or literature out there suitably for this kind of problem?

Many thanks for your help :)

methylation R conumee copy number phylogeny • 385 views
ADD COMMENT

Login before adding your answer.

Traffic: 2735 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6