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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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`ascat.runAscat` raw and ASCAT profile plots show different chromosome widths #176

Closed MikeWLloyd closed 4 months ago

MikeWLloyd commented 4 months ago

I am trying to understand why I am seeing different chromosome widths in the profile plots across samples (and in general). I have tried to look through documentation and methods papers, but can not find information on this. I am running tumor-only Illumina Cyto-SNP v2.1 data with GC and RT files I've made from the Illumina manifests. I am also running predictGermlineGenotypes as: gg = ascat.predictGermlineGenotypes(ascat.bc, platform = "IlluminaCytoSNP").

Below is an example plot with compressed widths. Can you provide details on what drives the patterns I am seeing?

tumorSepsample sample ASPCF sample ASCATprofile sample sunrise

zhangzhhcb commented 4 months ago

Hi, based on your first BAF plot, the data have large LOH regions in those narrow chromosomes. Without normal samples, it is a bit hard to identify those LOH regions. You could try to customize parameters in the platform based on https://github.com/VanLoo-lab/ascat/issues/73 to rescue segments within the LOH region. We are working on an updated version to deal with this situation, but not release yet.

MikeWLloyd commented 4 months ago

Thank you for the reply. Having this understanding to explain the patterns is a big help. I will see if I can rescue any region based on #73, and if not keep an eye out for the next release.