How to determine statistically significant recurrence or enrichment of LOH
0
1
Entering edit mode
8.2 years ago

Is anyone aware of an existing tool for identifying statistically significant recurring regions of loss-of-heterozygosity (LOH) in (for example) a cohort of tumor vs normal sequence or array data. I'm thinking of something like GISTIC but specifically for LOH.

LOH • 1.9k views
ADD COMMENT
1
Entering edit mode

I don't think there's any reason why you couldn't apply GISTIC with some tweaking of the inputs and params. If I'm wrong and that turns out to be impractical, the underlying algorithm isn't that crazy, IIRC, and wouldn't be awful to implement something similar. It's essentially peak finding, followed by random permutation of the same size events to establish significance.

ADD REPLY
0
Entering edit mode

Yeah. I figured as much but was curious if anyone out there had seen something that was LOH-specific.

ADD REPLY

Login before adding your answer.

Traffic: 1609 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