mskcc
Unlikely genome wide aUPD
Dear, Venkatraman!
Can't figure out why FACETs infers genome wide 2:0 state for one of my samples (that is highly unlikely to be the case) and finds 2:1 in another very similar (by logOR baseline) sample.
2:0
2:1
Thank you!
The UPD call is because the allelic imbalance (log-odds-ratio part) in the first figure is too high for balanced segments. Even though the second figure also has some allelic imbalance it doesn't seem to reach the threshold of being called UPD. The question is why is the allelic imbalance so high. Is the coverage depth too low?
Median coverage for T/N the first sample is 100/68. Can I change the allelic imbalance threshold to make the first sample 2:1? What are the possible reasons for such imbalance in raw data if we assume a sample is balanced?
Having stared at the plots even more you can see the log-ratio in the first plot is a lot more skewed (many points below -1.5) than in the second plot. It could be due to insert size being very different between tumor and normal which may have an impact on logOR as well.
Another possibility is that normal is contaminated. This can induce an imbalance in the ref-vs-alt ratio in the normal which in turn affects logOR. You can plot the vafN data to see if that maybe the case.
Thank you, Venkatraman! Looks like different T/N insert size is not the case - they have very similar distribution. We see not signs of contamination as well. There appears to be a cofactor for such logOR diturbance - GC content. For the samples with GC ~ 45% (like those two posted above) we see high imbalance and samples with GC ~ 55% have much better logOR. Does FACETs make GC correction for logOR metric?
Conceptually there is no reason to expect a relationship between GC content and logOR since it measures allelic imbalance between tumor and normal. There should be barely any difference in the GC content of DNA fragments with ref and alt alleles and this association implies that GC differentially affects them. I believe such and effect is an artifact.