How to determine LoH from sequenza output.

[TC]

I was wondering is there a straightforward way to determine loss of heterozygosity from sequenza output? My naive idea was to just take regions where the B allele is 0, but since the A and B counts are not to be considered to define zygosity, I'm left wondering if there's another way to determine it? As a followup question, what about regions where the CNt is >=2 and the B allele is 0?

Thanks!

[sysu.che...@gmail.com]

Hi, Do you have any answer? I want to ask the same question

在 2016年6月15日星期三 UTC+8上午7:12:02，TC写道：

[Francesco Favero]

Sorry I didn't addressed this sooner.

LOH can generally be determined when B is equal to 0.
If you are interested in copy neutral LOH, you should look at the A value, eg A == 2 and B == 0 means a genotype AA (copy neutral LOH in diploid chromosomes, whit genotyoe AB); A == 1 and B == 0 means a genotype A, indicating a copy number of 1 (non copy-neutral for a diploid chromosome) and also a loss of heterozygosity in the specific segment.

So in short you need to evaluate the B parameter to get all the LOH regions, and the A parameter if you want to further characterise the LOH.

Best

Francesco

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[Liu Xiaoqiao]

Hi Francesco,

how about region with A > 2 and B ==0? should these region also be considered as LOH region?

[Francesco Favero]

Hi Liu,

Yes, imagine the classic LOH occurs early in tumor evolution, and then a genome doubling event occurs, you will have a scenario as the one you described.

I would say that all the scenarios where one of the allele is depleted are equally interesting, it would be quite limiting to consider an LOH only the "AA" cases.

Hi Francesco,

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