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Old 04-25-2012, 02:13 AM   #1
ForeignMan
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Default Simulation of inversions and translocations

Hello everyone,

I was asking myself if it is possible so adequately simulate (simple) inversions and (inter-chromosomal) translocations. Does anyone have experience with this?
Well there are some tools, that simulate (small) indels or approaches which implement known indels into a reference genome. But I never read if someone put effort into simultating inversions and especially translocations. I'd say this could also be useful for testing.
I know, that especially translocations can be a very complicated and complex process, involving other variations like deletions, insertions and inversions at the breakpoint. But would be great if someone had some experience with this or even knew an appropriate tool.

Thanks in advance!
Kind regards,
Christoph
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Old 04-25-2012, 07:14 AM   #2
tonybolger
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Quote:
Originally Posted by ForeignMan View Post
I was asking myself if it is possible so adequately simulate (simple) inversions and (inter-chromosomal) translocations. Does anyone have experience with this?
Well there are some tools, that simulate (small) indels or approaches which implement known indels into a reference genome. But I never read if someone put effort into simultating inversions and especially translocations. I'd say this could also be useful for testing.
How biologically accurate does this need to be?

Simulating the effects of e.g. homologous recombination doesn't seem too hard, and i guess you don't need to accurately predict the likelihood of it happening, but merely the likely effect.
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Old 04-25-2012, 07:37 AM   #3
ForeignMan
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I had the evaluation of methods for structural variation detection in mind.
So, just "pasting" regions from different chromosomes together might be too simple, I guess (?). And subsequent evaluation may miss the difficulties of a real scenario. More complex breakpoint sequences may influence their detection e.g. by paired-end- or split-reads. At translocation breakpoints, sequences may get inserted or deleted. I'd say one would have to consider this as well. But I find it hard to estimate how complex this rearrangement really is in most cases. I'm mostly interested in aberrations in cancer samples and I've just seen also some pretty complex ones.
So, I'm not sure if a homologous recombination, by simply exchanging genomic regions is sufficient here. But if it's that simple, maybe there already exists such a simulation approach I missed so far.
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