Experience with ChIA-PET?

[Boel]

Hi All,

We are looking into ChIA-PET, a tool to look at genome wide chromatin interaction analysis. So far all publications seems to be from the group developing the procedure (PMID: 20181287 & 19890323). Does anyone out there have any experience with this technique, and any comments regarding the sensitivity and specificity, the pros and cons? Would be highly appreciated.

Thanks,
Boel

[arendon]

So are we. Should one interpret the lack of replies as CHIA-PET being really challenging?
thx,
augusto

[simonandrews]

We've done a fair bit of work with this kind of data, and I'm currently writing tools for handling this kind of paired sequence data which will appear in a future version of SeqMonk.

It's difficult to make general observations about this type of data as many of the problems we see are technical in nature and relate to the specific types of protocol being used (of which there are several related variants). I think it's fair to say that extracting biologically relevant information from these data is still very challenging, and it's pretty easy to draw incorrect conclusions by not accounting for factors which might introduce systematic bias in the frequency of interaction pairs you see. Also, if you're doing a comprehensive unbiased analysis then the volume of data is really problematic. Exponential increases in interactions from linear increases in measurement sites is no fun (well actually it is kind of fun in a masochistic way)!