Suggestions for workshops on case control data analysis of exome sequencing

Question

[peris]

Hi all,

I am trying to shift my field from model organisms to human genetics. I have started working on case-control studies using exome sequencing. I have experience in working on NGS and am well versed with its analysis. However, after generating the variants, I don't know how to proceed. So, can the members here give recommendations for any workshops or short courses that could give me an idea of what sort of analyses to perform in case-control studies and also what the relevant tools are for these studies?

Thanks and regards

[Devon Ryan]

I hope you don't mind, but I've taken the liberty of editing your post a bit.

BTW, you might have a look at ecSeq. I don't know if they're active in the US too, but they offer a number of courses on various topics (I haven't really looked, but perhaps case-control studies are among them).

Answer 1

[Katie D'Aco]

I haven't heard of any courses or workshops, but would be really interested to learn about them if they exist. I'm actually writing my own tutorial on this very topic, so it's good to know that it might be helpful to someone! I think part of the reason there isn't a ton of material about case/control studies is that there is no standard procedure yet. Each study is different, and each investigator has their own set of preferred tactics and assumptions.

Besides learning from colleagues and mentors, I've picked up stuff by reading results papers from other exome seq projects. One neat one that just came out is the FORGE Canada paper that is worth a look and gives you some good high level ideas. If you have any specific questions about your study, try asking them on biostars and maybe we can help point you in the right direction.

Another good source of information are the Golden Helix DNA-Seq Tutorials. Reading through them should give you some ideas of how to proceed.

[peris]

Thanks Katie. I will look forward for the tutorial whenever it will come online. Also thanks for the links.

Present I am trying to apply plinkseq and skat to get some idea.

Thanks and regards.