Entering edit mode
12.6 years ago
Liyf
▴
300
I have a question whether there is software to calculate the power of exome sequencing. As I know, there are many softwares to calculate the power of GWAS.
Hoping your reply, Thanks all.
It is not clear what you are asking. Power to detect what? Are you talking about performing GWAS using exome sequencing or finding a causative variant in a single pedigree or something else?
You are talking about finding a somatic variant in cancer samples where you are sequencing paired tumor and normal? I'm not sure what "controls" you are talking about here. If a patient has a somatic variant (in tumor and not in normal), then that is typically the quantity of interest.
Have you tried a web search for this yourself and did you find anything?
I tried, but only one: http://darth.ssg.uab.edu:8080/epc/exome-calculator.html?module=exome-power. In fact, it seems not work and it is fit for simple disease.
Power to detect the somatic mutation. Because I do not know how many patients and controls is enough for my study.
Yes, What I mean is just what you thought. But I did not understand why it is typically the quantity of interest? Because I want to evaluate how many pairs should I select. Thanks in advance.
See my answer below, but you will need to know what you are looking for (the expected percentage of samples showing the variant) before one can answer the question. When thinking about sample numbers, keep in mind that you will often want to think about a validation set that may not be subjected to exome sequencing but would be used to follow up on findings in the original exome screening set--this set may be larger than the original screening set.
Many thanks, in fact, I desire a validation set, so I need to calculate the power. Thank you very much.