I'm currently working on a feline project. We are looking at breed specific mutations but have been running into some problems. In the past, we have been able to identify mutations that affect a particular breed. The thing is, cats don't care who they mate with and without supervision will mate with the stray cat next door. The offspring will typically exhibit the same breed-specific traits (hairless, scrunched nose, etc.) but their gene pool gets tainted. We are seeing a lot of breed specific mutation in the domestic shorthair/longhair gene pool aka the "mutts", which isn't surprising based on the above. I was wondering if there was a way to determine how related individuals are to one another? I'm assuming if some kind of sick domestic cat mates with a purebred cat and passes their offspring a particular illness, there must be some way to identify the relatedness when you look at the WGS data? I ran a PCA on the data in the past for something completely different but also didn't see a correlation. I know for humans they have a program called "peddy" that looks at how related individuals are but is there a way to do something similar for cats?
The PCA just doesn't seem to be sensitive enough for this. It worked great for identifying breed as a whole but I think it falls short when comparing a cat 3/4th "purebred" cat to domestic short hair.
I'm just thinking that cats with a particular disease could be somehow related? They also could have a different mutation but I'm interested in trying to find a way to look at how related individuals are to one another?
What kind of data are you inputting into PCA? Is it SNPs?
Have you tried removing breed-specific SNPs? Also, I assume those are explained by PC1, so you can try ignoring that one.
That is correct, the PCA is just looking at SNPs. I guess I haven't tried removing breed specific SNP.. I honestly don't know how to do that. If you know of a way of doing that, I'd be interested. I generate every PCA plot possible when I run the data. You are right about the PC1 though. I'm really curious to see if there's any other way to look at the data? I just feel like there is a better way of looking at the data than a PCA