unplanned breeding

Question
I have 2 Russells, brother and sister, 4 yrs old.  I also have a son of the female from a previous litter, he's 2 yrs old.  I had planned to outcross this girl either next year or the following and then keep a female and cross that with one of the boys down the road.  However, one of the boys got to my girl during her heat last month and now she's pregnant.  I never saw a tie and the only time they were let out together was when I was sure she was out and the boys no longer seemed interested in her.  However, here I am with a lot of unknowns.  I know you can line breed a mother and son to set a particular type.  However, I don't know if it was the son that covered this girl.  My worry is that it was her brother instead.  What kind of problems might I wind up with in these puppies?  I know that there's a greater chance of genetic problems showing up and I will have to prepare for that.  Is there anything you can tell me?  As long as both the male and female are clear for certain genetic problems, will the puppies also be clear?  What if 1 is clear and the other is found to have a certain genetic problem ... what are the chances that the puppies will be effected?  Sorry, as you can see I'm a bit worried about this unexpected catastrophy.  

Answer
Hi JP

The thing with interbreeding is this, ANY genetic defects or flaws will come out 10 fold in the pups.  

According to the Canine Eye Registration Foundation, JRTs are afflicted with lens luxation. This is a displacement of the lens from its normal site behind the pupil and may result in glaucoma causing vision impairment or blindness. Lens luxation not associated with trauma or inflammation is presumed to be inherited.

Legg-Perthes Disease also affects this breed. It is very similar to hip dysplasia, however, instead of the acetabulum being shallow, necrosis is of the femoral head. This disease may be a simple autosomal recessive or polygenic (more than one gene involved) and results in painful hips.

While those are the two most common diseases, the breed can also be afflicted with epilepsy, skin conditions (including allergies), and genetic deafness.

You have to be prepared for some or all of these to be predominant in the resulting pups.

Good luck