Answer:
they never revealed the disease the character jenny had and was dying from
She didn't have cancer as is assumed. She had a degenerative, incurable genetic disease. When Ducky asked Abby to run blood from a non-existent John Doe earlier in season 5, Abby came back with results that indicated an unusual anomaly. I looked it up and it's a genetic disorder (I can't remember what it is called but I found it on Wikipedia by looking up the anomaly).