Sam developed an unusual form of cancer, that of the tonsils. While he's been gone in the short term because of his character loss, this is why he's been gone for more than an episode or two. Caught early, surgeries and therapy have been very successful. Expected to make a full recovery, but it's a "long row to hoe" as my dad would say.
Edit: Also, the source of the cancer was HPV. This is a virus that could be eradicated with vaccination. It is the source of > 99% of cervical and similar (but unknown to me) percentage of tonsilar cancer.
Also, no real reason to put it in spoiler tags, I guess. Removed. Reflexive habit when dealing with healthcare information...