So Tut's DNA results are in, and they are fascinating. I won't link you, because JAMA is charging 15.00 a pop for the article... but you can look at the stuff elsewhere in bits. (cough, EgytianDreams forum, cough.)
But basically- Tutankhamun is the offspring of full-siblings, the mummy in KV-55 and the mummy identified as the "Younger Lady". KV-55 and the younger lady are the son and daughter of Amenhotep3 and the mummy identified as the Elder Lady, now definitively identified as Queen Tiye. The babies in Tut's tomb are his kids, and also the kids of another unidentified female mummy. But the paper is silent on the relationship between KV-55 (putative heretic pharaoh) and said unidentified female mummy. Also silent on Younger Lady and unidentified female mummy.
More questions than answers right now. If no relationship between unidentified female and the parents of Tut, who the hell is this woman Tut was breeding with? Is it possible the relationships exist, and haven't been stated for some reason? Could further testing flesh this mess out?
I'll put my suspicions out there. When all is said and done, I'm betting the Younger Lady actually is Nefertiti- that we've been wrong about her nonroyal background. And I'm betting the unidentified female is Ankesenamun.... which would mean the babies were born of multi-generational inbreeding.
Of course, if Kv-55 mummy is potentially Akhenaten, there's equal chance he could be Smenkhare.... but that would mean he had a wife other than Meritaten, and that he was not the son of Akhenaten but rather Amenhotep and Tiye, making him the heretic's brother.
Again- more questions than answers.