Some of the technical stuff is over my head; I have never delved too deeply into the technical aspects of genetic research, so I'll leave it to posters more savvy than I to comment. However, other information is very surprising and interesting to those of us who study the history. For instance, most but not all researchers believe that Akhenaten was the father of Tutankhamun and that his mother was a secondary queen named Kiya. A tomb in the Valley of the Kings was discovered in 1907 by Theodore Davis and his archaeologist, Edward R. Ayrton. This tomb, KV55, has puzzled people ever since. It contained one badly decayed mummy (skeletonized) in a heavily damaged coffin that some argued was the body of Akhenaten; based on the examinations of more than one forensic anthropologist, however, the skeleton was that of a person no more than 25 years of age at death, which was too young for Akhenaten. Therefore, most of us have believed that the skeleton belonged to a very ephemeral and poorly understood king named Smenkhkare.
However, the SCA's genetic analysis has confirmed that this mummy was the father of Tutankhamun. Tut's dad, then, was this fellow (the skull of the skeleton in KV55). Because the genetic tests have confirmed that the mummy thought to be Amunhotep III was in fact him (long contested by some), we can now rule out that Amunhotep III was the father of the boy-king. This used to be a popular theory among some researchers.
KV35 is the tomb of Amunhotep II. It was discovered in 1898 by Victor Loret, and in the course of clearing the tomb Loret came upon a sealed side chamber containing mummies that had been moved in ancient history, some time following their original burials. Two of the mummies belong to regal-looking females and are known as Younger Lady and Elder Lady. So then, the genetic tests have confirmed that KV35YL, the Younger Lady, was both the full sister of Akhenaten and the mother of Tutankhamun. This presents a big mystery. It's unlikely that Kiya was Akhenaten's sister, so who is this woman? There are several possible candidates: Sitamen, Isis, Nebetah, or Baketaten, all royal ladies known from that time. There is also Nefertiti, of course, but as with Kiya, she was probably not Akhenaten's sister.
The tests have further confirmed that KV55 and KV35YL were the children of Amunhotep III and his principal queen, Tiye. At this point I may sound a little redundant, so please forgive me. This is all big news to those of us who study the history. Long suspected and also now confirmed is that KV35EL, the Elder Lady from that cache of mummies in KV35, is in fact the mummy of Queen Tiye. Some of you may remember the big fuss the British Egyptologist Joann Fletcher tried to make in identifying this mummy as Nefertiti, so now this officially sinks her theory. A theory she rushed to publish and which landed her in a heap of trouble.
Also confirmed is that KV35EL (Elder Lady) was the daughter of the nobles Yuya and Tjuya, who were buried in KV46 during the reign of Amunhotep III.
And yet more. A female mummy from KV21 (sorry, no photo) is quite possibly that of Ankhesenamun, queen of Tutankhamun. This is most likely going to be confirmed. Two stillborn mummified infant girls (photo of one here) were found in KV62, Tutankhamun's tomb, when it was being cleared in the 1920s. It has been verified that Tutankhamun was their father and the KV21 mummy their mother. Tutankhamun is not known to have another wife, so the KV21 mummy probably is in fact Ankhesenamun, long lost to history.
The genetic tests have clarified that there is no trace of Marfan's syndrome in Tut's family line. The odd appearance of Akhenaten and family in the early artwork of the Amarna Period most likely has nothing to do with disease, an idea most Egyptologists abandoned years ago but still popular among laypeople. However, other diseases were prevalent, malaria among them. It was a combination of weakening by malaria and the severe fracture to his left distal femur that most likely caused the death of Tutankhamun.
Here are some JAMA links (and one from National Geographic) where you can read more, including the one from which I quoted above:
Of course I would like to write more and there's a lot more to be said--all of you know how addicted I am to the study of ancient Egypt. Still, I've written enough, and I hope some of you will comment and contribute.