Neb-Ma'at-Re, genetic testing proves or disproves the family relationship of one person to another. That is how genetic testing would prove or disprove Nefertiti being Tut's stepmom or mother as i believe.
The real problem is getting hold of Nefertiti's genetic makeup to do such a test. That is if Islamic Egyptian authorities would allow such a test in the first place. (They don't normally allow it)
Okay say that problem the Islamic authorities allow the testing to be done. We return to the problem of getting Nefertiti's genetic makeup.
Myself i would chose the Elder Lady from Tomb KV35 for the first testing. I agree with Dr. Susan E. James in her article "Who is Mummy Elder Lady?" In KMT A Modern Journal of Ancient Egypt Volume 12, Number 2 Summer 2001. In that it is this mummy the Elder Lady that is Queen Nefertiti, not the Younger Lady.
The Elder Lady is more comonly believed to be Queen Tiye, Nefertiti's mother-in-law but Dr. James in the forementioned article explains (to my satisfaction anyway ) why the Queen Tiye identification is wrong.
Another reason i believe the Elder Lady to have been Nefertiti is on account of her head of hair, not a wig like so many other Royal women. The removal of all body hair was a common royal obligation due to their relation and service to the Ancient Gods of Egypt. Nefertiti is alone in that as Queen she did not serve those Gods and hence the need to remove her head of hair would not be so required.
Because i do not believe that Akhenaten loved Nefertiti so much as to overlook her common background (if she really was), excusing her for not providing him with a royal male heir, and making her Great Royal Wife over the mother of his sons. This rings more like Victorian fiction than Late Bronze Age Royal Egyptian reality to me. He needed a son, if not for tradition then for the sake of his religious reforms.
One might argue that his own common mother was Great Royal Wife, okay granted but at least Queen Tiye gave her husband 2 sons to earn that title.
I might add that neighter son was ever shown with their Royal parents as a child unlike Akhenaten's sisters who where shown in temple scenes. (See Dr. Joyce Tyldesley's book Nefertiti, Penguin Books (1998), page 52)
Dr. Nicholas Reeves in his book The Complete Tutankhamun, The King, The Tomb, The Royal Treasure, Thames and Hudson pubishers ,(1997) writes on page 23 about "the monuments which are now known to have been usurped from Akhenaten's scondary wife, Kiya." He follows this up on page 25 repeating again that Kiya's monuments are appropriated by Nefertitie's daughter Meritaten.
This is all agreed with in Dr. Joyce Tyldesley's book Nefertiti, page 153. Same book pages 155-157 we have Kiya's coffin being remade into a Kings coffin and being resealed in KV55 tomb under the sealings of Tutankhamun. Some son he doesn't elevate his mother to even King's Wife status but seals her coffin for his dad! While Tuthmosis III raised his common mother in statue to God's Wife. (see Women in Ancient Egypt, by Gay Robbins, Havard Press, (1993) page 151.)
No i do not believe Kiya was his mother or even the mother of Smenkhare, despite pg 130 in Tyldesley's book "There is also strong circumstantial evidence to suggest that Kiya gave Akhenaten at least two sons." She was just to DISRESPECTED after death to ever have been the mother of Pharaoh.
So this leaves us with who might have been their mother, Queens Tiye, or Sitamen? But if either of these Queens had been their mother, why no inclusion of her? They would not and did not suffer the comtamination of Akhenaten in later years. The mother of these boys could not be honored for some reason. I like to believe because she was the Queen of that Criminal Akhenaten.
Nefertiti, had no monuments destroyed after her death, or the death of husband. Why?
So if we go back to the Elder Lady and test her DNA against the KNOWN DNA of Tutankhamun. Remember she is thought to be Queen Tiye, (see Dr. James article), and we know that Queen Tiye was related to Tut either as,or as both grandmother and mother. If it is maternal DNA we can at least rule out poor abused Kiya as his mother and Tut gains in that he didn't disgrace his mother after her death.
Aw but the catch is Islamic Egyptian Authorities don't allow genetic testing at this time.