Dr Garry Nolan, professor of microbiology and immunology at the Stanford University School of Medicine, began the scientific exploration of Ata in 2012, when a friend called saying he might have found an alien.
Ata was found in northern Chile by Oscar Munoz, who sold the remains to Ramon Navia-Osorio, a Spanish businessman who believed it could be evidence of alien life.
Nolan said: "I heard about this specimen through a friend of mine. There had been some extraordinary claims put forward."
He added: "I managed to get a picture of it - you couldn't look at this specimen and not think it's interesting.
"It's quite dramatic.
"So I told my friend, 'Look, whatever it is, if it's got DNA, I can do the analysis'."
So Nolan and his team took DNA from bone marrow in Ata's ribs, and compared it with human and primate genomes. Nolan said that 2 per cent of the DNA could not be matched with human DNA, but that was due to degradation of the sample rather than evidence of extraterrestrial biology.
Further tests showed that the mummy was indeed human and female, with a mix of Native American and European ancestry typical of the region of Chile where it was found.
Researchers next looked for genetic clues that could explain Ata's small stature, multiple bone and skull abnormalities, abnormal rib count, and premature bone age.
The genomic results turned up a number of mutations in seven genes that separately or in combinations contributed to bone deformities, facial malformation and dwarfism. Some mutations, though found in genes already known to cause disease, had not before been associated with bone growth or development disorders.
Nolan believes further research into Ata's speedy bone ageing could one day benefit patients. "Maybe there's a way to accelerate bone growth in people who need it, people who have bad breaks," he said. "The symptoms and size of this girl were extremely unusual. Nothing like this has been seen before.
"Certainly, nobody has looked into the genetics of it."
Dr Atul Butte, director of the Institute for Computational Health Sciences at the University of California in San Francisco, said: "For me, what really came out of this study was the idea that we shouldn't stop investigating when we find one gene that might explain a symptom.
"There could be multiple things going wrong, and it's worth getting a full explanation, especially as we head closer and closer to gene therapy."
Nolan said he hoped that one day Ata would be given a proper burial. Judging from the skeleton's intact condition, he said, the baby girl's remains were probably no more than 40 years old.
"We now know that it's a child, and probably either a pre- or post-term birth and death," he said. "I think it should be returned to the country of origin and buried according to the customs of the local people."
The research was published in the journal Genome Research.
