It is known that astronauts' bodies adapt to micro-gravity, but it was generally assumed the effects wore off upon their return to Earth.
Scott landed in March 2016, and it appears his body has yet to return to normal.
Some of the genes that seem to have changed permanently involved DNA repair, bone formation and how the cells use oxygen.
Nasa took the unique opportunity of having astronaut twins to learn more about the genetic changes of long periods in space.
The long-term effects of space habitation are still unknown and the space agency said the experiment was a stepping stone for its mission to Mars.
While Scott was away, experts monitored the brothers' DNA.
"We really see an explosion, like fireworks taking off, as soon as the human body gets into space," said Dr Chris Mason, Twins Study investigator, of Weill Cornell Medicine. "We've seen thousands of genes change. This happens as soon as an astronaut gets into space, and the activity persists temporarily upon return to Earth."
He added that as well as understanding risks for space travel, the study could lead to finding ways to protect and fix genetic changes.
Nasa collected regular readings for metabolites, cytokines and proteins and discovered that spaceflight was linked to oxygen deprivation stress, increased inflammation and dramatic nutrient shifts which affect genes.
Scientists also discovered that Scott's telomeres — the caps at the end of chromosomes that shorten with age — stretched in space, suggesting a possible protection against ageing. They returned to normal within two days of landing back on Earth.
The study showed no cognitive difference between Scott and Mark after being on the space station.
Researchers are now evaluating what impact the findings might have upon space travel beyond Earth's orbit.
- Telegraph Group Ltd
