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The UK Border Agency "human provenance pilot project" is aimed at stopping people "swapping" nationality in the hope of remaining in the UK.
It is testing migrants to try to establish where they are from.
But scientists say it is not possible to tell what country a person comes from using the tests.
The pilot began earlier this month, targeting migrants from the Horn of Africa. Mouth swabs, hair and nail samples will be tested on a voluntary basis.
It is understood there is concern that some asylum seekers are pretending to be from countries like war-torn Somalia when making their asylum claims when in fact they are from neighbouring countries.
The Home Office said "nationality swapping is often used by fraudulent asylum seekers to help prevent their removal.
"That is why we are continuously looking at new and improved ways to ensure that we can ascertain the correct identity and nationality from every asylum seeker."
Professor Sir Alec Jeffreys of the University of Leicester pioneered human DNA fingerprinting. He described the pilot as "naive and scientifically flawed".
"It is...