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ROME — The body of Yara Gambirasio, a 13-year-old student, was found on a chilly day in a quiet northern city in Lombardy in February 2011, three months after she was reported missing following a gymnastics practice. The autopsy showed she had been beaten but not sexually abused, stabbed several times and left to die in a field less than 10 miles from her home.

The autopsy also revealed stains on the young girl’s frayed clothing: a liquid that contained the DNA of a person whom investigators called “Unknown Male No. 1.”

In the absence of other evidence, investigators embarked on the country’s largest DNA dragnet, taking genetic samples from nearly 22,000 people.

Finally, last month, they said they had found their suspect, Massimo Giuseppe Bossetti, a 43-year-old father of three from Lombardy.

But what some praised as a triumph of modern science and 21st century sleuthing, has also set off a debate about the risks of privacy violations and the darkened corners of the past they can expose after the DNA testing also revealed something unknown even...