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Seven years ago, Congress prohibited employers and insurers from discriminating against people with genes that increase their risks for costly diseases, but the case that experts believe is the first to go to trial under the law involves something completely different: an effort by an employer to detect employee wrongdoing with genetic sleuthing.

Amy Totenberg, the federal district judge in Atlanta who is hearing the case, called it the mystery of the devious defecator.

Frustrated supervisors at a warehouse outside Atlanta were trying to figure out who was leaving piles of feces around the facility. They pulled aside two laborers whom they suspected. The men, fearing for their jobs, agreed to have the inside of their mouths swabbed for a genetic analysis that would compare their DNA with that of the feces. Jack Lowe, a forklift operator, said word quickly spread and they became the objects of humiliating jokes.

“They were laughing at us,” he said.

The two men were cleared — their DNA was not a match. They kept their jobs but sued the company. On May...