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When Meg DeBoe decided to tap her Christmas fund to order a $99 consumer DNA test from 23andMe last year, she was disappointed: it arrived with no information on what her genes said about her chance of developing Alzheimer’s and heart disease. The report only delved into her genetic genealogy, possible relatives, and ethnic roots.

That’s because just a month earlier, in November 2013, the Food and Drug Administration had cracked down on 23andMe. The direct-to-consumer gene testing company’s popular DNA health reports and slick TV ads were illegal, it said, since they’d never been cleared by the agency.

But DeBoe, a mommy blogger and author of children’s books, found a way to get the health information she wanted anyway. Using a low-budget Web service called Promethease, she paid $5 to upload her raw 23andMe data. Within a few minutes she was looking into a report with entries dividing her genes into “Bad news” and “Good news.”

As tens of thousands of others seek similar information about their genetic disposition, they are loading their DNA data into...