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The flashy new industry of personalized gene testing is experiencing some early blowback.

Over the last six months, New York State's Department of Health has sent letters raising the specter of fines and jail time to six online gene-testing firms that offer consumers the ability to peer into their genome to assess their future risk of getting diseases such as cancer, heart disease and multiple sclerosis. Often, it turns out, the services offering these DNA deep-dives are doing so without the involvement of a doctor. That puts them on the wrong side of the law.

Targets in New York's letter-writing campaign include the high-profile 23andMe, in Mountain View, Calif, (run by the wife of Google co-founder Sergey Brin) and Navigenics, of Redwood Shores, Calif., as well as their publicly traded partners Illumina and Affymetrix. The letters say the companies cannot perform their gene scans on New York residents without a permit. Warning letters to three more online gene-scanning firms are due to go out soon, New York says.

California health regulators are also investigating 12 complaints from the public about...