The Supreme Court’s June decision banning certain kinds of human gene patents is making waves again this week, threatening to submerge diagnostic tests in legal wrangling. On Wednesday, a U.S. district court in San Francisco invalidated a patent on a new, blood-based prenatal test for Down syndrome. The reason, according to the judge, is that the patent poses a “risk of preempting [other uses of] the natural phenomenon” that the test focuses on—fetal DNA that can be isolated from the mother’s blood.

Judge Susan Illston wrote in her opinion that she invalidated the patent, held by the San Diego, California-based company Sequenom, based on several recent rulings, including the Supreme Court’s decision denying patent claims on BRCA genes used in cancer risk testing . She also cited an earlier court decision denying a patent for a blood test because it lacked inventiveness, offered by Prometheus Laboratories Inc. of San Diego, that measures risks linked to exposure to a therapeutic drug.

This week’s decision affects a test for Down syndrome patented and marketed in 2011 by Sequenom. The test works in a novel way, by isolating fetal DNA from the mother’s bloodstream rather than by the older and riskier method of taking tissue from the womb (as in amniocentesis, for example). Another part of the novelty is the test’s efficiency: It uses the father’s DNA to cue a search for fetal DNA in circulation, then examines the isolated DNA for Down syndrome’s anomalies. Although Sequenom’s patent on the test (U.S. patent 6,258,540) claims a method of testing and not a natural product, Illston still ruled that it could lock up a “natural phenomenon.”

If this decision stands, “I don’t see how you can maintain a genetic diagnostic claim anymore,” says Christopher Holman, a molecular biologist and professor of law at the University of Missouri, Kansas City. He finds two aspects of the decision striking: Its demand for greater inventiveness in the claimed method of testing, and its finding that Sequenom’s patent could preempt nature. Holman thinks some of the reasoning is “strange.” He points out that Sequenom had argued in court that other companies could continue to do fetal blood tests so long as they used a different method—and that there are other methods that could be used. But the judge didn’t buy this, Holman says: She ruled that other methods are not commercially viable, and for that reason, Sequenom’s claims were preemptive.

One of those cheering the judge’s ruling is Ariosa Diagnostics of San Jose, California. This company, one of several rivals in this field, was the first to enter the legal battle in 2011: It wanted to offer a fetal DNA test of its own and took Sequenom to court to prevent Sequenom from getting the first jump with a patent infringement lawsuit. Sequenom countersued. Two other diagnostic companies joined the fray. This week’s decision is the outcome of that legal brawl. Yesterday, Ariosa issued a press release claiming it had won a “complete victory.”