The outlook for the business of gene patenting has suddenly turned very, very murky. In a highly anticipated decision issued late Monday, Manhattan federal district court judge Robert Sweet invalidated patents on two gene mutations associated with breast and ovarian cancer. The patents are held by Myriad Genetics and the Utah Research Foundation. Here’s Judge Sweet’s 156-page opinion, which is sure to provoke hot debate in the IP world. And here’s preliminary analysis of the ruling from Patent Litigation Weekly columnist Joe Mullin.

The American Civil Liberties Union and the Public Patent Foundation had challenged the gene patents, arguing such patents violate the U.S. Constitution by restricting the rights of patients and researchers to genetic material found in nature. (Myriad charges women thousands of dollars for tests to determine whether they have the mutations, and it closely guards scientists’ use of the patented genes.) Myriad contends that its gene patents and others like them are responsible for bringing “personalized medicine” to the market.

At last month’s closely watched summary judgment arguments, lawyers for both sides debated whether the isolated DNA sequences covered by Myriad’s gene patents are “markedly different” from the same sequences as they exist in the human body. Myriad contended that they are; the ACLU said they are not.

Judge Sweet agreed with the ACLU. “The resolution of these motions is based upon long recognized principles of molecular biology and genetics: DNA represents the physical embodiment of biological information, distinct in its essential characteristics from any other chemical found in nature,” he wrote. “It is concluded that DNA’s existence in an ‘isolated’ form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issue directed to ‘isolated DNA’ containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter.”

In a brief interview on Monday, Chris Hansen of the ACLU said that Judge Sweet’s decision could potentially invalidate other gene patents. According to Hansen, approximately 20 percent of the human genome is patented.

Myriad’s lead counsel, Brian Poissant of Jones Day, declined to comment.