Jan 17 (Reuters) - A federal judge has ruled that an $83 million malpractice suit can move forward against law firm Ropes & Gray, which is defending its handling of patent applications for a major New York research facility.

U.S. District Judge Richard Stearns in Massachusetts on Friday threw out a motion to dismiss filed by Ropes & Gray, a 1,000-attorney firm based in Boston, which in February 2010 was sued by Cold Spring Harbor Laboratory over work the firm performed on patents for synthetic gene structures used in cancer research. The gene research was recognized as the "Breakthrough of the Year" by Science magazine in 2002.

Cold Spring Harbor Laboratory, a non-profit cancer, neuroscience and biology research center on Long Island, accused former Ropes & Gray partner Matthew Vincent of copying and pasting large portions of text on applications the laboratory submitted to the U.S. Patent & Trademark Office from a previous application filed by an unrelated party. The laboratory claimed that the copied text did not accurately reflect its patents and prejudiced and delayed the PTO's consideration of the applications.

Cold Spring Harbor Laboratory argued that Ropes & Gray knew of Vincent's alleged wrongdoing but did not tell the laboratory about it. It is seeking as much as $82.5 million in damages and has sued the firm for legal malpractice, breach of fiduciary duty, negligence and fraud.

Ropes & Gray did not respond to repeated requests for comment.

According to the Jan. 13 decision, Vincent resigned from practicing law after a disciplinary investigation revealed that he had established his own company while at Ropes & Gray and collected about $700,000 from the firm's clients for work that could not be verified or substantiated. Ropes & Gray billed the laboratory about $10,000 under the guise of work Vincent's company allegedly performed, the decision said.

In its motion to dismiss, Ropes & Gray said that the laboratory failed to state a valid malpractice claim, since the copying of text from other applications is standard practice and because the laboratory did not argue that Vincent's actions caused the delay or denial of the patent approvals.

Stearns disagreed.

"This argument does not appear to be based on a fair reading of the amended complaint, which repeatedly alleges a causal link between Vincent's conduct and the PTO's rejection" of the applications, he wrote.

The case is Cold Spring Harbor Laboratory v. Ropes & Gray, No. 11-1012, U.S. District Court in Massachusetts.

For Cold Spring Harbor Laboratory: Chad Ziegler, with Scully, Scott, Murphy & Presser, in Garden City, N.Y.

For Ropes & Gray: Irena Royzman, Patterson, Belknap, Webb & Tyler in New York.

(Reporting By Leigh Jones; Follow us on Twitter: @ReutersLegal)