A Boston federal judge has denied motions by Ropes & Gray and former partner Matthew Vincent to dismiss a malpractice case based on claims that they mishandled patent applications at the U.S. Patent and Trademark Office.

On Jan. 13, Judge Richard Stearns of the District of Massachusetts denied motions by the firm and Vincent to dismiss malpractice claims brought by Cold Spring Harbor Laboratory.

According to the order, Ropes & Gray was the principal outside patent counsel for Cold Spring Harbor, a biomedical research and educational institution in Cold Spring Harbor, N.Y., from 2001 until late 2008.

Cold Spring Harbor relied on the firm to patent inventions related to methods of regulating gene expressions by using synthetic RNA molecules. Vincent was the main Ropes & Gray attorney doing the work.

In September 2006, an examiner at the U.S. Patent and Trademark Office (PTO) rejected all pending claims in a particular Cold Spring Harbor application as anticipated by another patent awarded to a different researcher. Cold Spring Harbor claims Vincent copied extensive portions of text from the other earlier patent application instead of describing the Cold Spring invention. The laboratory claims it discovered this problem in early 2008 after its own investigation of Vincent’s prosecution of the patent applications.

According to Stearns’ order, Ropes & Gray would not inform the PTO what happened unless Cold Spring Harbor signed a waiver releasing the firm from any future liability. Cold Spring Harbor refused to sign the waiver.

Ropes & Gray fired Vincent in April 2009, according to Cold Spring Harbor’s complaint. Vincent resigned from the practice of law in September 2009, according to a Massachusetts Board of Bar Overseers disciplinary database.

From April 2002 through September 2008, Vincent billed and collected $733,771.30 from Ropes & Gray, which in turn billed its clients, through a business entity called “The IP Resource Company.” Vincent never told Ropes & Gray about the company, which purportedly did patent database searches.

Cold Spring Harbor first sued Ropes & Gray and Vincent in the Eastern District of New York. The case was transferred to the District of Massachusetts in January 2011. Cold Spring Harbor’s legal claims include legal malpractice, breach of fiduciary duty, fraud and fraudulent concealment and negligence. Its breach claims stem from the defendants’ simultaneous representation of two competitors: RXi Pharmaceuticals Corp. and Insert Therapeutics, and its successor Arrowhead Research Corp. and affiliate Calando Pharmaceuticals Inc.

RXi and Cold Spring Harbor entered into a license agreement concerning Cold Spring’s synthetic RNA molecule technology in March of 2007, but Cold Spring Harbor claims Ropes & Gray did not seek a waiver of conflict from it until that October.

As for the Insert Therapeutics-related allegations, Cold Spring Harbor claims Vincent was part of the group that formed Calando to exclusively license Insert’s technologies, including certain technology a Cold Spring Harbor employee developed. Vincent later proposed that Cold Spring Harbor form a business venture with Calando, but did not disclose his relationship with Calando.

The laboratory also claims that Ropes & Gray breached its fiduciary duty by allowing Vincent to represent Insert and co-own Calando.

Cold Spring Harbor claims it was forced to spend “no less than $500,000″ in attorney fees because of the defendants’ wrongdoing and it lost licensing opportunities worth between $36.5 million to $82.5 million. It also claims that its damages include all of the attorney fees it has paid to Ropes & Gray since 2001, which total at least $1.4 million.

Cold Spring Harbor seeks a judgment at trial between $36.5 million to $82.5 million, punitive damages and attorney fees and costs.

Stearns wrote that “Vincent and [Ropes & Gray] were necessarily made privy to confidential information about [Cold Spring Harbor's] patent licensing strategy. By putting themselves in a position where they could reveal such information to potential competitors such as Insert and RXi, defendants created a direct conflict of interest.

Ropes & Gray declined to comment, according to a firm spokesperson.

The firm’s lawyers at Patterson, Belknap, Webb & Tyler in New York declined to comment.

Vincent’s lawyers at Boston’s Sherin & Lodgen also declined to comment. Lawyers at L’Abbate, Balkan, Colavita & Contini in Garden City, N.Y., who also represented Vincent, did not respond to requests for comment. Vincent could not be reached for comment.

Peter Bernstein, a partner at Scully, Scott, Murphy & Presser in Garden City, N.Y., who represents Cold Spring Harbor, said, “We are pleased that the court has denied Ropes & Gray’s motion to dismiss and can now move forward with substantive aspects of the case.” Mirick, O’Connell, DeMallie & Lougee of Worcester, Mass., also represented Cold Spring Harbor.

Sheri Qualters can be contacted at squalters@alm.com.