As more details surface about the alleged misappropriation of tens of thousands of dollars by the Berkeley Divinity School, the controversy surrounding the school’s finances has forced Yale officials to re-examine Yale’s relationship with affiliated institutions.

Yale officials remain in the ongoing process of drafting a new affiliation agreement with Berkeley.

“We have had a lot of conversation already, so it is pretty far along,” Yale President Richard Levin said. “I am optimistic that we will have a satisfactory renewed agreement.”

Levin declined comment on what terms he desires, but the recent allegations may reshape the University’s entire framework for pursuing affiliation agreements.

“I think the whole issue with affiliation agreements and what they do and do not mean is one we will be looking at,” Provost Alison Richard said. “It is not a matter that we have given consistent strategic attention to. We have to look at our whole procedures for affiliations and how we conduct those affiliations.”

Levin said that the University is only approached occasionally by organizations seeking affiliation, but he said that the recent events surrounding Berkeley would color his consideration of future entities seeking University affiliation. He said Yale currently has such agreements with a handful of institutions, including the Haskings and John B. Pierce laboratories.

Yale does not allow its schools to have assets in accounts outside University jurisdiction. The Hartford Courant has reported that the Berkeley Divinity School had a private unregulated bank account of which Yale officials were not aware.

An audit this summer revealed Berkeley’s independent account.

“There was a change in deans occurring. It had been about 10 years since the last audit,” Vice President of Finance and Administration Robert Culver said. “It was to make sure all disbursements were properly controlled from an accounting perspective. There was no premeditated notion that we needed to look at the Divinity School at all.”

University officials maintain Yale’s 1985 reaffiliation agreement with Berkeley stated that the affiliation required all of Berkeley’s funds to go through Yale.

“It was explicit in the affiliation agreement … that stipulated the actual terms of affiliation that said that all of their funds had to flow through Yale,” Levin said.

University Secretary Linda Lorimer, who in 1985 worked as the liaison between the Yale Divinity School and the Berkeley Divinity School, said that the 1985 affiliation agreement represented over a year and a half of work by a subcommittee consisting of Berkeley trustees, the Yale Divinity and Berkeley Divinity deans and herself.

“The 1985 agreement brought Berkeley and Yale much closer together in terms of specifying how students would be admitted, how funds would flow and how the budget of Berkeley would be developed,” Lorimer said.

Yale, however, never directly handled Berkeley’s donations, Vice President for Development Charles Pagnam said. While Pagnam, who oversees Yale’s fund-raising efforts, said he knew some of the Berkeley Divinity School donors through their connections to the Yale Divinity School, he added that he did not know how Berkeley handled its donations and other transactions.

“I don’t know about the quote ‘secret checking account’,” Pagnam said. “Berkeley had always received gifts directly — how they process those gifts I have no idea.”

Christian Sonne, the chairman of the Berkeley Divinity School board of trustees, declined comment.