Paul Allen was working on the Allen Institute for Immunology before he died in October.

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Paul Allen’s estate is making its first major philanthropic gift after his death, giving $125 million to establish a research division focused on the immune system and related diseases.

The Allen Institute announced Wednesday that the Microsoft co-founder made the commitment to start the Allen Institute for Immunology, a project he was working on before he died at age 65 in October. It’s the fourth division to be established under the nonprofit, with others focused on cells, the brain and providing grants to further advances in medical science.

Allan Jones, chief executive officer of the institute, described the announcement as “bittersweet” after Allen’s death from complications of non-Hodgkin’s lymphoma. While other units have made important scientific advances that will ultimately translate into medical applications, Jones said, “this is really the first time that we’ve made a pretty significant investment in something that has a direct application to human health.”

Allen undertook a variety of business and philanthropic endeavors in the three decades after he left Microsoft. At least half his $26 billion fortune is probably earmarked for charitable purposes after he joined the Giving Pledge. He provided the bulk of funding for the Allen Institute, which was started in 2003 and employs about 500 people. Allen’s sister Jody is on the board.

Goals for the new division include a long-term study to collect data on 60 to 100 children, young adult and elderly volunteers and document changes in their immune systems, according to Thomas Bumol, a longtime Eli Lilly executive who leads the unit. Unlike studies that seek clean answers about the effectiveness of a drug in a specific situation, the institute will study the “normal variant noise” of people’s health, he said.

“That will be a pioneering way to study the immune system for the future,” Bumol said. The effort will involve 70 scientists internally, in addition to partnerships with hospitals and outside research centers.

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