This past July, philanthropist Paul Allen spent hours grilling his team about an ambitious plan they were hatching: Expanding the Allen Institute — the Seattle-based scientific research organization he founded and funded — to add a new division that would probe the mysteries of the human immune system.

For Allen, the quest was personal (he had survived two cancers of the immune system) as well as intellectual (the Microsoft co-founder was fascinated with complex biological problems). Allen kept pushing his team to articulate how it was going to maximize the impact of the research, according to one of the participants in those July meetings. Finally satisfied with the plans, Allen decided to commit $125 million to fund the immunology division.

Allen died three months later of septic shock stemming from non-Hodgkin’s lymphoma.

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On Wednesday, the Allen Institute announced its new division. With Allen’s gift, the Allen Institute for Immunology will hire 70 in-house scientists and operations staffers, partner with five clinical research groups, and become a new part of Allen’s legacy.

The researchers will analyze blood samples and other medical data collected over several years from both healthy volunteers and patients with diseases of the immune system. In its initial stage, the division will focus on studying two cancers (multiple myeloma and melanoma) and three autoimmune disorders (rheumatoid arthritis, ulcerative colitis, and Crohn’s disease).

The goal: to better understand normal variation in the human immune system — and what goes awry when people get sick.

“We aim to try to truly understand what [immune health] is. And we think that’s going to be a secret to understanding what goes wrong in these diseases,” said Thomas Bumol, a longtime executive at Eli Lilly who will lead the new division as its executive director.

The new division will not develop therapeutics, but in the future it may “partner and collaborate with others who would be interested in taking our observations and maturing them,” Bumol said.

The Allen Institute, which has no clinical operations, will partner in its new immunology research endeavor with two clinical research groups in Seattle (the Virginia Mason Health System’s Benaroya Research Institute and the Fred Hutchinson Cancer Research Center) and three more around the country (the University of Pennsylvania, the University of Colorado, and the University of California, San Diego). The partners will contribute patient samples while also collaborating scientifically.

The new immunology division marks a significant expansion of the Allen Institute, which has about 300 scientists studying brain science and nearly 70 studying cell science.

Bumol’s 70-person team will include the usual ingredients of a research organization: two large biology groups working on experimental immunology and molecular biology, as well as a small research administration staff. It will also include a significant investment in computational biologists and information technology specialists — an effort to honor Allen’s request that the researchers prioritize mining data in search of insight about the mechanism of disease.

As of the end of November, Bumol had already brought on eight staffers, with four more acceptances from hires who will start in the coming weeks.

Bumol worked as a consultant to help the Allen Institute develop the plans for the new division before he joined to lead it this past March. During his years running an immunology research group at Lilly, he found unusual success (his group discovered the autoimmune drug now sold as Taltz) but also experienced painful failure (he worked on an unsuccessful therapy for lupus).

Those experiences, Bumol said, made clear to him that “our understanding of the immune system was basically in preschool — and that we really needed to bring that up to a different level.”

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