Ahlquist’s focus was treating and researching colorectal cancer. Spurred by the understanding that early detection could prevent many deaths from colorectal cancer, he co-invented the Cologuard test, a noninvasive stool test that can detect DNA and hemoglobin markers associated with colorectal cancer. When Exact Sciences bought the license to further develop and manufacture the test, Ahlquist became the company’s chief scientific advisor. Cologuard was approved by the U.S. Food and Drug Administration in 2014.

Over the course of his career, Ahlquist authored more than 200 peer-reviewed manuscripts and received more than 80 patents. He was revered as a mentor and teacher. Among many awards, he received the first Mayo Clinic Distinguished Inventor Award, the Mayo Clinic Investigator of the Year, the Mayo Clinic Internal Medicine Research Career Achievement Award, and the William Beaumont Prize from the American Gastroenterological Association.