Janet D. Rowley, a medical researcher whose innovative study of chromosomes led to a revolutionary understanding that certain forms of cancer are caused by genetic abnormalities, died Dec. 17 at her home in Chicago. She was 88.

She had ovarian cancer, according to a statement from the University of Chicago, with which she had been affiliated since the 1940s.

Dr. Rowley, who was awarded the nation’s highest civilian honor, the Presidential Medal of Freedom, in 2009, was a part-time researcher who often worked at her dining room table in the early years of her career. She made her first landmark discoveries in 1972, when she became the first scientist to find evidence that alterations in chromosomes could lead to forms of leukemia and other kinds of cancer.

Some scientists were skeptical of her findings, and the New England Journal of Medicine refused to publish a research paper she had written. But over and over again, Dr. Rowley was able to demonstrate a link between genetic markers, or repeated chromosomal patterns, and particular diseases.

Before her groundbreaking studies, most scientists believed that genetic mutations occurred after cancer invaded the body. Dr. Rowley established that the opposite was true: that genetic abnormalities were the cause of cancer, not the result of cancer.

Janet Rowley died Dec. 17 at 88. (Courtesy of University of Chicago Medicine)

“Few would have thought this was possible,” National Institutes of Health Director Francis S. Collins said in an interview. “She was way ahead of the field on this.”

Before turning to laboratory work, Dr. Rowley treated children with Down syndrome and other developmental difficulties. In 1959, Down syndrome was one of the first conditions associated with a chromosomal aberration.

Dr. Rowley began her study of chromosomes in 1960 at a laboratory in England, where her husband — also a renowned medical researcher — was on academic sabbatical. When she returned to Chicago in 1961, she persuaded a former teacher to let her work in his laboratory. She had just enough space for a microscope.

She soon became adept at the analysis of chromosomes, then a new field of science called cytogenetics. (Chromosomes, which occur in pairs, carry genetic information in living organisms; humans have 23 pairs of chromosomes.)

Dr. Rowley often photographed the chromosomes in her laboratory, then arranged the images on her dining room table for further study. She warned her four sons not to move them out of sequence.

During a second tour of study in England in the early 1970s, Dr. Rowley learned a new technique called “banding,” or the use of stains to observe and identify chromosomes with greater precision.

The innovation allowed her to make her first major discovery. In examining the chromosomes of a patient with acute myeloid leukemia, she noticed that part of chromosome 8 had broken off and traded places with part of chromosome 21. She was the first to identify the phenomenon that became known as translocation.

Soon after, Dr. Rowley solved the mystery of the “Philadelphia chromosome,” which had been an enigma in the field of genetics. In the early 1960s, two researchers in Philadelphia had identified a structural anomaly in chromosome 22 that seemed to be correlated with chronic myelogenous leukemia.

But no one understood the full significance of the Philadelphia chromosome until Dr. Rowley realized that a portion had broken away and attached itself to chromosome 9. Through the process of translocation, part of chromosome 9 had, in turn, migrated to chromosome 22.

“It was a very striking finding,” Harold E. Varmus, a Nobel laureate and the director of the National Cancer Institute, said in an interview. “Virtually every case of [myelogenous] leukemia had a Philadelphia chromosome.”

When such a translocation occurs, NIH director Collins said, it is like tearing the pages from one chapter of a book and inserting them elsewhere. As a result, the normal functioning of the genes is disrupted and can lead to cancer or other diseases.

By the 1980s, other scientists were using Dr. Rowley’s findings to analyze the components of cancer cells produced by abnormal genes. In 2001, the Food and Drug Administration approved a drug, commercially known as Gleevec, that has proved effective in treating chronic myelogenous leukemia, the disease associated with the Philadelphia chromosome.

The incremental process — from initial observation to Dr. Rowley’s moment of discovery to the experiments that led to a form of therapy — has been cited as an example of the scientific method at its best.

“You can draw a line from Janet’s research to the development of a drug to treat a specific leukemia,” said Collins, who has also directed the worldwide Human Genome Project. “The development of Gleevec is a remarkable advance toward making what had been a fatal disease something that can be treated more as a chronic condition. We’re all standing on the shoulders of Janet Rowley and others like her who proved that the paradigm worked.”

Janet Davison was born April 5, 1925, in New York and grew up primarily in Chicago. Her father worked in stores and later taught retail management. Her mother was an elementary school teacher.

Dr. Rowley was 15 when she entered an advanced program at the University of Chicago and received a bachelor’s degree in 1944. She was accepted into the university’s medical school, but because of a quota that limited the number of women — only three in a class of 65 — she had to wait a year.

She received a second bachelor’s degree in 1946 and graduated from medical school Dec. 17, 1948. One day later, she married Donald Rowley, a fellow medical student who later became a University of Chicago pa­thol­ogy professor. He made important discoveries about the immune system and invented the gel electrode, a widely used tool to measure cardiac activity. He died in February.

A son, Donald Rowley Jr., died in a drowning accident in 1983.

Survivors include three sons, David Rowley, a geology professor at the University of Chicago, Robert Rowley of Stanardsville, Va., and Roger Rowley of Moscow, Idaho; and five grandchildren.

Since Dr. Rowley’s first discoveries in the 1970s, more than 70 diseases and disorders have been linked to genetic anomalies. Dr. Rowley’s laboratory, which focuses exclusively on leukemia and lymphoma, has found more than a dozen of those connections.

“I was 47 years old before I did anything that people would really look at twice,” she said in 1998. “So, patience is an important aspect . . . and good luck.”

After being forced to wait a year to enter medical school, Dr. Rowley became one of the first women to make major discoveries in a field dominated by men.

“She probably mentored over 100 women in her career,” said Michelle M. Le Beau, who began working in Dr. Rowley’s laboratory in 1981 and is now director of the University of Chicago’s Comprehensive Cancer Center and its Cancer Cytognenetics Laboratory. “She showed women that you could have a professional life, you could have a personal life and you could have a family. I think, in that respect, she was a remarkable role model.”

In 1998, Dr. Rowley received National Medal of Science and the Lasker Award for medical research, often called the American equivalent of the Nobel Prize. After publicly criticizing the ban on stem-cell research by the George W. Bush administration, Dr. Rowley was standing next to President Obama in 2009 when he reversed the ban.

Later that year, she received the Presidential Medal of Freedom, followed by a lifetime achievement award from the American Association for Cancer Research in 2010 and the $500,000 Albany Medical Center Prize in Medicine and Biomedical Research this year. She had 14 honorary doctorates, including from Oxford, Harvard and Yale.

Dr. Rowley continued to work at her laboratory until shortly before her death, riding her bicycle to work each day. Her colleagues expressed dismay that the biggest prize of all, the Nobel, never came her way.

“We wondered all the time,” Le Beau said. “She had an insatiable curiosity, a love of science and a love of discovery. And she was extremely humble.”