Caroline Morton, who serves as the clinic's executive director, said the Human Genome Project to map all of human DNA, completed in 2003, has "revolutionized" the treatment the clinic offers.
"Many disorders that were previously unrecognized and undiagnosed, now can be diagnosed through gene sequencing," she said. "And that was all made possible by the Human Genone Project."
Dr. Morton said that the public databases assembled from the genome project are "extraordinary" tools. "We use them literally every working hour of every day."
When researchers began mapping the genome in the late 1980s, Morton said, "I wasn't sure that the payoff would be as immediate and as direct as many people were selling it as. I have to say, I think I was wrong."
While the clinic treats only children with genetic disorders, it provides them with general care as well - mending broken bones and treating sore throats.
Among the clinic's biggest challenges, Caroline Morton said, is paying for the sophisticated care that children with rare diseases require. The Plain People generally shun government-provided health services.
"These are people who desperately need a fairly advanced level of care but do not have health insurance and are not wealthy people," she said.
Dr. Morton became interested in studying genetic disorders among the Amish and Mennonites in 1988 as a researcher at the Children's Hospital of Philadelphia.
One day, a 6-year-old Amish boy showed up with a mysterious ailment. Tests showed he had glutaric aciduria, a condition diagnosed only seven or eight times previously.
Intrigued, the pediatrician drove to the boy's home in rural Lancaster County. He realized that the condition might be caused by a genetic disorder. So, as The New York Times Magazine reported last year, he started looking for that disorder among the Amish. By the end of the summer, he found had 20 more cases.
Dr. Morton is only one of many researchers to study genetics among the Plain People. But he was one of the few to live and work among them and make a long-term commitment to their care.
Geneticists have long studied isolated human populations, where marriage to outsiders is uncommon. It's easier to trace the spread of genes through these communities, which also tend to have a higher incidence of inherited disorders.
Genetic testing could tell Amish or Mennonite couples their risk of having children with many genetic disorders. Prenatal testing could predict whether a specific child would develop these illnesses.
But those familiar with the Plain People say that the whole concept of genetic counseling conflicts with their beliefs.
"They believe that these children are literally special children, sent from God to test their belief and conviction in God," said Shuldiner, of the University of Maryland, who studies diabetes and heart disease among the Amish and Mennonites.
"There is no stigma whatever attached to these children or the families of these children," Shuldiner said. "They're revered in this community."
Morton hasn't decided what to do with his prize money, although he has some general goals.
He would like to expand clinic services, and ensure the clinic's financial survival. He also wants to find the time to publish more of the results of his research.
The physician, though, has no plans to do what a number of MacArthur recipients have done, using their grants to take a sabbatical. "I have a lot of work as a pediatrician, and that can't go away," he said.