In 1996, John Crowley’s two youngest children received what doctors at the time believed to be a death sentence.

John and his wife, Aileen, had noticed that their daughter, Megan, who was 15 months old at the time, had not yet taken her first steps and wasn’t pulling up in her crib.

“We got Megan's diagnosis when Patrick was 7 days old. They told us it was a rare disease, one we had never heard of, that it was fatal, that she wouldn't live to be but a couple of years old and that also, too, Patrick, who was with us there at the doctor's office … that he may have the disease,” Crowley, of Princeton, N.J. told FoxNews.com. “A few months later we had Patrick tested, and learned that he in fact did have Pompe disease as well.”

Pompe disease is a rare genetic neuromuscular disorder that causes progressive muscle weakness in people of all ages, according the Pompe.com. The genetic defect causes patients to be deficient in an important enzyme needed to break down sugar stored in the muscle cells throughout the body.

“We'd never heard of Pompe disease. Aileen and I are silent carriers … but it doesn't manifest until you have a baby with somebody else,” Crowley said. “And even then, there's only a one in four chance, so for us, the odds were very low.”

With no treatment for the disease available, doctors told the Crowleys that their children would get very sick and become very weak. Within 6 months of their daughter’s diagnosis, they found themselves in the intensive care unit of their local hospital where Megan was put on a ventilator.

“Those were six weeks in the ICU that we'll never forget, but she fought through it,” Crowley said. “And I realized that that fight in her eyes -- that she didn't want to give up -- and we knew then, that if she wouldn't give up, then we wouldn't either.”

A race against time

The grief-stricken parents admittedly had no idea what they were up against or where to start, but their love for their ailing children set them on a path to survival.

“We didn't know that we could change the course of their disease, but we wanted to never have any regrets that we didn't try to do everything we could,” Crowley said. “Ultimately, that's what we did, was to help move science forward and bring attention and resources to the disease.”

The Crowleys started working with non-profit organizations to raise money for Pompe disease research. By the year 2000, with the help of a scientist friend, John started a small biotech company in the hopes of finding a cure for Pompe disease.

“I had no idea how to run a biotech company, knew nothing about science, but was quickly immersed in that world,” Crowley told FoxNews.com. “That company helped to develop what became the first generation therapy that three years later the kids received, that they've been receiving now for 13 years.”

Megan and Patrick receive infusions of the enzyme replacement therapy, called Lumezyme through ports in their chests every other week.

“What the enzyme is designed to do is to replace the enzyme that's missing or defective in people with Pompe,” Crowley said. “It's designed to get to muscle cells, including the heart, which is a cardiac muscle, to get to the diaphragm, which is involved of course in breathing, and restore muscle function as best as it can.”

The drug proved life-saving for the Crowley children, and many of the estimated 5,000 to 10,000 Pompe sufferers around the world. Within the first year of receiving therapy, Crowley noted, Megan and Patrick’s hearts which had become enlarged due to the progression of the disease, were back to their normal sizes.

The quest for a cure

But Crowley knew that while the medication was a great start, there was still the potential for a cure. He sold his company, Novazyme Pharmaceuticals, to pharmaceutical giant, Genzyme Corp., and in 2005, started another biotech company called Amicus Therapeutics.

With nearly 20 years of Pompe research under their belts, today, his team has developed a second generation Pompe drug that is currently in clinical trials.

“The biggest drawback for the current therapy is that the drug is not targeted very well to where it needs to go,” Hung Do, chief science officer at Amicus Therapeutics, who helped develop Lumezyme, told FoxNews.com. “It doesn't reach the tissues and cells that need this particular drug to supplement the missing activity, and so we were able to address that in the development of this current second generation drug.”

As chairman and CEO of Amicus Therapeutics, headquartered in Cranbury Township, N.J., Crowley has made it his mission to find a cure not only for Pompe disease, but other rare diseases, as well. They have poured more than a decade of research into developing a drug to treat Fabry disease, a rare condition that causes fat to accumulate in the body that can cause life-threatening damage to the kidneys, liver and heart. The drug was approved in Europe, and the company hopes to see it approved in other parts of the world, including the United States.

Amicus also recently acquired another small biotech, MiaMed, started by a Long Island father desperate to find a cure for his daughter’s rare condition called CDKL5, characterized by severe seizures and developmental deficiencies.

“I've met many moms and dads who continue to be not just great champions and advocates for their children, but tremendous entrepreneurs and having that patient perspective is so vital,” Crowley said. “I think having that patient perspective is probably what sets Amicus apart from our peers. Many great biotech companies are patient-focused, we try to do it to an extraordinary level here.”

Coming full circle

Now 19, Megan attends her dad’s alma mater, the University of Notre Dame some 600 miles from home – something no one, save for her father, thought she would ever be able to do. She still requires 24-hour care from nurses, some of whom relocated from New Jersey to Indiana to continue caring for her.

“I had never been more than a few days without my parents or away for that long or that far, but I knew it was something in my heart that I really wanted and I knew Notre Dame was a place I really wanted to be,” Megan told FoxNews.com.

This summer, she had the opportunity to work side by side with many of the people who helped save her life when she interned in patient advocacy at Amicus Therapeutics.

“I just love that personal relationship with the other patients, I think that’s so important … so the scientists understand what the patient wants, and the patient understands what the scientists are doing to help them,” Megan said. “And it doesn’t happen overnight, and I know that more than anyone.”