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Monday’s approval of the first drug to treat the underlying cause of Duchenne muscular dystrophy offers hope to young patients handed a cruel sentence — almost certain death before their 25th birthday. But the impact of the Food and Drug Administration’s decision will extend beyond boys who suffer from a form of the disease — fewer than 2,000 in the United States — and raises complicated questions about the role patient advocacy should play in a regulatory process rooted in science.

In an e-mail announcing that Cambridge-based Sarepta Therapeutics will be allowed to market the drug, called eteplirsen, the FDA’s Janet Woodcock said the ruling showed the agency’s “ability to apply flexibility to address challenges we often see with rare, life-threatening diseases — while remaining within our statutory framework.” Put more plainly, regulators decided it was worth taking a chance on eteplirsen, even though only 12 patients were enrolled in Sarepta’s clinical trial; a study that an independent advisory panel – and even some FDA staffers — found woefully inadequate.

The drug produces a crucial protein needed for muscle movement that’s lacking in a subset of Duchenne patients, but there was disagreement within the agency about whether it’s enough to make a difference. Dr. Ronald Farkas, the FDA’s top drug reviewer, and a critic of Sarepta’s data, recently quit, and Woodcock — director of the Center for Drug Evaluation and Research — faced an internal backlash. An independent FDA advisory panel also was not convinced of the drug’s effectiveness. Following an April hearing in a crowded Maryland hotel ballroom, the panel narrowly voted to recommend against its approval, despite emotional testimony from patients and their families. Richard P. Hoffmann, a pharmacist named to the committee to represent consumers, ended up abstaining. “I was just basically torn between my mind and my heart,” he said.

That’s the crux of the dilemma facing the FDA. It’s supposed to only allow the sale of medicines that have been clinically proven to work, and don’t cause harm. If regulators were to be unduly swayed by anecdotal evidence and heartfelt pleas, drug companies could come to rely on armies of patient advocates to overcome spotty trial results. But if the approval process is completely dehumanized, the agency could been viewed as unwilling to put patients’ lives over strict adherence to bureaucracy.

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“The FDA needs to take a step back and re-evaluate how it’s going to do this going forward,” says Harry Glorikian, a health care consultant based in Lexington. “Historically, we’ve let science and data drive our decisions when it comes to therapeutics.”

The eteplirsen decision came with a large asterisk — Sarepta has to conduct a two-year study to better show whether the drug helps maintain or improve mobility — but its entry into the marketplace represents a major victory for the patient advocacy movement, and is bound to encourage more such engagement in the drug-approval process. Based on the infighting that went on over the Duchenne treatment, that’s going to be challenging for the FDA. It has to find a balance between public opinion and what’s truly in the public interest.